Two PhD fellowships in experimental brain tumor research and bioinformatics

The selected candidates will be part of professor, consultant neuropathologist Bjarne Winther Kristensens research group https://bric.ku.dk/research-groups/Research/kristensen-group/ Bjarne Winther Kristensen will be the principal supervisor. A main interest in the group is how the role of the tumor microenvironment influences brain tumor aggressiveness and therapy response and how this change between different types and subtypes of brain tumors. Most of our projects focus on glioblastoma. The PhD fellowships are supported by the Lundbeck Foundation.

Your job
You will join a multi-disciplinary research team that work with both patient tumor tissue, experimental in vitro and in vivo brain tumor models and advanced bioinformatics.

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

• Carrying through an independent research project under supervision.

• 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, e.g. human biology, neuroimmunology and bioinformatics. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

PhD fellowship in Bioinformatics/Data Science/Machine Learning

We are looking for a highly motivated and ambitious bioinformatician / data scientist / Machine Learning specialist for a three-year PhD fellowship commencing 1 October 2024 or as soon as possible thereafter.

The “Data Science for Drug Design” (DSDD) research group is dedicated to the development and application of cutting-edge and data-driven technologies to advance network medicine. The DSDD group has a broad expertise encompassing structural bioinformatics, cheminformatics, computer-aided drug discovery & design, research tool/database development and applying machine learning/AI approaches.

Department of Drug Design and Pharmacology is committed to research-based teaching and interdisciplinary research that supports the development and understanding of chemical and pharmacological properties of drugs and drug targets. We work as part of a dynamic academic community of research, education and innovation within the Pharmaceutical Sciences bridging Health Sciences and Life Sciences.

PhD Microbiome Monitoring for Food Safety

The Netherlands Food and Consumer Product Safety Authority (NVWA) enforces rules and regulations to guard the safety of foods throughout the food chain. And luckily, the current status of food safety in the Netherlands is quite high. Nevertheless, changes in the food production chain continuously challenge food safety. For example, production methods, societal preferences, economic drivers or consumer behavior may change over time, with potential consequences for food safety.

You will be enrolled in the Graduate School of the Faculty of Science and embedded at the Microbiology Theme at the Swammerdam Institute for Life Sciences at the University of Amsterdam, supervised by prof. dr. Linda Verhoef and prof. dr. Stanley Brul (promotors). You will closely collaborate with biosystems data analyses group (BDA). The work performed at WBVR will be co-supervised by dr. M. Brouwer.

In this research project, you will work with monitoring samples that NVWA collects in the context of AMR monitoring in food production animals. You will enrich this sample flow with microbiological and epidemiological data, aiming to identify indicators that are relevant for (changes in) food safety. By making smart use of monitoring data, and enriching the sample flow with epidemiological data, you will investigate whether genotype profiles can provide biomarkers as a sneak preview into changes in food production systems. 

You have/are

• a degree (MSc, or equivalent) in Food Safety, Microbiology, Molecular Biology, Biomedical Sciences, or closely related fields. Candidates in the final stages of obtaining their degree are eligible to apply;
• an excellent background in bio-informatics and molecular microbiology, expertise in the field of food safety, an interest in (epidemiological) data-analyses and hands-on experience in next gen sequencing;
• fuent in English, both written and spoken;
• strongly motivated, highly curious, problem-solving, a team player who can also work independently.

Do you have questions about this vacancy? Or do you want to know more about our organisation? Please contact: prof. dr. ir. Linda Verhoef, email l.p.b.verhoef@uva.nl or prof. dr. Stanley Brul email s.brul@uva.nl

For details click here

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PhD position in lipid metabolism engineering in microalgae

As a part of a European project, we are seeking a highly motivated and skilled early-stage scientist to join our highly dynamic team as a PhD candidate. The successful candidate will play a critical role in advancing our research and development efforts in the field of microalgae lipid metabolism engineering and photosynthesis, and will have the opportunity to join a highly exciting international European consortium and team. This position requires a strong foundation in molecular engineering, metabolic pathway analysis, and synthetic biology, along with hands-on experience in bioreactor operations.

Key Responsibilities:

• design, execute, and optimize experiments focused on lipid production in microalgae;
• engineer and manipulate metabolic pathways to enhance lipid biosynthesis;
• apply synthetic biology techniques to modify and optimize microalgal strains;
• operate and maintain bioreactors for the cultivation and experimentation of microalgae;
• analyze data and interpret results to drive project progress and innovation;
• prepare technical reports, scientific publications, and presentations to communicate research outcomes.

Your qualities

• MSc in Life Sciences related field, especially: Biochemistry, Biotechnology, Molecular Biology, or a related field;
• demonstrated enthusiasm and interest in molecular engineering and synthetic biology of eukaryotic microalgae;
• basic/advanced understanding of photosynthetic metabolism;
• strong background in metabolic pathway analysis and genetic manipulation;
• practical experience with bioreactor systems and microalgae cultivation;
• proficiency in molecular biology techniques, including gene cloning, CRISPR, and DNA assembly;
• excellent problem-solving skills and the ability to work independently and collaboratively;
• strong communication skills, both written and verbal, with the ability to present complex data clearly;
• valid English certificate (e.g., TOEFL) for non-Dutch degrees.

Preferred Qualifications:

• previous experience and/or knowledge in lipid metabolism and engineering and/or microalgae research within lipid metabolism or photosynthesis research;
• familiarity with omics technologies (genomics, transcriptomics, proteomics, metabolomics);
• experience with bioinformatics tools and software;
• experience with metabolic model is a plus.

For more information about the procedure, please contact Rutger Voorrips, recruiter, by email: rutger.voorrips@wur.nl.

For details click here

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Posted on July 10, 2024

Doctoral Researcher in Microbiome Systems Biology

The Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI) investigates the pathobiology of human-pathogenic fungi and identifies targets for the development of novel natural product-based antibiotics. The research group Microbiome Dynamics invites talented and highly gifted candidates to apply as Doctoral Researcher (m/f/div) in Microbiome Systems Biology for four years.

As part of a new EU-funded project, the Microbiome Dynamics (MBD) department contributes to developing microbiome-based creative solutions to address precision nutrition for immune health in obese people. We are seeking an excellent and enthusiastic Ph.D. student in the fields of metabolic modeling and/or microbiome data to work on this project and collaborate closely with an extensive network of top European scientists and start-ups. The objective of the Ph.D. project is to conduct extensive in silico microbiome metabolic modeling to predict food-microbiome interactions and their effects on immune health.

The candidate will also have the opportunity to contribute to several national and international research projects focused on the role of the microbiome in globally significant diseases. Together with renowned scientists and supported by an excellent infrastructure, you will have the opportunity to contribute to a healthier, cleaner, and fairer society. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

• A strong interest in conducting collaborative research on the topic outlined above is paramount
• Candidates are expected to be interested in working at the boundaries of several research domains
• Master’s degree in computational biology, bioinformatics, bioengineering, chemical engineering, or a related discipline
• Knowledge and experience in the analysis of biological high-throughput data
• Knowledge of statistical methods in the context of biological systems
• Experience with programming (Python, Perl, C++, R)
• Well-developed collaborative skills

Further information:
Prof. Dr. Gianni Panagiotou | +49 3641 532-1759 | career@leibniz-hki.de

The deadline for the advertisement is July 31, 2024, but applications will be reviewed on a rolling basis.

