Doctoral Researcher positions in Metagenomics

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 positions (m/f/div) in Metagenomics For 4 years.

The Microbiome Dynamics (MBD) Department contributes to the development of personalized microbiome-based strategies to aid in the detection, monitoring, treatment, and prevention of human diseases (e.g., Ni et al., Cell Metabolism 2023; Leung et al., Science Translational Medicine, 2022; Seelbinder et al., Nature Communications, 2023). MBD is currently coordinating the EU-funded consortium MiCCrobioTAckle (https://miccrobiotackle.eu/), the BMBF-funded consortium PerMICCion (www.permiccion.de), and is an active participant in the EU-funded consortia FOODGUARD and NUTRIMMUNE, the Cluster of Excellence "Balance of the Microverse" (www.microverse-cluster.de), and the CRC/Transregio 124 "Pathogenic fungi and their human host: Networks of interaction" (www.funginet.de) funded by the Deutsche Forschungsgemeinschaft and the consortium SynThera funded by the Carl Zeiss Foundation.

We are seeking an excellent and enthusiastic Ph.D. student in the field of metagenomics. The aim of this PhD project is to leverage advanced computational techniques to analyze extensive metagenomics datasets, uncovering the influence of diet on the gut virome and its subsequent impact on the development of metabolic diseases.

Your profile:

• 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, Systems Biology, Bioengineering, Chemical Engineering, or a related discipline
• Knowledge and experience in the analysis of metagenomics and/or 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 | carrer@hki-jena.de

The deadline for the advertisement is January 31, 2025, but applications will be reviewed on a rolling basis.

Apply here

Doctoral Researcher in Computational Biology

The University of Luxembourg is an international research university with a distinctly multilingual and interdisciplinary character.

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. The LCSB recruits talented scientists from various disciplines: computer scientists, mathematicians, biologists, chemists, engineers, physicists and clinicians from more than 50 countries currently work at the LCSB. We excel because we are truly interdisciplinary, and together we contribute to science and society.

Successful candidates will join the Computational Biology group, led by Prof. Antonio del Sol, which develops computational models to address challenges in stem cell research and aging. We employ methodologies from different areas of mathematics, engineering, and physics, and integrate multiple sources of biological information to study biological processes at different levels of organization.

Berlin Institute of Health PhD Program - Call for PhD candidates 2025

The BIH PhD program aims to promote interdisciplinarity and support young translational talents. The program co-funds PhD positions for excellent translational projects that fit one of the four BIH research priorities. PhD candidates can apply until February 10, 2025, 2:00 p.m., Central European Time (CET).

The Berlin Institute of Health at Charité (BIH) is publishing the second call for students for its PhD program, which consists of Six doctoral positions (PhD, MD/PhD, Dr. rer. nat., or equivalent)

The BIH PhD Program contributes to the overall translational mission of BIH. This PhD program aims at fostering interdisciplinarity and will support and promote young translational talents within the BIH ecosystem and beyond. Positions in the BIH PhD Program are intended for students who wish to obtain a doctoral degree and who are motivated to carry out translational research.

We are looking for excellent candidates with a Master’s degree in various fields (Life Sciences, Bioinformatics, Mathematics, Physics, Computational Biology or similar, depending on the project you are applying for) and who are qualified to pursue a doctoral degree. You must have a strong academic background, exceptional motivation in doing translational research and a track record that matches the project(s) for which you are applying.

Interested candidates can apply until February 10, 2025 (2:00 p.m., Central European Time (CET)) via the BIH application portal (see link below).

For details click here

Posted on January 05, 2025

PhD Position in Bioinformatics: Clinical Breast Cancer Proteomics

The position will be placed in the Cancer proteomics Mass spectrometry research group headed by Professor Janne Lehtiö at Science for Life Laboratory (SciLifeLab). The Lehtiö group is a translational group aiming to improve cancer treatment using multi-omics tumor data analysis. The group members are from various disciplines working as a team to study genes and proteins in the context of biological networks, understand how tumor molecular changes impact the proteome and discover new disease biomarkers to be exploited therapeutically. Scientists and engineers in our group work closely together using a variety of technologies to generate novel knowledge about the biology of the disease and implement tools to support the clinical-decision making in the oncology setting.

We seek a highly motivated PhD student in bioinformatics, interested in breast cancer ​omics data analysis of clinical cohorts characterized by mass spectrometry-based proteomics. The position requires solid interest and curiosity to learn proteomics data analysis as well as communication skills and willingness to work in a team environment. The work will involve integrative and translational analysis of multiple levels of omics data derived from breast cancer cohorts. The focus will be on developing and applying ‘omics’ methods on biologically/clinically oriented research questions and to analyze the acquired data as well as to validate the findings using public domain data.

Eligibility requirements 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.

Skills and personal qualities

Qualifications

• Master of science, or equivalent, in biology, medicine, bioinformatics, computer science, mathematical statistics, or another relevant field.
• Documented education and experience in bioinformatics data analysis
• Programming experience
• Knowledge in statistical methods
• Basic understanding of cell- and molecular biology of cancer
• Fluent in English language
• Excellent communications skills

Reference number STÖD 2-4972/2024

Last application date 03.Jan.2025 11:59 PM CET

For details click here

The CeMM International PhD Program in Molecular Technologies and Systems Medicin

Do you want to work in an environment that promotes free-minded scientific creativity, and translate your findings to impact medical practice and improve healthcare? Are you excited to gain a new understanding of the molecular physiology and pathology of humans? Do you want to join an international group of highly collaborative and successful colleagues that help you achieve your training and research goals? Are you a person who enjoys teamwork across disciplines and within a broader cultural and social context? If yes, apply now for one of our 15 fully funded PhD positions here: https://apply.cemm.at/

‍The next PhD Program at CeMM, the Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, together with our partners the Medical University of Vienna, the CCRI St. Anna Children’s Cancer Research Institute and AITHYRA, the newly founded Research Institute for Biomedical AI of the Austrian Academy of Sciences, will start in September 2025.‍

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.

Apply here

Posted on December 30, 2024

PhD-position in structure-based ligand design using artificial intelligence based methods

PhD position in the molecular and cellular communication between cancer and the nervous system

Umea University is one of Sweden’s largest higher education institutions with over 37,000 students and about 4,700 employees. The University offers a diversity of high-quality education and world-leading research in several fields. Notably, the groundbreaking discovery of the CRISPR-Cas9 gene-editing tool, which was awarded the Nobel Prize in Chemistry, was made here. At Umeå University, everything is close. Our cohesive campuses make it easy to meet, work together and exchange knowledge, which promotes a dynamic and open culture.

