PhD student project on AI-driven modelling and design of cell type-specific enhancers

The De Wit lab and Aerts lab at the VIB-KU Leuven Center for Brain & Disease Research, Belgium, are seeking a highly motivated Ph.D. student to work on a joint project on AI-driven modelling and design of cell type-specific enhancers. The VIB-KU Leuven Center for Brain & Disease Research is part of the VIB Life Sciences Institute and is embedded within the University of Leuven, which ranks among the world’s top 50 universities. At our Center, 340 researchers study the basic mechanisms of the central nervous system and related diseases.

The project, funded by an FWO Strategic Basic Research (SBO) grant, will focus on designing and testing enhancers to target transgenes to specific cell types in the mouse brain and in cultured human brain biopsies using adeno-associated viral vectors. The project will have both a computational and wet lab component.

The Ph.D. student will be stationed in the De Wit lab but will be embedded in both the De Wit and the Aerts lab as well as the Leuven Bioinformatics and Leuven AI community. The PhD student will be jointly supervised by Joris de Wit and Stein Aerts.

Profile

We are seeking a highly motivated, enthusiastic, critical, and creative individual to join our teams.

• You have a Master's degree in the Life Sciences, Bioinformatics, Computer Science, or a related field.
  The successful candidate must meet the requirements for enrollment at the Doctoral School Biomedical Sciences, which are:
  • a Master's degree (or an equivalent higher education degree) that is relevant for the doctoral research;
  • distinction (= cum laude) based on your study results or professional realizations.

• You must be proficient in English. The KU Leuven Admissions office might ask you to submit a certificate proving your proficiency in English.
• Experience with programming (Python, R )
• Experience with machine learning is a plus
• Experience with the analysis of (single-cell) gene expression and chromatin data is a plus
• Experience with molecular biology, viral vectors, animal surgery, or histology is a plus
• Team player

For further information and questions, please send an email to Joris De Wit (joris.dewit@kuleuven.be) or Stein Aerts (stein.aerts@kuleuven.be)

Apply here

PhD position in tumor immunology and genetic T cell engineering

The LIT - Leibniz Institute for Immunotherapy (foundation under civil law) (http://www.rcii.de/en/), formerly RCI – is a biomedical research center focusing on translational immunology in the fields of cancer immunotherapy, transplant rejection and autoimmunity. The objective of the LIT is to develop innovative and efficient cellular immune therapeutics in these areas. Our own GMP laboratories and close networking with University and University Hospital offer excellent opportunities for clinical translation of novel immune cell products.

We are offering a PhD position (m/f/d)The group of Prof. Philipp Beckhove at the LIT (https://www.rcii.de/en/research/departments/department-for-interventional-immunology/about/) is looking for a highly motivated and talented PhD student to pursue cutting-edge research in the field of experimental and molecular tumor immunology and genetic T cell engineering.

Requirements

We are looking for a highly motivated individual who is enthusiastic to work in an ambitious team on a competitive project, and who fits the following profile:

• Strong interest in immunology & cancer
• Master in biology/biochemistry/molecular medicine or related fields
• Creative mind that is eager to shape the project and who wants to make an impact on immunological and biomedical research
• Experimental training in molecular biology and immunology
• Keen interest in using modern technology (i.e. CRISPR, T cell engineering, imaging, etc.)
• Excellent oral and written communication skills and team spirit
• Experience in mouse models (FELASA certificate) would be advantageous.

For more information, please contact Prof. Philipp Beckhove (philipp.beckhove(at)ukr.de). We are looking forward to your detailed application.

Please apply via our homepage http://www.rcii.de quoting the reference PB-2023-3.

Application deadline is October 6^th, 2023.

Posted on September 25, 2023

PhD in Clinical and Biomedical Sciences

The GW4 BioMed2 MRC DTP is offering up to 22 funded studentships across a range of biomedical disciplines, with a start date of October 2024.

These four-year studentships provide funding for fees and stipend at the rate set by the UK Research Councils, as well as other research training and support costs, and are available to UK and International students.

About the GW4 BioMed2 Doctoral Training Partnership

The partnership brings together the Universities of Bath, Bristol, Cardiff (lead) and Exeter to develop the next generation of biomedical researchers. Students will have access to the combined research strengths, training expertise and resources of the four research-intensive universities, with opportunities to participate in interdisciplinary and 'team science'. The DTP already has over 90 studentships over 6 cohorts in its first phase, along with 38 students over 2 cohorts in its second phase.

The 80 projects available for application, are aligned to the following themes;

• Infection, Immunity, Antimicrobial Resistance and Repair
• Neuroscience and Mental Health
• Population Health Sciences

Applications open on 4th September 2023 and close at 5.00pm on 1st November 2023.

Apply here

Two PhD scholarships in analysis of aquatic eDNA

Are you interested in working with analysis of aquatic environmental DNA (eDNA) in relation to marine biodiversity conservation and sustainable fisheries resource management? Then, you have the opportunity to come and work with us at DTU Aqua!

We have two available positions at the National Institute of Aquatic Resources (DTU Aqua), Denmark:

A PhD Scholarship to study biodiversity at offshore wind farms using eDNA to monitor spatial and temporal biodiversity variation, and to develop eDNA into a robust cost-efficient tool for marine environmental impact assessment. The project will apply advanced autonomous robotic instruments for in situ eDNA sampling and DNA analysis. The scholarship is part of the “WINDNA” project, financed by the Independent Research Fund Denmark and the Velux Foundations.

A PhD Scholarship to develop eDNA based methods to estimate bycatch of non-targeted fish species in large catches of pelagic fish (e.g., herring and mackerel). The aim of the project is to develop a high quality, cost-effective pipeline for eDNA based catch composition assessment using DNA from samples of production water surrounding the catch. The vision is that the method can replace the currently used manual and labour-intensive methods, which to date is based on visual identification of subsamples.

Both positions are imbedded in the genetics/genomics group at DTU Aqua. The group applies cutting edge molecular methods with the aim to generate knowledge and develop DNA based tools for aquatic biodiversity conservation and sustainable fisheries management. The primary focus of the group is within population genetics/genomics and eDNA analyses. The group currently consists of around 15 people including researchers at different career stages, postdocs and PhD students as well as an experienced technical staff.

Responsibilities and qualifications
The ongoing climate and biodiversity crises call for new precise, fast, and cost-efficient methods for detection, monitoring and protection of biodiversity. For example, it has been decided that the massive build-up of offshore wind-power across the globe, should not be done at the expense of biodiversity. However, the monitoring of biodiversity using traditional methods is challenged by logistical, economical and time constraints.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

A background in eDNA analysis including metabarcoding is preferred and experience with bioinformatic analyses of large genomic data sets is an asset.

In addition, we are looking for candidates who have:

- Master of Science (M.Sc.) degree in Biology, Computer Science or Engineering

- Keen interest in research within marine and aquatic sciences, including “molecular ecology”

- Good collaborative skills

- Proficiency in written and spoken English

Further information
Further information may be obtained from Professor Einar Eg Nielsen, tel.: +45 40210231, email: een@aqua.dtu.dk.

General information may be obtained from Susan Zumbach Johannesen (szjo@aqua.dtu.dk).

Application procedure 
Your complete online application must be submitted no later than 22 October 2023 (23:59 Danish time). 

Apply here

Posted on September 20, 2023

PhD position in Preclinical data sciences

We have a vacancy for a 3-year PhD position for improving the reproducibility and translatability of preclinical drug response models, with specific focus on precision oncology applications. The funding comes from Helse Sør-Øst in the research group of Prof. Tero Aittokallio at Department of Cancer Genetics, Institute for Cancer Research (https://www.ous-research.no/aittokallio/). The group is also affiliated with University of Oslo, Oslo Centre for Biostatistics and Epidemiology (OCBE), a joint centre with Oslo University Hospital. Co-PIs of the project are Prof. Therese Sørlie and Prof. Åslaug Helland.

Joint PhD Program from BioNTech and TRON in translational medicine 

ATLAS - Joint PhD Program from BioNTech and TRON with a focus on translational medicine    

9 PhD positions in biology, biochemistry, life science, chemistry, medicine, computer science or related fields

BioNTech and TRON (Translational Oncology Mainz) are leading institutions in the field of immunotherapy. Our joint international PhD Program (ATLAS) is looking for talented, junior researchers of all nationalities.

Our international PhD program ATLAS (Talent Academy for TransLAtional Science), guides and supports PhD students to conduct excellent research projects and offers comprehensive training in cutting-edge technologies and professional skills. The scientific training within the program has a strong focus on "the art of translation", i.e. turning basic scientific discoveries into applications.

We offer the opportunity to work on innovative research projects focused on translational science in the field of medicine. As a PhD student*, you will join a community of world-class scientists working on diverse topics such as: 

• Immunotherapy of cancer, infectious diseases & autoimmunity
• Cardiovascular, aging & regenerative biomedicine
• RNA biochemistry
• Protein engineering
• Bioinformatics & systems biology
• Biomarker research
• Antimicrobial therapies

For details on the program and the specific projects, please visit www.atlas-phdprogram.com. 

Who can apply? 

Aspiring students seeking to advance knowledge and explore novel therapies. The requirements are:

• A master’s degree in Biology, Biochemistry, Chemistry, Life Science, Medicine, Immunology, Computer Science or Engineering related fields.
• Motivation and passion for science
• Ability to work independently and in an international, multi-disciplinary team
• Professional proficiency in both written and spoken English

Please carefully read "How to apply" and "Projects offered" before applying. 

The deadline for applications is October 31st, 2023. Interviews will take place in Mainz in February 2024.

If you have any further questions, please visit www.atlas-phdprogram.com or email us at info@atlas-phdprogram.com.

PhD position (DNA Repair & Genome Stability)

Thinking of doing your PhD in the Life Sciences? The International PhD Programme (IPP) Mainz is offering talented students the chance to work at the cutting edge of research. As an IPP PhD student, you will join a community of exceptional scientists working on diverse topics ranging from how organisms age or how our DNA is repaired, to how epigenetics regulates cellular identity or neural memory.

PhD project: Sources and consequences of intrinsic genomic instability across human cell types

As part of the SFB1361 consortium, this PhD project aims to characterise the sources of intrinsic DNA fragility and uncover how it may lead to recurrent rearrangements and tissue-specific oncogenesis. To this end, we will combine sophisticated genomics approaches from the Roukos and Beli labs (Bowman et al, Nat. Protoc, 2020; Longo, Puig et al., submitted; Mosler et al., Nat Commun, 2021) to  generate a compendium of intrinsic DNA fragility maps across human cell types, and characterise how they relate to gene expression, chromatin environment and 3D chromosomes organisation. We will then link the molecular and cellular sources of intrinsic DNA fragility, focusing on the roles of non-canoncial DNA structures, such as R-loops and G-quadruplexes, and of incomplete topoisomerase actions, and their interference with replication and transcription.

For more details on the projects offered and how to apply via our online form, please visit https://www.imb.de/phd

The deadline for applications is 8 November 2023. Interviews will take place at IMB in Mainz on 22-24 January 2024.

Starting date: 1 March 2024 – 1 August 2024

Posted on September 15, 2023

PhD position in Genomics

The Department of Medical Biochemistry and Microbiology (IMBIM) at Uppsala University provides a broad international environment for research and teaching. Research at IMBIM) broadly spans the areas of biochemistry, cell and molecular biology, tumour biology, comparative genetics, functional genomics, immunology, bacteriology, and virology. The research is essentially of fundamental nature, but with relevance and application in health and disease in both animals and humans. More info: https://www.imbim.uu.se/research-areas/.

Leif Andersson’s research group at IMBIM is now seeking a motivated candidate with the ability to work independently and with a strong interest in pursuing a PhD degree in Genomics with specialization in evolutionary population genomics at Uppsala University. The research project will focus on exploring mechanisms underlying genetic adaptation in natural populations.

More information about the group: https://www.imbim.uu.se/research-groups/genetics-and-genomics/Andersson_Leif/

Qualifications
Candidates should hold a Master’s degree or equivalent, with a focus on genetics, genomics and/or bioinformatics. Experience in population genetics, the analysis of whole genome sequence data, statistics and programming is required for the project. Good oral and written communication skills in English are required. Emphasis will also be given on personal qualities such as collaboration and communication skills as well as analytical capacity. The candidate is expected to take own initiatives as well as to collaborate with national and international colleagues both within and outside of the group.

For further details, please contact: Professor Leif Andersson, leif.andersson@imbim.uu.se

You are welcome to submit your application no later than September 27, 2023, UFV-PA 2023/3368.

Apply here

PhD position in Tumor Inflammation and Angiogenesis

The Laboratory of Tumor Inflammation and Angiogenesis, headed by Prof. Massimiliano Mazzone, is embedded in an international and multi-disciplinary research environment of the VIB Center for Cancer Biology (CCB), located on Campus Gasthuisberg of the University of Leuven. The mission of the lab is to unravel the interplay taking place in the tumor microenvironment (TME), and whenever suitable, exploit these insights to develop novel therapeutic approaches aimed to impact cancer progression through re-education of the immunosuppressive tumor ecosystem. De facto, the research topics span the fields of tumor biology, immunology, metabolism, and angiogenesis, focusing on the functional characterization of environmental cues of the TME dictating the cancer immune cell landscape. The end goal of the Team is to understand how manipulation of the identified signaling dynamics can impact the functional and phenotypic state of tumor-infiltrating immune cells. To gain groundbreaking insights, we exploit advanced spatial metabolomics, single-cell and spatial transcriptomics, gene manipulation (supporting new ways for fast transgenic mouse generation and gene editing), and pharmacologic approaches in mice to study immune metabolic functions.

Position

As a Ph.D. student with a strong background in Bioinformatics, you will be responsible for leading the analysis of the generated datasets. Able to organize and troubleshoot your work you will be in charge of the advancement of your own in silico project; nonetheless, you are willing to support and contribute to several research projects of the lab, have a collaborative spirit, and are eager to liaise with academic collaborators, but also technology transfer experts and industrial partners. Communicative and collaborative you will be expected to share results and experiences with the team in a transparent and professional manner. The successful candidate should thrive in small-team environments where self-sufficiency, initiative, and flexibility are key and lines of communication are short. You will join a young international team and you will contribute to a collaborative, interactive, diligent, and science-driven culture in order to meet milestones set by the lab head.

Profile and skills

We are looking for a highly motivated, well-organized, and dynamic candidate with creative thinking.

• You hold an MSc. degree in (Bio)informatics / Computational Biology / Computer Science or a related field
• You have a strong interest in translational research in the immuno-oncology space
• You are familiar with single-cell or spatial biology workflows
• Working proficiency in R and Python
• Experienced in handling and managing the analysis of large biological datasets would be advantageous
• Knowledge of computing environments, cloud-based solutions, and hardware specifications to manage data would be advantageous
• Fluency in English, both oral and written, is mandatory
• Team player, applying your expertise to drive projects within a small team.
• Strong interpersonal and communication skills that you can use within the team and with collaborators.
• Meticulous, independent, and motivated.
• Keen to take on responsibilities.

How to apply?

Please send a detailed CV, a motivation letter, and the contacts of at least two reference contacts to massimiliano.mazzone@kuleuven.be and marcello.delfini@kuleuven.be

Apply here

Posted on September 11, 2023

PhD student on Deep Learning for Virus and Host Genomics

Through cutting-edge research in the fields of ENERGY, HEALTH and MATTER, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) solves some of the pressing societal and industrial challenges of our time. Join our 1.500 employees from more than 70 nations at one of our six research sites!

The Center for Advanced Systems Understanding (CASUS) is a German-Polish research center for data-intensive digital systems research. CASUS was founded in 2019 in Görlitz and conducts digital interdisciplinary systems research in various fields such as earth systems research, systems biology and materials research.

The global SARS-CoV2 Pandemic has demonstrated the urgency to develop new tools for our arsenal against pathogens and human disease. If you are passionate about designing the next generation of genomic algorithms for host-pathogen interactions – we are looking for your talent!

Your tasks:

• Design of deep learning tasks to interrogate questions of genome biology
• Devise novel approaches to incorporate Biology-informed knowledge into the model architecture
• Engage with our international collaborators (Dresden, London, Zurich, Taipei etc.) to understand existing approaches and datasets
• Collaborate with the research team on other questions of machine learning, functional genomics, genome instability
• Supervise junior lab members
• Present results and publish high-impact peer-reviewed research

Your profile:

• Master or Diploma in a relevant field, such as Molecular Biology, Computational Biology, Bioinformatics, Genetics, Computer Science, Mathematics, Linguistics or equivalent scientific background
• A solid background in biology, mathematics, software engineering, machine learning or in a related subject
• Excellent programming skills in languages such as Python
• Familiarity with modern deep learning frameworks like Tensorflow 2.x.x, PyTorch
• Previous experience or interest in Bioinformatics, Systems Biology, Natural Language Processing, Deep Learning, Git version control and Slurm cluster environments is a plus
• Strong motivation to work in a collaborative environment
• Excellent communication skills in English and in a professional context (presentation of research results at scientific meetings, colloquial discussions, writing of manuscripts)

Apply here

PhD Studentship: Understanding the risk and preparing for arboviruses

An exciting joint funded PhD studentship between Surrey University and APHA (Weybridge) to characterise two neglected arboviruses, that are zoonotic and have potential to cause significant livestock and human disease burdens if introduced and established in the UK mosquito population. This is a unique opportunity to undertake fundamental virological studies, in relevant mosquito vectors, alongside state-of-the-art genomic analysis and molecular diagnostic test development. The accumulated data will be utilised to develop an epidemiological risk model which can be used to inform UK policy makers on whether the viruses would establish within the UK mosquito populations.

