PhD scholarship

 PhD positions in Bioinformatics, Genomics and Life Science:


Update on March 01, 2024

9 Funded PhD fellowships in European Doctoral Network TAME

The neuronal tau protein is associated with tauopathies, most notably Alzheimer’s disease. Tauopathies are characterised by intraneuronal aggregation of tau protein into filaments causing neurofibrillary degeneration and synaptic dysfunction, which lead to dementia.

There is an urgent need to provide society with better diagnostics and disease-modifying treatments for these diseases. It is to meet this urgent need that TAME (TAuimMunE), Europe’s first Tau network, has been created. To this end, TAME‘s research and training activity goals are to improve and protect the health and well-being of citizens of all ages by generating new knowledge, developing innovative solutions and integrating, where relevant, a gender perspective to diagnose, monitor and treat diseases, in order to make public health systems more cost-effective and sustainable.

The TAME network expands the scope of research collaboration geographically connecting 9 beneficiaries in 7 European countries and 7 associated partners, across tauopathies and across disciplines. We have teamed-up to combine molecular and cellular neuroscience with computing, chemical and bio-engineering and their technology expertise between academia (7 beneficiaries) and industry (2 beneficiaries). Each beneficiary is recruiting a doctoral candidate.

We are looking for talented, highly-motivated experimentally skilled young scientists with Master degrees or equivalent in disciplines related to Life or Medical Sciences : (Bio)Chemistry, Neurosciences, Applied Mathematics or Machine learning, Molecular Biology, Genetics, Cell Biology. Candidates are in the first four years of their research careers and not yet awarded with a doctoral degree. We are committed to equal opportunity recruitments. TAME is dedicated to promoting the role of women in science, and, therefore, explicitly invites women to apply.

Join us to contribute to a better understanding of tau-related diseases and supports the development of new, safer, personalised and more effective diagnosis and interventions for Alzheimer’s disease and the less common tauopathies.

Closing date 9 Mar 2024

For details click here


PhD Scholarship in Pathogen Genomics

Applications are invited from suitably qualified candidates for a full-time funded PhD scholarship starting in September 2024, affiliated to the Discipline of Bioinformatics, School of Mathematical and Statistical Sciences, at the University of Galway.

University of Galway

Located in the vibrant cultural city of Galway in the west of Ireland, the University of Galway has a distinguished reputation for teaching and research excellence

Since the onset of the COVID-19 pandemic, the benefits of whole-genome sequencing for pathogen research, and for understanding infectious disease transmission and evolution in a public health context, have been brought into sharp relief. Large datasets of pathogen genomes have been and continue to be published, offering substantial opportunity for new biological insights to be obtained through their (re-)analysis.

We wish to recruit a student with keen interests in infectious disease, in using “big data” computational population genomics approaches, and in maximising the utility of genomics to study bacterial pathogens of national and international importance. The project will study the genomics of aetiological agents of enteric and diarrhoeal disease – as well as antimicrobial resistant Gram-negative bacteria – of public health significance in Ireland and overseas.

Based in the School of Mathematical and Statistical Sciences, and with primary supervision from Dr. Matthew Dorman, the student will benefit from an environment with strong expertise in quantitative data analysis. There will be scope to work with colleagues affiliated to the Discipline of Bacteriology (School of Medicine, University of Galway) and Galway University Hospital. The student will join Dr. Dorman’s newly-established group while it is in a phase of growth, and will have opportunities to contribute to shaping the team’s research direction as it matures. The student will also benefit from opportunities to interact with an international network of collaborators and contacts in acadaemia and public health.

Contact Name: Dr Matthew Dorman

Contact Email: matthew.dorman@universityofgalway.ie


Posted on Feb, 29, 2024

PhD Research Fellow in marine food webs and metagenomics

The World Health Organization (WHO) lists antibiotic/antimicrobial resistance (AMR) among top 10 threats for global health. AMR threatens human and animal health and welfare, the environment, food security, economic development, and equity within societies. This RCN funded projects overarching goal, is to generate new knowledge about measures that help us to understand, handle and prevent the development of antimicrobial resistance (AMR) from a One Health perspective.

About the position

PhD Research Fellow in marine food webs and metagenomics available within the Center of Biogeochemistry in the Anthropocene, University of Oslo.

The fellowship period is 3 years. Starting date no later than 2024-06-01.

A fourth year may be considered with a workload of 25 % that may consist of teaching, supervision duties, and/or research assistance. This is dependent upon the qualification of the applicant and the current needs of the department.

No one can be appointed for more than one PhD Research Fellowship period at the University of Oslo.

Required qualification:

  • Master’s degree or equivalent in biology, ecology, genetics or marine biology
  • Foreign completed degree (M.Sc.-level) corresponding to a minimum of four years in the Norwegian educational system
  • Fluent oral and written communication skills in English
  • Experience with R, Python and bash programming

Desired qualification:

  • Field experience including handling and identification of marine animals, marine fish and crustations
  • Knowledge of laboratory work ideally with experience in DNA extraction, quantification and library preparation
  • Experience with stable isotope techniques (in particular compound specific stable isotope analysis) is an advantage
  • Experience with experimental design and application of diverse statistics
  • Experience with bioinformatics in particular handling of large sequencing datasets

Contact information

For further information about the position please contact: Professor Alexander Eiler, phone: +47 46501671, e-mail: alexander.eiler@ibv.uio.no or Odd-Gunnar Wikmark, phone: +47 46807320, e-mail: ogwi@norceresearch.no

For questions regarding Jobbnorge, please contact HR Adviser Nina Holltan, +47 228 54424, e-mail: nina.holtan@mn.uio.no

Deadline 19th March 2024

For details click here


PhD position: In vivo gene editing and functional genomics

The Laboratory for Biological Engineering (Prof. Randall J Platt) of the ETH Zurich in Basel, Switzerland develops genome engineering technologies and applies them to a range of fundamental and disease-focused areas. To advance these efforts, the Platt group is recruiting a full-time (100%) PhD Student to develop and apply in vivo functional genomic methods.