Apply here

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Doctoral student in Cardiac genomics

The University of Gothenburg tackles society’s challenges with diverse knowledge. 56 000 students and 6 600 employees make the university a large and inspiring place to work and study. Strong research and attractive study programmes attract researchers and students from around the world. With new knowledge and new perspectives, the University contributes to a better future.

The Department of Molecular and Clinical Medicine is located at the Institute of Medicine at the Faculty of Medicine at Sahlgrenska Academy, University of Gothenburg. Our primary research at the department focus on metabolism, diabetes, obesity and cardiovascular disease. We support and promote research and teaching in translational medicine to improve health and to benefit society.

The PhD education in Medical Science comprises carrying out a scientific project and completing at least 30 credits of courses at third-cycle level. The doctoral student must also write a scientific compilation thesis or monograph corresponding to at least 120 credits. The project "Dissecting cardiac genomes in human heart failure" aims to determine the contribution of somatic mutations to heart failure (HF). HF is a leading cause of death and disability which results when the heart is unable to generate sufficient output of blood for the needs of the body. The causes and mechanisms underlying HF are poorly understood and therapy mainly targets the consequences rather than causes of HF.

Eligibility   

Education at third-cycle level requires general eligibility and specific eligibility as set out in the general syllabus for the subject.

The general eligibility requirements for education at third-cycle level are:
1. having completed a degree at second-cycle level, or
2. the fulfilment of course requirements totalling at least 240 credits, of which at least 60 credits must be at second-cycle level, or
3. the acquisition of equivalent knowledge in some other way, either in Sweden or abroad.

Specific entry requirements for this subject, according to the general syllabus, are:
having completed the English B/6 course or is considered to have acquired equivalent knowledge through previous studies.

Contact information 

For more information about the project please contact principal supervisor,
Gustav Smith, Professor, Institute of Medicine,
e-mail: gustav.smith@wlab.gu.se

For details click here

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PhD student: Deep learning in Genomics

The Yves Moreau and Stein Aerts research labs are looking for a shared PhD student to apply deep representation learning and large language models to decipher the genomic regulatory code, with a focus on the human brain. You will engineer new AI models to predict cell-type specific expression of all protein-coding genes in the genome, across diverse cell types in different regions of the human brain. Techniques will include Transformers, self-supervised learning, reinforcement learning, and generative AI models. Explainability of your models is essential, to discover new biological rules of the genomic regulatory code. As a secondary aim, your trained models can be applied to interpret human genetic variation and to improve the prediction of disease risk from the genome sequence.

The project, funded by an FWO Strategic Basic Research (SBO) grant, will focus on designing and testing genomic enhancers to target transgenes to specific cell types in the mouse brain and in cultured human brain biopsies using adeno-associated viral vectors. Whereas you will focus on AI modeling, other members in the consortium will perform wet-lab experiments to test your predictions and designed DNA sequences. This provides an opportunity to get acquainted with “wet-lab” experimental research. The PhD student will be stationed at ESAT-STADIUS in the Moreau group but will be embedded in both the Moreau and the Aerts labs as well as the new VIB Center for AI & Computational Biology and the Leuven Bioinformatics and AI community. The PhD student will be jointly supervised by Yves Moreau and Stein Aerts.

Profile

• You obtained a Master's in Computer Science, Artificial Intelligence, Bioinformatics, Physics, Engineering, Bio-engineering, or equivalent. Please note that to be admitted to the doctoral training distinction (= cum laude) based on your study results or professional realizations is a strict requirement.
• Comprehensive AI background (deep learning, probabilistic modeling, generative AI)
• Proficient in Python programming
• Experience with machine learning is a plus (e.g., PyTorch/Tensorflow/Keras)
• Experience with explainable AI (e.g., SHAP) is a plus
• Experience with high-performance computing, software containers
• Experience with genomics is a plus, but not essential
• Ability to work independently and in a team.
• Proficiency in oral and written English.

How to apply?

Please complete the online application procedure and include a detailed CV, two reference letters, and a motivation letter.

For further information and questions, please send an email to Yves Moreau (yves.moreau@kuleuven.be) or Stein Aerts (stein.aerts@kuleuven.be)

For details click here

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Posted on July 03, 2024

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.

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.

Skills and personal qualities

•  We are seeking a highly motivated person who is guided by scientific creativity.
•  We welcome applicants with a background in medicine, biomedicine or molecular biology with:
  1) interest and skills in bioinformatics
  or

         2) experience from wet-lab research and interest in analysing complex datasets.

• Emphasis will be placed on personal suitability, scientific interests, and hypotheses within the research-related area.

Terms and conditions

The doctoral student will be employed on a doctoral studentship maximum 4 years full-time.

Reference number STOD 2-2770/2024

Last application date 19.Jul.2024 11:59 PM CEST

Apply here

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PhD Studentship in Immunotherapy/ Bioinformatics

Award Summary:

100% tuition fees and an annual stipend of £19,237 (2024/2025 UKRI rate). International candidates will be required to fund the difference between the home and international fees.

Location: Newcastle University, UK

Overview

This studentship will computationally investigate the heterogeneity of CAFs in NASH-HCC patients, employing bioinformatics and AI led image analysis of single-cell and spatial datasets, identifying features of disease stage, progression and therapeutic response.

Objective 1: Profile cancer-associated fibroblast heterogeneity in patients with NASH-HCC.

Bioinformatics analysis of pre-existing scRNA-seq data from HCC patient tissue. The student will learn to perform quality control, normalisation, dimensionality reduction, clustering, differential gene expression and trajectory analysis of scRNAseq data.

Objective 2: Develop new AI technologies to analyse multiplexed spatial imaging data of NASH-HCC patient tumours.

The student will analyse the first spatially resolved multiplexed analysis of NASH-HCC immunotherapy responders and non-responders, performing imaging mass cytometry analysis using standard published workflows. The student will work to develop advanced AI tools for image analysis, centred on detailed spatial relationships and specific cell-cell interactions, potentially limiting immunotherapy responses.

Objective 3: Perform an integrated analysis to identify serum signatures associated with CAF heterogeneity, tumour stage, progression, and response to therapy.

The connection between tumour stroma composition and immune cell presence and over 4000 circulating serum markers (O-link assays) will be explored, pinpointing serum signatures indicative of disease stage, progression, and treatment response.

Methodology and skills gained

The student will develop computational analysis skills, analysing and integrating large bulk RNAseq and scRNAseq datasets and highly multiplexed imaging data, also learning the fundamentals of machine learning AI analysis. They will be immersed in a thriving laboratory environment, with the opportunity to develop wet lab skills alongside their predominantly computational research.

Eligibility Criteria

You must have or be expected to gain a minimum 2:1 Honours degree or international equivalent in a subject relevant to the proposed PhD project. A master’s qualification will be advantageous.