A 4-year PhD position in understanding the molecular and cellular crosstalk between cancer and the nervous system has become available at Umeå University, Sweden. We encourage applications from highly motivated individuals with a keen interest in cancer, neuroscience and developmental biology. The PhD is open to anyone who meets the criteria outlined below. The studentship provides an excellent training opportunity for a talented and ambitious student. The working ‘day to day’ language in the laboratory is English.

Eligibility:

Basic eligibility for doctoral education is for those who have completed a degree at advanced level, completed course requirements of at least 240 higher education credits (credits), of which at least 60 credits at advanced level, or who have acquired essentially equivalent knowledge in some other way within or outside the country (HF Chapter 7, Section 39). Within the medical and dental programs, eight semesters of study constitute basic eligibility.

Further information and informal enquiries: Associate Professor Dr. Sara Wilson sara.wilson@umu.se

Application deadline 2025-02-23

Apply here

Doctoral (PhD) student position in Metastatic preclinical modelling

The Translational embryonal neural tumor research laboratory is located at BioClinicum in Stockholm and affiliated with the Childhood Cancer Research Unit, Dept of Women’s and Children’s health, Karolinska Institutet. The Baryawno laboratory consists of 2 Ph.D. students and a postdoc, and is part of the group constellation of professor Per Kogner, associate professor John Inge Johnsen and associate professor Malin Wickström. The group consists of a total of 12 Ph.D. students and postdoctoral fellows. The focus of our research is to increase our biological understanding of the embryonal tumor neuroblastoma, to develop new therapies leading to better survival, less side effects and increased quality of life.

The current project will be focused on characterising the bone marrow stroma of a bone metastatic mouse model of neuroblastoma by single-cell RNA-seq, creating organoid models of human bone metastases, and testing the function of seven genes that are overexpressed in human bone metastatic tumours when compared to primary tumours – in childhood neuroblastoma, adult prostate cancer and adult kidney cancer. The aim is to characterise and create novel preclinical models, and to investigate if the seven genes are direct contributing to the metastatic process. We will either knock-down the gene expression with shRNA in bone metastatic cell lines, or overexpress use the genes using cDNA in cell lines that are not bone metastatic.

Eligibility requirements for doctoral education:

A) General eligibility requirement

ou 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 2-5051/2024

Last application date 31.Dec.2024 11:59 PM CET

Apply here

Posted on December 19, 2024

PhD Position in Bioinformatics: Clinical Breast Cancer Proteomics

The position will be placed in the Cancer proteomics Mass spectrometry research group headed by Professor Janne Lehtiö at Science for Life Laboratory (SciLifeLab). The Lehtiö group is a translational group aiming to improve cancer treatment using multi-omics tumor data analysis. The group members are from various disciplines working as a team to study genes and proteins in the context of biological networks, understand how tumor molecular changes impact the proteome and discover new disease biomarkers to be exploited therapeutically. Scientists and engineers in our group work closely together using a variety of technologies to generate novel knowledge about the biology of the disease and implement tools to support the clinical-decision making in the oncology setting.

SciLifeLab is a national infrastructure and research center in technology driven life sciences and Karolinska Institutet is one of the four founding universities for SciLifeLab. We offer a very stimulating and diverse work in a team of very motivated co-workers with expertise in cutting-edge technology.

We seek a highly motivated PhD student in bioinformatics, interested in breast cancer ​omics data analysis of clinical cohorts characterized by mass spectrometry-based proteomics. The position requires solid interest and curiosity to learn proteomics data analysis as well as communication skills and willingness to work in a team environment. The work will involve integrative and translational analysis of multiple levels of omics data derived from breast cancer cohorts. The focus will be on developing and applying ‘omics’ methods on biologically/clinically oriented research questions and to analyze the acquired data as well as to validate the findings using public domain data.

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.

Qualifications

• Master of science, or equivalent, in biology, medicine, bioinformatics, computer science, mathematical statistics, or another relevant field.
• Documented education and experience in bioinformatics data analysis
• Programming experience
• Knowledge in statistical methods
• Basic understanding of cell- and molecular biology of cancer
• Fluent in English language
• Excellent communications skills

Reference number STÖD 2-4972/2024

Last application date 03.Jan.2025 11:59 PM CET

Apply here

PhD student in Structural Bioinformatics

We have the power of over 40,000 students and co-workers. Students who provide hope for the future. Co-workers who contribute to Linköping University meeting the challenges of the day. Our fundamental values rest on credibility, trust and security. By having the courage to think freely and innovate, our actions together, large and small, contribute to a better world. We look forward to receiving your application!

The research group of Björn Forsberg will recruit 1-2 PhD students in machine learning and computer vision methods to improve methods structural bioinformatics of 3D molecular representations.

In this position, you will use machine learning methods and tailored feature engineering to design new methods that aim to understand the complexity of molecular life in 3D. Specifically, you will extend existing methods to quantify variation in ensembles and averages of molecular structures like proteins and incorporate established methods from computer vision to unsolved problems where they have not been deployed previously. You will have the opportunity to learn and develop high-performance computing solutions using national super-computing infrastructure and apply these methods at scale to investigate new biology. There are also opportunities for national and international collaboration in both software development and applied biological research, and integration of e.g. AlphaFold.

Your qualifications

You have graduated (or completed courses with at least 240 credits) at master's level, either in a computational or mathematical field of study, or with demonstrated experience in structural biology or bioinformatics.

You will be expected to independently write and evaluate software in python and C++, using git for versioning, collaborative development, testing and deployment. Evidence of experience (e.g. through GitHub user contributions) is beneficial to your application. You are expected to be resourceful and independent, but also transparent and open to both provide and receive feedback. You are expected to look for opportunities to develop your own skills and interests, and encouraged to participate in international conferences, workshops, and collaborations. Excellent oral and written communication skills in English is essential.