Project background

Investigating gene function using direct in vivo screening is revolutionising the way we study brain biology. We have previously developed AAV-based molecular methods for direct in vivo CRISPR screening and are continuing to develop novel tools to be able to interrogate new aspects of brain biology.

Job description

We are looking for a highly motivated and collaborative researcher to be integrated in a multidisciplinary team of scientists. The candidate will develop novel molecular methods and apply them to ask fundamental questions about brain development and function in the context of health and disease. The candidate will be passionate about science, technology, collaboration, and communication.

Your profile

The ideal candidate should have a Master’s degree or equivalent in Biology, Neurobiology, Molecular Biotechnology, Molecular Medicine, or a related field. The successful candidate will have experience across several of the following areas:

  • cloning, molecular biology techniques and synthetic biology
  • virus production and/or evolution and delivery (AAV, LV)
  • in vivo interrogation of mouse models, including histological techniques, imaging and quantification
  • primary cell isolation, cell culture, and flow cytometry
  • preparation of deep sequencing libraries for functional genomics experiments
  • bioinformatics, statistics, and programming

Application submission deadline: 18th March 2024

Apply here


Posted on Feb 24, 2024

PhD fellowship in Bioinformatics

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. The project is a part of the large PIG-PARADIGM consortium (https://pig-paradigm.net/), funded by the Novo Nordic Foundation, has the overall goal to prevent spreading of AMR by reducing antibiotic use in pig-production.

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.

Project description

The PhD project concerns how commensal and pathogenic microbiota modulate host signaling 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.

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, Systems Biology, 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).

Other important criteria are:

  • The grade point average achieved
  • Professional qualifications relevant to the PhD project. This include (but not limited to):
    For the following criteria the level has to be at level where you are able to work independently:

    • A solid knowledge of network biology
    • Knowledge of Machine and Deep learning algorithms
    • Python and knowledge of C/C++, shell scripting and Unix/Linux operating system

Application deadline: February 26, 2024, 23.59pm CET (extended from February 12 2024)

Apply here


PhD student in Evolutionary Genomics

he Department of Ecology and Genetics (IEG) is an international environment with staff and students from all over the world. Our research spans from evolutionary ecology and genetics to ecosystem studies. Learn more at www.ieg.uu.se.

A PhD student position in evolutionary genomics, with specific focus on biology and evolution of lichen photobionts is now available within the Evolutionary Biology Program at IEG.

Project description

Lichens, symbiotic organisms composed of fungi, photobionts (algal partners), and bacteria, play crucial roles, particularly in cold environments, contributing significantly to biogeochemical cycles and trophic interactions. Recent scientific evidence suggests that lichen photobionts play decisive roles in lichen adaptation to different environments, yet the mechanisms behind this are poorly understood.

Duties
The selected candidate will be responsible for performing molecular laboratory work, including DNA/RNA extraction, quantitative PCR, library preparation, and sequencing using short and long read sequencing technologies. Additionally, the PhD-student will be tasked with growing and maintaining Trebouxia axenic cultures, conducting experimental evolution studies on cultures, analyzing different types of ‘omics’ data, and utilizing microscopy techniques to describe the morphological characteristics of identified Trebouxia species.

Qualifications required
To meet the entry requirements for doctoral studies, you must

  • hold a Master’s (second-cycle) degree in Evolutionary Biology, Systematic Biology, Population Genomics, or a related field
  • 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.

Please submit your application by 18 Mars 2024, UFV-PA 2024/510.

Apply here


Doctoral (PhD) student in Data-driven imaging and Bioinformatics

The Department of Molecular Medicine and Surgery (MMK) and the research group of Vascular Surgery is looking for a curious and highly motivated Ph.D. student to join Prof. Ulf Hedin, Dr. David Marlevi, and Dr. Melody Chemaly to improve stroke risk prediction for patients with carotid atherosclerosis using a multidisciplinary combination of advanced image processing, dedicated bioinformatic analysis, and experimental vascular biology. Based in a dynamic translational research environment of vascular surgery, biology, and imaging, you will join a diverse research team focused on atherosclerotic plaque instability based on data from the Biobank of Karolinska Endarterectomies (BiKE): the world’s largest resource for molecular studies on carotid atherosclerosis, offering unprecedented opportunities for both scientific and clinical impact.

The overall goal of the proposed project is to investigate clinical, diagnostic, and molecular features of tissue hypoxia, angiogenesis and intraplaque haemorrhage (IPH) in relation to stroke risk, seeking to improve on current paradigms for clinical risk predictions and individualize diagnostic precision. Improving atherosclerotic risk prediction has been a primary focus of our team’s efforts over the last couple of decades, seeking insights into pathways steering plaque instability, as well as identifying novel biomarkers improving on clinical routine.