Applicants whose first language is not English require an IELTS score of 6.5 with a minimum of 5.5 in each subsection. International applicants may require an ATAS clearance certificate prior to obtaining their visa and to study on this programme.

How To Apply

You must apply through the University’s Apply to Newcastle Portal

Contact Details

jack.leslie@newcastle.ac.uk 

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PhD position: Bioinformatics and Evolutionary Genomics

For the Van de Peer Lab (Bioinformatics and Evolutionary Genomics), in collaboration with the Flemish Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, we are looking for a m/f/x doctoral fellow.

About the project

Global climate change will challenge the productivity of major agricultural crops. Therefore, more resilient crops are required to secure sufficient food production worldwide. To create plants with desired productivity and better environmental stress tolerance, strategies such as genome doubling of agriculturally important crops and generating hybrids hold great promise. Yet, just how a plant manages to maintain a double set of chromosomes and how all alleles interact in dynamic genetic networks to create more phenotypic plasticity remains poorly understood.

This fully funded PhD project is part of the Methusalem project granted to Prof. Yves Van de Peer and aims to gain a deeper understanding of polyploidy through genomics, experimental evolution, modeling, and artificial intelligence. Partner institute ILVO explores the benefits of polyploidization in crop breeding by studying genome doubling and interspecific hybrids.

About your job

In this project, you will investigate the phenotypic, physiological, and molecular response of interspecific, tetraploid hybrids and their diploid parents in drought experiments and yield trials. Experiments will span the range from single cells to plant populations at the field level, with both fundamental research questions and direct practical applications in plant breeding, through an interdisciplinary approach. You will collect genomic data with high throughput sequencing (HTS) methods, and combine it with phenotypic field observations. Additionally, you will apply molecular markers to study genome constitution and perform single-cell RNA-Seq experiments to study differential gene expression networks.

Profile

• You have a keen interest in applied plant research and in combining wet-lab experiments with bio-informatics.
• Practical experience in a molecular lab and/or HTS data analysis/bio-informatics expertise is strongly recommended.
• You have programming skills in Python or another scripting language, or you are willing to learn it.
• You have good communication and writing skills and have an excellent knowledge of written and spoken English.
• You are highly motivated, enthusiastic and self-critical. You work with attention to detail, and you have an open mindset to learn new skills.
• You combine being a team player with a strong sense of autonomy and responsibility.
• You are willing to apply for additional funding when eligible.
• You are willing to participate in the training and supervision of graduate students.

How to apply? 

Please complete the online application procedure and include a detailed CV, a letter of motivation and the contact details of two referees no later than August 21st, 2024.

For more information about this vacancy please contact Prof. dr. Tom Ruttink or dr. Marlies Peeters (tom.ruttink@ilvo.vlaanderen.be; marlies.peeters@ilvo.vlaanderen.be).

Selected candidates will be informed no later than August 28th. Interviews will be held in the second week of September.

Apply here

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Posted on July 01, 2024

PhD student in Cancer Precision Medicine

The Department of Immunology, Genetics and Pathologyat Uppsala University has a broad research profile with strong research groups focused on cancer, autoimmune and genetic diseases. A fundamental idea at the department is to stimulate translational research and thereby closer interactions between medical research and health care. Research is presently conducted in the following areas: cancer precision medicine, cancer immune therapy, genomics and neuro-biology, molecular tools and functional genomics, neuro-oncology and neuro-degeneration and vascular biology. Department activities are also integrated with the units Oncology, Clinical Genetics, Clinical Immunology, Clinical Pathology, and Hospital Physics at Akademiska sjukhuset, Uppsala.

Duties
We are looking for a doctoral student with a special interest in the area of cancer precision medicine with a focus on hematological tumors and epigenetic regulation of gene expression.  The candidate will devote most of the time towards his/her research level education. Within this research level education the candidate will mainly focus on studies on epigenetic mechanism and the impact of these for tumor transformation and progression of the tumor clone in two hematopoietic tumors, multiple myeloma and acute leukemia in infants.

Requirements
We are looking for applications from highly motivated candidates that hold a Master’s (second-cycle) degree in Medical Science, or 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. Previous experience in experimental research within the area and methods is highly warranted. A requirement is that the candidate manage well the English language both in written and spoken form.

For further information about the position, please contact: Helena Jernberg Wiklund, helena.jernberg_wiklund@igp.uu.se

Please submit your application by 15th August 2024, UFV-PA 2024/1573.

Apply here

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PhD Studentship: Proteotranscriptomic

University of Surrey - Veterinary Medicine and Science

Exercise-induced pulmonary haemorrhage (EIPH) has serious welfare implications for racing Thoroughbreds (TB). Long term prognosis is poor and the only recovery recommendation is arbitrary rest time between severe EIPH episodes or retiral. With no ability to monitor varying severity within the pulmonary vasculature and tissue in vivo there is a clear unmet need to qualify and quantify EIPH severity and progression. In human medicine, the advent of ‘omics’ technology and biomarker discovery has allowed for more precise disease classification leading to stratified disease management. Human acute lung injury changes are reflected in circulating microRNA biomarkers, before changes in the lung occur. Excitingly microRNAs can also act as ongoing lung remodelling markers. Proteomic profiling of human pulmonary fibrosis and interstitial lung disease has also revealed a circulating protein signature pattern.

We hypothesise that the pathophysiology of EIPH leads to proteotranscriptomic changes at the tissue level with varying severity allowing us to identify signature patterns that differentiate between controls and EIPH cases. We further hypothesise that tissue level changes are reflected in circulating serum and such signature patterns can be utilised as biomarkers to determine disease severity and consequently develop a more targeted approach to managing EIPH. You will utilise our impressive bank of tissue samples and data collected from each horse to take a proteotranscriptomic and bioinformatics approach to start to answer some of the questions we do not know in relation to equine EIPH.

Entry requirements

Open to candidates who pay UK/home rate fees. See UKCISA for further information. Starting in October 2024. Later start dates may be possible, please contact Dr Susan Armstrong once deadline passes.

You will need to meet the minimum entry requirements for our Veterinary Medicine and Science PhD programme.

This is basic research with a strong molecular and bioinformatic focus project and undergraduates with a degree in a related discipline would be expected. Medical and veterinary graduates are encouraged to apply.  A Master’s degree in related subject is desirable and previous experience in statistical methodology is desirable. Potential students should provide an overview of how their qualifications and training fit with the project and can contact Dr S. K. Armstrong informally prior to application to discuss the project.

How to apply

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

Application deadline: 1 July 2024

Enquiries: Contact Dr Susan Armstrong

Ref: PGR-2324-085

For details click here

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PhD student in structure-based drug design with focus on machine learning

The Department of Cell and Molecular Biology is one of the most international, broad and distinguished molecular bioscience departments in Europe. The department comprises sju research programs with about 220 employees (http://www.icm.uu.se). The PhD position is available in Jens Carlsson’s group in the computational biology and bioinformatics programme. Jens Carlsson’s research focuses on using molecular modeling techniques to study protein-ligand interactions. The Carlsson group uses structure-based methods (e.g., molecular docking and molecular dynamics simulations) to understand protein function and to design ligands of pharmaceutically important targets, often in close collaboration with experimental groups. The Carlsson group is an international research team and is also part of the Science for Life Laboratory (http://www.scilifelab.se/). Visit the group website for more information (http://www.carlssonlab.org/).

