PhD scholarship

 PhD positions in Bioinformatics, Genomics and Life Science:


Update on November 25, 2022

Marie Curie PhD fellowship in NAD and Aging (DNA damage)

Our group and research
Our group ( approx. 15 people) utilizes computational science, animal models, and clinical trials to understand and manipulate the aging process with a particular focus on the role of DNA damage in aging. We develop and utilize high-throughput approaches such as high-content microscopy and omics investigations to understand the molecular basis of aging and age-associated phenotypes. Lab generated data is routinely analysed through AI-assisted pipelines such as novel cellular senescence classifiers and fully automated animal tracking

Project description
DNA damage accumulates with age and may contribute to age-associated diseases. A major DNA damage responsive enzyme is poly-ADP-ribose polymerase 1 (PARP1). Activation of PARP1 may contribute to decline of NAD with age however it is unclear how PARP activation can contribute with this in a steady state system. This PhD project will focus on understanding how DNA damage might impact systemic changes in NAD levels across tissues, a critical point for our ability to treat age-associated diseases.

This project is funded through the EU-Horizon NADis Marie Skłodowska-Curie Network (grant agreement #101073251) and the chosen candidate will become part of a larger network of researchers across top universities in Europe. NADIS is a MSCA Doctoral Network.

Application deadline: Tuesday, December 6, 2022, at 23.59 p.m. CET.

Apply here


Three PhD positions in Materials Chemistry, Peptide Chemistry, and Computational Chemistry

Polytechnic University of Catalonia (https://www.upc.edu/en), located in Barcelona (Spain), and University of Milan (https://www.unimi.it/en), located in Milan (Italy), are looking for talented, enthusiastic young scientists who are highly motivated to boost their research career in the areas of nanotechnology, nanoscaffolds and peptide-based nanomaterials.

The successful candidates will be part of an emerging project carried out with the funding of Marie Skłodowska-Curie Doctoral Networks HORIZON-MSCA-DN-2021 project called NanoReMedi (Functional Nano-Scaffolds for Regenerative Medicine https://www.nanoremedi.eu/). Repair or replacement of tissue and organ functions lost due to age, disease or damage represents one of the most urgent medical needs of our aging society. The NanoReMedi consortium will contribute to addressing this fundamentally important issue by using a new and efficient scientific approach relying on the design, preparation, characterization and validation of conceptually innovative peptide-based functional nanomaterials for regenerative medicine applications.

NanoReMedi stems from six Doctoral Courses/Schools at six beneficiary institutions, providing research and training in the field of nanomaterials for Regenerative Medicine. An active contribution of enterprises in training activities is a relevant feature of the programme. At the end of the project a join doctoral degree will be obtained.

  • Position 1 (ESR06): Desirable some computational experience that includes working a range of biological and/or material simulation methods such as the molecular dynamics or the density functional approach, as well as experience with peptide materials and proteins. Also, some knowledge on scripting and programming is desired, but not mandatory.

Specific Requirements: Master Degree or equivalent in Computational Chemistry/ Computational biology/ Chemistry/Physics/Biochemistry

  • Position 2 (ESR13): Desirable synthetic experience that includes working a range of chemical synthesis methods, as well as experience with polymers and peptide materials, including self-assembled polymers. Also, some knowledge on molecular characterization, such as NMR, UV-Vis-NIR, micro-Raman and FTIR, XPS and/or chromatography, as well as materials properties (i.e. rheology, particle sizing – DLS, TEM, SEM and AFM, electrospinning) is desired, but not mandatory.

Specific Requirements: Master Degree or equivalent in Chemistry/Pharmaceutical Chemistry/Biotechnology/Material Sciences

  • Position 3 (ESR4): Desirable synthetic experience that includes in solution and solid phase peptide synthesis, as well as experience with polymers and peptide materials, including self-assembled polymers. Also, some knowledge on molecular characterization, such as NMR, UV-Vis-NIR, micro-Raman and FTIR, XPS and/or chromatography, as well as materials properties (i.e. rheology, particle sizing – DLS, TEM, SEM and AFM) is desired, but not mandatory.