This is a joint funded PhD studentship between the Virology department at Animal and Plant Health Agency (Weybridge, Surrey) and the Vet School at Surrey University (Guildford, Surrey). The successful applicant will be based at APHA, immersing themselves within the arbovirology team, while benefitting from the support, expertise, and research culture in the schools of Veterinary Medicine and Bioscience at Surrey.

Posted on September 08, 2023

EMBL International PhD Programme

The EMBL International PhD Programme (EIPP), originally established in 1983, provides PhD students with an excellent starting platform for a successful career in science by fostering early independence and interdisciplinary research.

EMBL is dedicated to promoting excellence in the molecular life sciences throughout Europe. To achieve this goal, we inspire and train talented young scientists to become skilled and creative future leaders in academia, industry and other sectors.

Characterised by first-class training, internationality, dedicated mentoring and early independence in research, the EMBL International PhD Programme is among the world’s most competitive PhD training schemes.

EMBL-EBI provides a highly collaborative, interdisciplinary environment in which research and data service provision are closely allied.

We are a world leader in bioinformatics, at the centre of global efforts to collect and disseminate biological information. We share a campus with the Wellcome Sanger Institute, 20 km (11 miles) south of Cambridge in the United Kingdom.

EMBL-EBI’s PhD students are all part of the EMBL International PhD Programme, and also are registered with the University of Cambridge and enjoy all the benefits of university membership.

Posted on Septmeber 05, 2023

PhD scholarship in single-cell proteomics

A 3-year PhD Scholarship, starting 1 Dec 2023 or soon thereafter is available in the Cell Diversity Lab, led by Associate Professor Erwin M. Schoof. If you are establishing your career as scientist and are looking for a solid foundation to fulfill your dreams and ambitions in the context of single-cell biology, it is right here in front of you. At DTU Bioengineering, you will break new ground at the absolute forefront of single cell proteomics by Mass Spectrometry (scp-MS) and other single-cell technologies and use your skills to answer fundamental clinical questions and develop the next-generation experimental and computational workflows.

The PhD project, which is fully funded, is part of the department’s major long-term strategy to combine experimental and computational approaches to establish scp-MS as a routine tool for deciphering cell heterogeneity in complex biological systems. The focus of the project is applying scp-MS to primary Acute Myeloid Leukemia patient samples, to decipher the cellular heterogeneity within these leukemia hierarchies and better understand the differentiation trajectories that exist. The work is conducted in close collaboration with the University of Copenhagen and Rigshospitalet.

Qualifications The successful candidate must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree. Relevant subject areas are biochemistry, biomedicine, medicinal chemistry, molecular biology, immunology or related subjects. You should be curious, ambitious, organized, highly motivated and a team player, and are expected to have a strong interest in fundamental scientific discoveries and elevating their translational potential.

Further information may be obtained from Associate Professor Erwin Schoof at DTU Bioengineering. He can be contacted at erws@dtu.dk, or via Twitter @erwinschoof

Apply Before 18/09/2023, 22:59

Apply here

PhD students in Bioinformatics

SciLifeLab (SciLifeLab) is a national center for molecular biosciences with a focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource hosted by Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. The center also collaborates with several other universities.

The employment will be placed at the Department of biochemistry and biophysics, at Stockholm university.

Protein structure is essential for understanding their function and developing drugs targeting proteins. Recently, a deep learning method that can predict the structure of most proteins was made freely available and released a database with predicted protein structures. However, proteins do not act alone - they work together with other proteins. Therefore, the next major challenge is using these methods for predicting protein-protein interactions. Our initial studies have shown that it is possible to predict accurate structures of a large part of dimeric proteins using either a modified version of AlphaFold2 or AlphaFold-multimer. However, many proteins cannot be built accurately, nor can we always distinguish interacting from non-interacting protein pairs and building larger complexes accurately is still an unsolved problem.

Qualification requirements
In order to meet the general entry requirements, the applicant must have completed a second-cycle degree, completed courses equivalent to at least 240 higher education credits, of which 60 credits must be in the second cycle, or have otherwise acquired equivalent knowledge in Sweden or elsewhere.

In order to meet the specific entry requirements, for acceptance in the Biochemistry, especially Bioinformatics, program the applicant must have passed courses within the first and second cycles of at least 90 credits in either, a) Chemistry/Molecular Biology/Biotechnology, or b) Computer Science/Mathematics/Physics and at the second cycle level, 60 credits in Life Science, Computer Science Mathematics, Physics or Bioinformatics including a 30 credit Degree Project (thesis).

The qualification requirements must be met by the deadline for applications.

Contact
For more information, please contact the project leader, Professor Arne Elofsson, arne.elofsson@dbb.su.se.

General information about the PhD programs can be given by the Director of Doctoral Studies, Pia Ädelroth, pia.adelroth@dbb.su.se or the Head of the Department, Martin Högbom, martin.hogbom@dbb.su.se.

Apply here

Posted on September 01, 2023

Doctoral position in Medical Systems Biology

Microbiome research has experienced vast advances in the last two decades with the advent of culture-free techniques to study the composition and function of bacterial communities. This has elucidated the importance of host-associated microbial communities for health and adaptation to changing environments. In the Research Group Medical Systems Biology at the Institute of Experimental Medicine, we use systems biological approaches incorporating a large variety of molecular data sets to better understand microbiome-host interactions and how these interactions can be therapeutically targeted.

In this project, we want to understand the role of metabolic interactions on microbial community dynamics in a host-associated context. We will use the freshwater polyp Hydra as a model system to study how nutrient changes in the water column impacts the microbial community dynamics living on Hydra, and how well these changes are predicted by metabolic interactions between the community members.

Your role:

• As part of our highly interdisciplinary research group, you will be responsible for the integrative analysis of large-scale experimental data sets (microbiome amplicon sequencing, transcriptomics, metabolomics, genomics) in the context of microbiome-host interactions
• Reconstruct metabolic models for the Hydra-associated bacteria from metagenomic and amplicon sequencing data using an in-house developed pipeline
• You will use these models to simulate metabolic interactions between different members of the bacterial community in Hydra and you will validate these experiments in lab rotations with our research partners
• Develop a new metabolic model for the host and will use metabolic modeling and experimental validation to investigate the role of the host on the metabolic factors determining community assembly

Your profile:

• You are a highly motivated PhD candidate with the willingness to learn new and challenging methods and concepts as well as excellent (English) communication skills
• You solve problems and have a can-do mindset
• During your studies, you gained first experiences in bioinformatics or systems biology (omics analysis, metabolic modeling) and possess excellent programming skills (preferentially R and Python) preferably in a Linux environment
• Further, you have experience in microbiological work and are interested in basic research with a unique model system.

We look forward to receiving your application by October 1st, quoting the tender number 22406.

For more details on the position, please get in touch with Dr. Jan Taubenheim, Institute of Experimental Medicine, Kiel University / University Hospital Schleswig-Holstein, via phone at +49-431 5000-30345 or via email at j.taubenheim@iem.uni-kiel.de. More information about the research group and the UKSH is available here

PhD candidate in Genetic Epidemiology

We have a PhD vacancy for three years at the K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing (ISM),NTNU Norway. The Department of Public Health and Nursing (ISM) is responsible for research, teaching, innovation and dissemination in community medicine, nursing, primary health care and public health and thus actively contributing to the knowledge for a better world mission of NTNU.

We currently have a vacancy at the K. G. Jebsen Center for Genetic Epidemiology for a PhD Fellowship. This is a 3-year temporary position within the field of genetic epidemiology and statistical genetics focused on investigating the etiology of chronic kidney disease. We seek a talented, self-motivated and enthusiastic person with experience in genetic epidemiology, statistical genetics, bioinformatics, medicine, epidemiology or biostatistics. For more information about the center, see www.ntnu.edu/huntgenes and our videopresentation: K. G. Jebsen Center for Genetic Epidemiology

Duties of the position

This PhD project will involve investigation of genetic and causal risk factors for chronic kidney disease (CKD) using large population-based data sets including HUNT and UK Biobank. The candidate is expected to use a wide range of statistical approaches such as genome-wide association analyses, Mendelian randomization, functional bioinformatic follow-up and network analysis to investigate which modifiable risk factors are most important for CKD. The period of employment for the position as a PhD candidate is 3 years full-time. Admission to a doctoral degree program is a requirement.

Required selection criteria

PhD position in Human Genomics

At the Faculty of Medicine, Department of Clinical Science, a full-time PhD position is available for a period of four (4) years or max 4 months after completed the PhD-degree, if this is achieved within a shorter time than four years. The positions include 25 % required duties such as teaching, exam work or supervision, depending on the demands at the department. The position is part of the project “People of Norway”, and is funded by the University of Bergen.

About the project/work tasks:

PhD position in Molecular and Computational Neurogenomics

We are a highly motivated international team of researchers at the Molecular Neurogenomics group (Jordanova Lab) and the Computational Neurobiology group (Malysheva Lab) at the VIB CMN. We are excited to announce a call for a joint Ph.D. student in our labs to work on a challenging project at the interface of neurodegeneration, genomics, computational and systems biology.

Charcot-Marie-Tooth disease (CMT) represents the most common genetic disorder of the peripheral nervous system. Patients experience progressive distal muscle weakness and wasting, sensory loss, and skeletal deformities ultimately leaving them severely disabled. This lifelong disorder is currently incurable. The largest protein family implicated in the etiology of CMT are aminoacyl-tRNA synthetases (ARS). Ubiquitous and essential enzymes, ARS catalyse a critical step in protein biosynthesis by charging tRNA with their cognate amino acid.

The candidate should:

• have an MSc in Systems Biology, Molecular Biology, Natural Sciences, or related disciplines
• be very motivated and enthusiastic to learn and expand both computational and experimental skill sets
• be able to summarize data extracted from the literature and clearly shape research objectives
• be able to efficiently communicate with experimental and computational scientists
• have excellent communication and writing skills in English

Required skills

• confident in basic molecular biology techniques, such as cell cultures, basic genomics data generation
• basic/intermediate programming skills in R and/or Python
• Ability to adapt to the research environments while being full members of two labs

Desirable skills

• knowledge of gene regulatory mechanisms
• statistical analysis
• basic processing of NGS data
• experience with iPSC culturing
• knowledge of and some experience with genetic perturbation assays, such as CRISPR

You can apply for this job through the online VIB job application platform.

Don’t forget to include the following document(s):

• a detailed CV, detailing set of mastered experimental and computational skills and publications if any
• a letter of motivation describing your relevant research experience and competitive advantages
• contact details of two referees

For more information: please contact albena.jordanova@vib.be, valeriya.malysheva@vib.be or jobs.cmn@uantwerpen.vib.be

Apply here

PhD Position- Radiomics, Deep Learning and Artificial Intelligence in Patients with Brain Tumors

The Institute of Neuroscience and Medicine, Medical Imaging Physics (INM-4) of the Research Center Jülich led by Prof. Dr. N. Jon Shah focuses on the development, experimental validation and clinical implementation of novel brain imaging methods such as quantitative MRI, PET, EEG as well as combinations thereof. The position is situated in the department Brain Tumor Diagnostics led by Prof. Dr. Karl-Josef Langen, that focuses on the preclinical and clinical evaluation of novel radiopharmaceuticals for brain tumor diagnostics and the correlation with MRI, in close collaboration with the University Hospital RWTH Aachen as well as the surrounding University Hospitals Bonn, Cologne and Duesseldorf. Details

Your Job:

The PhD student will work in the framework of a DFG (German Research Foundation) funded project on the development, implementation, and application of methods from the broad field of Artificial Intelligence such as Deep Learning or Radiomics towards an improved diagnosis of brain tumor patients based on MRI and PET. Especial emphasis will be put on the correlation of novel neuroimaging techniques and radiomics features and machine learning models with the underlying histopathology by access to local tissue samples. During the project an integration into other related projects within the INM is conceivable, to address individual interests of the applicant, e.g., in PET/MRI hardware or sequence development.

Your Profile:

• Master’s degree in Bioinformatics, Medical Physics, Biomedical Engineering, or a related field of study
• Experience with UNIX-like operating systems
• Solid experience in one or several relevant programming languages (i.e., Python, R, Matlab, C++) or the strong wish to acquire such skills
• Ideally some experience or solid knowledge on the concepts of radiomics and machine learning
• Ideally experience with medical image processing including PET and MRI
• Experience or strong interest in clinical research with a focus on brain cancer
• Excellent oral and written communications skills in English are required
• Knowledge of German is a plus

We look forward to receiving your application by 18.9.2023

Apply here

Posted on August 23, 2023

Three PhD positions in AI for the Life Sciences

Are you ready for a challenge? There are three PhD positions available in the AI Technology for Life group at Utrecht University. All positions have in common that you will use recent developments in AI technology to gain understanding of complex living systems.

The three PhD projects available are:

1. PhD in AI Technology for plant-microbiome interactions.
2. PhD in Explainable AI for Multi-Modal Life Science Data.
3. PhD in explainable AI in a multi-task setting.

You will become part of the vibrant interdisciplinary research group “AI Technology for Life”, a new interdepartmental research group between the Department of Information and Computing Sciences and the Department of Biology. The group is created as a result of the great importance attached by the Faculty of Science to stimulate research and teaching between departments. Together with the members of the group you work at the interface between the Life Sciences and AI.

Qualifications

• A (nearly) completed MSc degree in a relevant area such as Artificial Intelligence or Bioinformatics with a strong AI component;
• Demonstrable experience with development of machine learning methods;
• An interest in working with life science data, for example omics data or medical images;
• As you will have to collaborate with researchers in the life sciences

PhD fellowship in bioinformatic analysis of host - pathogen interactions

A PhD fellowship is available in the Computational Biology and Bioinformatics research group (https://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk) at Department of Veterinary and Animal Sciences (https://ivh.ku.dk/english), Faculty of Health and Medical Sciences at University of Copenhagen. Anti-microbial resistance (AMR) is a fast-increasing challenge for human health. Within the large PIG-PARADIGM consortium (https://pig-paradigm.net/), funded by the Novo Nordic Foundation, the goal is to prevent spreading of AMR by reducing antibiotic use in pig-production.

The Bioinformatics group and research
The Computational Biology and Bioinformatics research group holds a long-standing interest in Computational RNA biology and transcriptomics but works in general on many different topics covering computational, algorithmic and biological aspects. The group holds a long interest in RNA structure, RNA interactions and transcriptome analysis, which over the years have evolved in different directions from gene network analysis and CRISPR.

Job description
Your key tasks as a PhD student at SUND are:

• Carrying through an independent research project under supervision, with content as outlined above in the project description.
• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PhD project
• Teaching and disseminating your knowledge.
• Writing a PhD thesis on the grounds of your project

Application deadline:  August 23, 2023, 23.59pm CET

Jan Gorodkin E-mail: gorodkin@sund.ku.dk 

Apply here

Posted on August 21, 2023

PhD scholarship in climate change population genomics

Are you interested in working at the interface between genomics, climate change and biodiversity conservation and in answering the question: “How can we gain and use knowledge about climate change biodiversity effects and response for aquatic conservation and resource management?” Then, come and work with us at DTU Aqua!

A PhD Scholarship to study climate change biodiversity effects using comparative population genomic methods is available at the National Institute of Aquatic Resources (DTU Aqua), Denmark, with starting date November 2023 (or earlier). The scholarship is part of a larger Nordic collaborative project, “BlueBioClimate”, financed by the EU Interreg Öresund-Kattegat-Skagerrak Programme, the Danish Rod and Net License Funds, the Innovation Fund Denmark, private foundations and the National Institute of Aquatic Resources. The project will primarily be carried out at the Section for Marine Living Resources’ population genetics group situated in Silkeborg, Denmark. DTU Aqua is an institute at the Technical University of Denmark.

The overall purpose of the PhD project is to develop novel approaches to integrate genomic information with spatial management and conservation of biodiversity in collaboration with resource management practitioners at national and regional level. The successful student will apply a comparative population genomics approach and will, in collaboration with other project participants, take advantage of integrated information across multiple aquatic taxa (e.g. fish, shellfish, plants) and combine genomic data already available with new data produced in the project.

A background in population genetics is preferred and experience with bioinformatic analyses of large genomic data sets is an asset.

In addition, we are looking for candidates who have:

- Master of Science (M.Sc.) degree in Biology, Computer Science or Engineering

- Keen interest in research and the field of marine and aquatic sciences

- Good collaborative skills

- Proficiency in written and spoken English

Further information
Further information may be obtained from Senior Researcher Jakob Hemmer-Hansen, tel.: +45 93511088, email: jhh@aqua.dtu.dk.

General information may be obtained from Susan Zumbach Johannesen (szjo@aqua.dtu.dk).

Your complete online application must be submitted no later than 15 September 2023 (Danish time).

For apply click here

PhD in Tumor heterogeneity in glioblastoma

The DNA Repair and Chemoresistance Group (DRC) headed by Dr. Eric Van Dyck at the Department of Cancer Research (DoCR) carries out fundamental and translational research on the molecular mechanisms governing DNA repair, chromatin dynamics and chemoresistance in cancer. Our main research interest resides in the identification & validation of novel strategies to improve cancer treatment, with a particular focus on gliomas. As part of a collaborative Télévie Research Project with the GIGA-Neurosciences (ULiège, Belgium) and the Laboratoire National de Santé (LNS, Luxembourg), the DRC is seeking to recruit a highly motivated PhD student.