Project description
The objective of the PhD project is to develop computational approaches to identify small molecule and peptide ligands that target therapeutically relevant receptors, with the vision to accelerate the drug discovery process. The project will be focused on addressing several challenges in structure-based drug design using artificial intelligence. Recently developed techniques for the prediction of the three-dimensional structures of proteins and protein-ligand complexes will be optimized for drug discovery applications.

Requirements
The applicant must hold a master’s degree in biology, chemistry, pharmacy, physics, computer science or within another subject which the employer considers to be equivalent. The applicant must have good ability to work independently as well as in a group. Excellent written and oral knowledge of English is required as the work takes place in an international environment.

For further information about the position, please contact: Jens Carlsson, jens.carlsson@icm.uu.se, Tel: +46 (0)72 227 7976.

Please submit your application by 17 June 2024, UFV-PA 2024/1634.

Apply here

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Posted on June 25, 2024

PhD candidate for Spatial multi-omics data integration

Project Overview

This PhD position is one of multiple positions within a larger project aimed at optimizing spatial omics analysis for a variety of biological applications. Your research will primarily focus on the integration of spatial omics data, working closely with leading experts. including the Martin Guilliams lab and the Chris Marine lab, VIB-UGent Center for Inflammation Research, Belgium

What you will do

• Analyze and integrate spatial omics data generated from advanced technologies such as MERFish Vizgen, MACSima Miltenyi, and 10X Visium-HD generated at the VIB.
• Develop new computational methods and tools for spatial omics data analysis.

Profile

Essential

• You obtained a Master's in Computer Science, Artificial Intelligence, Bioinformatics, Physics, Engineering, Bio-engineering, or equivalent.
• Background in AI (deep learning, probabilistic modelling, generative AI) or machine learning
• Proficient in Python or R programming
• Strong communication skills in English

Desirable but not required 

Preference will be given to candidates with experience with

• experience with processing scRNA-seq or spatial transcriptomics data
• experience with high-performance computing and software containers
• a background in systems biology

Key personal characteristics

• Strong interpersonal skills
• Ability to work independently and as part of a team

We offer

•  Competitive stipend and benefits package
• Fully funded PhD scholarship, but encouraged to apply for a national PhD fellowship (e.g., FWO)
• A versatile and challenging academic position with very diverse contacts in a world-class research environment operating at an international level, and various opportunities to broaden your expertise.
• Access to state-of-the-art compute & GPU infrastructure
• Collaborative and supportive research environment
• Attendance of national and international conferences
• Training courses in academic, technical, and career skills.

How to apply?

Please complete the online application procedure and include a detailed CV, two reference letters, and a motivation letter.

For further information and questions, please send an email to Yvan Saeys  (yvan.saeys@ugent.be).

For details click here

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PhD in Computational Biomedicine / Machine Learning / Spatial Omics

We are looking for a highly motivated and talented PhD student to join the newly created Translational Spatial Profiling Center at the Heidelberg University Hospital, managed by the Institute for Computational Biomedicine and the Institute for Pathology.

PhD Studentship: Data analytics to disentangle molecular level interactions in microbiomes

Posted on June 15, 2025

PhD scholarship in Single Cell Bioinformatics

Are you interested in becoming a bioinformatics researcher working with state-of-the-art methods and data? Would you like to contribute to research that will deepen our understanding of the interplay between the viruses and the immune system? Then this is the PhD project for you. In this project, you will be working with single cell proteomics and transcriptomics data from clinical trials testing virus vaccine strategies, as well as pre-clinical data from model organisms. During this project, you will be joining the Single Cell Omics group at the Section for Bioinformatics at the Technical University of Denmark.

About the Single Cell Omics group
We are a bioinformatics outfit working on the development and application of data analysis tools, with a specific (though not exclusive) focus on single cell data, such as single cell cytometry (flow, mass, and barcode-based cytometry), single cell sequencing (tag-based, full transcript-based), and single cell mass spectrometry. We collaborate with clinicians on prognostics, diagnostics, and therapeutics for various diseases, including cancer and inflammatory bowel disease.

Responsibilities and qualifications
Your overall focus will be to handle, analyze, and communicate results from single cell studies of the immune response to viruses. You will apply existing tools for analysis of single cell data and develop new methods if gaps in the repertoire are identified.

The following requirements must be met by the successful candidate:

• Strong background in biology (e.g. through a relevant degree programme or relevant work experience)
• Strong programming skills

The following are desirable, but not required:

• Experience working with data analysis in R (the research group you will be joining works primarily in R)
• Experience working with RNA sequencing data
• Experience working with, or working knowledge of single cell RNA sequencing data
• Basic understanding of immunology

Further information
Further information may be obtained from Lars Rønn Olsen, email: lronn@dtu.dk.

Application procedure 
Your complete online application must be submitted no later than 20 June 2024 (23:59 Danish time). Applications must be submitted as one PDF file containing all materials to be given consideration.

Apply here

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PhD Student: Machine Learning Applications and Data Analysis in Translational Psychiatry

At the Max Planck Institute of Psychiatry in Munich, basic scientists and clinicians are working in close cooperation to understand the causes of complex diseases of the brain, searching for new prevention and treatment strategies. This translational research strategy is supported by a modern psychiatric research hospital as well as a number of research departments and research groups with expertise ranging from neurobiological research methods as well as clinical and behavioural studies to molecular genetics and computational approaches. The overarching goal is to optimise the benefit of research advances for the patients by way of close and innovative networking of basic research-oriented and clinical neuroscience.

The Project Group “Translational Deep Phenotyping” offers a position from 01.03.2024 as PhD student (m/f/x) for development and implementation of machine learning applications and data analysis in Translational Psychiatry.

Your group

The MPIP Fellowship led by Prof. Dr. med. Falkai at the Max Planck Institute of Psychiatry focuses on developing transdiagnostic biomarkers across the spectrum of mental illness. The project group “Translational Deep Phenotyping” explores and validates biomarkers that identify and predict disease severity and treatment response in schizophrenia spectrum disorders and depression. This approach enhances the comprehension of mental illness pathophysiology through a highly interdisciplinary, integrative, and multimodal approach.

Your profile

• You studied in the field of life science or bioinformatics
• You have experience in basic molecular and optionally also in cell biology techniques
• You have beginner-intermediate level experience on the use of R or Python for data analysis
• You are a team player
• You work carefully and independently
• You have excellent skills in spoken and written English

Please contact Dr. Dr. David Popovic for further questions: david_popovic@psych.mpg.de.

For details click here

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Posted on June 01, 2024

19 fully funded PhD scholarships in Computational Biology, Structural Biology, Genomics, Neurogenomics or Biophysical modelling

Human Technopole is offering up to 19 fully funded PhD scholarships to young scientists from the national and international community who wish to undertake a doctoral degree on a project focused on Computational Biology, Structural Biology, Genomics, Neurogenomics or Biophysical modelling.