Skills and personal qualities

We are looking for a highly motivated, independent, and analytical person, with:

  • A degree or the equivalent in scientific data analysis, data science and machine learning , biomedicine or bioinformatics
  • Skills in bioinformatics (Python, R or others) and biostatistics (SPSS, STATA etc.)
  • Specific knowledge of big data analysis, quantitative medical image analysis, or application of data-driven methods for clinical application purposes in general and vascular applications in particular is advantageous, but not required.
  • Experience from experimental cellular or vascular biology is meritorious, but not required.
  • Previous experience with scientific data analysis is advantageous, with involvement in previous scientific publications meritorious.

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..

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 2-647/2024

Last application date 07.Mar.2024 11:59 PM CET

Apply here


PhD Candidate in Epigenetics & Gene Regulation

Epigenetic regulation of cell identity is essential for cell functionality and tissue homeostasis. Understanding the dynamics of epigenetic programming holds significant impact for deciphering the complexities of disease and developmental processes. If you share our fascination for this captivating process, join our team and embark on this exciting journey together!

Within this project we aim to unravel the gene regulatory mechanisms of a newly identified chromatin bound protein that acts as a dynamic switch between opposite epigenetic histone marks H3K27me3 (repressive) and H3K79me2 (activating). We will assess this both in human cancer cell lines and mouse developmental models (mouse embryonic stem cells and gastruloids).

The project, led by Dr. Rutger Gjaltema, is embedded in the Molecular & Cellular Epigenetics (MCE) group at the Swammerdam Institute for Life Sciences (SILS) and in close collaboration with Dr. Thijs van Boxtel (Developmental, Stem Cell and Cancer Biology Group, SILS).

Tasks and responsibilities: 
•    complete a PhD thesis within 4 years;
•    be an active member of our research group and take responsibility for shared tasks;
•    maintain an open and organized work environment;
•    keep accurate records of experiments and data by thorough documentation;
•    stay up to date with latest literature and technological developments;
•    present your results at (inter)national scientific meetings;
•    assist in teaching and supervising Bachelor and Master students;
•    take a leading role in writing and publishing manuscripts.

What do you offer? 

You are a person that has:
•    a MSc degree in Molecular biology or Biomedical Sciences;
•    drive and passion for epigenetic/chromatin research
•    preferential experience with molecular cloning, CRISPR/Cas9 genome editing,

ChIP-seq/CUT&Tag/ATAC-seq, qRT-PCR, NGS library preparation, and (mESC) cell culture;
•    interest to perform bioinformatic analyses in R and bash;
•    talent for setting up and developing new molecular tools and techniques;
•    intrinsic motivation to keep learning and improving;
•    fluent capabilities in English, both written and spoken.

Questions?

Do you have questions about this vacancy? Or do you want to know more about our organisation?

Please contact: Dr. Rutger Gjaltema, email r.a.f.gjaltema@uva.nl

Apply here


PhD position in Population Genetics

The Vienna Graduate School of Population Genetics is an interdisciplinary and interinstitutional PhD program in evolutionary and population genetics. We provide an integrated program of training opportunities to prepare students for a career in population genetics on an internationally competitive level.

We encourage young, enthusiastic students intrigued by the interdisciplinary nature of the Vienna Graduate School of Population Genetics to apply for the program within the application deadline. Our students show a high level of dedication and activity and integrate into an international team with English as the working language.

We welcome candidates with backgrounds in either theoretical, computational or experimental fields such as bioinformatics, biomathematics, statistics, evolutionary genetics, functional genetics, theoretical and experimental population genetics. Applicants with a genuine interest for interdisciplinary research in evolution will be preferred.

Applicants are requested to email the following information as a single pdf document to the program coordinator:

  • application form with indication of two preferred topics
  • CV
  • a motivation letter with a statement of research interests
  • university certificates including grades. Please enclose a copy of your university degree that enables you to pursue a PhD study (diploma, master; credit hours need to be equivalent to 300 ECTS); if you will earn your degree after the deadline: please supply recent transcripts
  • at least two reference letters assessing your scientific qualifications need to be e-mailed directly to us (please contact your referees proactively and use the referee request below as a guideline). Please consider that your referees may need some time to prepare and send their letters within the deadline!

Apply here


Posted on February, 2024

PhD position in Bioinformatics and Artificial Intelligence

Information about the department
The Department of Mathematical Sciences at Chalmers University of Technology and the University of Gothenburg has about 200 employees and is the largest department of mathematics in Sweden. The department has three scientific divisions: Algebra and Geometry, Analysis and Probability Theory, and Applied Mathematics and Statistics, and conducts successful research in pure and applied mathematics and mathematical statistics in a wide range of research areas. We have an international environment with frequent exchanges with other universities around the world. The department provides a friendly, creative, and supportive atmosphere with a steady flow of international guests. There are many committed teachers with extensive and broad experience in all aspects of higher education.  More information about us can be found on our website: http://www.chalmers.se/math/

About the position One Ph.D. position is available in bioinformatics with a focus on large-scale data analysis using artificial intelligence. The research project is centered around DNA sequence analysis, inference in biological networks, and modeling of evolution. The primary applications will be related to antibiotic resistance and bacterial genomics.