PROJECT

Despite surgery and a combination of radio- and chemotherapy, the outcome for patients with glioblastoma (GBM) remains dismal. Intratumoral heterogeneity manifested by the presence of tumor cells with different properties and levels of resistance to chemoradiation poses a crucial challenge in GBM therapy. We have described a unique gene expression signature that classifies GBM specimens in two major groups displaying profound differences in proliferation as well as DNA repair and cell cycle gene expressio.

KEY responsibilities

• Participate in the setting-up and implementation of a collaborative research project
• Conduct a research project with the aims of submitting a PhD thesis dissertation and obtaining a PhD degree
• Publish results in scientific journals and/or file patents if applicable
• Participate in training and international scientific conferences
• Disseminate results to the scientific community and the public
• Participate in laboratory activities including seminars and interaction with other team

Posted on August 18, 2023

12 fully funded PhD positions in Life Sciences

The Cologne Graduate School of Ageing Research (CGA) in Germany is a joint venture of the University of Cologne Excellence Cluster on Stress Responses in Aging-Associated Diseases (CECAD), the University Hospital Cologne, the Max Planck Institute for Biology of Ageing and the Max Planck Institute for Metabolism Research. Cologne has emerged as a leading global research cluster with a stellar constellation of institutes and scientists dedicated to ageing research in Life Sciences. We offer up to 12 fully funded PhD positions to highly motivated and talented researchers.

The structured Ph.D. training programme within a cutting-edge research environment will start on an individual basis between July 1 and October 1, 2024. The initial contract is limited to three years. Payment is based on the German TV-L E13 scale, 65% if terms and conditions under collective bargaining law are fulfilled or on an equivalently remunerated Ph.D. support contract of the Max Planck Society.

We offer

• An outstanding international research environment at on of the most prestigious ageing research clusters in Europe
• Excellent infrastructure for training and research by internationally recognized scientists in facilities with state-of-the-art technologies
• Ph.D. projects that can be carried out in up to 52 participating research groups of the above mentioned institutes
• An interdisciplinary and structured Ph.D. programme in the vibrant city of Cologne, Germany, completely conducted in English
• An individual career mentoring programme, extensive methods courses and soft skill workshops
• Intensive support and guidance for international students in all administrative matters

We are looking for

• Highly qualified and motivated students holding a M.Sc. or equivalent degree in Biology, Cell/Molecular Biology, Biochemistry, Bioengineering, Bioinformatics, Biophysics, Genetics, Medical Biology, Translational Medicine or a related field
• Students who have already proven their motivation, interest and qualification for the above-mentioned research areas by achieving very good grades in their B.Sc. and M.Sc. studies
• Candidates with very good English skills (C1 level, written and spoken)

Further Information

• Application period:Aug 15 - Nov 6, 2023
• Online application portal: https://application.ageing-grad-school.de
• Contact: cga-coordination@uni-koeln.de

PhD fellowship in computational CRISPR guide RNA design

A PhD fellowship is available in the Computational Biology and Bioinformatics research group (https://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk) at Department of Veterinary and Animal Sciences (https://ivh.ku.dk/english), Faculty of Health and Medical Sciences at University of Copenhagen. The CRISPR field is developing rapidly and is continuously providing novel technological possibilities by several types of applications including gene editing and gene surgery. A key challenge is to pick the most efficient on-target guide RNA (gRNA) among several possible ones in a specific target region while taking the possible off-targets, i.e., unintended edits elsewhere in the genome, into account. This PhD project aims to make computational methods for on-target gRNA design while taking the off-target potential into account. The position is funded by the Novo Nordisk Foundation.

The PhD project is focused on designing computational methods for gRNA design while taking the off-target landscape, developed by others in the group, into account. The PhD project will take outset in the in-house deep learning (DL) model, CRISPRon, to be applied on data generated by project collaborator Prof Yonglun Luo. The initial model will encode both on- and off-target data (as ranked by our CRISPRoff method) to predict gRNA efficiency while also being used for model-driven data generation of novel gRNA efficiency data by collaborator.

Principal supervisoris Professor, Jan Gorodkin, Department of Veterinary and Animal Sciences, Phone: +45 23375667, Email: gorodkin@sund.ku.dk.

Start: November 1, 2023 or as soon as possible thereafter.
Duration: 3 years as a PhD student

Job description
Your key tasks as a PhD student at SUND are:

• Carrying through an independent research project under supervision, with content as outlined above in the project description.
• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PhD project
• Teaching and disseminating your knowledge.
• Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants    
Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project such as Bioinformatics, Computer Science or similar areas. Most importantly that you meet the technical requirements in bullet #2 below. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Application deadline:  August 23, 2023, 23.59pm CET 

Kontakt:  Jan Gorodkin E-mail: gorodkin@sund.ku.dk

Apply here

PhD fellowship in bioinformatic analysis of host - pathogen interactions

A PhD fellowship is available in the Computational Biology and Bioinformatics research group (https://ivh.ku.dk/bioinformatics), Center for non-coding RNA in Technology and Health (RTH), (http://rth.dk) at Department of Veterinary and Animal Sciences (https://ivh.ku.dk/english), Faculty of Health and Medical Sciences at University of Copenhagen. Anti-microbial resistance (AMR) is a fast-increasing challenge for human health. Within the large PIG-PARADIGM consortium (https://pig-paradigm.net/), funded by the Novo Nordic Foundation, the goal is to prevent spreading of AMR by reducing antibiotic use in pig-production. Several strategies will be taken including microbial therapies that can diminish the need for antibiotics by production of more resilient pigs. Within this PhD project the goal is to explore and establish the molecular interactions between host and commensal as well as pathogenic microbes in various sections of the pig's intestine. The research aims to identify and associate these interactions in pigs with and without diarrhoea. By gaining a deeper understanding of these interactions, the project will offer valuable insights into the characterization of resilience against pathogens.

The PhD project concerns how commensal and pathogenic microbiota modulate host signalling in the intestine and aims to elucidate fundamental aspects of disease progression. Within the gut microbiome component, the project will identify microbial species, microbial gene functions, and gene clusters through DNA sequencing by PIG-PARADIGM consortium partners. Combined with tissue/fecal metabolomics, this will lead to microbial species/gene interaction networks and pathways. Conversely, on the host side gene networks and pathways will be identified through total and small RNA-seq data likewise established by PIG-PARADIGM consortium partners.

Principal supervisoris Professor, Jan Gorodkin, Department of Veterinary and Animal Sciences, Phone: +45 23375667, Email: gorodkin@sund.ku.dk
Start:     January 1, 2024 or as soon as possible thereafter.
Duration:     3 years as a PhD student

Job description
Your key tasks as a PhD student at SUND are:

• Carrying through an independent research project under supervision, with content as outlined above in the project description.
• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PhD project
• Teaching and disseminating your knowledge.
• Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants  
Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project such as Bioinformatics, Computer Science or similar areas. Most importantly that you meet the technical requirements in bullet #2 below. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Application deadline:  August 23, 2023, 23.59pm CET

Kontakt: Jan Gorodkin E-mail: gorodkin@sund.ku.dk

Apply here

Posted on August 14, 2023

PhD student on Deep Learning for Virus and Host Genomics

Through cutting-edge research in the fields of ENERGY, HEALTH and MATTER, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) solves some of the pressing societal and industrial challenges of our time. Join our 1.500 employees from more than 70 nations at one of our six research sites! The Center for Advanced Systems Understanding (CASUS) is a German-Polish research center for data-intensive digital systems research. CASUS was founded in 2019 in Görlitz and conducts digital interdisciplinary systems research in various fields such as earth systems research, systems biology and materials research.

Natural Language Processing has substantially improved deep learning of language and our understanding of linguistics due to unprecedented possibilities for text analysis. In a collaboration between the TU Dresden and CASUS, we use transformer-based deep learning algorithms that treat genomes as text. The project will encompass using deep learning to understand the phylogeny of SARS-CoV-2 and Mpox (monkeypox). Furthermore, the project will involve the analysis of genome-wide siRNA screening data to decipher unknown host-pathogen interactions.

Your tasks:

• Design of deep learning tasks to interrogate questions of genome biology
• Devise novel approaches to incorporate Biology-informed knowledge into the model architecture
• Engage with our international collaborators (Dresden, London, Zurich, Taipei etc.) to understand existing approaches and datasets
• Collaborate with the research team on other questions of machine learning, functional genomics, genome instability
• Supervise junior lab members
• Present results and publish high-impact peer-reviewed research

Your profile:

• Master or Diploma in a relevant field, such as Molecular Biology, Computational Biology, Bioinformatics, Genetics, Computer Science, Mathematics, Linguistics or equivalent scientific background
• A solid background in biology, mathematics, software engineering, machine learning or in a related subject
• Excellent programming skills in languages such as Python
• Familiarity with modern deep learning frameworks like Tensorflow 2.x.x, PyTorch
• Previous experience or interest in Bioinformatics, Systems Biology, Natural Language Processing, Deep Learning, Git version control and Slurm cluster environments is a plus
• Strong motivation to work in a collaborative environment
• Excellent communication skills in English and in a professional context (presentation of research results at scientific meetings, colloquial discussions, writing of manuscripts)

Deadline: 4 October 2023

Apply here

Doctoral Researcher (Biology)

The department Ecology and Emergence of Zoonotic Diseases of Prof. Dr. Fabian Leendertz at the Helmholtz Institut für One Health (HIOH) in Greifswald, Germany is offering a position as Doctoral Researcher (f/m/d).

We offer a position as doctoral researcher within the “BCOMING” project (Biodiversity Conservation to Mitigate the risks of emerging infectious diseases) which aims at understanding how biodiversity conservation measures can prevent the insurgence of zoonotic diseases. BCOMING is a highly interdisciplinary international consortium, encompassing ecology, infectious research, geography, social sciences and anthropology.

Qualifications:

• Master’s Degree/Diploma in Veterinary medicine, Biology, Genetics, or a related field of the life sciences
• Previous field experience in tropical countries is desirable
• Experience in working in a molecular lab environment
• Flexible mindset, teamwork oriented and excellent communication skills
• English proficiency necessary, French (B1) necessary
• Ability to work independently and as part of an international team

Advantageous for this position:

• Familiarity with R environment, bioinformatics (or interest in learning it)
• Interest in living in West Africa for extended periods of time (3-6 months stays over project duration)
• Strong interest in applied molecula ecology.

Closing date: 31.08.2023

Apply here

PhD program in Medical Biotechnology

The VIB-UGent Center for Medical Biotechnology (CMB) focuses on the development of new and innovative molecular tools and technologies to challenge human health problems. The Center translates its novel technologies and insights to widely applicable research tools, vaccines, diagnostics, and biopharmaceuticals. Our research pushes the boundaries of protein- and DNA-focused biomolecular and bioinformatics research and engineering technologies. CMB educates and trains the next generation of medical biotechnology researchers and informs the public on the impact of biotechnology on human health.

Ph.D. projects:

• Multi-omics characterization of immune triggers in Moyamoya disease – Impens Lab
• Computational mass spectrometry – Martens Lab
• Development and exploitation of a novel glycosylation-enabled antibody-drug conjugate technology – Callewaert Lab
• Development and exploitation of novel proteomics technology to hunt for novel immunotherapy targets on cancer cells – Callewaert Lab
• Functional studies on N-terminal proteoforms of tRNA ligases – Gevaert Lab
• Coronavirus control – Saelens Lab

PhD position in Molecular and Computational Neurogenomics

We are a highly motivated international team of researchers at the Molecular Neurogenomics group (Jordanova Lab) and the Computational Neurobiology group (Malysheva Lab) at the VIB CMN. We are excited to announce a call for a joint Ph.D. student in our labs to work on a challenging project at the interface of neurodegeneration, genomics, computational and systems biology.

Charcot-Marie-Tooth disease (CMT) represents the most common genetic disorder of the peripheral nervous system. Patients experience progressive distal muscle weakness and wasting, sensory loss, and skeletal deformities ultimately leaving them severely disabled. This lifelong disorder is currently incurable. The largest protein family implicated in the etiology of CMT are aminoacyl-tRNA synthetases (ARS). Ubiquitous and essential enzymes, ARS catalyse a critical step in protein biosynthesis by charging tRNA with their cognate amino acid. Jordanova Lab reported that dominant mutations in the tyrosyl-tRNA synthetase (YARS) cause a clinical variant of CMT and so far six additional cytoplasmic ARS have been implicated in the same pathology.

The candidate should:

• have an MSc in Systems Biology, Molecular Biology, Natural Sciences, or related disciplines
• be very motivated and enthusiastic to learn and expand both computational and experimental skill sets
• be able to summarize data extracted from the literature and clearly shape research objectives
• be able to efficiently communicate with experimental and computational scientists
• have excellent communication and writing skills in English

Required skills

• confident in basic molecular biology techniques, such as cell cultures, basic genomics data generation
• basic/intermediate programming skills in R and/or Python
• Ability to adapt to the research environments while being full members of two labs

Desirable skills

• knowledge of gene regulatory mechanisms
• statistical analysis
• basic processing of NGS data
• experience with iPSC culturing
• knowledge of and some experience with genetic perturbation assays, such as CRISPR

For more information: please contact albena.jordanova@vib.be, valeriya.malysheva@vib.be or jobs.cmn@uantwerpen.vib.be

For application click here

PhD position in Bioinformatics

At the Faculty of Medicine, Department of Clinical Science, a full-time PhD-position is available for a period of four (4) years or max 4 months after completed the PhD-degree, if this is achieved within a shorter time than four years. The positions include 25 % required duties such as teaching, exam work or supervision, depending on the demands at the department. The position is part of the project “People of Norway”, and is funded by the University of Bergen.

Qualifications and personal qualities:

Your application must include:

Posted on August 08, 2023

PhD student in computational analysis of health trajectories

The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is the leading supercomputing center in Spain. It houses MareNostrum, one of the most powerful supercomputers in Europe, was a founding and hosting member of the former European HPC infrastructure PRACE (Partnership for Advanced Computing in Europe), and is now hosting entity for EuroHPC JU, the Joint Undertaking that leads large-scale investments and HPC provision in Europe. The mission of BSC is to research, develop and manage information technologies in order to facilitate scientific progress. BSC combines HPC service provision and R&D into both computer and computational science (life, earth and engineering sciences) under one roof, and currently has over 800 staff from 55 countries.

• Integration of heterogeneous data sources using advanced data mining techniques.
• Preparation and presentation of scientific articles
• Collaborate in the preparation and presentation of scientific projects
• Establish and maintain collaborations with international researchers

• Education
  • Bachelor in biology, biotechnology, medicine, or a degree in science or engineering with sufficient knowledge and interest in biology.
  • MSc in bioinformatics, computational biology or similar.

Deadline The vacancy will remain open until suitable candidate has been hired. Applications will be regularly reviewed and potential candidates will be contacted.

Apply here

PhD position in Neurology and Stroke

Posted on August 05, 2023

PhD position in human Palaeogenomics

In the framework of the research project GenIn Characterizing the deep roots of Gender Inequalities through molecular archaeology, the CNRS Occitanie-Ouest is offering a fully-funded 3-year position in human palaeogenomics. The PhD student will receive training from experts and undertake cutting-edge research in archaeo-anthropology and palaeogenomics. The project GenIn aims at leveraging the latest advances in molecular archaeology, combined with archaeology, anthropobiology and geochemistry, to better understand the deep roots of gender inequalities by exploring the status and life of women and men during the late Neolithic in present-day France territory.

The primary aim of the PhD project is to reconstruct and analyse ancient genomic data of late Neolithic individuals. When integrated to archeo-anthropological contexts, this new molecular data will enable the exploration of potential contrasts between men and women regarding their health, their position in familial and social networks as well as their respective contribution to the genetic make-up of the population. The analyses will use state-of-the art palaeogenomics methods to screen and recover ancient DNA data (using whole genome sequencing or targeted enrichment techniques depending on preservation conditions) from human skeletal remains dating ~3500-2500 Before Common Era and excavated in present-day Southern France.

The PhD candidate should have a background in molecular genetics, evolutionary biology, bioinformatics, palaeogenomics or a related field. Knowledge in statistical and bioinformatics analyses is expected, as well as an interest in archaeology and anthropology. Experience in a molecular biology laboratory will be a plus. T

he successful candidate will be involved in all aspects of the project (except for field work), from laboratory work and data analysis to the dissemination of results. Research results will be published in international peer-reviewed journals, and disseminated through oral presentations in national or international conferences and in general public seminars. Candidates must have excellent communication skills, be self-motivated and able to work both independently and as part of a team. Candidates should be able to communicate (speaking + writing) in English. Being able to communicate in French is not required. The CAGT wishes to reflect the diversity of society and welcomes applications from all qualified candidates regardless of social background, disability, gender, nationality, religion or sexual orientation.

For details click here

PhD student in Metabolism and Cell Biology

The Leibniz Institute of Plant Biochemistry in Halle (Saale), a research institute of the Leibniz Association, is offering a three-year position in the frame of a DFG-funded project for a PhD student (m/f/d) at the Department of Metabolism and Cell Biology, working group Jasmonate Function & Mycorrhiza.