Contact persons Björn Forsberg Assistant Professor bjorn.forsberg@liu.se

Apply here

Posted on December 12, 2024

PhD Studentship: AI solutions to guide treatment strategies for Cancers

Applications are invited for a 3.5-year funded PhD studentship at the Sussex Cancer Research Centre available from September 2025 under the supervision of  Dr Frances Pearl, School of Life Sciences, University of Sussex. It will be co-supervised by Prof Laurence Pearl FRS FMedSci, (Sussex), Dr Max Whibley (RSCH) & Dr Eleni Ladikou (BSMS).

In general, the types of treatment available to a cancer patient is determined by the type or ‘site’ of the original tumour. However, for 3-5% of all cancers, termed 'cancer of unknown primary' or 'CUP’s,' the original tumour site is unknown, making it particularly challenging to decide on the best treatment strategy for the disease as it presents at diagnosis, in secondary sites. For a minority of CUP patients (15–20%), the tumour can be attributed to a distinct clinical entity that benefits from primary site-specific treatment; however, the remaining 80–85% of patients belong to a group with a poor CUP prognosis.  In Sussex, despite extensive clinical & diagnostic work-up, including physical examination, radiological imaging, and histopathological investigation, approximately 300-500 of the cancers diagnosed annually, are designated as CUPs.

This project is a collaboration between the bioinformatics group at the University of Sussex, Brighton and Sussex Medical School (BSMS) and the CUP Multi-Disciplinary Team (MDT) at the Royal Sussex County Hospital (RSCH), University Hospitals Sussex NHS Foundation Trust.  At Sussex the student will be trained in genomics, programming, bioinformatics, big data and data science, cancer biology and therapeutics.  They will attend weekly online MDT meetings with the CUP team and will be trained in the interpretation of pathology & radiology outputs, at the RSCH and/or Brighton and Sussex Medical School.

Informal enquiries about the project can be made to Frances Pearl f.pearl@sussex.ac.uk

For details click here

PhD Student in Microbiome Research with a Bioinformatic Focus

Marie Curie (MSCA) PhD Student in Microbiome Research with a Bioinformatic Focus (We are targeting applicants of all genders.) Full time | Limited to three years | Announcement number: 917-2024

The Department of Hematology / Oncology at University Hospital Frankfurt offers a broad diagnostic and therapeutic spectrum for patients with solid tumors and malignant diseases of the hematopoietic system.

The research group led by Dr. Sebastian Scheich is dedicated to investigating the crosstalk between the microbiome and disease outcomes, particularly cancer, in preclinical rodent models and clinical patient samples. The current project is funded through an EU Horizon MSCA doctoral network. The lab is embedded within the Frankfurt Cancer Institute (FCI) and is further supported by grants from the Else Kröner-Fresenius-Stiftung, Deutsche Krebs­hilfe, and BMBF. It is part of a vibrant research environment within the FCI and maintains lively international collaborations.

The research team is also integrated into the excellent research infrastructure of the University Hospital Frankfurt, the Frankfurt Cancer Institute, and the DKTK partner site Frankfurt. Moreover, the department works closely with the Institute for Medical Microbiology and Hospital Hygiene and the Department of Infectious Diseases. The lab maintains a close collaboration with the group of Prof. Dr. Florian Büttner to develop bioinformatic tools.

Your role

• The current research position is embedded in the TargetRNA project, an EU Horizon funded Marie Skłodowska-Curie Action (MSCA) doctoral training network (https://www.uib.no/en/targetrna).
• Study of microbiota changes upon administration of compounds active against riboswitches and novel small molecules developed in other project parts in the consortium
• Conduction of microbiota-related experiments in small rodent models (mice)
• Utilization of 16S sequencing and metagenomic sequencing of complex samples, including library preparation and hands-on sequencing on own sequencers
• FACS-based immune profiling
• Single-cell RNA sequencing on two in-house platforms (BD Rhapsody and 10x Genomics)
• Bioinformatic analysis of sequencing data together with other datasets (e.g. FACS data, single-cell data) using multiomic integration models

Who you are

• A master’s degree or equivalent in biology, biochemistry, molecular medicine, bioinformatics, or a related field
• Mobility rule: No residence or main activity (work, studies, etc.) in Germany for more than twelve months in the last three years
• Comfort in working with rodent models
• Strong bioinformatic background or a high level of interest in large-scale data analysis using e.g. R

Join our team
Use the time until December 15, 2024, to apply. Please submit your online application including a possible starting date and your salary expectations. For further information regarding the position and project, please contact Dr. Sebastian Scheich via e-mail (s.scheich@med.uni-frankfurt.de) or Hanne Platzer via phone (+49 69 6301-6566).

Apply now: https://unimedizin-ffm-karriere.career.softgarden.de/application/?jobId=51396548

6 PhD Positions in Biosciences

The joint Research Training Group of Technische Universität Berlin – Freie Universität Berlin – Humboldt-Universität zu Berlin – Universität Potsdam – FMP Berlin offers 6 PhD Positions in Berlin/​Potsdam, Germany (salary E 13 TV‑L, 67 %, for three years starting at 01 April 2025)

Peptide research has become very important in both academia and industry, and there is a high demand for well-trained and knowledgeable researchers in this field. For this reason, the Bioactive Peptides Research Training Group offers a modern research training programme in peptide research for scientific staff. The RTG comprises 12 different research groups with scientific backgrounds in molecular biology, biochemistry, biotechnology, computational chemistry, synthetic techniques and methods, providing state-of-the-art bioanalytical and structural characterisation of peptides. More detailed information on the participating groups and the specific vacancies (with reference number) can be found at: https://​www.synpepbio.de/​apply. If you have any questions, please contact Dr Erik Werner (erik.​werner@​tu-berlin.de).

The research assistant has successfully completed an academic university degree (master's, diploma, or equivalent) in (bio‑)chemistry, molecular biology, biophysics, biotechnology, or a related field (or completes it soon). In addition, specialised knowledge should also be available:

Focus I: basic knowledge of micro- and/or molecular biology in theory and practice (cultivation of E. coli and fungi, cloning techniques, PCR, etc.) and/or protein biochemistry (protein purification by chromatography, protein characterisation by MS and spectroscopic methods).

Focus II: theoretical and practical experience in the fundamentals of peptide synthesis chemistry, very good knowledge of bioanalytical techniques for the identification of synthesis products (MS, NMR).

Focus III: theoretical and practical experience in fundamentals of structure elucidation, biophysics or structural biology with particular interest in biomolecular NMR spectroscopy and/or experience in peptide chemistry or protein biochemistry combined with dedication to learn biomolecular NMR.