In the multi and interdisciplinary scientific environment of the European School of Molecular Medicine (SEMM) network, that includes 8 Italian Research Centers and 7 Italian Universities, we offer an innovative PhD program in Systems Medicine.
The PhD Program aims to train young and motivated researchers in the wide field of modern Biomedicine. The general idea is that complex systems, such as diseases and their pathogenesis, cannot be understood taking into account a single point of view. The expertise of different scientists, biologists, medical doctors, computer scientists, physicists and mathematicians is needed to provide new insights.

AWARDING BODIES

SEMM PhD program is a 3^rd-cycle university degree, fully academic in nature and it is released by SEMM's collaborating universities that acts as awarding bodies: The qualification of Doctor of Philosophy, abbreviated "PhD", is awarded jointly by the Rectors of the University of Milan (administrative site), the University of Naples "Federico II", the University of Bari, the University of Turin, the University of Trento, the Catholic University of the Sacred Heart, and Hunimed of Milan in compliance with the Ministerial decree dated 14 December 2021, n. 226; in the title and the certificate the institutional/scientific role of the Fondazione SEMM as well as the curriculum attended are expressly mentioned.
The title gives full access to post-doctoral research positions in Europe and worldwide.

RESEARCH CENTERS

Research centers include: European Institute of Oncology (IEO), FIRC Institute of Molecular Oncology (IFOM), Center for Genomic Science of IIT, National Institute of Molecular Genetics (INGM), Italian Institute of Genomic Medicine (IIGM), Human Technopole (HT), Center for Genetic Engineering (Ceinge), Telethon Institute of Genetics and Medicine (TIGEM). Science covers virtually every aspect of modern Cell and Molecular Biology, from both the basic and applied research points of view, it is highly multidisciplinary and is supported by know-how extending from functional genomics to developmental model systems.

FELLOWSHIPS

All admitted students will have a fellowship. It consists of an annual gross amount of € 20.266,50. The amount is not subject to IRPEF taxation, as per the art. 4, Law n. 476 dated 13/8/1984, and subject to the regulations of the art. 2, subs. 26, Law n. 335, dated 8 August 1995, as far as the pension contributions are concerned. Fellowships are mostly offered by the Universities, but can also may be available at host research centres. These fellowships will be independently managed by the individual granting institutions with specific awarding and delivery modalities; these will not be in any way ascribable either to SEMM or the Universities. The number of available positions/fellowships will be communicated at the time of the call.

We encourage applications from highly motivated graduates with outstanding academic qualifications. Successful candidates will join research groups headed by top-level scientists and will carry out their research in cutting-edge fields in a stimulating environment.

The PhD positions are available through the SEMM PhD Program in Systems Medicine.

Detailed information on the call and on the application process here.

Deadline 27 June 2024.

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Posted on May 23, 2024

Doctoral (PhD) student position in computational network-based cancer precision medicine

Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.1 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

During 2024 the DDLS Research School will be launched with the recruitment of 20 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see:Data-Driven Life Science (DDLS) - SciLifeLab

The doctoral studies will be conducted in the Cancer Proteomics Mass spectrometry research group headed by professor Janne Lehtiö. The research group is placed at SciLifeLab in Solna, Stockholm. The Lehtiö research group is a translational team of scientists dedicated to advancing human proteome analysis. We develop innovative methods to enhance personalized cancer treatments.

Proteomics is the large-scale study of proteomes - entire sets of proteins in a biological system. This field of science focuses on understanding the proteins in biological processes. By analysing the proteome, we can gain insights into cellular behaviour, disease mechanisms, and potential therapeutic targets. Proteomics involves various technologies and methods, such as mass spectrometry and bioinformatics.

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.*

Reference number STOD 2-2069/2024

Last application date 06.Jun.2024 11:59 PM CEST

For details click here

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Doctoral scholarship holder omics driven drug discovery

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.

The Center of Medical Genetics in the Faculty of Medicine and Health Sciences is looking for a full-time (100%) doctoral scholarship holder in the field of “Omics driven drug discovery in hereditary aortopathy”

The Antwerp Center of Medical Genetics (CMG) is a large clinical, diagnostic and research department that is embedded within the University of Antwerp and the Antwerp University Hospital. The CMG has built up a substantial know-how and infrastructure in the field of the clinical, molecular and pathophysiological study of several hereditary diseases: heart diseases, hearing loss, cancer, bone diseases and mental retardation.

Position

• You will work actively on the preparation of a PhD thesis in the field of cardiogenomics, more specifically hereditary aortic aneurysm and dissection.
• You are eager to take on a challenging PhD project investigating the molecular mechanisms of aortic aneurysmal disease, making use of human DNA, mouse models, cells (iPSC-derived models), -omics datasets and bioinformatics tools.
• You will publish high-quality scientific articles related to the research project.
• You will present your work at national and international scientific workshops and conferences.

Profile

• You hold a Master degree in (Bio)medical sciences, Biochemistry, Biotechnology or closely related discipline, or you will have obtained it by the time you start to work.
• You are eligible to apply for FWO(-SB) scholarship.
• You can demonstrate excellent study results.
• Your research qualities are in line with the faculty and university research policies.

Want to apply?

• You can apply for this vacancy through the University of Antwerp’s online job application platform up to and including June 17, 2024 (by midnight Brussels time). Click on the 'Apply' button and complete the online application form. Be sure to include the following attachments:
• a motivation letter
• your academic CV (including honors, grades, skills, prior mobility, publications,…)
• 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.
• 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 Prof Dr Bart Loeys (bart.loeys@uantwerpen.be)

For details click here

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PhD position at the Department of Biomedicine

PhD Position in Coleoptera Phylogenomics

The Senckenberg Gesellschaft für Naturforschung (SGN) was founded in 1817 and is one of the most important research institutions in the field of biodiversity. At its eleven locations throughout Germany, scientists from over 40 nations conduct cutting-edge research at an international level. At the Senckenberg Research Institute and Natural History Museum Frankfurt we seek to fill the position of PhD Position – (m/f/d) in Coleoptera Phylogenomics.

The project focuses on Dorynotini, a Neotropical tribe of tortoise beetles, to explore trait evolution, including antipredator traits, in relation to shifts between savanna/dry forest and tropical rainforest biomes. Moreover, the project seeks to understand the tribe’s spatiotemporal evolution, more specifically, the role of seasonally dry tropical forests for dispersal across South America, and how the morphological diversity on the Caribbean islands evolved. The PhD student will engage in diverse activities spanning field work in South America and the Caribbean, fossil description, alpha taxonomy, phylogenomics, historical biogeography, and bioinformatics.

Your profile

• Master’s degree in evolutionary biology (ideally in entomology)
• strong interest in entomology and systematics
• a background in phylogenomics (preferentially anchored hybrid enrichment, low-coverage whole-genome sequencing), including assembly and wet lab methods
• Experience with methods of divergence time estimation, ancestral range reconstruction and trait evolution is also beneficial, as is publication in peer-reviewed journals
• Ability to work independently and as part of a team
• Ability to conduct field work in the Tropics
• Good communication and writing skills in English
• Strong organizational skills

How to apply

Please send us your complete and informative application documents (letter of motivation, including a possible start date, summary of previous research experience, a CV and contact information for at least two references, and copies of certificates, transcripts and grades) mentioning the reference of this job offer (ref. #01-24019) until 14.06.2024, by e-mail (attachment in a single pdf document to: recruiting(at)senckenberg.de.