We are looking for a highly motivated PhD student (m/f/d) to study the genetic and molecular interactions of different transcription factors during gynoecia development and fruit set in tomato. The work is based on our previous data (Schubert et al. [2019], Plant Cell 31:1043-1062; Israeli et al. [2023], Plant Physiology 192:2336-2355) and will provide insight into the coordinated function of MYBs and ARFs in the cross-talk between auxin and JA in tomato reproduction. Molecular biological and biochemical methods will be applied. The project is a collaborative project with the Hebrew University of Jerusalem, Israel.

The successful applicant (m/f/d) with a degree that was not obtained at a German university must submit a certificate assessment for foreign university qualifications (Statement of Comparability for Foreign Higher Education Qualifications) from the Central Office for Foreign Education (https://www.kmk.org/zab/central-office-for-foreign-education).

Please send your complete application documents including the reference number 11/2023 until 15.08.2023 exclusively by email to bewerbungen(at)ipb-halle.de

Contact for further information:

Prof. Dr. Bettina Hause, bettina.hause(at)ipb-halle.de

For details click here

Posted on August 02, 2023

Two PhD fellows in Human Diet-Gut-Brain interactions

Department of Nutrition, Exercise and Sports, Faculty of Science at University of Copenhagen is offering two PhD scholarships to study interactions between dairy products, gut movements, the microbiome, cognition and brain function in humans commencing 01.10.2023 or as soon as possible thereafter.

The scientific environments

The two positions are available in the Research Groups of Gut Microbes, Diet and Health and Motor Control and Neuroplasticity, respectively, at the Department of Nutrition, Exercise and Sports.

The Gut Microbes, Diet and Health Research Group

The group conducts research to understand the mechanisms by which the gut microbiota contributes to digestion and health. The group conducts human cohort and intervention studies, apply cutting-edge metabolomics and microbiomics, and collaborate with leading microbiome researchers and researchers in immunology and intestinal host receptors to elucidate host-microbial cross-talk.

Responsibilities and tasks
The two PhD positions are part of a project called YourGutBrain - Yoghurt to alter gut movements and brain function supported by Arla Food for Health, a public-private research partnership between the University of Copenhagen, Aarhus University, Arla Foods Amba and Arla Foods Ingredients.

The project brings together a multi-disciplinary team of experts across nutrition, diet-microbiome interactions, cognitive performance and brain activity to uncover novel causal and mechanistic evidence of fermented dairy as an approach to optimize gut health and cognition.

To be eligible for the PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. in Neuroscience, Human Physiology, Psychology or Microbiology, Biotechnology, Bioinformatics, Human Nutrition or related fields with excellent results.

Principal supervisorsare Associate Professor Henrik Munch Roager (hero@nexs.ku.dk) and Associate Professor Anke Karabanov (anke@nexs.ku.dk), Department of Nutrition Exercise and Sports, University of Copenhagen.

The deadline for applications is 6 August 2023, 23:59 (GMT+2).

Apply here

PhD steering soil microbiomes for crop quality

The Institute of Environmental Sciences (Faculty of Science at Leiden University) is looking for:

1 PhD candidate Steering soil microbiomes for better crop quality: The holy grail to improve human health

Note: this is an advertisement for one PhD student that will work at the Institute of Environmental Sciences in close collaborations with another PhD student advertised by the Institute of Biology . Students will be working together on a larger project on ‘Steering soil microbiomes for better crop quality: The holy grail to improve human health’

Project:
Are you a motivated researcher who is excited to implement novel methods and work in an interdisciplinary consortium with experts in human health, governance and biology? Do you have a MSc degree in soil science, ecology, microbial ecology or a related field? And do you like variation in your activities with laboratory, field, and analytical work? Then this could be the ideal PhD position for you!

We are hiring two PhD students who will work on a project that is an interdisciplinary collaboration between several institutes within Leiden University, University of Groningen, NIOO-KNAW, LUMC, van Hall Larenstein and Maastricht University. The PhDs, one of which will be situated at the Institute of Environmental Sciences (CML) and the other one at the Institute of Biology (IBL), will work at the interface of soil microbiomes and soil ecology, plant health, and in collaboration with LUMC.

Selection criteria

• a team player with a collaborative attitude and ability to work within a multidisciplinary team;
• a completed (or about to be completed) MSc degree in soil science, plant sciences, ecology, microbial ecology or a related field;
• hands-on experience in, or strong affinity with, at least two of following topics: field experiments, laboratory (manipulative) experiments, molecular laboratory analyses (including molecular analyses, 13C tracing techniques), plant quality analyses, (multivariate) statistical analyses;
• excellent English language proficiency;
• we value experience with scientific writing.

This vacancy will be listed up to and including Sunday 3 September 2023. Interviews will be scheduled in end of September 2023.

For more information:

For more information about these position please contact Dr. Emilia Hannula s.e.hannula@cml.leidenuniv.nl (for PhD position at CML) and/or Prof. Martijn Bezemer t.m.bezemer@biology.leidenuniv.nl (for PhD position at IBL).

Apply here

Posted on July 31, 2023

PhD student position: Machine learning and systems biology

The Max Planck Institute of Biochemistry (MPIB) in Martinsried, Munich is one of the leading international research institutions in the fields of biochemistry, cell and structural biology and biomedical research. With about 30 scientific departments and research groups and about 800 employees, the MPIB is one of the largest institutes of the Max Planck Society.

The Department of Machine Learning and Systems Biology headed by director Prof. Dr. Karsten Borgwardt is seeking a PhD student (m/f/d).

Scientists in the Department of Machine Learning and Systems Biology develop and apply novel machine learning algorithms to detect patterns and statistical dependencies in large datasets from biology and medicine. Machine learning on graphs, machine learning in medicine and machine learning in protein research are current and future foci of the department. We seek a highly motivated doctoral student (m/f/d) to join an enthusiastic and collaborative team in an outstanding scientific environment.

Your qualifications

The successful candidate should have a Master's degree or similar qualification in bioinformatics, computer science, mathematics, statistics, engineering, physics, or related fields. He/she should be motivated to  develop new machine learning methods and/or to apply machine learning algorithms to solve problems in the life sciences. Written and oral command of the English language is essential.

Your application

Then please upload your complete application documents, containing a one-page letter with a personal statement describing your scientific accomplishments and your interests in our department and its research, your CV and bibliography, as well as contact information for at least two references, in electronic form via the online application website. Deadline: September 15, 2023.

PhD student in structural biology of glycan-modifying enzymes

The Faculty of Science Leiden and Leiden Institute of Chemistry are looking for a PhD student in structural biology of glycan-modifying enzymes Join our research team as a PhD student in structural biology of glycan-modifying enzymes! Expand your knowledge in biochemistry and structural biology while working on cutting-edge research projects.

A PhD position is available in the research team of Dr. Zach Armstrong working on the structural biology of glycan-modifying enzymes. The project is aimed at the structural biology of human and viral enzymes that modify glycocalyx sugars. This will be achieved through protein production in insect and human cells, protein purification, enzyme kinetics, application of precision chemical tools and structural biology of enzymes and their complexes (X-ray/CryoEM). The research associate must be flexible and communicative and have knowledge of both biochemistry and structural biology.

The key responsibilities of the project will be:

• Expression of mammalian (and viral) genes in insect and human cell systems
• Enzyme kinetics, including enzyme inhibition kinetics and determination of substrate specificity
• Structure solution by X-ray crystallography (CryoEM where appropriate): crystallization, data collection and structure solution / refinement / deposition
• To keep up-to-date, in a pro-active manner, with scientific literature in the field of carbohydrate chemistry and glycobiology and help disseminate this information through to the group
• To provide guidance to other staff and students, as required, as well as coordinating the work of small research teams
• To supervise Masters and Bachelors project students in the laboratory

Selection Criteria

• Masters degree in Structural Biology or Biochemistry;
• Experience with protein expression;
• Knowledge of Structural biology, Cryo-EM or X-ray Crystallography;
• Knowledge of enzyme kinetics is preferred but not essential;
• Excellent communication skills in the English language are essential

Do you have questions about this position? Please contact Dr. Zach Armstrong, z.w.b.armstrong@lic.leidenuniv.nl.

For details click here

Posted on July 28, 2023

PhD student tin Microbiome/ Bioinformatics

The University of Antwerp is a dynamic, forward-thinking, European university. We offer an innovative academic education to more than 20,000 students, conduct pioneering scientific research and play an important service-providing role in society. We are one of the largest, most international and most innovative employers in the region. With more than 6,000 employees from 100 different countries, we are helping to build tomorrow's world every day. Through top scientific research, we push back boundaries and set a course for the future – a future that you can help to shape.

The Lebeer Lab performs cutting edge research on Lactic Acid Bacteria and their habitats, including the human microbiome (with a special focus on the vaginal microbiome) but also vegetable fermentations, insects and plants. Prof. Sarah Lebeer holds a prestigious ERC Starting Grant on the ecology, evolution and beneficial potential of lactobacilli. In 2020, the group launched the Isala citizen science project on the female microbiome, with more than 3,000 participants.

Position

• You will work actively on the preparation and defense of a PhD thesis on the topic of the ecology and evolution of female microbiome. Your own research interests and ideas surrounding this topic are welcomed and encouraged.
• Your research will mainly entail the development and application of computational pipelines for DNA and RNA sequencing data analysis.
• You will publish scientific articles on your research.
• You will present your work at national and international workshops and conferences.
• You will apply for an FWO PhD fellowship on the topic of the female microbiome, again with considerable room for your own interests and ideas. There is in-house funding available so failing to obtain such a fellowship poses no problem.
• You will carry out a limited number of teaching and research support tasks for the department of Bioscience Engineering.

Profile

• You hold a Master degree in bioinformatics or you hold a Master degree in biology, bioscience engineering, biochemistry or biomedical sciences and you have experience with bioinformatics. Last year Master students can also apply.
• You can work fluently with Linux and Bash.
• You can code in Python and/or R.
• You have a solid understanding of molecular biology and microbiology.
• You are interested in microbial ecology and evolution and in the human microbiome.
• You are interested in learning how to analyze microbial genome, metagenome and (meta)transcriptome sequencing data through various techniques, including (meta)genome assembly, read mapping to reference genomes and phylogenetic analysis.

Want to apply?

• You can apply for this vacancy through the University of Antwerp’s online job application platform up to and including 21 August 2023 (by midnight Brussels time). Click on the 'Apply' button, complete the online application form and be sure to include the following attachments: (1) a motivation letter, (2) your CV and (3) contact info for one or two references.
• The selection committee will review all of the applications as soon as possible after the application deadline. As soon as a decision has been made, we will inform you about the next steps in the selection procedure. The interviews will take place on 6 September 2023.
• If you have any questions about the online application form, please check the frequently asked questions or send an email to jobs@uantwerpen.be. If you have any questions about the job itself, please contact dr. Stijn Wittouck, senior bioinformatician at the Lebeer Lab, (stijn.wittouck@uantwerpen.be).

Apply here

PhD Researcher in Bioinformatics: Investigating protein evolution using machine learning

The Bioinformatics Group at Wageningen University is seeking a motivated and talented PhD researcher to join our team. In this role, you will delve into the fascinating world of orphan genes – genes that are unique to a single species, with no homologs found in other organisms.

In this project, we will investigate orphans in human gut microbiome species. We will use state-of-the art machine learning approaches to study the properties of orphans and to learn about their evolutionary origin and potential function. In particular, we plan to use predicted protein structures to detect remote homology and to investigate the properties of proteins with potentially novel functions. This work will contribute to a fundamental understanding of how proteins evolve.

The ideal candidate must have the following qualities:

• A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline;
• Proficiency in programming (e.g. in Python);
• Experience in applying machine learning to biological data;
• Strong affinity with molecular evolution and/or prokaryote genomics;
• Good statistical and mathematical skills;
• Perseverance in problem solving;
• Excellent writing and oral communication skills in English.

For more information about this position, please contact dr. Anne Kupczok by email: anne.kupczok@wur.nl and dr. Aalt-Jan van Dijk by email :aaltjan.vandijk@wur.nl.
For more information about the procedure, please contact Noorien Abbas, Corporate Recruiter, by email: vacaturemeldingen.psg@wur.nl.

Apply here

Posted on July 25, 2023

PhD Position in Protein science

Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 54,000 students, more than 7,500 employees and a turnover of around SEK 8 billion.

The Department of Medical Biochemistry and Microbiology (IMBIM) at Uppsala University provides a broad international environment for research and teaching. Research at IMBIM) broadly spans the areas of biochemistry, cell and molecular biology, tumour biology, comparative genetics, functional genomics, immunology, bacteriology, and virology. The research is essentially of fundamental nature, but with relevance and application in health and disease in both animals and humans.

Qualifications: The person we are looking for should have a master’s degree or equivalent (240 ECTS) in molecular biology, biochemistry, structural biology or similar, providing basic theoretical and practical knowledge. Experience in working with proteins should be demonstrated through a MSc project.

The applicant must be fluent in written and spoken English (see entry requirements at: https://www.uu.se/en/study/masters-studies/application/entry-requirements). The candidate is expected to take initiative driving the project, but also to collaborate with the other members of the doctoral network. Emphasis will be given on personal qualities, including analytical capacity, accuracy, flexibility and collaborative skills.

For further details, please contact: Per Jemth, Per.Jemth@imbim.uu.se

Application: Please submit your application using the Uppsala University application portal, by including a CV, a letter describing your research interest and skills, publications or a copy of master thesis or equivalent, contact information of two referees (phone number and e-mail address).

You are welcome to submit your application no later than September 21, 2023, UFV-PA 2023/2601.

Apply here

PhD position in insect microbiome ecology

An NSF-funded PhD position is available in Dr. Alison Ravenscraft’s laboratory at the University of Texas at Arlington. Ravenscraft Lab (https://www.ravenscraftlab.com) focuses on ecological interactions between insects and their microbial symbionts. The available position will focus on the role of the caterpillar gut microbiota in the plant-insect chemical arms race. Start date is flexible but ideally will correspond with the start of the Spring 2024 or Fall 2024 semesters.

The idea that gut flora may assist insects in breaking down plant defenses has been often proposed, but rarely tested. The graduate student will join a team of collaborative researchers who are working together to ask whether, and how much, the insect gut flora help to detoxify an herbivorous diet. The research will involve a combination of field work, insect rearing experiments in the lab, microbial cultivation, and high-throughput metagenomics. The student will acquire highly desirable skills including microbial culture techniques, use of analytical chemistry equipment (HPLC, LCMS), and the generation and analysis of high-throughput sequencing datasets. The position is fully funded by a prestigious NSF grant, and the student will also benefit from three years of preliminary data and sample collection, including a library of hundreds of insect gut bacterial isolates.

Qualifications

Fundamental requirements include:
• A bachelor’s degree or higher in Biology, Ecology, Microbiology, Chemistry, Bioinformatics, or a related field
• Strong work ethic and independence
• Excellent communication and teamwork skills
• Excellent English writing and speaking ability.

Although not required, the preferred candidate will have prior research experience, programming experience (R or Python), and demonstrated scientific writing skills.

Interested students should send an email with their CV and a brief description of their research interests to Dr. Ravenscraft (alison.ravenscraft@uta.edu). Please include "caterpillar graduate position" in the subject line. Review of applications for spring entry will begin on Sep 1, 2023 and review for fall entry will begin on December 1, 2023.

For details click  here

PhD student Cardiac regeneration and remodeling

The Max Planck Institute for Heart and Lung Research in Bad Nauheim is an interdisciplinary research institution with international flair. Our researchers have the possibility to work on various model systems by making use of latest cutting-edge technologies. A successful applicant will have the opportunity to become a member of the International Max Planck Research School for Molecular Organ Biology.

The Max Planck Society wishes to increase the share of women in areas in which they are underrepresented. Women are strongly invited to apply. The Max Planck Society is committed to employing more handicapped individuals and especially encourages them to apply.

he Max Planck Institute for Heart and Lung Research, Department Cardiac Development and Remodeling, Prof. Dr. Thomas Braun, in Bad Nauheim (near Frankfurt am Main) is offering a PhD student position (f/m/d) in the field of cardiac regeneration and remodeling, ref. nr. 2023_09.

Job Description

We seek enthusiastic, highly motivated people to join our international research group working on immune cell heterogeneity during cardiac regeneration and remodeling. The current project involves the characterization of mouse mutants in different disease models, including functional, histological, transcriptional, and protein biochemical analysis. Experience with animal models and solid knowledge in bioinformatics to analyze single cell RNAseq data and of immunology is highly appreciated. Salaries will be based on previous experience according to TVöD guidelines.

Your application

Applicants should submit a statement of interest, a full CV including certificates, and names and addresses of two references via our applicant portal.

Posted on July 19, 2023

PhD student position in genomic analysis of brain tumors

We are looking for a bioinformatics PhD student to join the research team of Dr. Sevin Turcan at the University Hospital Heidelberg/National Center for Tumor Diseases. Our laboratory uses advanced omics techniques to analyze patient samples and preclinical in vitro/in vivo models to study brain tumor biology. As a key member of our team, the PhD student will have the opportunity to analyze, interpret, and make a significant impact on the computational projects in the lab by analyzing genomics datasets obtained from primary brain tumor samples and preclinical glioma models (e.g., single-cell RNA-seq/ATAC-seq and spatial transcriptomics). This work will be critical in uncovering biological insights into adult brain tumors. The project is initially limited to 3 years, with the possibility of extension.