Focus IV: experience or a solid understanding of molecular modelling and molecular dynamics simulations. Candidates with additional experience in peptide chemistry or natural products are strongly encouraged to apply.

Good knowledge of German and/or English required; willingness to acquire the respective missing language skills. Successful applicants will have a strong interest in interdisciplinary collaboration in research, including molecular biology, (protein) biochemistry, bioanalytics, bioinformatics and structural biology.

Interested candidates should send their application, quoting the reference number, focus and target group, together with a cover letter (background and motivation), curriculum vitae, certificates (including university degree), and contact details of at least one person who would be willing to provide a letter of reference, by email as a single PDF file (max. 5 MB) to contact@synpepbio.tu-berlin.de by 02 January 2025. A candidate may apply for more than one position but must indicate first, second or third priority in their email.

Posted on December 10, 2024

PhD Position in Deep Learning on Single-Cell Sequencing Data

Do you enjoy using computational approaches to study biological problems? Are you interested in developing and applying deep learning methodology to investigate cells at the molecular level? We invite enthusiastic and dedicated candidates to join our cutting-edge research team as a PhD student to work on developing novel methodology for the analysis of single-cell sequencing data using deep learning based approaches.

Come work at the largest university of Amsterdam!

You will be part of the Biosystems Data Analysis group (BDA) of the Swammerdam Institute for Life Sciences (SILS). BDA works on the development of methodology for data mining, machine learning/deep learning, data fusion, and modelling and application of these methods to answer biological questions, in close collaboration with domain experts. Within SILS, various experimental groups have started or will soon start to use single-cell sequencing data, and we will closely collaborate with researchers in these groups.

You will work on the following research objectives:

1)    Develop methodology to integrate existing biological knowledge in single-cell sequencing analysis e.g. towards cell-cell communication analysis or trajectory analysis.

2)    Develop methodology for unsupervised learning of embeddings to integrate single-cell sequencing data with other data modalities.

3)    In collaboration with researchers in SILS, apply the methodology to address specific biological questions of interest e.g. in plant science, immunology or neuroscience.

Tasks and responsibilities

You will:

•    develop computational approaches;

•    make use of available single-cell sequencing data and data newly obtained by our collaborators, as input for training machine learning models;

•    collaborate with both experimental researchers as well as with computational researchers (other PhD students working at UvA);

•    be an active member of the research group and take responsibility for shared tasks; incorporate feedback and give input to others;

•    take a leading role in writing manuscripts and complete a PhD thesis within the official appointment duration of four years;

•    participate in the Faculty of Science PhD training program;

•    assist in teaching and supervise Bachelor and Master theses.

Your profile

You are passionate about science and have a particular interest in deep learning applications in biology. You enjoy close collaboration with domain experts. You have a creative mind and look forward to work at the cutting-edge of computational technology. Finally, you are a team player and a pleasant colleague who enjoys being part of an interdisciplinary team of computational researchers and experimental researchers.

You have/are

•    an MSc in Data Science, Artificial Intelligence, Computational Science, Bioinformatics, or similar;

•    interested in using machine learning/deep learning on single-cell sequencing data;

•    able to communicate with non-experts on computational issues;

•    professional command of English.

Do you have any questions or do you require additional information? Please contact:

• prof. dr. Aalt-Jan van Dijk
• Email: a.d.j.vandijk@uva.nl
• T: +31  20 525 5519

Apply here

PhD position in Cancer Immunotherapy

Applications are invited for a 3 year position in a Research Fellowship as a PhD Candidate in the Experimental Cancer Immunotherapy Group lead by Johanna Olweus, MD, PhD, at Dept. of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet. The PhD position is available at the University of Oslo, Institute of Clinical Medicine.

Olweus is Head of the Dept. of Cancer Immunology at Oslo University Hospital Radiumhospitalet and leads a research group in the department, and holds a position as Professor at the University of Oslo (UiO). The main focus of the research group of Olweus is to develop novel T-cell receptor-based cancer immunotherapies and new technologies for target and TCR identification, and to couple clinical immunotherapy trials with penetrating mechanistic analyses. To this end, Olweus was awarded an ERC Consolidator Grant 2020-25. The research is performed in an interdisciplinary and translational program. The enthusiastic research team of 22 persons is highly international and conducts research in close collaboration with world-leading international collaborators at institutions such as Netherlands Cancer Institute and Karolinska Institutet.

http://ous-research.no/olweus

Qualification requirements and personal skills

PhD Studentship: Investigating Genetic Markers

Volcanic emissions are a natural source of mercury (Hg) to the atmosphere and Mt. Etna (Italy) is a major natural source of Hg to the Mediterranean region. Previous research has shown that Hg deposited on the low pH and organic-poor soils of Etna's south-eastern flank may not be retained, but instead released to groundwater or re-emitted to the atmosphere, indicating that the deposition of volcanic Hg has clear environment impacts. The potential for Hg to disrupt local ecosystems is particularly concerning, as it may alter microbial activity, including their capability to oxidise trace gases such as carbon monoxide (highly abundant at Etna volcano). This plays a crucial role in atmospheric chemistry and climate regulation. In this proposal, you will investigate if Hg affects the microbial communities and specifically their capability of oxidising trace gases, such as carbon monoxide.

Primary supervisor - Dr Marcela Hernández García

The project

You will be answering theses key questions: 1) How do bacterial communities in recently formed soils from Mt Etna utilise CO, and what specific metabolic pathways are involved? and 2) Does exposure to mercury influence the expression and activity of CO-dehydrogenase enzyme in bacteria isolated from Mt. Etna soils?

To answer these questions, you will join sampling campaigns at Mt. Etna followed by soil incubations and trace-gases measurements. You will be trained in cutting-edge tools for isolation and identification of microbes, including whole genome sequencing, proteomics, metagenomics and bioinformatics.

Specific training will include the cultivation of soil bacteria; quantitative PCR; amplicon-based sequencing (metagenetics); whole genome sequencing, (meta)genomic analysis and proteomics.

Person specification

We are looking for a pro-active, highly motivated student willing to join sampling campaigns at Etna Volcano in Italy. The successful candidate should have a strong background in Microbial, biochemistry, Soil or Environmental Sciences (BSc/Masters in Soil Microbiology, Environmental Microbiology, or similar).