Specific Requirements: Master Degree or equivalent in Chemistry/Pharmaceutical Chemistry/Biotechnology/Material Sciences

Applications must be submitted on https://www.nanoremedi.eu/submit-application/ from November 28th, 2022 at 17:00 central European time (http://www.timeanddate.com/time/zones/cet) to December 31st 2022 at 17:00 central European time.

Applicants are required to submit the following documents by uploading them as a PDF file along with (or as one PDF attachment to) the application form. Instructions on submission are provided on https://www.nanoremedi.eu/download-documents/. For more information you may also contact nanoremedi@nanoremedi.eu

For details visit here


Posted on November 24, 2022

CRUK 4 Year PhD Studentships (Biomedical Research)

We are pleased to announce the following exciting postgraduate opportunities at the CRUK Manchester Institute for 4 year fully funded PhD Studentships

We welcome applications from enthusiastic and ambitious candidates with a strong academic track record to our PhD programme.  Applicants should hold or expect to graduate with a First or minimum upper-second class undergraduate honours degree (or equivalent from a non-UK university) in a relevant subject and Masters-level and/or other laboratory research experience in cancer.   Laboratory research experience as part of, or outside of a university degree course or a Master-level degree in a relevant subject is advantageous but is not a conditional requirement in making an application.
The Cancer Research UK Manchester Institute is proud to be a diverse, open and global Institute.  Our priority, and that of the University of Manchester, is to support our current students and welcome new ones from Europe and other continents, we therefore encourage students of all nationalities to apply for the programme.
Cancer Inflammation and Immunity Research Group
Leukaemia Biology Research Group

NIHR Manchester Biomedical Research Centre funded 4 year PhD Studentships - September 2023

Systems Oncology Research Group
Principle Investigator: Dominic Rothwell, Simon Pearce,Caroline Dive(Lab), Natalie Cook & Alicia Conway (clinical)
Nucleic Acid Biomarkers Team, Cancer Biomarker Centre
All applications will be considered equally irrespective of ethnicity, disability, sexual orientation, gender, religion/belief, age and nationality.  To help us monitor equality, diversity and inclusion within the Institute, you will be asked to complete and submit an EDI monitoring form during the application process.  Equal opportunities information will not be shared and will not form any part of the selection process or divulged to members of the selection, recruiting or interview panels.
Successful applicants will receive a non-taxable annual stipend (living allowance) of £21,000 GBP per annum, fully funded bench and tuition fees (home and international) for 4 years.  This applies to the CRUK funded and NIHR Manchester Biomedical Research Centre studentships.  Registration and graduation will be affiliated to the University of Manchester, UK.
The CRUK Manchester Institute is currently located over two sites at the Oglesby Cancer Research Building, Manchester Cancer Research Centre and our temporary site at Alderley Park, Cheshire until our new research facilities are re-established on our former site in Withington, South Manchester next to the The Christie NHS Foundation Trust.  The rebuilding of our world-class Paterson research facilities is well underway, and we anticipate returning to our original site in Withington, Manchester in 2023.

4 Year PhD Studentship – Weizmann Institute of Science/CRUK Manchester Institute, University of Manchester

“The interplay between the intratumoural microbiome, the type of cancer inflammation and the response to immunotherapy”

Dr Santiago Zelenay, CRUK Manchester Institute, UK & Dr Ravid Straussman, Weizmann Institute, Israel

We are pleased to announce this exciting new PhD opportunity at the Cancer Research UK Manchester Institute and the Weizmann Institute, Israel.

Immunotherapies hold great potential for improving cancer patient outcomes. However, we do not fully understand why some patients respond to therapy while others do not. We know that inflammation can both speed up and slow down tumour progression and can both promote and limit the response to immunotherapy. Different types of intratumoural inflammatory responses occur, but the instructive signals that dictate the ‘flavour’ of inflammation within the tumour bed are poorly defined. Dr Santiago Zelenay’s (CRUK Manchester Institute, University of Manchester) and Dr Ravid Straussman (Weizmann Institute) propose to tackle this central gap in knowledge building on recent ground-breaking work from their teams. Within this framework, the main aim of this PhD project will be to investigate the interplay between the intratumoural inflammatory response and the tumour microbiome with the overarching goal of providing new insights into the principles that dictate immunotherapy outcomes. The successful candidate will undertake this 4-year research project by combining the expertise established in the Zelenay & Straussman research groups at the CRUK Manchester Institute, UK and the Weizmann Institute, Israel.