To learn more about our lab and the work we do, please visit our website at: here

Responsibilities:

Design and implement bioinformatics pipelines for data analysis (particularly single cell RNA-seq and spatial transcriptomics)
Develop and apply computational methods for the analysis and integration of genomics and epigenomics data
Communicate results effectively in both written and oral formats

Personal qualifications:

Master’s degree in bioinformatics, computational biology, or a related field Proficiency in at least one programming language (e.g., R, Python) Familiarity with single cell data analysis tools and software Excellent communication skills in spoken and written English. A high level of motivation, flexibility, and reliability.

For details click here

PhD Researcher in Bioinformatics

Are you looking for a PhD position and interested in research on protein evolution in bacteria? Are you a bioinformatician who wants to apply state-of-the-art machine learning methods on gene sequences and protein structures to analyze evolutionary patterns? Then this PhD vacancy may be of interest to you!

Job description:

The Bioinformatics Group at Wageningen University is seeking a motivated and talented PhD researcher to join our team. In this role, you will delve into the fascinating world of orphan genes – genes that are unique to a single species, with no homologs found in other organisms.

Even though more and more sequencing data is available, we cannot find homologs of these genes outside of that single species. The evolution of such genes is particularly intriguing, since they might arise from very fast divergence beyond recognition or entirely novel “from scratch” from a region that did not code for a protein before. Alternatively, some might simply be artefacts of the automatic annotation.

The ideal candidate must have the following qualities:

• A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline;
• Proficiency in programming (e.g. in Python);
• Experience in applying machine learning to biological data;
• Strong affinity with molecular evolution and/or prokaryote genomics;
• Good statistical and mathematical skills;
• Perseverance in problem solving;
• Excellent writing and oral communication skills in English.

For more information about this position, please contact dr. Anne Kupczok by email: anne.kupczok@wur.nl and dr. Aalt-Jan van Dijk by email :aaltjan.vandijk@wur.nl.
For more information about the procedure, please contact Noorien Abbas, Corporate Recruiter, by email: vacaturemeldingen.psg@wur.nl.

Apply here

Posted on July 17, 2023

Doctoral (PhD) position in genetics

Our vision is to use human genetics to understand how our evolutionary history impacts health and disease. We do so by leveraging large-scale biobanks, omics data and experimental techniques in our wet-lab. We are interested in the gene flow from Neandertals and Denisovans into modern humans and the genetic legacy of archaic gene variants. In addition, the group is interested in genetic variability in general and the functional consequences thereof, particularly for membrane-bound proteins such as receptors and ion channels. Other topics of interest include the genetic predisposition to infectious diseases, such as COVID-19.

The doctoral student project and the duties of the doctoral student

The doctoral student will perform analysis of medical genetics, archaic DNA, population-scale biobanks, and conduct experimental research. This includes challenging tasks in computational biology, bioinformatics, and wet-lab work including molecular biology and pharmacology. Overall, the project strives to leverage combined insights in genetics with medical knowledge to gain insights of pathophysiological and pharmacological relevance.

What do we offer?

A creative and inspiring environment full of expertise and curiosity. Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. As a doctoral student you are offered an individual research project, a well-educated supervisor, a vast range of elective courses and the opportunity to work in a leading research group.

Eligibility requirements for doctoral education

In order to participate in the selection for a doctoral position, you must meet the following general (A) and specific (B) eligibility requirements at latest by the application deadline.

It is your responsibility to certify eligibility by following the instructions on the web page Entry requirements (eligibility) for doctoral education.

A) General eligibility requirement

You meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:

1. have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
2. have satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the advanced/second-cycle/master level, or
3. have acquired substantially equivalent knowledge in some other way in Sweden or abroad.*

Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.

*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.

B) Specific eligibility requirement

You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:

- Show proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school.

Reference number STÖD 2-2752/2023

Last application date 11.Aug.2023 11:59 PM CEST

For details click here

PhD candidate in Biochemistry / Cell Biology / Neurobiology

Using a wide range of molecular biological, protein biochemical and microscopic techniques as well as cell biological assays, our institute conducts groundbreaking basic research on molecular implementation and control of the cellular processes underlying the development and plastic adaptations of cellular features required for proper organ function.

Proper neuronal cell shape development and plasticity e.g. are essential prerequisites for the formation of neuronal networks, the information transfer in the brain, as well as for plastic adjustments representing an important basis for learning and memory processes. All of these processes are largely brought about by actin cytoskeletal and membrane topology-modulating proteins. Identifying and molecularly understanding such components therefore is our top research focus.

PhD project:
The aim of the project offered is to understand cell morphology development and plastic adaptations thereof by studying molecular players at the actin cytoskeleton/membrane interface both at cellular/functional as well as at molecular/mechanistic levels. Additionally,
revealing and studying interaction partners and regulatory mechanisms (phosphorylation; Ca2+ sensor protein association, Arg-methylation) will lead to broader insights into mechanisms of cellular development, plasticity, stress adaptation and repair.

We welcome applications from candidates fulfilling the following criteria:
• Master of Science or Diploma (in biochemistry,
neuroscience, biology or similar)
• High level of motivation and enthusiasm for scientific research in an ambitious, international team
• Reliability, accuracy, responsibility
• Sound, basic knowledge in: Molecular biology, protein biochemistry, cell biology, imaging
• Specialized experience with e.g. membrane
interaction studies, high-resolution or electron microscopy, signal transduction work is an advantage but not required
• Software knowledge (e.g. Office; Excel; Prism; ImageJ)

We are looking forward to your application!

In order to join us, please direct your complete application
- CV incl. Publ. & honors,
- certificates & transcripts of both Bachelor and Master,
- 2-3 ref. addresses, cover/motivation letter
to: Michael.Kessels@med.uni-jena.de

For details click here

Posted on July 14, 2023

Doctoral scholarship holder artificial intelligence for bioinformatics 

The University of Antwerp is a dynamic, forward-thinking, European university. We offer an innovative academic education to more than 20000 students, conduct pioneering scientific research and play an important service-providing role in society. We are one of the largest, most international and most innovative employers in the region. With more than 6000 employees from 100 different countries, we are helping to build tomorrow's world every day. Through top scientific research, we push back boundaries and set a course for the future – a future that you can help to shape.

The Department of Computer Science in the Faculty of Science is looking for a full-time (100%) doctoral scholarship holder in the field of artificial intelligence for bioinformatics.

Position

• You will work actively on the preparation and defence of a PhD thesis in the field of artificial intelligence under the supervision of Prof. Dr. Wout Bittremieux.
• You will build on recent advances in artificial intelligence to develop deep neural network models for the analysis of molecular data. You will develop algorithmic and high-performance computing solutions to derive novel biological insights from large-scale mass spectrometry proteomics data and study the role of proteins as fundamental building blocks of life.
• You will be part of the Adrem Data Lab, an internationally renowned research group known for its contributions to the theory as well as practical application of data sciences, and Biomina (biomedical informatics research network Antwerp), a multidisciplinary network that brings data science technology and challenges in life sciences and biomedicine together.
• You will publish scientific articles related to the research project.
• You will carry out a limited number of teaching and research support tasks for the Bittremieux Lab, such as assisting practical teaching sessions and supervising Bachelor and Master students in the group.

Profile

• You hold a Master degree in Computer Science, Machine Learning, Bioinformatics, Chemistry, Biology, Biomedical Sciences, or related fields, or you will have obtained it by the time you start work.
• Although a background in molecular biology or the life sciences is an advantage, it is not a prerequisite. If this is the case, please address it in your cover letter.
• You can demonstrate excellent study results.
• Foreign candidates are encouraged to apply.
• Your teaching competences are in line with the University of Antwerp’s educational vision.
• Your research qualities are in line with the faculty and university research policies.
• You act with attention to quality, integrity, creativity, and cooperation.
• You have excellent programming skills (Python preferred, knowledge of additional programming languages is a plus) and have a keen interest in machine learning, big data analytics, and their application in the life sciences.
• You have excellent oral and written communication skills, have an inquisitive mindset, and have strong interpersonal skills. You are fully fluent in English.

Want to apply?

• You can apply for this vacancy through the University of Antwerp’s online job application platform up to and including 7 August 2023(by midnight Brussels time). Click on the 'Apply' button and complete the online application form. Be sure to include the following attachments:
  • a strong motivation letter
  • a detailed academic CV
  • a software portfolio (e.g. GitHub)
  • two recommendation letters or contact information of two scientific references
• The selection committee reviews all applications as soon as possible after the application deadline. As soon as a decision is made, we will notify you. If you are still eligible after the pre-selection, you will be informed about the possible next step(s) in the selection procedure. Interviews of the candidates, after a preselection by the selection committee, will take place in August 2023.
• If you have any questions about the online application form, please check the frequently asked questions or send an email to jobs@uantwerpen.be. If you have any questions about the job itself, please contact Dr. Wout Bittremieux (wout.bittremieux@uantwerpen.be) with as email subject “DOCPRO AI for bioinformatics.”

Apply here

PhD student to work on somatic variation (Genomics)

The University of Antwerp is a dynamic, forward-thinking, European university. We offer an innovative academic education to more than 20000 students, conduct pioneering scientific research and play an important service-providing role in society. We are one of the largest, most international and most innovative employers in the region. With more than 6000 employees from 100 different countries, we are helping to build tomorrow's world every day. Through top scientific research, we push back boundaries and set a course for the future – a future that you can help to shape.

The Rademakers team (Genetics of Frontotemporal Dementia) at the VIB-UAntwerp Center for Molecular Neurology, Belgium is seeking a highly motivated PhD student to work on somatic variation as a potential cause of frontotemporal dementia using bioinformatic analysis and statistical evaluation of multiple omics datatypes. The Rademakers lab performs research on disease modeling, epigenetics, transcriptomics, proteomics, and short and long-read sequencing in Frontotemporal dementia and related dementias.

Position

Frontotemporal dementia is clinically characterized by language and behavioral impairment. About half of the individuals do not have a positive family history yet show remarkably similar symptoms with asymmetrical pathology found in the brain. Somatic variants in the brain are an attractive explanation based on these observations. In this genetics project, the candidate will investigate the role of somatic variation based on the most extensive collection of frontotemporal dementia patients with TDP-43 brain pathology gathered through international collaborations. This project will be performed with a combination of state-of-the-art short and long read DNA and RNA sequencing methods, and an in-depth genetic and biostatistical analysis. The successful candidate will contribute to systematically evaluating this challenging type of variant.

Profile

We seek a highly motivated, enthusiastic, critical, and creative individual to join our team. The candidate should have a strong interest in bioinformatics, biostatistics, and genetics, and experience in sequencing data analysis is considered an advantage.

Essential:

• Master’s in biochemistry, biomedical sciences, bioinformatics, related disciplines or equivalent through experience
• Proficient in verbal and written English.
• Ability to summarize data extracted from literature and to define research objectives.
• Passion for science, self-motivation, flexibility, and team spirit

Desirable but not required:

• Programming experience, preferably in Python or R
• Experience with data analysis and working in the Linux environment
• Experience with large-scale data from genomics and transcriptomics
• Experience with data analysis of short- and long-read sequencing and awareness of the biotechnological background
• Experience with a workflow management system such as Snakemake or Nextflow

Want to apply?

• You can apply for this vacancy through the University of Antwerp’s online job application platform.
• Be sure to include:
  • a detailed CV incl. a list of previous experience
  • a letter of motivation explaining why you are interested in our work and aspire this PhD position
  • the names and contact details of 3 references
• The selection committee will review all of the applications and as soon as a decision has been made, we will inform you about the next steps in the selection procedure.
• If you have any questions about the online application form, please check the frequently asked questions or send an email to jobs@uantwerpen.be. For questions about the job itself you can contact wouter.decoster@uantwerpen.vib.be

For more information please contact wouter.decoster@uantwerpen.vib.be

For details click here

Posted on July 10, 2023

PhD in Bioinformatics, Biostatistics and Artificial Intelligence

We (Luxembourg Centre for Systems Biomedicine) seek a highly motivated bioinformatician or biostatistician who is well versed in the statistical and machine learning analysis of biomedical data and bioscientific programming for a project on the study of neurodegenerative diseases. The candidate should have experience in the analysis of large-scale biomedical data (omics, clinical, imaging, or other large biological datasets), using statistical methods, pathway/network analysis or machine learning/artificial intelligence. The candidate will conduct integrative analyses of biomedical datasets, focusing on omics and clinical data to predict clinical outcomes of interest (e.g., disease progression scores). This will include implementing and applying software analysis pipelines and interpreting disease-related data together with experimental and clinical collaborators.

Classification models guided by prior mechanistic knowledge will be built, exploiting the known grouping structures among features in the omics data, using dedicated structured learning algorithms. With the help of statistics, machine learning and pathway- and network- and analyses, the goal is to improve the mechanistic understanding of disease-associated alterations in neurological disorders.

Skills/Qualifications
Your Profile

• The candidate will have an MSc or equivalent degree in bioinformatics, biostatistics, machine learning, computational biology, or related subject areas
• Prior experience in large-scale data processing and statistics / machine learning is required
• Previous work and publications in bioinformatics or biostatistics analysis of large-scale biomedical data (e.g., omics, clinical, imaging, other biomedical data) should be outlined in the CV
• Demonstrated skills and knowledge in omics data analysis, machine learning, pathway and network analysis are highly advantageous
• The candidate should have a cross-disciplinary aptitude, strong organizational and interpersonal skills, and a keen interest in collaborative biomedical research
• Fluency in oral and written English

We offer

• A fully funded position with a highly competitive salary.
• An opportunity to join the Luxembourg Centre of Systems Biomedicine with an international and interdisciplinary ethos.
• Working in a scientifically stimulating, innovative, dynamic, well- equipped, and international surrounding.
• Opportunity to work closely with international academic partners.
• State-of-the-art research facilities and computational equipment

Where to apply E-mail enrico.glaab@uni.lu

Apply here

PhD student position to uncover gene regulation in heart failure

We offer a PhD student position (fully funded for 3 years, start of PhD project in September 2023) as part of the structured PhD program RTG2344 MeInBio. The PhD project will focus on identifying the dynamics of spatial organization of cell types as well as activity patterns of transcription factors and chromatin regulators associated with heart failure pathogenesis through integrative analysis of single cell transcriptomes, epigenomes and subcellular spatial transcriptomes.

The PhD candidate will be a member of the MeInBio PhD research training group (RTG2344, funded by the German Research Foundation) and profit of their structured training curriculum. MeInBio aims at a dual education in bioinformatics and wet laboratory approaches to explore the spatio-temporal dynamics of gene regulation using high-throughput and high-resolution methods (www.meinbio.uni-freiburg.de).

​

Qualifications:

• Master’s degree in any field with strong interest in gene regulation and high dimensional data analysis.

• Experience with analysis and/or generating epigenomic datasets (ATAC-seq, ChIP-seq, CUT&Tag) and single cell genomics datasets (single cell RNA-seq, single cell ATAC-seq) are preferred, but not required.

• Candidates with experience in both wet and dry lab are highly encouraged to apply.

• Excellent communication and collaborative skills. 

We offer:

• An exciting modern research project in a well-equipped laboratory using state-of-the-art technologies.

• Intensive supervision secured by a thesis advisory committee.

• Regular exchange with a tandem laboratory to ensure low-threshold interdisciplinary communication.

• Regular courses in bioinformatics and wet laboratory techniques as offered by the RTG2344 MeInBio.

• Additional “soft skills” courses and networking possibilities with all RTG MeInBio members for scientific exchange.

• Yearly funds for conference visits.

Interested candidates please send one pdf with following documents to sebastian.preissl[at]pharmakol.uni-freiburg.de:

1) Motivation letter including your research interests

2) CV

3) Contact information for two to three references

Apply here

Posted on July 10, 2023

PhD Scholarship in Spatial Transcriptomics and Bioinformatics

The Brewer group at the Bioimaging section, Department of Biochemistry and Molecular Biology, invites applications from outstanding candidates who are interested in joining our group as a PhD student. The position is available from 1 September 2023, or as soon as possible thereafter. Application deadline: 29 July 2023.

The applicant will be working in the group of Associate Professor Jonathan Brewer at the Danish Molecular Biomedical Imaging Center (DaMBIC), but will also be integrated into the Center for Functional Genomics and Tissue Plasticity (ATLAS).

We are looking for a highly motivated candidate, who will work with development and application of data analysis tools for state-of-the-art spatial transcriptomics. The revolution in single-cell transcriptomics have shown the need for spatially resolved technologies to visualize cellular diversity and interactions in the context of intact tissues. This has led to the recent development of new technologies to acquire full transcriptome-wide data at single cell level and with high spatial resolution. These new technologies are likely to transform our understanding of biological processes and human diseases and form the basis for development of new treatments.

PhD scholarship qualifications/requirements:
We are looking for a highly motivated, dedicated, and ambitious candidate with:
•    A Master’s degree in Life Science, preferably Molecular Biology, Biomedicine, or Computational Systems Biology. If you have not yet completed your Master programme, you can apply to be enrolled in our 4+4 PhD programme, which is a way to commence the PhD study whilst concurrently completing the Master programme.
•    Molecular biology skills such as qPCR and in vitro transcription for MERFISH probe design.
•    Experience with single molecule localization microscopy (STORM).
•    Experience with image analysis, bioinformatics, programing languages such as Python and R. Previous experience with MERFISH data analysis would be an advantage.
•    Strong communication and collaborative skills and an interest in working in an interdisciplinary environment.
•    Proficiency in spoken and written English.