Senckenberg Gesellschaft für Naturforschung

Senckenberganlage 25

60325 Frankfurt a.M.

E-Mail: recruiting(at)senckenberg.de

For information regarding the scientific aspects of the project please contact Marianna Simões (marianna.simoes(at)senckenberg.de).

For details click here

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Posted on May 20, 2024

PhD student Bioinformatics

PhD position MetaHealth

Location: Academisch Centrum Tandheelkunde Amsterdam

This PhD project is supported by the NWA program METAHEALTH, which focuses on oral and metabolic health in the first 1000 days of life. The PhD candidate will collaborate closely with fellow PhD students studying social behaviour, mathematical modeling and gut microbiome modelling in METAHEALTH.

Your duties

Your responsibilities are 1. improving the existing 3D reconstructed human gingiva model in order to better mimic the microbial exposure infants encounter in their oral cavity; 2. exploring various factors influencing the host-microbiome interactions, including the impact of diet components and immune factors, with the improved model. Through comprehensive phenotypic and functional analyses you will elucidate the host responses crucial for maintaining tolerance and fostering homeostatic interactions with oral microbes.

PhD in Metabolomics

Location: Utrecht University

Would you like to understand how endocrine disruptors affect human health? Are you passionate about metabolomics? Then a PhD position at the One Health Chemical group of the Institute for Risk Assessment Sciences (IRAS) might be just for you! We are offering an exciting PhD position to investigate the health effects of endocrine disrupting chemicals (EDCs) on multimorbidity, with a focus on metabolic dysfunction-associated steatotic liver disease (MASLD), metabolic and immune related diseases.

Wat breng je mee?

As the ideal candidate for this position, you feel at ease working in a multidisciplinary environment and are a team player. You are enthusiastic, ambitious,  independent thinker, and have excellent writing skills. The nature of the position allows for diverse backgrounds, which include biology, chemistry, chemometrics, epidemiology, bioinformatics, statistics, computational epidemiology, or a related discipline. Affinity with OMICs data analysis is valued, and any experience with Large Language Models is considered valuable. You have experience with programming (e.g. R, Matlab, Python).  Most importantly: you are willing to learn.

PhD position in structure-based RNA-ligand design

At the Faculty of Medicine, Department of Biomedicine in the group of Professor Ruth Brenk (http://www.uib.no/en/rg/brenk), a PhD-position (100 %) 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 candidates must be able to start the position latest mid-August 2024.

The position is part of the project “Paving the way for rational RNA-ligand design” financed by The Research Council of Norway.

The main objectives for the advertised PhD position are

• to carry out structure-based design of RNA-ligands
• to establish computational methodology on how to harvest the potential of large, chemically accessible combinatorial spaces for the design of RNA ligands
• to determine the binding affinities of RNA ligands
• to determine the crystal structures of RNA-ligand complexes

This PhD project will be conducted in collaboration with the group of Prof. Jens Carlsson at Uppsala University in Sweden implying that this position will involve research stays in his lab.

Qualifications and personal qualities:

Posted on May 07, 2024

PhD scholarship in Proteomics Bioinformatics

DTU Health Tech engages in research, education, and innovation base on technical and natural science for the healthcare sector. The Healthcare sector is a globally expanding market with demands for the most advanced technological solutions.

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

In our research group, I don't perceive myself as an authoritative figure who makes all the decisions. Rather, I see myself as a guide and facilitator for you. My primary role is to provide unwavering support to help you achieve our shared goals by navigating the right paths and eliminating obstacles along the way. I am committed to fostering an environment where scientific ideas, diversity and personal growth thrive.

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

• Strong R programming skills
• Experience with applied analysis of proteomics or transcriptomics (bulk/single-cell)

Further information
Further information may be obtained from Kristoffer Vitting-Seerup, krivi@dtu.dk.

Application procedure 
Your complete online application must be submitted no later than 1 June 2024 (23:59 Danish time). Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply now", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

• A letter motivating the application (cover letter – max 1 page)
• Curriculum vitae
• Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
• Letters of recommendation (mandatory)

For details click here

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PhD in Bioinformatics, Biostatistics and Artificial Intelligence

The Luxembourg Centre for Systems Biomedicine (LCSB) is an interdisciplinary research centre of the University of Luxembourg. We conduct fundamental and translational research in the field of Systems Biology and Biomedicine – in the lab, in the clinic and in silico. We focus on neurodegenerative processes and are especially interested in Alzheimer’s and Parkinson’s disease and their contributing factors.

Your Role...

We 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).

Posted on April 30, 2024

PhD position in bioinformatics and artificial intelligence

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.

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

About the position
Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data- Driven Life Science (DDLS) aims (https://www.scilifelab.se/data-driven/) to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.1 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

During 2024 the DDLS Research School will be launched with the recruitment of 20 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see https://www.scilifelab.se/data-driven/ddls-research-school/

The position is in the field of data-driven epidemiology and biology of infection, which covers research that will transform our understanding of pathogens, their interactions with hosts and the environment, and how they are transmitted through populations. The research in this field have a strong focus on computational analysis or predictive modelling of pathogen biology or host-microbe systems for which multidimensional, genome-scale experimental data are now available or it may use population-scale genetic, clinical, or public health data from pathogen surveillance efforts and biobanks.

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 October 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: 2024-06-07

Apply here

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PhD student position in stochastic modelling of infectious diseases

One Ph.D. position is available in stochastic modelling of infectious diseases. The research project is focused on healthcare-acquired infections with the long-term goal of developing computational tools for outbreak surveillance, inference of transmission chains and evaluating interventions.

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

Project description
Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data- Driven Life Science (DDLS) aims (https://www.scilifelab.se/data-driven/) to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.1 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

During 2024 the DDLS Research School will be launched with the recruitment of 20 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see https://www.scilifelab.se/data-driven/ddls-research-school/

The position is in the field of data-driven epidemiology and biology of infection, which covers research that will transform our understanding of pathogens, their interactions with hosts and the environment, and how they are transmitted through populations. The research in this field have a strong focus on computational analysis or predictive modelling of pathogen biology or host-microbe systems for which multidimensional, genome-scale experimental data are now available or it may use population-scale genetic, clinical, or public health data from pathogen surveillance efforts and biobanks.

Qualifications
Candidates for this position must have obtained an M.Sc. degree in mathematics, mathematical statistics, bioinformatics, computer science, physics or an equivalent topic (obtained latest October 1, 2024). Previous experience in stochastic modelling and inference is desirable. Candidates should also have good computing and programming skills (e.g. Python and R) and previous experience in mathematical modelling of biological systems. Good presentation and communication skills in oral and written English are also required.