Major responsibilities
You will be enrolled in a graduate program in Applied Mathematics or Bioscience depending on your background. You will also be part of the CARe – the Centre for Antibiotic Resistance Research in Gothenburg, an interdisciplinary excellence center connecting multiple universities and hospitals in the region. As a Ph.D. student, you are expected to develop your own ideas and communicate scientific results orally as well as in written form. In addition, the position will normally include 20 % departmental work, mostly teaching duties.

Qualifications
Candidates for this position must have obtained an M.Sc. degree in bioinformatics, mathematical statistics, mathematics, computer science, physics, molecular biology, or any equivalent topic (obtained latest September 1, 2024). Previous experience in analysis of large-scale biological data is desirable. Candidates should also have good computing and programming skills (e.g. Python and R), experience in the Linux/UNIX computer environment, and, preferably, previous experience in working with machine learning and/or artificial intelligence. Good presentation and communication skills in oral and written English are also required.

Application deadline: 2024-02-19

For questions, please contact:
Irina Pettersson,
irinap@chalmers.se

Erik Kristiansson,
erik.kristiansson@chalmers.se

Apply here


The CeMM International PhD Program in Molecular Technologies and Systems Medicine

The CeMM PhD program focuses on the thematic areas of infection, immunity, metabolism, cancer, rare diseases, network medicine, design chemistry, patient-derived organoids and aging research. These areas are built on the pillars of epigenetics and genome integrity, bioinformatics and systems biology, high-throughput genetics, genomics and proteomics, molecular and cell biology, high content automatic imaging, chemical biology, and organic chemical synthesis.

Our goal is to enable and empower students with the ability to successfully design, execute, manage and explain a research project in modern molecular medicine, through a strongly participatory and interactive program. The program is conceptualized in three ‘modes’: collect, connect and contribute. These will guide you through scientific excellence in data generation and validation to responsible and professional scientific citizenship.

 

Eligibility

To be eligible to enroll in the CeMM PhD program all candidates are required to have a Bachelor’s or Master’s degree in medicine, biology, chemistry, bioinformatics, mathematics or any scientific/technical, subject-relevant degree.

Candidates applying with a Bachelor's degree must have completed a four year course and need to demonstrate that they have acquired a significant amount of research experience. In addition they must achieve a first class honors or a 2:1.

Candidates do not need to have completed their degree at the time of application, however they should obtain their final degree certificate by the end of September.

The working language at CeMM is English, so excellent written and oral communication skills in English are required.

Submission deadline : 23 January, 2024

Apply here


 

PhD Studentship: Machine Learning Models for Zoonotic Disease Surveillance

In this PhD project you will join a team of scientists from the University of Surrey and the UK Animal and Plant Health Agency (APHA) to develop novel bioinformatic approaches to detect and predict a type of infectious diseases termed zoonotic disease that can be transmitted between species, from animals to humans (and vice-versa).

The aim of the project is to integrate DNA sequence from samples routinely collected by the APHA with laboratory experimental data to detect with high accuracy the pathogen strain and predict their preferred animal host(s), and as such help the government to delineate strategies to prevent and control infectious disease outbreaks.

Together with our team of collaborators, you will develop novel computational methods to identify genetic signatures that predict phenotypic characteristics of pathogens such as strain, host reservoir, and host preferences. You will harness the power of the large APHA data bank of DNA sequences matched to pathogen phenotypes and outbreak characteristics to map at single nucleotide resolution the genetic makeup of pathogen outbreaks.

INTERVIEW DATE: 30 January 2024, 9am-12noon

Supervisors: Dr Alexessander Couto Alves, Dr Jennifer Ritchie, Dr Mark Arnold and Dr Liljana Petrovska

Entry requirements

Open to candidates who pay UK/home rate fees. See UKCISA for further information. Starting in April 2024.

You will need to meet the minimum entry requirements for our PhD programme.

Applicants should hold or expect to gain a minimum of a 2:1 Bachelor Degree, Masters Degree with Merit, or equivalent, in bioinformatics, data science, statistics, machine learning, artificial intelligence, computer science, mathematics, physics, biology, or a closely related life, environmental or physical science. The project will involve analysis of large data sets and some familiarity with programming, especially R or Python would be required. We will also consider candidates with different academic paths but with experience acquired from a research position, or equivalent, that is relevant to the topic of the PhD project.

How to apply

Applications should be submitted via the Biosciences and Medicine PhD programme page.

Apply here


Posted on December, 2023

PhD position in computational single-cell cancer biology

Project description Anti-cancer drugs targeting signaling pathways often show great initial response, but resistance inevitably develops. One major reason for this is cell-state heterogeneity, where the response of a cell to a drug is influenced by the state the cell is in. In this project, we will use state-of-the-art single-cell multi-omics techniques (Radboud) and computational modelling (VU/NKI) to understand cellular responses to drugs over time, and develop strategies to rationally control cell behaviour to achieve better therapeutic efficacy.

This is a collaborative project between the Vrije Universiteit (VU), the Netherlands Cancer Institute (NKI) in Amsterdam, and the Radboud University in Nijmegen. It is funded by the Dutch Cancer Society.

Responsibilities: Your role will be to develop and apply computational approaches to analyze the data generated in the project and build computational models of the signaling networks. You will use these models to understand how the targeted signaling pathways behave under the various perturbations and how this determines the response of the cells to treatment. You will formulate testable hypotheses that will be validated experimentally Finally, you will contribute to designing more effective drug treatment strategies.