PhD / Doctoral Position in Biomedical Data Sciences & Bioinformatics

The University of Konstanz is one of the eleven Excellence Universities in Germany. Since 2007 it has been successful in the German Excellence Initiative and its follow-up programme, the Excellence Strategy.

This position is an exciting opportunity for you, if you wish to develop strong data science skills and gain significant knowledge in cell biology by conducting research that will investigate the molecular mechanisms underlying normal and diseased cellular states. The position is available within the research group of Tenure Track Prof. Dr. Andreas Gruber, which has a focus on developing and applying data science approaches to study gene activity regulation in human health and disease (further information: https://www.biologie.uni-konstanz.de/gruber.

Amongst others, you will be developing data science approaches to analyze Next Generation Sequencing data from wet laboratory experiments and from the clinics. By applying molecular multi-level data science models to large patient cohorts you will enable a panoramic view on the gene activity programs that are vital to healthy cell function, unravel disease regulomes and biomarkers. The results of your work will contribute to current efforts to foster precision medicine via personalized analytics.

Posted on July 10, 2023

PhD Student Computational Biology/ Bioinformatics

The mission of the Berlin Institute of Health at Charité (BIH) is medical translation: transferring biomedical research findings into novel approaches to personalized prediction, prevention, diagnostics and therapies and, conversely, using clinical observations to develop new re-search ideas. The aim is to deliver relevant medical benefits to patients and the population at large. The BIH was founded in 2013 and is funded 90 percent by the Federal Ministry of Education and Research (BMBF) and 10 percent by the State of Berlin. Since 2021 the BIH has been integrated into Charité as its so-called third pillar.

The bioinformatics group "Computational Genome Biology" of Prof. Martin Kircher performs research in the fields of sequence analysis, data mining, machine learning and functional genomics. We devise computational approaches to score and identify functionally relevant genetic changes in the human genome. Understanding how gene regulation is encoded in our genomes across development and the diversity of cell-types is one of our fundamental research questions. You will develop and implement new methods to analyze the regulatory genome of patients with rare genetic disease. The work is part of the Case Analysis and Decision Support (CADS) platform of the BIH and in close collaboration with the Medical Genetics Department of the Charité.

You will be co-supervised by Dr. Max Schubach. https://kircherlab.github.io/

Job description:       

• Training in computational biology and independent research
• Work on cutting-edge projects using state-of-the-art technology:
  • Analyze the regulatory genome of patients with rare diseases
  • Model regulatory sequence in convolutional neural nets or integrate sequence features, DNA shape, epigenetic marks, and interactions between DNA binding factors in classical machine learning models
  • Study the regulatory mechanisms through model interpretation
  • Gain insights into the sequence encoding of regulatory function and its relation to epigenetic annotations
• Receive guidance on PhD requirements and thesis work
• Have access to BIH facilities and computational resources
• Collaborate with internal and external partner
• Career development

Requirements:      

• M.Sc. or equivalent in bioinformatics, computational biology or similar, alternatively in computer sciences with experience in molecular biology and large-scale data analysis
• Fulfilling all registration requirements at a University (preferentially in Berlin) for an aspired PhD program
• Basic knowledge of molecular biology, gene regulation and epigenetics
• Highly skilled in a programming language such as Python, R, C++, or Java
• Deep understanding of statistical concepts and machine learning
•  Intermediate to advanced skills in an analysis environment like R or Python scipy/scikit learn

Please submit your application via the BIH Career portal https://jobs.bihealth.org by 19.07.2023, quoting the reference number BIH-52.23 We are looking forward to hear from you!

For details click here

PhD student to work on somatic variation (Bioinformatics)

The University of Antwerp is a dynamic, forward-thinking, European university. We offer an innovative academic education to more than 20000 students, conduct pioneering scientific research and play an important service-providing role in society. We are one of the largest, most international and most innovative employers in the region. With more than 6000 employees from 100 different countries, we are helping to build tomorrow's world every day. Through top scientific research, we push back boundaries and set a course for the future – a future that you can help to shape.

The Rademakers team (Genetics of Frontotemporal Dementia) at the VIB-UAntwerp Center for Molecular Neurology, Belgium is seeking a highly motivated PhD student to work on somatic variation as a potential cause of frontotemporal dementia using bioinformatic analysis and statistical evaluation of multiple omics datatypes. The Rademakers lab performs research on disease modeling, epigenetics, transcriptomics, proteomics, and short and long-read sequencing in Frontotemporal dementia and related dementias.

Position

Frontotemporal dementia is clinically characterized by language and behavioral impairment. About half of the individuals do not have a positive family history yet show remarkably similar symptoms with asymmetrical pathology found in the brain. Somatic variants in the brain are an attractive explanation based on these observations. In this genetics project, the candidate will investigate the role of somatic variation based on the most extensive collection of frontotemporal dementia patients with TDP-43 brain pathology gathered through international collaborations. This project will be performed with a combination of state-of-the-art short and long read DNA and RNA sequencing methods, and an in-depth genetic and biostatistical analysis. The successful candidate will contribute to systematically evaluating this challenging type of variant.

Profile

We seek a highly motivated, enthusiastic, critical, and creative individual to join our team. The candidate should have a strong interest in bioinformatics, biostatistics, and genetics, and experience in sequencing data analysis is considered an advantage.

Essential:

• Master’s in biochemistry, biomedical sciences, bioinformatics, related disciplines or equivalent through experience
• Proficient in verbal and written English.
• Ability to summarize data extracted from literature and to define research objectives.
• Passion for science, self-motivation, flexibility, and team spirit

Desirable but not required:

• Programming experience, preferably in Python or R
• Experience with data analysis and working in the Linux environment
• Experience with large-scale data from genomics and transcriptomics
• Experience with data analysis of short- and long-read sequencing and awareness of the biotechnological background
• Experience with a workflow management system such as Snakemake or Nextflow

If you have any questions about the online application form, please check the frequently asked questions or send an email to jobs@uantwerpen.be. For questions about the job itself you can contact wouter.decoster@uantwerpen.vib.be

Posted on July, 2023

PhD scholarship in Bioinformatics and Transcriptomics

Do you want to be part of a team that is pushing the boundaries of transcriptomic? Do you want to help us shape the future of omics analysis? We are looking for a skilled and enthusiastic PhD student in bioinformatics to conduct advanced transcriptomic analyses, with a focus on transcript/isoform level analysis of vast amounts of transcriptomics data.

If so, consider joining the Isoform Analysis group in the Section for Bioinformatics at the Technical University of Denmark (DTU). Here you will work closely with talented researchers that want to make a difference. Importantly you will be joining a collaborative group where you get a lot of support but also a lot of autonomy in a section where you will get a diverse set of inputs.

Responsibilities
Your objective will be to create bioinformatic tools, databases, and applied analysis of transcriptomics data that empower and inspire other researchers to analyze transcripts/isoforms.

About Us
My leadership philosophy can be simply stated as: people first. Our research is driven by a passion for science, but never at the expense of personal wellbeing! I firmly believe that science should be an exhilarating and enjoyable journey. Although I am not yet an experienced group leader, I take my role seriously and remain committed to continuous learning.

Requirements
The following requirements must be met by the successful candidate:

• Strong programming skills

Any of the following features are highly desirable, but not strictly required:

• Experience with applied analysis of proteomics or (bulk/single cell) RNA-seq
• Experience with developing bioinformatic tools (webserver/package)
• Strong background in molecular/cellular biology
• Experience with analyzing large and complex datasets
• Experience working with data analysis in R (the research group you will be joining works in R)

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Application procedure 
Your complete online application must be submitted no later than 14 July 2023 (Danish time). Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• A letter motivating the application (cover letter)
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• Letters of recommendation (not mandatory)

Apply here

PhD position (4 years) in structure-based RNA-ligand design

Posted on June, 2023

PhD Student, Computational Biology

VTT is one of the leading applied research organisations in Europe. What unites us are curiosity, a passion for learning, and a purpose: to solve the biggest challenges of our time and turn them into sustainable growth and well-being. Our cross-disciplinary community of over 2000 brilliant minds focuses on creating impact through science-based innovation. In recent years, we have created ground-breaking innovations such as the world's fastest and most accurate radiation detector, a cancer-sniffing sensor device for smartphones, and a headphone set entirely made of microbial materials. Get to know us further by exploring VTT's tech & infra.

We are now looking for a PhD Student to join our Computational Biology team.

Join us to develop process models and Digital Twins of biotechnological processes of all flavours, advancing automation, digitalization and efficiency in industrial biotechnology. In your work, you will study various biotechnological systems and describe their dynamics, parameter correlations and interdependencies through mathematical and data-driven models. You will work with a range of organisms – yeasts, filamentous fungi, bacteria and algae. In addition to the modelling work, you will support experimental work in the lab and conduct experimental planning.

As PhD Student, you will:

• Have the possibility to fulfil your passion and ambition as a researcher
• Create process models of microbial cultivations through analysis of bioreactor data/measurements
• Apply computational modeling and machine learning to develop tools and pipelines
• Collaborate with other experts to develop model-guided solutions to bioprocess development
• Plan and execute experimental work
• Contribute to research and development projects and to writing proposals for public funding
• Present and report your findings in conferences and scientific papers
• Complete your doctoral studies

Who we are looking for:

• You have a Master of Science or equivalent degree in control engineering, biotechnology, bioprocess engineering or a related field and are eligible for PhD studies
• You have high ambition to work as an independent researcher
• You have expertise of modelling dynamic systems through ordinary differential equations and simulating these systems
• You have prior experience with or interest in microbial physiology
• You can communicate fluently in English both verbally and in writing

Additionally, you ideally have one or more of the following skills

• Control theory for nonlinear dynamic systems, especially model predictive control
• Programming skills in Matlab, Julia, Python or similar computing languages
• Prior experience with metabolic and/or process modelling
• Prior experience with bioprocess engineering
• Experience in any of the following areas: bioprocess engineering, microbiology, bioanalytics, machine learning

PhD studentship in Precision medicine

Primary mitochondrial diseases are clinically-heterogeneous and genetically-diverse conditions that can be caused by pathogenic variants in either mitochondrial or nuclear DNA.

The Newcastle Highly Specialised Mitochondrial Diagnostic Service is a component laboratory of the North East and Yorkshire GLH and is integrated within the Wellcome Centre for Mitochondrial Research at Newcastle University (http://www.newcastle-mitochondria.com).  In partnership with teams in London (UCLH) and Oxford, we provide a comprehensive diagnostic and clinical management service for patients with mitochondrial disease across the UK.

Working with colleagues in the mitochondrial clinical and research services in London and Oxford, we have partnered with the leading UK Mitochondrial Disease charity, the Lily Foundation, to lead a research project incorporating emerging technologies (e.g. RNAseq, long-read sequencing) to establish the genetic basis of patients with mitochondrial disease who remain undiagnosed by conventional genomic testing.

This studentship will support the wider project through wet laboratory studies of novel and rare mitochondrial variants, using a repertoire of functional assays to characterise novel disease genes and support functional validation of genetic findings. The studentship will be supervised by Professor Rob Taylor, Dr Monika Oláhová and Dr Charlotte Alston who together have a long-standing track record of mitochondrial gene discovery and the characterisation of post-transcriptional molecular disease mechanisms.

Eligibility Criteria

You must have/expect to achieve a 1st or 2:1 honours degree or international equivalent in an appropriate scientific speciality (Biomedical Sciences, Biochemistry, Human Genetics or similar); a Masters degree (grade Merit or above) in a relevant subject would be advantageous.

Applicants whose first language is not English require an IELTS score of 6.5, with a minimum of 5.5 in each subsection.

Knowledge/experience of human genetics, human primary cell culture and SDS-PAGE is desirable.

Applicants must be willing to learn novel assays including CRISPR/Cas9 editing of model cell lines.

How To Apply

You must apply through the University’s Applications and Offers | Newcastle University - Postgraduate - Newcastle University (ncl.ac.uk)

In the ‘Course choice’ tab:

• select ‘Postgraduate Research’ in the 'Type of Study' field
• select ‘Full Time’ in the ‘Mode of Study’ field
• select ‘2023’ in the ‘Year of Entry’ field
• enter programme code 8440F in the ‘Course Title’ field
• leave the ‘Research Area’ field blank
• press ‘Search’
• Select ‘PhD Translational and Clinical Research (FT)’
• Save selection

Contact Details Prof Rob Taylor (robert.taylor@ncl.ac.uk)

Application Closing Date 29th June 2023

Apply here

Posted on May 31, 2023

PhD student in Molecular Biology

The position is funded through the German Research Foundation (DFG) in the context of the Collaborative Research Centre 1565 (Molecular mechanisms and interplay of gene expression processes) with the aim to better understand the roles and regulation of ribonucleases during the cellular stress response.

About us

Gene expression determines the characteristic features of different cells and tissues. Dynamic regulation of gene expression is essential for cellular adaptation in response to changing conditions but is also the molecular basis of numerous diseases. Our research group aims to understand mechanisms of gene expression regulation. RNA processing and decay are key aspects of gene expression mediated by ribonucleases. We explore ribonuclease functions using a broad spectrum of leading-edge methods from the fields of biochemistry, cell and molecular biology, including various high-throughput transcriptomics and proteomics approaches. Our lab is embedded in the excellent, international context of the Göttingen Campus allowing a dynamic, stimulating and collaborative working environment.

Your tasks

• Developing a research project studying the functions ribonucleases and elucidating mechanisms of regulation
• Using diverse experimental methods, including human cell culture, genome editing, molecular biology, RNA analyses, fluorescence microscopy, recombinant protein expression/purification, in vitro biochemical assays
• Generating and analysing transcriptomic datasets

Your profile

• Motivated and enthusiastic researcher, interested in developing a scientific project
• MSc degree in molecular or cell biology, biochemistry or a related subject
• Experience with standard molecular biology and biochemistry techniques as well as a practical background in RNA biology
• Experience with or interest in bioinformatics is advantageous
• Ability to work independently and also in a team
• Good command of the English language

PhD Student biology, genetics, bioinformatics

The Leibniz Institute for the Analysis of Biodiversity Change (LIB), formed by the merger of the Zoological Research Museum Alexander Koenig (ZFMK), Bonn and the Centre for Natural History (CeNak) of the University of Hamburg, is an internationally operating research institute. As a research museum of the Leibniz Association, the LIB contributes to taxonomic and molecular biodiversity research and to the conservation of global biodiversity, documents and analyses evolutionary and ecological biodiversity change and participates in public communication about biodiversity change and its possible causes.

PhD Student (f/m/d)

in the DFG-funded project "Exploration of genomic methods for species delimitation in terrestrial snail radiations". In the project, the systematics, evolution and biogeography of land snail radiations in Indonesia will be investigated with the help of various genomic methods. The project is supervised by Prof. Bernhard Hausdorf (B.Hausdorf(at)leibniz-lib.de), who is also happy to answer project-related questions.

Your work tasks are in particular:

• Generate genomic datasets using methods such as ddRAD and target capture.
• Species delimitation and reconstruction of evolution and biogeography of land snail radiations using generated genomic data
• Evaluation of advantages and disadvantages of different methods for species delimitation and optimisation of methods

Our requirement profile:

• Qualifying university degree (master's degree/diploma) in biology, genetics, bioinformatics or a related field
• Experience with molecular biology methods, especially genomic methods such as ddRAD or target capture
• Experience with the analysis of population genetic and genomic data
• Programming skills are an advantage

Apply here

Posted on May 29, 2023

PhD Candidate in bioinformatics and multi-omics analyses for cancer signaling

NTNU is a broad-based university with a technical-scientific profile and a focus in professional education. The university is located in three cities with headquarters in Trondheim.

We have a vacancy for one PhD candidate in bioinformatics at the Department of Clinical and Molecular Medicine within the field of computational precision medicine, and with a focus on multi-omics data integration for cancer signalling modelling. The PhD candidate will be supervised by associate professor Åsmund Flobak at the DrugLogics group, and associate professor Morten Rye at the Group of Bioinformatics. You will be part of, and bridge, two established research groups tackling various aspects of cancer diagnostics and therapy. The two groups have affiliated researchers at all stages of their careers, meaning other phd candidates, postdocs, researchers and PIs. In addition, both groups have large academic networks throughout Europe, and are in close collaboration with leading bioinformatics groups at major cancer centres.

The focus in the proposed project will be to integrate multi-omics data from spheroids derived from cancer patients at our hospital with public data on cancer tissue and models. Spheroids will span several cancer disease entities, including colon cancer and prostate cancer. The goal is to identify single and combinatorial drug targets for cancer precision medicine, and increase our understanding of druggable pathways and adaptive resistance mechanisms through computational modelling of these pathways. The research work in the project will be related to our well established activity in several ongoing projects, including the PRESORT, DrugLogics, IMPRESS, PROSTOMICS, LINKS initiatives. Knowledge within programming and bioinformatics is required for this position.

Required selection criteria

Deadline 15th June 2023

Apply here

PhD in Genetics and Addiction

The Complex Trait Genetics lab (www.ctglab.nl) at the Center for Neurogenomics and Cognitive Research in Amsterdam (www.cncr.nl) is seeking applicants for a PhD position in Genetics and Addiction. The successful candidate will be part of the BRAINSCAPES project, which is a 10-year nationwide collaboration funded by the Dutch Government (Gravitation Program), and led by the department of Complex Trait Genetics. The main aim of BRAINSCAPES is to gain mechanistic insight into several brain disorders by leveraging results from recent genetic discoveries, utilizing large-scale bioinformatic resources, and testing genetically informed hypotheses in experimental studies.