Entry requirements

The successful candidate will have a strong background in Microbial, Soil Microbiology, Environmental Sciences or similar, with a minimum entry requirement 2:1 in a Bachelor’s degree.

Start date: 1 October 2025

Apply here

Posted on December 06, 2024

PhD in Computational Biology

We are currently looking for a talented PhD student in the context of the FWO-SBO funded project ‘MATCHMAKING: Unveiling Optimal Soybean-Rhizobia Matches in Northwestern European Environments’ (4-year position). This PhD position is a shared position between the VIB-UGent Center for Plant Systems Biology and ILVO.

The VIB-UGent Center for Plant Systems Biology (PSB, www.psb.vib-ugent.be) is a world-leading plant science institute with the mission to integrate genetics, genomics and computational biology to unravel the biology of plants and to improve the sustainability and climate resilience of crops. The Maere lab at PSB (http://www.maerelab.be) is active in the fields of computational biology, systems biology and evolutionary genomics. Current research topics include testing a novel experimental setup (single-plant omics) to unravel the molecular wiring of plant phenotypes under field conditions, studying dosage balance-sensitive genes in plants, and investigating factors affecting soybean yield and rhizobial inoculant performance in the field.

The institute for Agriculture, Fisheries and Food Research (ILVO) is a multidisciplinary research institute of the Flemish government with focus on research and innovation in sustainable agriculture, horticulture, fisheries and food business. Positive, proactive, professional, working together and being an example are the 5 values that guide ILVO employees in the way they approach their work.

Project description

Soybean is not only a major source of protein for food and feed worldwide but also, by interaction with nitrogen (N)-fixing rhizobia in the root nodules, a sustainable alternative for N fertilizers. The growing global demand for plant-based protein, coupled with the need to reduce reliance on imports from deforestation-prone areas, drives expansion of soybean cultivation into higher latitudes. Indeed, to meet European demands for sustainable soybean products, production must extend to north-western regions of the continent. However, existing soybean varieties and commercial rhizobia inoculants are not adapted to these environmental conditions, resulting in insufficient nodulation and consequently inconsistent high-protein bean yields.

Profile

• You have a MSc degree in Bioengineering, Biotechnology, Computational Biology or Bioinformatics.
• You have a solid background in plant biology, statistical data analysis, machine learning, R and Python programming
• Experience with plant field trials is a plus
• You are fluent in English (spoken and written).
• You can work in a team as well as independently.
• You are meticulous, well-organized, responsible and self-critical.
• You take pride in delivering high-quality work.
• You have a passion for science and you can think outside the box.

We offer

• An exciting work environment in both a top basic research institute (VIB) and a top applied research institute (ILVO).
• The opportunity to be part of a dynamic, interdisciplinary and international team.
• A challenging project with high societal value.
• Ample opportunity to learn new skills.
• An attractive salary.

Please complete the online application procedure and include a detailed CV, a letter of motivation and the contact details of two referees. Applications are accepted until the position is filled.

For more information, contact Steven Maere (steven.maere@psb.vib-ugent.be) and Hilde Muylle (hilde.muylle@ilvo.vlaanderen.be).

PhD student in Computational Biology

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 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. We conduct successful research in pure and applied mathematics and mathematical statistics in a wide range of research areas and offer 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. The department plays a crucial role as a collaborator in various scientific disciplines and industrial projects.

The announced PhD position is in the group of Marija Cvijovic (http://www.cvijoviclab.org/), located at the Division of Applied Mathematics and Statistics. In our division there are several research groups in the area of computational biology and bioinformatics. Gothenburg offers a vibrant computational/systems biology environment with many excellent research groups actively collaborating and organizing a number of life science seminars, summer schools and workshops.

Our department continuously strives to be an attractive employer. Equality and diversity are substantial foundations in all our activities. We work actively to be a parent-friendly organization.

The PhD student is supervised by Professor Marija Cvijovic and Associate Professor Umberto Picchini and is funded by a grant from the Swedish Research Council.

Subject area
Computational Biology

Specific subject description
The research project is performed in an international and highly collaborative multidisciplinary environment. We study the complexity of cellular ageing using experimental and computational methods. The work is highly interdisciplinary with close collaboration with a number of experimental research groups in other areas.

Job assignments
You will work in a highly dynamic research environment at the interface between mathematics and biology to address the central problems of cellular ageing. The work involves a tight integration of mathematical modelling and biological experiments, considering the intricate interplay of numerous subsystems in the ageing process.

Eligibility  
The Swedish Higher Education Ordinance provides eligibility criteria for academic positions. To qualify for the position, the applicant must have obtained a Master’s degree or a four-year Bachelor’s degree in mathematics, applied mathematics or mathematical statistics, or expect to complete such a degree by December 31, 2024.

Candidate should have excellent communication skills, strong self-organizing skills and the capacity to work effectively in an interdisciplinary environment. Fluency in English is expected.

International PhD Program in Microbiology

We are excited to invite applicants with a strong interest in interdisciplinary research in modern microbiology to apply for fully funded PhD positions at the International Max Planck Research School Principles of Microbial Life.

Applicants should hold an MSc degree or equivalent in biology, biochemistry, genetics, molecular biology, microbiology, bioinformatics, chemistry, chemical biology, physics, biophysics, or another relevant field.

The International Max Planck Research School Principles of Microbial Life is a joint initiative of the University of Marburg, the Max Planck Institute for Terrestrial Microbiology, and the Center for Synthetic Microbiology. More than 30 research group leaders participate in the program and cover research in

• Cellular organization and architecture
• Microbial communities and host-microbe interactions
• Natural products and chemical biology
• Physical biology
• Physiology and metabolism
• Signal transduction and information processing
• Systems and synthetic biology

We offer:

• A research project in a vibrant, international research community
• Mentoring by world-class scientists through a thesis advisory committee
• Access to state-of-the-art research facilities
• Structured interdisciplinary training program, which includes lectures, seminars, scientific and transferable skill workshops, attendance to retreats and conferences
• Salary based on the Collective Agreement for the Public Service in Germany (TVöD), which includes health and social insurance coverage
• Assistance service for international researchers

Deadline for applying is January 31, 2025. Apply directly via the online application system: https://imprs-marburg-appl.mpg.de/public/

Accepted candidates can start their PhD projects already in summer of 2025. The PhD program starts in October 2025.