Research groups: This project will be jointly supervised by dr. Evert Bosdriesz (www.evertbosdriesz.org), assistant professor in the Bioinformatics group at the VU Amsterdam and prof. Lodewyk Wessels, who heads the Computational Cancer Biology group at the Netherlands Cancer Institute (ccb.nki.nl). The successful candidate will be employed at the VU and will spend at least two days per week at the NKI. The project is in close collaboration with the research group of prof. Klaas Mulder (https://www.ru.nl/personen/mulder-k-w) at the Radboud Universiteit Nijmegen.

Requirements

  • a degree in a quantitative discipline such as bioinformatics, computer science, physics, (applied) mathematics, or a related field
  • proficiency in bioinformatics programming languages (e.g. R, Python)
  • good cross-disciplinary collaborative and communication skills
  • experience in molecular and/or (cancer) biology and is a plus
  • experience in statistics, machine learning and/or pattern recognition is a plus
  • experience in analyzing high-throughput molecular data is a plus

Vacancy questions
If you have any questions regarding this vacancy, you may contact:

Name: Evert Bosdriesz
Position: Assistant professor
E-mail: e.bosdriesz@vu.nl

Application deadline: 22/10/2023

Apply here


PhD position in structure-based RNA-ligand design

PhD position At the Faculty of Medicine, Department of Biomedicine, 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 “Paving the way for rational RNA-ligand design” financed by The Research Council of Norway.

In this project, two PhD students, one postdoc and one researcher will tightly collaborate on compound design, synthesis and testing. More information about the project can be found here: https://www.uib.no/en/rg/brenk/162656/paving-way-rational-rna-ligand-design

Qualifications and personal qualities:

  • The applicant must hold a master`s degree or equivalent in the field of cheminformatics, bioinformatics, pharmacy, medicinal chemistry, or a related discipline.
  • The applicant must have a thorough understanding of the physico-chemical properties of small molecules and the principles of small molecule-RNA interactions.
  • Basic knowledge of a scripting language is required.
  • Experience with RDKit is a distinct advantage.
  • Experience with modelling RNA structures or RNA-ligand interactions is a distinct advantage.
  • Experience with using supercomputer clusters is a distinct advantage
  • Training in organic synthesis is a distinct advantage.
  • The candidate must demonstrate a strong commitment and enthusiasm for structure-based drug design of RNA-ligands and for research in general.
  • The candidate must be able to work independently and interactively in a team setting.
  • Experience from relevant research projects will be considered as positive

Deadline 30th October 2023

Applu here


Posted on October, 03, 2023

PhD scholarship within cattle Genomics and Bioinformatics

The Department of Animal- and Aquacultural Sciences (IHA), Faculty of Biosciences at the Norwegian University of Life Sciences (NMBU) has a vacant 3-year PhD - position related to cattle genomics and bioinformatics.

The main objective of the PhD project is to create haplotype-separated reference genomes in the Norwegian Red breed. These reference genomes will serve as basis for mapping structural variants in this population. Additionally, the project aims to compile comprehensive catalogs of structural variants, represented as genome graphs. These resources will allow us to examine functional consequences of structural variants and create opportunities for developing SV genotyping approaches.

The successful candidate will join CIGENE (https://cigene.no/), a multidisciplinary genome biology research group possessing expertise in genetics, functional and comparative genomics, bioinformatics and evolutionary biology. CIGENE has excellent wet and dry lab facilities for automated high-throughput omics, and bioinformatics.

Required Academic qualifications:

  • Master’s degree in genetics, genomics, bioinformatics, or similar field

The following experiences and skills will be emphasized:

  • Experience with analysing omics data
  • Experience with command-line-based operation of the High-Performance Computing (HPC) system
  • Familiarity with at least one programming language (R, python, etc)
  • Ability for independent work displaying initiative and creativity
  • Analytical and academic approach to research questions

You need to:

  • have good collaborative skills
  • a high proficiency in English, both written and spoken

Application deadline: 15.10.2023

Apply here


PhD fellowship in Mucosal Immunology

We are looking for a highly motivated PhD student to join the Mucosal Immunology Group headed by Professor William Agace at the Department of Immunology and Microbiology, Copenhagen University.

The successful candidate will join a superb team of international researchers within the newly established NovoNordisk Foundation challenge grant-funded ‘Center for Intestinal Immune Regulation (CIIR)’. CIIR comprises of 4 collaborating teams (Agace, CU; K. McCoy, Calgary (Canada); F. Bendtsen, Hvidovre hospital; L. Rønn-Larsen, DTU) whose combined expertise in mucosal immunology, gastroenterology, microbiota-host interactions, bioinformatics and state-of-the-art animal models aims to identify intestinal immune-stromal interactions important in intestinal homeostasis and in inflammatory bowel disease (IBD).

Key criteria for the assessment of applicants
Applicants must have a master’s degree in molecular biology with specialization in Medical Biology.

The applicant should have performed their master practical project in the field of mucosal Immunology and have a strong educational background in Immunology, as well as some training in bioinformatics. (basic R programming).

The applicant should have practical experience in breeding and maintaining mice colonies as well as working with mice, including flow cytometry-based assessment if intestinal immune populations and the intestinal microbiota.