Application deadline: 2024-05-29

Apply here

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PhD position on the regulatory networks underlying temperature tolerance in cauliflower

Are you looking for a PhD position and interested in genetic regulation in cauliflower? Do you want to combine data collection in the field with computational data analysis to investigate a complex trait? Then this PhD vacancy may be of interest to you.

Cauliflower is an important vegetable that can grow in various climatic regions. However, it is sensitive to high ambient temperatures during development, which might result in delayed curd induction and poor curd quality. Some cauliflower accessions are more sensitive than others. The genetic basis underlying temperature tolerance is not well understood yet. In this project, we aim to optimize field phenotyping for the timing of curd initiation and curd architecture under various temperature conditions and to perform genomic and transcriptomic analysis to identify associated genomic regions and genes. This will ultimately contribute to the breeding of climate-proof cauliflowers.

As a PhD student you will work on this complex trait, by:

• performing independent research, supported by your supervisors;
• combine experimental fieldwork with bioinformatics to collect and analyze data;
• writing publications on your scientific work, culminating in a PhD thesis.

In particular, you will collect genomic, transcriptomic and phenotypic data from several large field experiments with 100-200 cauliflower genotypes. You will perform genome-wide association studies and transcriptomics to identify associated genomic regions and genes and investigate these further using state-of-the-art pangenomic tools.

You will work here
This is a position in the team of Guusje Bonnema at the Laboratory of Plant Breeding (http://www.pbr.wur.nl/), co-supervised by Sandra Smit from the Bioinformatics Group (http://www.bif.wur.nl/) and Richard Immink from Bioscience (Wageningen Plant Research). To fully benefit from the surrounding expertise, the PhD student will divide its time between Plant Breeding and Bioinformatics. Plant Breeding is a merged unit of Wageningen Research and Wageningen University which conducts both fundamental and strategic research and teaching at BSc, MSc and PhD level.

Your qualities
You are driven to unravel complex traits in plants by combining your expertise in plant breeding with your computational skills. You are also an enthusiastic team player, with well-developed communication and collaboration skills.

You also possess:

• a successfully completed MSc degree in plant sciences, plant biotechnology, bioinformatics, or a related discipline;
• knowledge of plant breeding and genetics;
• experience in the analysis of (gen)omics data using command-line tools;
• a demonstrable proficiency in programming (in R and Python);
• perseverance in problem solving;
• good writing and oral communication skills in English.

For more information about this position, please contact dr. Guusje Bonnema, by phone +31 317 484028 or e-mail guusje.bonnema@wur.nl, or dr. Sandra Smit, by e-email sandra.smit@wur.nl.

For more information about the procedure, please contact Dax Teunissen, corporate recruiter (+31 317 487820, dax.teunissen@wur.nl).

This vacancy will be listed up to and including May 13, 2024. We hope to schedule the first job interviews in the week of May 27.

For details click here

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Posted on April 20, 2024

PhD position in AI for biomedical data analysis

PhD position (all genders) in AI for biomedical data analysis Part time  | Temporary | Arbeitsort: Hamburg-Eppendorf

UKE_Zentrum für Molekulare Neurobiologie (ZMNH)

Better together. For life.

We are the University Medical Center Hamburg-Eppendorf (UKE) - and we stand for excellent competence in research, teaching and comprehensive healthcare in our clinics. Every day, our approximately 14,900 employees strive anew to make the world a little healthier with their contribution.

It is our aspiration to be one of the leading university hospitals - and at the same time the best employer in our industry. At UKE, for example, we firmly believe that successful and fulfilling work should be in harmony with employees' personal needs and individual lifestyles. And as diverse as these are, so is our range of individual solutions.

You will join the Institute of Medical Systems Biology and the bAIome Center for Biomedical AI (baiome.org) to complement our lively and enthusiastic team of machine learning engineers.

Your main tasks will encompass the development of novel machine and deep learning algorithms to understand, predict, and treat human disease. Using multi-modal genomic, image, and patient data, in conjunction with graph, transformer, and diffusion models, you will help us understand and treat immune-related maladies. Together with clinical disease experts, you will translate your findings into targeted applications.

Your profile

• Master’s degree in computer science, bioinformatics or related fields
• Solid understanding of machine and deep learning and relevant frameworks (e.g. Pytorch or Tensorflow, Keras, scikit-learn, OpenCV)
• Proficiency in Python, Linux and HPC environments
• Good communication skills to interact with collaborators ranging from machine learning researchers to pathologists or medical students
• Knowledge of biology and medicine is a plus
• Highly motivated with an interest to work in an interdisciplinary team spanning machine learning, bioinformatics, and medicine
• Strong English language skills to communicate and collaborate in our diverse work environment

We look forward to receiving your complete appli­cation by 22^nd April 2024.

Contact to the department
Prof. Dr. Stefan Bonn
s.bonn@uke.de

Apply here

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PhD student 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.

Project description
Your studies in Bioinformatics will be in the project: "Deep Learning for protein structure prediction”.

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.

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).

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

Closing date: 23/04/2024

Apply here

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PhD student in Pollinator Genomics

The Department of Zoology is one of the departments at the Faculty of Science with about 50 employees and 40 students, with research topics in Ecology, Ethology, Functional Morphology, Systematics and Evolution, and Population Genetics. The Centre for Palaeogenetics is a research centre jointly funded by Stockholm University and the Swedish Museum of Natural History

Project description
The Department of Zoology invites applications for a four-year PhD position based at the Centre for Palaeogenetics in Stockholm. The project is aimed at investigating temporal patterns of population structure and genomic diversity in pollinating insect populations. The analyses will use state-of-the-art genomic and palaeogenomic methods with focus on recovering DNA from museum specimens collected throughout the last 200 years. This will be a conservation genomics project part of a research programme funded by the Swedish Research Council and focused on investigating the genomic effects of population decline in insect pollinators. The PhD student will join the research group led by David Díez-del-Molino (see www.palaeogenetics.com) at the Centre for Palaeogenetics located on the Stockholm University campus.

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, the general syllabus for doctoral studies in the field of Population Genetics stipulates that applicants must have completed at least 120 higher education credits in biology, and at least 30 credits from a degree project within population genetics, molecular systematics, evolutionary biology, ecology, bioinformatics or a similar subject.

Contact
For more information, please contact David Díez-del-Molino, david.diez@zoologi.su.se or diez.molino@gmail.com

Closing date: 30/04/2024

Apply here

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PhD student in Molecular Biophysics

Are you interested in working with powerful new single-molecule imaging approaches to unravel fundamental principles of genome organization, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favourable working conditions? We welcome you to apply for a PhD position at Uppsala University.

The Department of Cell and Molecular Biology is organized into seven research programmes which all focus on different areas of cell and molecular biology: Computational Biology and Bioinformatics, Microbiology and Immunology, Molecular Biology, Molecular Biophysics, Molecular Evolution, Molecular Systems Biology and Structural Biology. The scientific basis of what we do lies in biology, but our research overlaps with other areas such as medicine, computer science, mathematics, chemistry, engineering sciences and physics. In total, we are over 200 staff and ~60 Ph.D. students. Please read more about the department’s work at https://icm.uu.se.