For more information about the International Max Planck Research School Principles of Microbial Life, please visit our website: https://imprs-marburg.mpg.de/

Contact:
IMPRS Office
Email: imprs@mpi-marburg.mpg.de
Web: http://www.imprs-marburg.mpg.de

Apply here

Posted on December 02, 2024

PhD student Chemoinformatics and machine learning

The Leibniz Institute for Food Systems Biology at the Technical University of Munich (Leibniz- LSB@TUM), a legal foundation under civil law in Freising, is a research institution of the Leibniz Association that combines methods of biomolecular basic research with analysis methods of bioinformatics and analytical high-performance technologies to investigate the complex interplay between the human organism and food ingredients.

The research group “Molecular Modeling” at Leibniz-LSB@TUM is looking for a

PhD student (w/m/d)

to start on 13/01/2025 (65% TV-L 13). The position is to be filled for initial 1 year with the option to extend it by another 3 years.

Project

The straightforward identification of chemosensory active molecules in food is largely hampered by the complex food composition, which can lead to masking effects and molecular interactions in the food matrix. The applicant will work on the development of machine learning prediction models for the identification of food-derived taste and odor active compounds.

Area of responsibility includes

• Chemoinformatics and machine learning: chemical space analyses, QSAR modeling, machine learning and relevant tools, pharmacophore modeling, molecular docking, virtual screening

Requirements

The ideal applicant might have various backgrounds. These backgrounds may include but are not limited to: computational chemistry, computer science, applied mathematics, computational biology, bioinformatics, and many other subjects relevant to the project. Excellent communication skills in English, verbally as well as in scientific writing, are required. Above-average interest in the topic, we consider self-motivation and the ability to face new professional challenges as self-evident prerequisites. The ability to work independently, outstanding team skills and organizational aptitude round-out the ideal profile.

In addition to a highly stimulating workplace where your performance counts, we offer

• a performance-related salary in accordance with TV-L, in-line with your personal qualifications and the personal prerequisites
• an interesting and varied task area in the field of university research
• a motivated team that is looking forward to welcoming you
• scientific development opportunities in an international and interdisciplinary research environment
• training and advanced qualifications within the Leibniz Association and the Technical University of Munich
• flexible working times and therefore good compatibility of work and family
• company pension scheme
• special annual payment

In the case of essentially reciprocal suitability, severely-disabled applicants as defined SGB IX will be preferred.

Please address any questions on current topics to Assoz. Prof. Dr. Antonella Di Pizio (a.dipizio.leibniz-lsb(at)tum.de) and get in touch if you think you would be interested in working as part of our team.

Send your application with the usual documents, containing your comprehensive CV and transcripts as well as names of three potential references electronically as a PDF file to the following address, citing the reference number 2024-16-S3-ADP:

Anja Albrecht (Human Resources Department) recruiting.leibniz-lsb(at)tum.de.

PhD Studentship: Integrative Bioinformatics Approaches for The Identification of Novel Targets

We ( University of Birmingham - Department of Cancer and Genomic Sciences ) are looking for a PhD candidate with a passion to combine bioinformatics and computational biology, as well as next-generation sequencing and high-throughput 'omic technologies, to target cells and their development.

This project focuses on using integrative bioinformatics approaches and next-generation sequencing technologies to develop an in-silico framework for the identification of new targets (genes and proteins), as well as potential novel therapies that target cell cycle changes (cellular oscillation), cell plasticity, and cell apoptosis. Cell growth and invasion is a fundamental mechanism of many diseases, and plays a key role in other notable cell changes such as ageing. By investigating genetic and protein changes at different points of the cell cycle, we can identify how these different molecules are active at different stages of the cycle, and how they change during cell development. This has wide-reaching applications, as it can lead to the identification of potential markers that can be targeted at specific stages of cell development, changes related to ageing or to specific disease, and changes that should be targeted to prevent cell death.

The first axis of the project involves the development of a large-scale repository of single-cell RNA sequencing (scRNAseq) data and spatial transcriptomic data, and high-throughput ‘omic technologies (whole genome sequencing, whole exome sequencing). In particular, the project will focus on single-cell sequencing, and spatial transcriptomics, to probe genetic changes at a cellular level, using data from several large-scale scRNAseq repositories. The second axis of the project focuses on 3D protein information and protein interaction data pertaining to cell-cycle oscillations and cell death. This work will also involve using high-throughput drug docking and molecular-dynamics simulations of protein-drug interactions. Both axes of the project will allow the candidate to develop an in-silico pipeline for rapid identification of potential therapeutics against genetic and proteins targets involved in cell death.

Please reach out to Dr Gendoo by email at (d.gendoo@bham.ac.uk) for an informal discussion prior to applying.
Application Deadline: 16th January 2025

Birmingham MIBTP page - https://www.birmingham.ac.uk/research/activity/mibtp

Doctoral (PhD) student position in Tumor Biology

Do you want to contribute to top quality medical research?

To be a doctoral student means to devote oneself to a research project under supervision of experienced researchers and following an individual study plan. For a doctoral degree, the equivalent of four years of full-time doctoral education is required.

The research group

We are seeking a highly motivated and ambitious person for exploring the molecular and cellular mechanisms regulating the tumor microenvironment in childhood brain tumors. The position is placed in Margareta Wilhelm’s research group at The Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum at Karolinska Institutet, in a strong medical research environment with extensive possibilities for interaction and support. MTC conducts research and teaching within immunology, infection biology, cell biology and cancer. MTC have about 40 research groups and our key words are multidisciplinary, bridging, national and international collaborations.

The doctoral student project and the duties of the doctoral student

Specifically, the student will work on a project aimed at understanding the development of medulloblastoma, with a focus on the crosstalk between myeloid cells and cells that initiate the cerebellar tumor formation. The project involves advanced stem cell culturing techniques, cerebellar organoid and in vivo modelling, high-content imaging, and statistical and bioinformatics analyses of sequencing and patient data. The candidate is expected to work within the general framework of the research project but is encouraged to contribute with ideas and suggestions for experiments.

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.

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.*

Reference number STÖD 2-4638/2024

Last application date 12.Dec.2024 11:59 PM CET

Apply here

PhD Candidate in Spatial Metabolomics

The Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V. develops efficient analytical methods for health research. Thus, it contributes to the improvement of the prevention, early diagnosis, and therapy of diseases like cardiovascular diseases, autoimmune diseases or cancer. Overall, the institute strives to advance precision medicine by combining knowledge from different fields such as biology, chemistry, pharmacology, physics, and computer science.