Other important criteria are:

  • Experience in PCR, qPCR and ELISA
  • A curious mind-set with a strong interest in Mucosal Immunology
  • Proficiency in English

Application deadline: Deadline for applications: 3 October 2023. 23.59pm CET

Apply here


Posted on September 29, 2023

PhD fellowship in Biophysics

We invite applications for a PhD position in biophysics. The research aim is to use different computer simulations to understand how the shape of mitochondrial membranes emerges. The project is part of a research project entitled “Coupling Architectures of the Cellular Powerhouse to Energy Production States”, which is financed by Sapere Aude: DFF-Forskningsleder. Niels Bohr Institute, Faculty of SCIENCE, University of Copenhagen

The inner membrane of mitochondria, the powerhouse of the cell, is highly folded, exhibiting intricate dynamical structures called cristae that are integral to a multitude of cellular processes, in particular bioenergetic demand. Abnormal cristae architectures are associated with many diseases, such as liver dysfunction. However, it remains obscure how exactly the crista shapes emerge and are connected to molecular activities. The goal of this project is to use multiscale computer simulation to understand how the activities and cooperativity of key molecular players shape crista membranes.

Who are we looking for?
A PhD candidate should have a background in physics, chemistry, biology, bioinformatics, or related fields. It is considered a strength to have knowledge of molecular dynamics simulations, and computer programming.

Contact person and supervisor: Assistant Professor Weria Pezeshkian, Niels Bohr International Academy, Niels Bohr Institute, Faculty of SCIENCE, University of Copenhagen, weria.pezeshkian@nbi.ku.dk

The deadline for applications is 1 October 2023, 23:59 GMT +2.

Apply here


PhD position in Neural Reprogramming and Cell Replacement therapies

Join our cutting-edge research team of Dr. Marc Thier (HI-STEM and Department of Prof. Andreas Trumpp, DKFZ) and make a significant impact on the lives of people affected by chronic progressive neurodegenerative diseases. We are offering a prestigious PhD position in our Neural Reprogramming and Clinical Translation Research Group (led by Dr. Marc Christian Thier), where we are dedicated to developing regenerative cell replacement therapies for the growing number of people affected by neurodegenerative diseases.

Requirements:
We are looking for a PhD student with a strong background in molecular cell biology. The advised candidate is excited to explore the “unknown” in science at the edge of knowledge, able to work precise and independently, and likes working in a team. Previous experience in stem cell culture, bioinformatic analysis of single-cell RNA-sequencing data, and knowledge in animal experimentation (FELASA B) are highly desirable. The project is already running and most technologies are already established. The candidate should be dedicated to the project, willing to learn bioinformatic analysis, and perform animal experiments.

Location:
HI-STEM gGmbH (www.HI-STEM.de) is a non-profit public-private partnership between the German Cancer Research Center (DKFZ) in Heidelberg and the Dietmar Hopp Stiftung. HI-STEM performs cutting-edge research on normal and malignant stem cells with the aim of translating these results into novel clinical applications. HI-STEM is located within the German Cancer Research Center (DKFZ, which is the largest biomedical research institution in Germany.

Apply here


Posted on September 27, 2023

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 6th, 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

Summary:

During this PhD, you will use innovative bioinformatic techniques to investigate how epigenetic processes contribute to rare genetic disorders that affect insulin secretion. Critically, you will use these disease-specific epigenetic patterns to develop classifiers termed “episignatures” to assist with the interpretation of novel genetic variants and as a diagnosis tool.

Description:

Mendelian disorders, while individually rare, are collectively common affecting around 3.5% of the population. New sequencing technologies have revolutionised medical genetics and enabled the identification of rare mutations as the cause of many different disorders. However, determining the exact genetic cause can still be challenging when dealing with variants with unknown or uncertain clinical significance. Recently there has been increasing evidence that epigenetic modifications can assist in the interpretation of genetic variation.

Academic criteria:

Applicants for a studentship must have obtained, or be about to obtain, a first or upper second-class UK honours degree, or the equivalent qualification gained outside the UK, in an appropriate area of medical sciences, computing, mathematics or the physical sciences. Applicants with a lower second class will only be considered if they also have a Master’s degree. Please check the entry requirements of the home institution for each project of interest before completing an application. Academic qualifications are considered alongside significant relevant non-academic experience.

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.

Work task

The research group of Prof. Tero Aittokallio develops computational approaches that combine multi-omics genomic/molecular profiling and clinical information from cancer patients using mathematical and statistical approaches such as machine learning and network modelling. The medical aim is to optimize treatment outcomes for individual patients using maximally predictive models and minimal biomarker signatures.

The group is now seeking a motivated PhD student, with strong computational and chemoinformatic skills, for developing methods for personalized treatment predictions. The PhD candidate will be working in a multi-disciplinary environment at Oslo University Hospital to develop methods for improved statistical designs and analysis of pre-clinical experiments to maximize their reproducibility and translatability.
The successful candidate will be employed at the Department of Cancer Genetics, located at the Institute for Cancer Research, and will work in a team of computational biologists in a close collaboration with experimental scientists, medical doctors and lab engineers. The PhD student will have the possibility to attend relevant courses at the University of Oslo, and present at national and international conferences.

The position will offer a vantage point in the rapidly developing field of functional precision medicine, with versatile opportunities to learn and become an expert in the field, where there is a growing requirement for data scientists. Our multicultural and multidisciplinary organisation prides itself in a working community that fosters creativity and diversity, and a relaxed workplace with a Nordic style of work-life balance.