The work of the candidate will focus on applying existing tools (e.g. FUMA, MAGMA, TWAS, LDSC, fine mapping) that integrate bioinformatic resources with results from genetic discovery studies for brain-related disorders, with a focus on addiction. The aim of the project will be to identify the neurobiological mechanisms linking genes to addiction susceptibility and investigating their overlap with other neuropsychiatric disorders. The candidate will work in an enthusiastic team of PhD students and postdocs with diverse backgrounds including statistics, bioinformatics, artificial intelligence, neuroscience, psychology, and stem cell biology.

We are seeking a highly motivated, talented individual. The successful candidate needs to have experience with genetic research, an affinity for working with large datasets, and familiarity with genome-wide association studies. Knowledge of the UNIX environment, R, some scientific programming experience, and genetics and/or neuroscience background is preferred.

Your duties

• apply bioinformatic tools for integrating results from genome-wide association studies with biological resources to data on brain-related traits
• actively take part in the BRAINSCAPES consortium including frequent contact with other, mostly neuroscience oriented, labs
• authoring and co-authoring manuscripts submitted to high quality journals
• some support (10% of time) for teaching is expected
• frequently present work to the international scientific community

Requirements

• MSc in any of the of the following fields: statistical or behavioral genetics, bioinformatics, computational biology or related computational field
• strong ability to write and read in English
• experience with Python, the R statistical language, and working in a UNIX environment is preferred
• demonstrable experience in (large) genetic data analysis is preferred
• support ‘open science’: share tools and data with the wider scientific community

Application

You are requested to write a letter in which you describe your abilities and motivation, accompanied by your curriculum vitae, a list of grades of your MSc and the names and contact details of two scientific referees. Please compile all this together in one document and convert it to pdf.

Are you interested in this position? Please apply via the application button and upload your documents as mentioned above until 01/06/2023.

Apply here

Posted on May 26, 2023

PhD students in Data Science (Bioinformatics)

The Novo Nordisk Foundation Centre for Biosustainability (DTU Biosustain) together with the departments of Bioengineering, Compute and Chemical engineering at the Technical University of Denmark are opening multiple PhD positions.

This initiative follows a strategy to educate the next generation of bilingual biotechnology scientists at the intersection of data science, engineering, and life sciences. Bilingual scientists capable of translating domain-specific (e.g., strain design, process systems engineering and multi-scale modeling, bio- discovery, scalability, and manufacturability) problems into data science and engineering solutions are highly needed. Further, bilingual profiles are the hardest to find and the most demanded in industry and academia. We want to fill this gap and offer multiple data science-focused PhD projects supervised by at least two of the involved departments and by helping candidates to customize their course curricula to ensure that they become bilingual in the domains covered in the project.

We are seeking highly motivated PhD candidates with skills in data science, machine learning, deep learning and bioinformatics and strong interest in biology, multi-scale modeling and in-silico experimentation applying them to solve sustainability and biotechnology challenges. If your areas of interest and competence are digitalization, data science, machine learning, deep learning and/or software development, and you are looking to gain experience while working on projects that will make an impact on the world, this is your chance.

Requirements
Two-year master's degree (120 ECTS points) or equivalent in computational biology, bioinformatics, machine learning, or related topics.

Ideal competencies required for the projects

You are willing to work in an international environment with colleagues and partners from all over the world. The following competencies are advantageous for successful execution of these PhD projects:

• MSc in data science, machine learning, computer science, biology, bioengineering, Chemical/Process Engineering, or related fields
• Background in data science, machine learning, deep learning, and/or bioinformatics including programming and mathematical modelling
• Proficiency in software development and data management (Python, R, and other relevant programming language)
• Interest in sustainability and biotechnology challenges
• Ability to translate domain-specific problems into data science and engineering solutions
• Excellent communication and interpersonal skills for working in a multi-disciplinary team environment

Also desirable

• Knowledge in the biosustainability areas: Sustainable chemicals, Microbial Foods, and Natural Products
• Knowledge of multi-scale modeling and in-silico experimentation
• Knowledge of process modeling and simulation

Application procedure 
Please submit your online application no later than 31 July 2023.

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• A letter motivating the application (cover letter)
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale

Apply Before 31/07/2023, 22:59

Apply here

PhD position to investigate the biophysical basis of neural computation with machine learning

The Gonçalves lab is a recently founded research group at the Neuro-Electronics Flanders (NERF), Belgium. We are currently exploring a range of exciting topics at the intersection between computational neuroscience and probabilistic machine learning. In particular, we develop machine learning methods to derive mechanistic insights from neuroscience data, and apply them to challenging neuroscience problems: from the retrieval of complex input-output functions of biophysically-detailed single neurons to the full characterisation of mechanisms of compensation for perturbations in neural circuits. We work in an interdisciplinary, collaborative, and supportive work environment, which emphasizes diversity and inclusion.

The project

We are looking for a Ph.D. candidate interested in using computational methods to investigate how the complex biophysics and morphology of single neurons give rise to the dynamics of neural populations. One question we are particularly excited about is how much these single-neuron mechanisms underlie the remarkable robustness of neural systems. This project will make use of our previously developed machine learning methods and toolbox (e.g., [2-3]), and depending on the selected candidate’s interests, can involve further method development. There will be flexibility to customize the project and ample opportunities to collaborate with top experimental partners locally and internationally.

Your profile

• You have, or are about to finish, a Master’s degree in a quantitative discipline (e.g., Physics, Computer Science, Mathematics, Machine Learning, Statistics, Bioinformatics, Computational Neuroscience).
• You have a genuine interest in interdisciplinary work at the interface between neuroscience, modeling, and machine learning.
• You have good programming skills (ideally in Python).
• You are a team player with excellent communication skills.
• Prior experience in deep learning, or/and the statistical analysis of neural data is a plus.

We offer

• A stimulating, international, interdisciplinary, collaborative, and supportive work environment, which emphasizes diversity and inclusion
• Scientific guidance at an internationally recognized high-level
• Access to state-of-the-art compute
• Competitive salary and benefits
• Fully-funded position. Although funding is available, the successful candidate will be encouraged and supported in obtaining a personal fellowship (FWO or other)
• The position is available immediately
• An environment that promotes personal development

How to apply?

Please complete the application through the VIB online application tool. A complete application file (English) should contain the following documents:

• your motivation letter stating career goals, past experience, and how these relate to the current position
• your CV
• contact information of two references (a minimum of one Professor; one reference can be a Postdoc)

Posted on May 24, 2023

PhD position in ageing and Alzheimer’s disease

PhD Student Biology, Genetics, Bioinformatics

The Leibniz Institute for the Analysis of Biodiversity Change (LIB), formed by the merger of the Zoological Research Museum Alexander Koenig (ZFMK), Bonn and the Centre for Natural History (CeNak) of the University of Hamburg, is an internationally operating research institute. As a research museum of the Leibniz Association, the LIB contributes to taxonomic and molecular biodiversity research and to the conservation of global biodiversity, documents and analyses evolutionary and ecological biodiversity change and participates in public communication about biodiversity change and its possible causes.

The LIB has a vacancy for a doctoral student (f/m/d) at the Hamburg location, limited to three years TzBfG, 65% hours, remunerated according to E13 (TV-L).

PhD Student (f/m/d)

in the DFG-funded project "Exploration of genomic methods for species delimitation in terrestrial snail radiations". In the project, the systematics, evolution and biogeography of land snail radiations in Indonesia will be investigated with the help of various genomic methods. The project is supervised by Prof. Bernhard Hausdorf (B.Hausdorf@leibniz-lib.de), who is also happy to answer project-related questions.

Your work tasks are in particular:

• Generate genomic datasets using methods such as ddRAD and target capture.
• Species delimitation and reconstruction of evolution and biogeography of land snail radiations using generated genomic data
• Evaluation of advantages and disadvantages of different methods for species delimitation and optimisation of methods

Our requirement profile:

• Qualifying university degree (master's degree/diploma) in biology, genetics, bioinformatics or a related field
• Experience with molecular biology methods, especially genomic methods such as ddRAD or target capture
• Experience with the analysis of population genetic and genomic data
• Programming skills are an advantage

Applications should be submitted in English. The documents should include a covering letter (including the date when the position can be started and the motivation for this position), a CV in table form, final certificates and a reference contact.

Apply here

PhD position in Biostatistics

A doctoral student position is available within the biostatistics group at the Department of Medical Epidemiology and Biostatistics (MEB) at Karolinska Institutet, Stockholm. The biostatistics group at MEB, KI comprises 4 professors, 3 senior lecturers, 9 PhD-level statisticians, 4 masters-level statisticians, and 10 doctoral students. The group is involved in a wide variety of research projects, including population-based cohort and case-control studies, twin and family studies, survival analyses, predictive modeling, genetic epidemiology and bioinformatics.

The successful applicant will work on the development and application of statistical models for studying breast cancer tumour progression, patient survival and mammography screening outcomes. The project will include analyses of data from large, detailed studies of breast cancer and mammography screening (with large-scale genetics and image data). The student will interact with other academic statisticians and with specialists in other fields, e.g. cancer epidemiology and screening.

A creative and inspiring environment full of expertise and curiosity. Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. As a doctoral student you are offered an individual research project, a well-educated supervisor, a vast range of elective courses and the opportunity to work in a leading research group. Karolinska Institutet collaborates with prominent universities from all around the world, which ensures opportunities for international exchanges. You will be employed on a doctoral studentship which means that you receive a contractual salary. Employees also have access to our modern gym for free and receive reimbursements for medical care.

Eligibility requirements for doctoral education

In order to participate in the selection for a doctoral position, you must meet the following general (A) and specific (B) eligibility requirements at latest by the application deadline.

It is your responsibility to certify eligibility by following the instructions on the web page Entry requirements (eligibility) for doctoral education.

A) General eligibility requirement

You meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:

1. have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
2. have satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the advanced/second-cycle/master level, or
3. have acquired substantially equivalent knowledge in some other way in Sweden or abroad.*

Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.

*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.

B) Specific eligibility requirement

You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:

- Show proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school.

Follow the instructions on the web page English language requirements for doctoral education.

Skills and personal qualities

Applicants should have a masters degree in mathematical statistics, statistics, or biostatistics and have an interest in statistical methods in medical/biological applications. Since theoretical development is a part of the project, strong mathematical training is preferred. Programming skills in R and/or C++ are considered a merit. Personal qualities for the role include being structured, performance-oriented and having good analytical, as well as communication skills.

Reference number STÖD 2-2107/2023

Last application date 13.Jun.2023 11:59 PM CEST

Apply here

Posted on May 22, 2023

PhD in developing targeted approaches for manipulating the human microbiome

The Deng lab at the Institute of Virology at Helmholtz Munich and the Technical University of Munich uses an integrative approach combining single-cell technologies, culture-independent techniques, multi-omics, and machine learning to understand the underlying mechanisms of phage-host interactions and their impact on the human host. Ultimately, we aim to develop personalized phage-based treatments against multiple human diseases and conditions.
We are looking for a highly motivated Ph.D. candidate (f/m/x) with a background in biotechnology and molecular microbiology to work on a project aiming to develop novel tools for targeted manipulation of the human microbiome in dysbiosis-associated diseases.

Your mission

Developing a targeted approach for manipulating the human microbiome by

• Using culture-independent and single-cell approaches to isolate phages
• Study the interactions between phages and their bacterial host on both population and single-cell levels using multi-omics

Your qualifications

• MSc in microbiology, molecular biology or a related field
• Being familiar with flow cytometers and cell sorting, qPCR or digital PCR, anaerobic chambers and/or bioreactors
• Good written and verbal communication skills in English

Interested?
If you have further questions, simply contact Mohammadali Khan Mirzaei, m.khanmirzaei@helmholtz-muenchen.de, who will be happy to be of assistance.

Apply here

PhD candidate for tracer-based metabolomics

The Metabolomics & Analytics Centre at the Leiden Academic Centre for Drug Research (LACDR) at Leiden University is looking for a:

PhD candidate for tracer-based metabolomics to study Gaucher disease

The Metabolomics and Analytics Center (MAC) seeks to hire a PhD student for the study and optimization of treatment of Gaucher disease using tracer-based metabolomics and advanced metabolomics and lipidomics methods. You will be part of a larger EU project (Reconstruction and Computational Modelling for Inherited Metabolic Diseases; www.Recon4IMD.org) for accelerating the diagnosis and personalize the management of inherited metabolic diseases, and especially of Gaucher disease. You will develop a tracer-based metabolomics workflow using liquid chromatography (LC) coupled to high resolution mass spectrometry (MS) and using advanced MS/MS methods (such as electron activation dissociation technology). The data acquisition workflow will be integrated with a computational workflow to process data; a first version of such a workflow has been recently developed at MAC.

Key responsibilities 
You will focus on 1) developing advanced tracer-based metabolomics technologies and methods, 2) applying your methods to analyze disease pathways and interventions in in-vitro models, and 3) screening for novel metabolites and lipids involved in Gaucher's disease. You will integrate and interpret your data using computational reconstructed metabolic networks and using multi-omics data integration in collaboration with other researchers.

Selection criteria 
•    Recent Master degree in Chemistry, Biochemistry, Biopharmaceutical Sciences, Life Sciences, Biomedical Sciences, preferably with a Major in Analytical Chemistry or Biochemistry
•    Interest in the field of metabolomics, lipidomics, mass spectrometry, in-vitro cell culture experiments, biochemistry and computational modeling
•    Independent and creative team player with good communicative skills
•    Proficient in spoken and written English

Information  
Enquiries can be made to Prof. dr. Thomas Hankemeier, e-mail: hankemeier@lacdr.leidenuniv.nl.
If you have any questions about the procedure, please contact Mrs. Ina Hazejager (e-mail:
abs@lacdr.leidenuniv.nl, telephone: +31 71 527 4220).

Instructions for applications 
To apply for this vacancy, please send an email to abs@lacdr.leidenuniv.nl. The closing date is 7 June 2023. Please ensure that you include the following additional documents quoting the vacancy number:
•    Motivation letter;
•    Full curriculum vitae;
•    A list of grades;
•    Two references.

Posted on May 19, 2023

Doctoral researcher in Lifestyle EpiGenetics/ Bioinformatics

The Epigenetic Epidemiology Lab at the Department of Human Genetics - Faculty of Medicine KU Leuven in Belgium - seeks a PhD candidate with strong skills in (epi)Genetics and Bioinformatics, as well as high interest in lifestyle related exposures in human.
The Epigenetic Epidemiology Lab has an international reputation in the design of epigenetic studies in humans. Major research topics include epigenetic changes because of ageing, obesity-related factors, nutrition, lifestyle, pollution, and other environmental factors. These changes can adversely affect overall health, fertility, childhood growth, pregnancy, as well as health of the next generations.
More information about our university: here

Project

PhD position in Bioinformatics/ Genomics

University of Birmingham (UK) - School of Biosciences

Genomic surveillance from wastewater was used successfully during the SARS-CoV-2 pandemic to inform public health measures by monitoring case numbers and the emergence of new variants. This project seeks to develop a low-cost, highly accessible technique that shares similarities with these methods but that is pathogen agnostic i.e. has the ability to detect a large variety of different pathogens. It will require research and technical innovation in the area of molecular biology to develop highly sensitive ‘ultraplex’ amplification techniques that are able to amplify a very large number of targets simultaneously. The project will also develop cutting edge library preparation methods to enable real-time nanopore sequencing as well as data analysis tools. Applicants will need to have a broad interest in the fields of diagnostics, genomics and bioinformatics and be open to developing new skills in molecular biology and data analysis.

The project seeks to build on existing skills and experience developing amplicon sequencing for outbreak use by the group over the last 7 years. Since the first use of real-time genomic surveillance during the 2014-2016 West African Ebola Outbreak (Quick 2016), it has become an invaluable source of information supporting epidemiological, typing and phylogenetic efforts. More than 10M SARS-CoV-2 genomes were sequenced during the pandemic, the vast majority of which were generated using amplicon schemes developed by the group. Building on this success we will develop multi pathogen schemes for use primarily in wastewater surveillance and clinical diagnostics by real-time sequencing.

Opportunities:

1. Cutting-edge research into techniques for real-time surveillance and wastewater monitoring.
2. Learn within an experienced team new genomics and bioinformatics skills which provide excellent opportunities for your future career.
3. Collaborate with our international partners and travel for fieldwork and conferences.

Applications should be directed to Joshua Quick (j.quick@bham.ac.uk). To apply, please send:

• Application form available here (https://drive.google.com/uc?export=download&id=1CSazI0eQgfXDcunFcj0L-eLUPgcRLZrH)
• CV
• Academic transcripts
• Names and contact details of two referees

Short listed candidates will be interviewed on Thursday June 22 or Friday June 23.

Apply here

Posted on May 17, 2023

Fully-funded PhD positions in Biomedical Sciences

Are you passionate about discovering the basis of health and disease, and applying your findings to answer clinically-relevant questions? Are you interested in one of the following topics?

Topic 1: Genes, Cells and Cell‑based Medicine
Topic 2: Molecular Processes and Therapies
Topic 3: Integrative Biomedicine

We are committed to meet today’s challenges in biology and medicine and realize that excellent science requires outstanding researchers. If you aspire to be one of them – we are looking forward to your application!

Available projects

A list of participating group leaders and available projects, with detailed project descriptions, is available on our application portal upon registration.

Who are we looking for?