PhD Candidate (m/f/d): Spatial Metabolomics

We are looking for an exceptional Doctoral Candidate and therefore we welcome applications from well- qualified data science researchers/students to work on projects mainly focused on improving treatment outcomes in cardiovascular and cancer diseases using mass spectrometry based metabolomics, machine learning and imaging technologies. The PhD project will focus on applying advanced data analytics and cheminformatics to expand boundaries of metabolomics applications in biomedical research.

You will be responsible for

• Data integration and bioinformatic analysis for mass spectrometry metabolomics and multi-modal imaging
• Effectively utilize and customize available resources for metabolite annotation, statistical, visualization and metabolic flux analysis of data generated from mass spectrometry analysis of biological samples.
• Communicating results effectively to interdisciplinary group of scientists

Your profile

• Masters, Diploma or equivalent degree in Bioinformatics, Biotechnology or Data Science related subjects.
• Experience in programming languages such as python, R or MATLAB is required.
• Knowledge of data analysis and data integration of omics data is advantageous.
• Overall understanding of biomedical research and knowledge of biochemical processes can be useful.
• Good presentation and writing skills
• Proactive, independent and solution-oriented way of working
• Fluent English (spoken and written)

The closing date for applications is December 21, 2024. Please apply via our applicant portal. Informal requests (reference number 328_2024) are welcome and can be directed to the  Human Resources team (bewerbungen(at)isas.de). Further information about the institute can be found at: http://www.isas.de/en.

For detail click here

PhD Researcher Computational Population Genetics

The Department of Archaeogenetics at the Max-Planck-Institute for Evolutionary Anthropology invites applications for the position of a PhD Researcher (m/f/d) in Computational Population Genetics.

We seek an innovative PhD researcher who enjoys working in an international research environment.

The research environment

The Max Planck Institute for Evolutionary Anthropology is one of the leading institutions investigating the evolution of humankind. Located in Leipzig (Germany), we unite scientists with diverse backgrounds who work together to gain insights into the human past.

The Department of Archaeogenetics utilizes the recent advances in generating genome-wide ancient DNA data to uncover an entirely new spectrum of information retrievable from anthropological and archaeological collections. This data unlocks fascinating insights into genetic relationships, geographical origin, selective processes, or genetic structure of historic and prehistoric human, plant, animal, or pathogen populations.

The project

The position will be part of the computational population genetics research group led by Harald Ringbauer. It is supported by the ERC Starting grant EPIDEMIC (see here). You will develop and apply powerful population genetic tools and pioneer linking medieval and modern genomes using shared haplotypes (IBD segments) to study historic European population structure.

Your qualifications

• You hold an MSc degree (or are nearing completion) in Bioinformatics, Computer Science, Mathematics, Physics, or a related field.
• Strong quantitative skills, ideally experience in data science and software development.
• Excellent intuition for empirical data analysis.
• Proficiency in English, enabling you to present and discuss research results in a multidisciplinary and international environment. Knowledge of German is not required, although we can support learning German.
• Self-motivated work style and work ethic.

What we offer

• Fully funded PhD Position for three years (with possible extension).
• Full salary via Max Planck support contracts (65 percent of Pay Group 13 of the Collective Wage Agreement for the Civil Service, TVöD), including the corresponding social benefits.
• A budget to attend international conferences, visits, or invite collaborators.
• You will closely interact with leading research groups in ancient DNA (see here) as a member at the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) in Leipzig, Germany.
• Living in Leipzig, an up-and-coming German city with a young demographic.
• The Max Planck Society offers flexible working hours, active support of healthy work-life balance, and a family-friendly working environment.

Term of Appointment:
The position will start in 2025. The exact date is negotiable.

How to apply

Electronic Applications (link to the application form only via the job offer on the institute’s career website: PhD position) will be considered until January 15th, 2025.

Posted on November 23, 2024

PhD Studentship in Cardiovascular Development

Interested in the morphogenetic processes underlying cardiovascular development? This PhD project will investigate the mechanisms by which key genes control the development of the aortic arch arteries.

Congenital cardiovascular abnormalities occur in ~1% of live births and cause a high level of death and morbidity, including defects affecting the major arteries, such as interruption of the aortic arch. These arteries form by a highly complex process that is tightly regulated by genetic and cellular interactions that are not fully understood.

To uncover the gene regulatory networks and signalling events between the different cell types required for arch artery formation we have been using state-of-the-art single cell sequencing technologies. In this PhD project you will interrogate this data using bioinformatic techniques to identify candidate genes for further analysis. These genes will be investigated in model organisms using a range of laboratory techniques including RNA and protein visualisation by in situ hybridization (using the RNAscope technique) and immunohistochemistry, fluorescent activated cell sorting (FACS), quantitative real-time RT-PCR, molecular cloning and cell culture assays.

Supervisors

Dr Simon Bamforth https://www.ncl.ac.uk/medical-sciences/people/profile/simonbamforth.html

Dr Helen Phillips https://www.ncl.ac.uk/medical-sciences/people/profile/helenphillips.html

Dr Rachel Queen https://www.ncl.ac.uk/medical-sciences/people/profile/rachelqueen.html

Newcastle University Biosciences Institute

Eligibility Criteria

You must have, or expect to achieve, at least a 2:1 Honours degree in biology, genetics, biomedicine, or a related area. The candidate must be willing to learn bioinformatics. A further qualification such as an MRes is advantageous.

The studentship covers fees at the Home rate only. Successful international candidates will be required to make up the difference between home fees and international fees.

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

How To Apply

You must apply through the University’s Apply to Newcastle Portal. Once registered select ‘Create a Postgraduate Application’.

Contact Details

Dr Simon Bamforth (simon.bamforth@newcastle.ac.uk)

For detail click here

PhD fellowship in Forensic Medicine

Research on human DNA recovered from sediments is a rapidly developing field. This area has implications for both forensic and ancient DNA research, where recovered DNA could be used for human identifications or to understand past environments and people. However, there is still a lack of understanding of how DNA is preserved in sediments, how to maximize its recovery, and how to adapt computational methods to this metagenomic data. This project will utilize bronze age sediments from England in order to study DNA preservation and recovery from different geological conditions. Methodological findings from this study will then be applied to sediments from various bronze age sites to study human population dynamics and agricultural practices. In addition, there will be the opportunity to apply these methods to human identification scenarios. This project will be performed at the Section of Forensic Genetics, Department of Forensic Medicine and will include collaborations with the Section for GeoGenetics, The Globe Institute.