Qualifications

  • Master degree in chemoinformatics, computer science, biostatistics, bioinformatics, biomathematics, or other relevant field
  • Confident communication skills in English and good scientific writing skills
  • Experience in various bioinformatics data analysis tools for large-scale omics data analyses
  • Good programming skills (e.g. Python, R) and ability to work with version control tools (e.g. Git)
  • Previous knowledge of cancer research and preclinical experiments is considered an advantage
Personal qualities

  • High work capacity and productivity
  • Able to work independently and in teams
  • Motivated and solution oriented
  • Multidisciplinary communication skills
  • Commitment to meeting deadlines

Application deadline: 15.10.2023

Webcruiter ID: 4709271937

Apply here


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.

Eligibility criteria

You will need to meet the minimum entry requirements for our PhD programme Veterinary Medicine and Science PhD research course. The successful candidate would be required to undergo enhanced security clearance to work at APHA and health surveillance including additional vaccinations to gain access to the high containment laboratory facilities.

Candidates with relevant experience in virology, molecular biology, bioinformatics (including working with ‘R-program’), or entomology would be considered preferential, but not essential. As this studentship requires integration between two organisations the successful candidate will be highly motivated and have excellent communications skills.

How to apply

Applications should be submitted via the Veterinary Medicine and Science programme page. In place of a research proposal you should upload a document stating the title of the project that you wish to apply for and the name of the relevant supervisor.

Application deadline:

Contact details: Denise Marston E-mail: d.marston@surrey.ac.uk

Apply here


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.

How it works

Application opens: August 2023

Application submission deadline: 09 October 2023, 23:59 CEST

Reference deadline: 11 October 2023, 23:59 CEST

Interview dates: To be confirmed

Written application results: Will be announced around mid-November 2023

Expected start date: Flexible, by October 2024 at the latest

For details click here


PhD: Single-cell transcriptomics and epigenetics

About the position

A three-year PhD fellowship on the project EPICOD – Novel insights into the epigenetic landscape of puberty onset in Atlantic cod - is available at the Faculty of Biosciences and Aquaculture, Nord University (Bodø, Norway).

Faculty of Biosciences and Aquaculture (FBA)

The FBA is responsible for research, teaching and dissemination of knowledge within biosciences and aquaculture. In recent years, FBA has undergone a major development both in terms of faculty and infrastructure, and has an exceptionally international academic environment.

The FBA aims to be a leading international arena in the High North for education, research and knowledge dissemination in aquaculture and marine ecology, fostered by a unique genomic platform and characterized by strong interaction between the disciplines. It possesses state-of-the-art laboratory facilities and operates a modern Research Station about 10 minutes from campus. The Faculty seeks to strengthen the relations between students, the research community, public sector and the industry. For more information visit the Faculty’s website.

Qualification requirements

At the time of taking up the appointment, the candidate should have completed an MSc degree (or equivalent) in a relevant discipline, namely epigenetics, genomics and bioinformatics.

This challenging project requires a highly motivated, creative and ambitious applicant with an excellent academic record and the ability to collaborate with other members of a multidisciplinary team.

Documented experience in bioinformatics is an essential requirement for this position. Hands-on experience in single-cell sequencing and epigenetic analysis is advantageous.

Proficiency in oral and written English is essential and must be documented either by the Norwegian Higher Education Entrance Qualification or internationally recognised certificates, such as TOEFL, IELTS, APIEL or similar.

The successful candidate will join the PhD programme in Biosciences at Nord University and is expected to complete a doctorate within the three-year project period. The candidate should fulfill the admission requirements of this PhD programme at the Faculty of Biosciences and Aquaculture and participate in the training components stipulated in regulations of the PhD program. Application for admission to the programme must be submitted within three months after taking up the position. For admission requirements and regulations, see our web page.

Deadline 18th September 2023

For details click here


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

  • You must have a professionally relevant background in field such as genetic epidemiology, statistical genetics, bioinformatics, public health, health sciences, epidemiology, biostatistics, molecular biology, or a medical degree
  • Your education must correspond to a five-year Norwegian degree program, where 120 credits are obtained at master's level
  • You must have a strong academic background from your previous studies and an average grade from the master's degree program, or equivalent education, which is equal to B or better compared with NTNU's grading scale. If you do not have letter grades from previous studies, you must have an equally good academic basis. If you have a weaker grade background, you may be assessed if you can document that you are particularly suitable for a PhD education.
  • Experience in quantitative statistical analysis
  • Proven experience in academic writing
  • Relevant technical knowledge and experience with statistical software (R or equivalent), programming languages (Python, Perl, C++ or equivalent) and/or distributed computation
  • Proficiency in spoken and written English
  • You must meet the requirements for admission to the to the PhD programme in medicine and health sciences

Application deadline: 20.09.2023

 

Apply here


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:

People of Norway is an unprecedented initiative combining large-scale genomic data with highly interdisciplinary analysis to reveal the fine-scale genetic and cultural history of the Norwegian population. Due to the influence of Norwegian migration throughout history, its findings will provide insights across both national and international scopes. The foci of the project are:

i) how current populations in Norway are shaped by past population structure and dynamics;
ii) the relationship with geographically neighbouring populations;
iii) coupling between genetic structure and prevalence of cultural and linguistic features in the population
iv) the effect of demographic changes on genetic structuring
v) improving accounting for genetic structure in medical association studies and precision medicine strategies.