To apply, a master’s degree (or equivalent) in in biology, biotechnology, medicine, molecular medicine, chemistry, computer science, data science, engineering, mathematics, physics or a related field, is required. You should hold or expect to obtain your degree not later than four months after the onsite interview week in Berlin (see below for the exact interview dates). Please check further details of your Eligibility for application here.

Details on the Recruitment process can be found here.

We offer:

• An excellent scientific, international and collaborative learning environment
• Individualised PhD supervision & mentoring
• Support of the thesis committee
• Advanced scientific, research-related & methods training
• Access to state-of-the-art infrastructure & core facilities
• Regular lectures, journal clubs & seminar series
• Participation in one of our specialised research programs
• A structured program for personal & career development
• Participation in PhD symposia, retreats & social activities
• Travel grants for external courses & conferences
• Active alumni network

Students may, in addition, join our MDC-NYU PhD Exchange Program in Medical Systems Biology, iNAMES – MDC-Weizmann Helmholtz International Research School for Imaging from NAno to MESo, or become associated with the interdisciplinary HEIBRiDS Data Science School.

How to apply? 

Calls for applications for central MDC recruitment are open twice a year, for Spring and Fall recruitment round. Applications are accepted exclusively via our online Application portal. Email applications for the central recruitment rounds can unfortunately not be accepted. Detailed information about the application process, including Application manual, are available here.

Contact and information

phdmdc@mdc-berlin.de

Apply here

PhD Positions - Quantitative Plant Sciences

Would you like to contribute to solutions to climate change and resource scarcity? Work with us at the Institute of Bio- and Geosciences, Plant Sciences (IBG-2, FZJ) on innovative use, production and technology concepts related to "plants", "sustainability" and "bioeconomy". We conduct interdisciplinary research in international or regional teams using state-of-the-art sensors and measurement concepts - and novel model systems.

The IBG-2 - Plant Sciences offers a unique, interdisciplinary and international working environment and access to excellent infrastructure and state-of-the-art plant physiology techniques. We are world leading in the development or Root Architectural models and the simulation of root growth, nutrient, and water uptake.

Your Job:

Doctoral theses are offered in the following subject areas:

Topic 1: ROOTED: Root plasticity responses to low P as modulated by N availability
Topic 2: Root2Resilience: Simulation of root system architecture for the discovery of traits covering resilience to Climate Change.

Your Profile:

You have a deep interest in how plants optimize nutrient acquisition and acclimate to different soil conditions. You are curious about root functioning and preferably have some experience within plant root research, for example during your master thesis work. You enjoy designing, conducting, and analysing experiments. You enjoy math and quantitative approaches in science and have some affinity with modelling and or computer programming.

Required applicant Profile: Master’s degree in Agriculture, Plant Biology, Soil Science, related natural sciences.

Desire attitude and skills:

• Self-motivated
• Creative problem solver
• Curious
• Collegial
• Good knowledge of plant and crop eco-physiology, especially in relation to plant nutrition and/or hydrology.
• Experience in conducting plant experiments in greenhouses or other growth conditions.
• Good basic knowledge of chemistry and physics
• Knowledge of mathematical models, especially dynamic crop models or functional structural plant models.
• Knowledge of numerical mathematics is a plus
• Programming skills, preferably in C++ and or statistical language R
• Good writing and oral presentation skills.
• Languages: High level English (C1/2)

For inquiries contact Johannes Postma at OSR@fz-juelich.de

Apply here

PhD Positions in Structural Biology

Two positions for talented and self-motivated PhD students are open in the Structural Parasitology group at IOCB Prague led by Dr. Sebastian Zoll. The group focuses on understanding the structural basis of interactions between parasite surface proteins with human host factors to elucidate immune defence strategies of the parasite and foster the development of novel therapeutic strategies against neglected diseases.

The lab is well-funded and supported by a diverse network of international collaborators, providing excellent opportunities for the candidate to receive additional training in foreign host institutions.

The successful candidate will adopt an integrated structural biology approach, utilising single-particle cryo-electron microscopy, X-ray crystallography, and small-angle X-ray scattering, alongside various biophysical techniques to characterize protein-protein interactions (such as SPR, ITC, MALS, MST). The position will provide hands-on training in a protein biochemistry lab, as well as training in structural data processing using Linux work stations.

Posted on May 15, 2023

PhD student in Cancer Systems Biology

The Department of Immunology, Genetics and Pathology (IGP) at Uppsala University has a broad research profile with strong research groups focused on cancer, autoimmune and genetic diseases. A fundamental idea at the department is to stimulate translational research and thereby closer interactions between medical research and health care. Research is presently conducted in the following areas: medical and clinical genetics, clinical immunology, pathology, neuro biology, neuro-oncology, vascular biology, radiation science and molecular tools.

Duties
Unlike many fatal forms of cancer, the brain tumor glioblastoma causes death not by distant metastasis but by local invasion. The local invasive growth of glioblastomas is multi-faceted: tumor cells invade along multiple anatomical routes, including the perivascular spaces, white matter fibers, and directly through brain parenchyma. Studies from our lab and others have linked these invasion routes to cellular pathways; the emerging picture is that invading glioblastoma cells appear to co-opt numerous pathways from embryo development and wound healing, including mesenchymal transformation and differentiation along oligodendrocyte and astrocyte lineages.

The research will focus on computational methods to score invasion in patient-derived xenograft brain slice assays (time-lapse confocal data) and spatial transcriptomics data (done with Mats Nilsson, SU and Dr. Hitesh Mangukiya, IGP). In the project's second part, we aim to stratify patients for invasion-targeted therapy and to work with experimental team members to test its performance. In brief, we will build a computational predictor that links signatures of newly collected patient samples to a list of invasion-targeted drugs. The predictor will combine molecular features with features derived from MRI imaging of patients (collaboration with dept of Neurosurgery).

Requirements
To meet the entry requirements for doctoral studies, you must

Hold a Master’s (second-cycle) degree in biotechnology, computational biology, applied mathematics, engineering, biomedicine, medicine, or similar. Have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or have acquired substantially equivalent knowledge in some other way.

The successful applicant must also

• Have working knowledge of, and interest in, real-world, data analysis.
• Have substantial experience in at least one programming language (typically Python, R, or MATLAB)
• knowledge of the mathematics needed to conduct research work in computational biology (corresponding to a degree in engineering or equivalent). Examples of mathematical concepts relevant for the project include: linear algebra, machine learning, regression, dimensionality reduction, Ising models, neural networks, probability, statistical testing, image analysis)
• Have documented knowledge of molecular biology, cell biology, cancer biology, biotechnology, or related areas.
• Have strong communication skills (oral and written English)
• Have strong interpersonal skills consistent with working in a team

For further information about the position, please contact: Sven.Nelander@igp.uu.se, +46 76 1380123

Please submit your application by 25 May 2023, UFV-PA 2023/1219

Apply here

PhD student position in tumor evolution and drug resistance

The student will be a part of the Kallioniemi research group, Karolinska Institutet,. Our group focuses on optimizing treatments for individual cancer patients based on molecular profiling and functional drug testing. Specifically, the student will be in the pediatric oncology team lead by Dr. Kasper Karlsson. The team focuses on improving survival for children with cancer by identifying efficient therapy combinations. We do this by applying several different methods and techniques, including cell barcoding to study individual tumor subclones, state-of-the-art organoid technologies, high-throughput drug screening and single-cell sequencing.

In this project we will use a technique called cell barcoding to identify efficient drug combinations to overcome metastatic heterogeneity in pediatric neuroblastoma. In cell barcoding a molecular barcode is inserted into cells’ genomes which makes it possible to monitor thousands of tumor subclones simultaneously and see how they evolve as they respond to drugs. We use this to identify and characterize cell populations that survive standard of care treatment, and to identify drugs specifically targeting those cell populations – a concept we have termed Precision Lethality.

Your work will be carried out at the Science for Life Laboratory (SciLifeLab), that is a leading national infrastructure for next-generation life science research in Sweden. SciLifeLab is jointly operated by the four host universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University, and it has facilities in four other universities across Sweden. There are over 1 000 people working at SciLifeLab, either in research groups or in the infrastructure facilities, most of them in the KI Solna campus and in Uppsala. This position resides at the Solna campus.

A) General eligibility requirement

You meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:

1. have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
2. have satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the advanced/second-cycle/master level, or
3. have acquired substantially equivalent knowledge in some other way in Sweden or abroad.*

Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.

*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.

B) Specific eligibility requirement

You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:

- Show proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school.

Skills and personal qualities

The successful candidate should be highly motivated to pursue a 4-year doctoral education and must hold an MSc in a relevant field, such as biomedical science, molecular and cell biology or biotechnology. The applicant must be fluent in English and be eager to work in a cross disciplinary and international team. The candidate should possess excellent interpersonal and communication skills, enjoy working in a collaborative setting, be willing to learn new techniques and be self-driven.

• Experience in tissue/cell culture techniques is required
• Previous programming experience in Python or R will be prioritized
• Handling of small-molecule drugs and high-throughput screening is desirable
• Assay development for next generation sequencing is desirable
• Experience analyzing single cell and cell barcoding data is desirable

Reference number STÖD 2-1934/2023

Last application date 30.May.2023 11:59 PM CEST

Apply here

Posted on May 12, 2023

10 PHD POSITIONS IN VIROLOGY AT THE LIV GRADUATE SCHOOL

The Leibniz Institute of Virology (LIV)in Hamburg is seeking talented and enthusiastic candidates to join our interdisciplinary PhD program – also known as LIV Graduate School – and offers 10 PHD POSITIONS IN VIROLOGY AT THE LIV GRADUATE SCHOOL.

OUR PHD PROGRAM:

The LIV Graduate School is an interdisciplinary structured training program for all doctoral candidates working at the LIV. We offer our PhD students the opportunity to conduct cutting-edge research in a world-class environment of basic and translational research in virology. As a PhD candidate in our program, you will have the opportunity to study human pathogenic viruses with a diverse team of experts in the fields of molecular biology, immunology, structural systems biology, bioinformatics, and machine learning.
Our program is designed to provide you with multidisciplinary training that will prepare you for a successful career in infection research.

YOUR COMPETENCES:

• Highly motivated individual with completed or pending master’s degree (or equivalent) in life science or natural sciences
• Previous experience in molecular and cell biology, virology, structural biology, bioinformatics, or related fields is a plus
• Strong commitment, team spirit, and quick comprehension
• Very good English skills, both written and orally
• Scientific curiosity and interest in interdisciplinary research

OUR OFFER:

• The opportunity to conduct the doctoral thesis at one of the leading German institutes with internationally recognized excellence in virological research
• Excellent working environment with a wide range of further training and career development opportunities within the structured PhD Program of LIV
• Access to cutting-edge technologies (next generation sequencing, high-resolution imaging, proteomics, high-performance computing, and more) and a global network of collaborators, giving you exposure to a variety of research perspectives
• A vibrant and highly motivated team in the scientific environment of LIV and CSSB
• Participation in the multidisciplinary Leibniz Center of Infection (LCI), including an annual summer school
• Three-year PhD position with payment and social benefits in accordance with regulations of the German TV-AVH (salary agreement for public service employees)

We look forward to receiving your complete and informative application documents in English language by June 10, 2023, by email. For application requirements and procedures, please check here

Leibniz Institute of Virology (LIV)
Human Resources
Martinistraße 52, 20251 Hamburg
e-mail: personalabteilung@leibniz-liv.de

Apply here

PhD scholarship in oat genomics

The Department of Plant Sciences, Faculty of Biosciences at the Norwegian University of Life Sciences (NMBU) has a vacant 3-year PhD position in genomics research on oats, focusing on broadening the genetic base of future oat breeding. This is a unique opportunity for candidates wanting to pursue a research career in plant breeding and getting practical experience in the rapidly evolving fields of genomics and phenomics, including genome sequencing, SNP genotyping, bioinformatics, statistical modelling, and analysis of high-throughput phenotyping data as well as classical genetic analyses and field-based plant breeding.

The overall aim of this PhD project is to broaden the genetic base for future oat breeding by phenotypic and genetic characterization of novel genetic diversity in a diverse and agronomically improved recurrent selection population based on crosses with Avena sterilis.

Main research tasks may include:

• Genetic characterization of the recurrent selection population using SNP marker data.
• Possibly whole genome sequencing of the parents and genotyping-by-sequencing (GBS) profiling of progenies (depends on external funding).
• Identification of signatures of selection and beneficial Avena sterilis-derived chromosome segment that have been retained through recurrent selection.
• Phenotypic evaluation of the recurrent selection population in field trials for agronomic and seed composition traits  for use in genetic studies.
• UAV-based multispectral imaging of field trials to assess canopy vegetation status.

Required Academic qualifications:

• MSc degree in plant breeding, plant genetics, molecular biology, bioinformatics or related fields that are relevant for the research project.
• Good scientific writing skills in English.
• The candidate which finishes their education within the spring/summer of 2023 can also apply but must provide documentation of their degree before employment.

The following experiences and skills will be emphasized:

• Competence in genetics and statistical data analysis
• Computer programming skills
• Some basic knowledge of plant science and plant breeding
• Experience in molecular genetics lab work or field trial research

For further information, please contact Prof. Morten Lillemo

E-mail: morten.lillemo@nmbu.no; phone +47 98039348.

Deadline 23rd May 2023

Apply here

Posted on May 10, 2023

PhD Scholarship in Bioinformatics and Data analysis

We are looking for a highly motivated computational student for a 3-year PhD position, to join the group of Associate Professor Kedar Natarajan from the 1 October 2022 or soon thereafter.

Our group investigates mechanisms underlying cell-fate decisions in stem cells (ES/iPS) and complex tissues, particularly in development and during differentiation. We develop and utilise experimental single-cell methods including transcriptomics, ATAC-seq, multi-omics and spatial transcriptomics, and also develop computational approaches for large-scale analysis of next-generation sequencing data.

Our science and team is highly collaborative and interdisciplinary, and welcomes new members with competences in relevant fields.

Responsibilities and qualifications
You will be mainly driving analysis of single-cell genomics (scRNA-seq, scATAC-seq, imaging/seq-based spatial Tx) and bulk datasets (RNA, ATAC, ChIP-seq and other chromatin profiling methods) in projects aimed at understanding molecular mechanisms driving cellular differentiation. Alongside setting up workflows/pipelines, you will also be involved in development of computational methods and datasets (transcriptomics, spatial analysis) for ongoing lab projects.

The candidate should have a two-year master’s degree in Bioinformatics, Computational Biology, Biostatistics or in a related quantitative field (e.g. Mathematics, Physics, Statistics), with documented experience in analysing and interpreting bulk and single-cell sequencing datasets. Prior experience with big-data integration and software development is desirable. As a part of a multidisciplinary team and research environment, the candidate is expected to be passionate about science, hardworking, learning oriented and work collectively within the group and with collaborators.

Profile
We are looking for a motivated and enthusiastic researcher with following competences:

Essential experience and skills:

• Master’s degree in Bioinformatics, Computational Biology, Biostatistics or in a related quantitative field (e.g. Mathematics, Physics, Statistics)
• Proficiency with programming languages (Python or R) and documented experience analysing bulk NGS datasets (RNA-seq, ATAC-seq, ChIP-seq etc.,) and single-cell datasets (scRNA-seq, scATAC), and working on computing cluster.
• Proficiency in written and spoken English and ability to work in collaborative environment.

Desirable experience and skills:

• Prior experience in setting up analysis pipelines on computing cluster (Nextflow, Snakemake) for NGS applications.
• Prior experience in developing computational methods and/or software development.
• Experience with different graphical packages for scientific manuscripts and illustration.

Further information 
Further information may be obtained from Assoc. Prof. Kedar Natarajan (kenana@dtu.dk)

You can read more about the lab at http://www.bioengineering.dtu.dk/Kedar-Natarajan and DTU Bioengineering at www.bioengineering.dtu.dk/english

Application procedure
Your complete online application must be submitted no later than 2 June 2023(Danish time).

Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• Cover/motivation letter of application, describing your relevant competences and how you will fit the group (max. 2 pages).
• CV incl. education, work/research experience and skills relevant for the position.
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale.
• List of publications.
• Contact information for 3 referees.

Apply here

PhD position on machine learning-based prediction of protein-protein interactions

Are you looking for a PhD position and like to participate in an exciting interdisciplinary research project to discover how proteins select their partners to interact with? Are you a bioinformatician with interest in machine learning, and its application to predict protein interactions? Then this PhD vacancy may be of interest to you.

Biological processes are controlled by transcription factor proteins (TFs), which interact in many different combinations to regulate gene expression. However, it is still largely unclear how the specificity of protein-protein interactions is encoded in protein sequence and structure and how this determines which combinations of proteins with unique functions can be formed. Ultimately, this knowledge is important to steer and control biological processes, and investigate for example the cause of human diseases or govern modern plant breeding approaches.

The Bioinformatics Group focuses on fundamental and applied bioinformatics research in the green life sciences. In particular, they develop and apply novel computational methods for the analysis and integration of –omics data. The group has a strong track record in genome analysis, algorithm development (including the application of machine learning to study protein function and interaction), and tool construction. There are many national and international collaborations with researchers studying plant development, biotechnology and genomics.

Your qualities

You have

• A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline
• Demonstrable experience in applying machine learning to biological data
• Good statistical and mathematical skills

• Proficiency in programming (e.g. in Python)
• Affinity with molecular biology and be interested in collaborating with researchers in this discipline
• Perseverance in problem solving

Apply here