The Deindl lab offers a stimulating multidisciplinary environment where you will work closely with experts in biophysics, biochemistry, structural and molecular biology. Our overall mission is to investigate the molecular mechanisms underlying genome-interacting processes using a highly multidisciplinary approach that combines advanced single-molecule fluorescence imaging with a range of biophysical, structural, and biochemical techniques. For more information about the research in the Deindl laboratory, please visit http://www.deindl-lab.com/.

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

• hold a Master’s (second-cycle) degree in physics, biophysics, biochemistry or similar, or
• 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.

We are looking for a highly motivated candidate with a master's degree or equivalent proficiency in physics, biophysics, biochemistry or similar. Excellent knowledge of English is a prerequisite, as the position is located in an international environment. We value personal characteristics such as good co-operative ability, a self-motivated personality, and a keen interest in basic research and in addressing fundamental biological questions with quantitative approaches.

Please submit your application by 3 May 2024, UFV-PA 2024/1166

For details click here

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Posted on April 05, 2024

PhD position bioinformatics and immunogenomics

The overall project aim is to identify infectious disease (ID) triggers that can potentially cause immune-related noncommunicable diseases (IR-NCDs) like inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis and post-COVID-19-condition. In this project, we aim to 1) identify IDs triggering IR-NCDs by screening for antibody responses against >500,000 ID antigens from infections, microbiome and environment, and 2) to disentangle environmental and genetic factors affecting the transition from IDs to IR-NCDs. We will combine novel multi-omics approaches and technologies for personalized genotyping of HLA and adaptive immune receptor genes to deeply profile samples of patients at time of diagnosis as well as before diagnosis. This project will represent the largest and most deeply profiled systematic study of multiple IR-NCDs in a large population cohort Lifelines. The analysis of antibodies will take into account other multi-omics measurements available for participants, such as genetics and gut microbiome. The project is part of EU-funded grant Dark Matter, and will be performed in UMCG in collaboration with partners from Austria, Germany, Hungary and other countries.

The candidate will work on the generation and analysis of wide-scale antibodies data in pre- and post-disease samples from individuals with several non-communicable diseases (such as rheumatoid arthritis, chronic fatigue and post-COVID19), who are part of Lifelines population cohort. The antibodies profile will be linked with host environment, genetics and microbiome data. The work will be performed in close collaboration with colleagues from Groningen Microbiome Hub

Required Expertise
- Master’s degree with a focus on bioinformatics expertise ..
- A collaborative spirit to work effectively within an international interdisciplinary team and with clinical partners
- Excellent organizational skills to manage complex workflows and data collection processes
- Strong communication skills, both written and verbal, with the capability to present research findings to both a specialist and non-specialist audience
- Team player with excellent communication and collaborative skills

Additional experience in the following areas is highly desirable
- Experience handling large databases
- Knowledge of developing and debugging in Java/Python/R.
- Knowledge of immunology

Meer informatie

PhD student Bioinformatics

The LIT - Leibniz Institute for Immunotherapy (foundation under civil law) (www.lit.eu) 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.

The Algorithmic Bioinformatics research group is a purely computational lab developing and investigating new algorithms for solving bioinformatics problems on genome sequencing data. The problems we address include read alignment, variant detection & genotyping, genome assembly, whole-genome alignment and more in the context of human and population genetics, immunology, cancer and other biomedical research areas.

Requirements:

• Master’s degree in bioinformatics, computer science, or a related field
• Creative mind that is eager to shape the project and who wants to make an important biomedical impact through computational research
• Good programming skills, preferably in C++ and Python
• Good understanding of sequence analysis algorithms and data structures would be an advantage
• Hands-on experience in high-throughput sequencing data analysis is a plus
• Excellent oral and written communication skills in English

We offer:

• An international cutting-edge research environment that offers exciting and diverse opportunities
• Perspectives for further scientific qualification
• Possibility to visit international conferences and collaborating centers
• Flexible working hours
• Flat hierarchies and short decision-making processes
• A highly motivated and cooperative team
• Job ticket

For more information, please contact Birte Kehr (birte.kehr(at)ukr.de). We are looking forward to receiving your application including a cover letter, CV, and certificates. Please apply via our homepage https://rci.hr4you.org/job/view/55 quoting the reference BK-2024-1. The application deadline is April 7th, 2024.

Apply here

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Posted on April 02, 2024

PhD student on Graph Algorithms with Applications in Bioinformatics

There is an opening for a 4-year PhD position between Centrum Wiskunde & Informatica (CWI) and VU Amsterdam. We are looking for a motivated PhD student with a special interest in algorithms and data structures and their application in bioinformatics. The joint project will be supervised by Yasamin Nazari (VU) and Solon Pissis and Daniel Dadush (CWI).

Job description

Genomes are strings containing four characters {A, C, G, T} which encode the DNA and the genetic information of an organism. Computational genomics studies algorithms that can efficiently process such strings. The human genome project effort led to a single genome sequence representing the genome information of human DNA. While the vast majority of genome information is similar for all humans, the small individual differences can still offer important insights.

Recently, there has been a growing interest in pangenomics, where the goal is to process genome information coming from a huge sample of the population. Pangenomic data is often modeled by a graph that captures interaction between different samples. This has motivated the move from string algorithms to graph algorithms. However handling pangenomic graphs is computationally more expensive than single genomes. Even processing a single genome involves many computational challenges, and a wide range of algorithmic solutions have made such tasks possible. This project aims to develop efficient algorithms for processing pangenomic graphs as well as designing pangenomic graphs that “best fit” a given data set. This also involves graph algorithms in different computational paradigms such as dynamic, distributed or parallel models, as well the use of optimization techniques to design pangenomic graphs.

Requirements

Candidates are expected to obtain a Master’s degree in Computer Science, Mathematics or a related discipline before starting the position. Expected qualifications include mathematical maturity, and familiarity with algorithms and discrete mathematics. Prior knowledge of bioinformatics is not required. Candidates are expected to have an excellent command of English.

Apply here

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 PhD student 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.

Project description
Your studies in Bioinformatics will be in the project: "Gene Regulatory Network Inference and Systems Biology”.

The goal of this project is to develop computational algorithms and methods that use omics data to infer gene regulatory networks (GRNs), and apply these to understand regulatory mechanisms that lead to cancer formation. Cancer cells are subjected to scRNA-seq to measure the transcriptomic response of gene knockdown perturbations via CRISPR interference on a large scale. The Sonnhammer group has recently shown that such data data offers a significant improvement in GRN quality compared to non-perturbed data. The project involves developing and applying computational methods that can work optimally with this new type of data, either by adapting and optimizing existing methods, or designing new methods based on deep learning neural networks and variational autoencoders. Also new methods for quality assessment need to be developed.  The resulting predicted regulatory mechanisms will be forwarded for evaluating their clinical relevance.

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.

Contact
For more information, please contact the project leader, Professor Erik Sonnhammer, erik.sonnhammer@dbb.su.se.

Closing date: 23 April 2024.

Apply here

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Posted on April 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.

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

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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.

PhD position: In vivo gene editing and functional genomics

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

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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

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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

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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.

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

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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

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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.

 

 

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

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Posted on December, 2023