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
• Participate in the undergraduate teaching of students in forensic genetics.
• Participate in national and international congresses and scientific meetings.
• Stay at an external research institution

Preferred qualifications

We are looking for a highly motivated candidate with a strong background in biochemistry, molecular biology, or geochemistry and interest in ancient DNA. Previous experience in DNA extraction, library preparation and sequencing is preferred. Previous experience in bioinformatics and genetics is preferred.

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. genetics, biology, or biochemistry. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Application deadline:  28 November 2024, 23.59pm CET

For detail click here

Doctoral scholarship in Mucin biology and Omics

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

The Laboratory of Experimental Medicine and Pediatrics in the Faculty of Medicine and Health Sciences is looking for a full-time (100%) doctoral scholarship holder in the field of gastroenterology, mucin biology and omics.

Position

• You will work actively on the preparation and defence of a PhD thesis in the field of gastroenterology, mucin biology and omics. You will investigate the role of unique mucin mRNA isoform panels that fill in the gap in predicting and monitoring appropriate barrier healing which is an urgent dire need to improve treatment strategies in patients with inflammatory bowel diseases (i.e. Crohn’s disease and ulcerative colitis).

Profile

• You hold a master’s degree in medicine, science, bioscience engineering, bioinformatics, pharmaceutical or biomedical sciences.
• You can demonstrate excellent study results.
• You have good knowledge in molecular (cell) biology, high throughput sequencing technologies (long-read (Pacbio, Nanopore) & short-read (Illumina) platforms, biostatistics and bioinformatics or are eager to submerge into these fields. Practical experience with next-generation sequencing and the use of bioinformatics will favour your application.

Want to apply?

You can apply for this vacancy through the University of Antwerp’s online job application platform up to and including 12 December 2024 (by midnight Brussels time).

Apply here

Posted on November 23, 2024

PhD position in Computational Biology

Your tasks

Your profile

We are looking for a highly motivated and enthusiastic candidate with a strong background in computational biology or a related field, who wants to pursue cutting-edge research oriented towards direct clinical applications.

PhD in Biostatistics, Computational Biology and Bioinformatics

The University of Luxembourg is an international research university with a distinctly multilingual and interdisciplinary character.

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 biostatistician or computational biologist who is well versed in the statistical and machine learning analysis of biomedical data and bioscientific programming for projects on neurological and cancer diseases. The candidate should have experience in the analysis of large-scale biomedical data (omics, clinical or other large-scale biological data), using statistical methods, pathway/network analysis or machine learning. The candidate will conduct integrative analyses of biomedical datasets, focusing on single-cell omics and clinical data to predict clinical outcomes of interest and therapeutics.

14 PhD Positions in Microbiology and Immunology

The University Hospital Erlangen, founded in 1815, is a center of state-of-the-art research and clinical medicine. More than 9,600 employees from around 50 professions carry out excellent research and care for our patients. Immunomedicine is a major research and clinical focus of the University Hospital Erlangen and the Friedrich-Alexander-University Erlangen-Nürnberg.

The Research Training Group 2740 (RTG, “Graduiertenkolleg 2740”), which has started in January 2022, is a research consortium funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). It consists of 15 outstanding research groups located in Erlangen, Regensburg, and Cologne and focuses on the in situ analysis of micromilieu factors and metabolites in the context of microbial infections (“immunomicrotope”).

Essential experience / qualifications

• Candidates for the doctoral positions in natural science (Dr. rer. nat.) or human biology (Dr. rer. biol. hum.) must hold a M.Sc. degree in immunology, microbiology, cell and molecular biology, biochemistry, molecular medicine, applied mathematics, theoretical physics, or in bioinformatics.
• Enthusiasm for experimental in vitro and in vivo research, self-reliance, ability to work in a team, excellent skills of the English language and an intrinsic motivation for the specific training program of the RTG 2740 are expected.

The recruitment symposium will take place on October 1 and 2, 2024, in Erlangen.

For details click here

12 fully funded PhD positions in Biology/ Bioinformatics

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

The structured Ph.D. training programme within a cutting-edge research environment will start on an individual basis between July 1 and October 1, 2025. The initial contract is limited to three years. Payment is based on the German TV-L E13 scale, 65% if terms and conditions under collective bargaining law are fulfilled or on an equivalently remunerated PhD support contract of the Max Planck Society.

We are looking for

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

Further information

Application period: August 12 - November 4, 2024 Online application portal: https://application.ageing-grad-school.de

Contact: cga-coordination@uni-koeln.de

Internet: https://www.ageing-grad-school.de The associated institutes are committed to diversity, diversity of perspectives and equal opportunities. Applications from people with disabilities and their peers are especially welcome, and preference will be given to people with disabilities if they are equally qualified. We are also committed to increasing the number of women in areas where they are under-represented and therefore strongly encourage women to apply.

Posted on August 10, 2024

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

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

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

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

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

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

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 

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

 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

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

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

PhD student in Evolutionary Genomics

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

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

Project description

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

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

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

• hold a Master’s (second-cycle) degree in Evolutionary Biology, Systematic Biology, Population Genomics, or a related field
• have completed at least 240 credits in higher education with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.

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

Apply here

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

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

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

Skills and personal qualities

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

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

Eligibility requirements for doctoral education

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

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

A) General eligibility requirement

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

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

B) Specific eligibility requirement

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

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

Reference number STÖD 2-647/2024

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

Apply here

PhD Candidate in Epigenetics & Gene Regulation

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

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

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

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

PhD position in Population Genetics

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

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

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

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

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

Apply here

Posted on February, 2024

PhD position in Bioinformatics and Artificial Intelligence

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

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

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

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

Application deadline: 2024-02-19

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

Erik Kristiansson,
erik.kristiansson@chalmers.se

Apply here

The CeMM International PhD Program in Molecular Technologies and Systems Medicine

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

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

PhD Studentship: Machine Learning Models for Zoonotic Disease Surveillance

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

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

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

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

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

Entry requirements

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

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

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

How to apply

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

Apply here

Posted on December, 2023