Qualifications and personal qualities:

  • The applicant must hold a master`s degree or equivalent in bioinformatics, genetics, or a related discipline
  • Experience with large scale genetic data sets and bioinformatics is essential
  • Experience in the following fields is desirable: genetic population structure analyses, statistical genetics
  • Interest in several of the following fields is desirable: biomedical sciences, demography, archaeology, linguistics
  • Experience from relevant research projects will be considered as positive
  • The candidate should be able to work independently and in a structured manner, and have the ability to cooperate with others
  • Ability and motivation to carry out a PhD project
  • The applicant must be fluent in oral and written English, see documentation requirements

General information: For further information please contact Ellen Røyrvik e-mail: ellen.royrvik@uib.no - phone: +47 966 23 255

Apply here


Posted on August 30, 2023

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

The application deadline is 2 October 2023.

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.

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

KEY SKILLS, EXPERIENCE AND QUALIFICATIONS

  • Master’s degree (or equivalent) in molecular/cellular biology/biochemistry, with a solid background and research experience in cancer biology and knowledge of DNA repair or chromatin dynamics
  • Wet laboratory and analytical skills, demonstrated experience in cell culture, as well as in the characterization of nucleic-acids, proteins, IHC, RNAi and bioinformatics will be considered as strong assets,
  • Excellent time management, rigour, perseverance, scientific creativity and originality, writing skills, conciseness, sense of priority and ability to work with others,
  • Language skills: fluent command of English, knowledge of other languages of the European Union is an asset

SCIENTIFIC CONTACT Dr Eric Van Dyck (eric.vandyck@lih.lu)

Apply here


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


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

What we are looking for

  • You have a Master's degree in the field of life sciences, with a focus on bioinformatics, biomedical sciences, bioscience engineering, (bio)chemistry, (molecular) biology, biotechnology, medicine or related disciplines.
  • You have analytical problem-solving skills, and you are a team player, creative, critical, and open-minded.
  • You have excellent oral and written communication skills in English.

For more information, please contact Nele Vervaet (cmb@vib-ugent.be)

Apply here


Posted on August 11, 2023

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:

  • The applicant must hold a master`s degree or equivalent in bioinformatics, genetics, or a related discipline
  • Experience with large scale genetic data sets and bioinformatics is essential
  • Experience in the following fields is desirable: genetic population structure analyses, statistical genetics
  • Interest in several of the following fields is desirable: biomedical sciences, demography, archaeology, linguistics
  • Experience from relevant research projects will be considered as positive
  • The candidate should be able to work independently and in a structured manner, and have the ability to cooperate with others
  • Ability and motivation to carry out a PhD project
  • The applicant must be fluent in oral and written English, see documentation requirements

Your application must include:

  • A brief account of the applicant`s research interests and motivation for applying for the position
  • Certified copies of diplomas and transcripts of grades
  • Applicant whose education is from another country than Norway, need to also attach a certified translation of the diploma and transcript of grades to English or a Scandinavian language, if the original is not in any of these languages. It is required that the applicant enclose a review from NOKUT whether the education in question (bachelor and master degree) is of a scope and level that corresponds to the level of a Norwegian master’s degree.

For further information please contact Ellen Røyrvik e-mail: ellen.royrvik@uib.no - phone: +47 966 23 255

Deadline 30th August 2023

Apply here


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.

The PhD student will work in a highly sophisticated High-Performance Computing (HPC) environment, have access to state-of-the-art systems and computational infrastructures, and establish collaborations with international and local experts in different areas of biomedical research.
Key Duties
  • 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
Requirements
  • 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

Are you passionate about utilizing cutting-edge data-driven approaches to address critical healthcare challenges? Are you eager to make a meaningful impact in the field of stroke prevention? If so, we invite you to join our dynamic research team of the Neurology department of the University Hospital Basel as a PhD/MD-PhD student working on an exciting SNF funded international project focused on data-driven approaches.

The position is limited to three years and the earliest starting date is September 1st, 2023.

Your position

As a PhD or MD-PhD student, you will be an integral part of our research team and actively contribute to the development and implementation of data-driven approaches to identify strategies to prevent stroke recurrence. You will have access to a vast array of anonymized patient data, a blood biobank and state-of-the-art computing resources, and a collaborative work environment. Under the guidance of experienced researchers (clinical-research and data-science), you will have the opportunity to shape the direction of the project and conduct cutting-edge research in the field of healthcare analytics.

Responsibilities:

  • Conduct a comprehensive review of existing literature on stroke, current preventative strategies secondary stroke, data analytics, and machine learning techniques
  • Data harmonization of several international clinical datasets, organization of the overall logistics of the Swiss Stroke Biobank
  • Collaborate with clinicians and researchers to identify relevant data sources and variables for analysis

Your profile

  • A master's degree in computer science, data science, computational biology, biomedical engineering, or a related field; or a masters degree in medicine with a strong data science interest
  • Strong programming skills, preferably in Python
  • Some experience working with large datasets and data processing tools
  • Solid understanding of data analysis and machine learning techniques- Excellent written and oral communication skills
  • Good knowledge (written/oral) of English
  • Ability to work independently and collaboratively in a team environment
  • Highly organized with excellent communication and interpersonal skills

Please send your application by e-mail to Prof. Mira Katan (mira.katan@unibas.ch).

Questions regarding the position should be directed to Prof. Mira Katan and Prof. Catherine Jutzeler, by e-mail at mira.katan@unibas.ch and catherine.jutzeler@hest.ethz.ch.

For details click here


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

An extensive resource for Bioinformatics, Epigenomics, Genomics and Metagenomics