Registration and graduation will be affiliated to the University of Manchester.

For further information on the Weizmann Institute of Science PhD Studentships please see here

For further project details, entry criteria and information please click here

Entry: September 2023

Application Deadline: 23 January 2023

Apply here


Posted on November 23, 2022

PhD position in computational genomics for natural products discovery

Microorganisms are an untapped resource for natural bioactive compounds that constitute a source of candidates for the development of pharmaceuticals and crop protection agents. Computational integration of different types of omics data, such as genomics and metabolomics profiles, constitutes a promising avenue to uncover this potential. Within the European network, a PhD position is available at the University Hospital Tübingen within the group Translational Natural Products Genome Mining.

PhD position in computational genomics for natural products discovery (f/m/d; E13 TV-L, 65%) Would you like to participate in an exciting interdisciplinary European network of scientists to transform natural product discovery using computational omics approaches? Do you enjoy collaboration and teamwork while being at the cutting edge of scientific progress? We are looking for a PhD candidate (f/m/d; E13 TV-L, 65%) with expertise in computational genomics to pioneer new technologies for omics-based natural product discovery.

In the project, the candidate will develop innovative computational approaches to chart the biosynthetic diversity found in microbial (meta)genomes. You will improve current software and workflows and develop phylogenetic methods of biosynthetic enzymes to enhance predictions of their metabolic products. Extensive international collaboration is foreseen, as these positions are part of a European training network and also will include a secondment at an international company. Specifically, the Doctoral Network MAGic-MOLFUN aims to integrate Natural Products Genome Mining, computational metabolomics and state-of-the art metabolic engineering and pathway discovery to develop ground-breaking tools and approaches to improve natural products discovery and characterization in bacteria and fungi, two major sources of bioactive compounds for applications in medicine, agriculture, food and biotechnology.

The research is embedded within the Translational Genome Mining for Natural Products Group at the Institute for Bioinformatics and Medical Informatics (IBMI) and the Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT) led by Prof. Dr. Nadine Ziemert.

Your profile

We are looking for an enthusiastic and complementary team player with all or a subset of the following skills:

  • a solid academic record (MSc) in bioinformatics, biology, chemistry or a related discipline
  • experience in computational omics analysis and proficiency in programming (in, e.g., Python)
  • at least basic to intermediate statistical and mathematical skills
  • demonstrable experience in working with next-generation sequencing data
  • affinity with microbiology, metabolism and/or biosynthetic pathways
  • team player attitude, enjoying multidisciplinary science
  • a very good level of oral and written English.

The deadline for application is January 15th, 2023.


Two PhD positions in computational genomics and metabolomics

Would you like to participate in an exciting interdisciplinary European network of young scientists to transform natural product discovery using computational omics approaches? Do you enjoy collaboration and teamwork while being at the cutting edge of scientific progress? We are looking for two PhD candidates with expertise in computational genomics and computational metabolomics, respectively to pioneer new technologies for omics-based natural product discovery.

Microorganisms are an untapped resource natural bioactive compounds that constitute a source of candidates for the development of pharmaceuticals and crop protection agents. Computational integration of different types of omics data, such as genomics and metabolomics profiles, constitutes a promising avenue to uncover this potential. Within the European network, two PhD positions are available within the Bioinformatics Group at WUR.
In project 1, the candidate will develop innovative computational approaches to chart the biosynthetic diversity found in microbial (meta)genomes. You will improve current software and workflows for analysing the modular architecture and composition of biosynthetic gene clusters, to facilitate enhanced comparative analysis as well as predictions of their metabolic products. To validate the efficacy of the approach, you will apply it to microbiome data.
In project 2, the candidate will improve current computational metabolomics workflows to make them better compatible with natural products metabolomics profiles, integrate the metabolomics workflow with omics-based bioactivity predictions into a genome-metabolome mining workflow, and apply this pipeline to paired omics data obtained by network partners.

We are looking for two enthusiastic and complementary team players with all or a subset of the following skills:

  • a solid academic record (MSc) in bioinformatics, biology, chemistry or a related discipline
  • experience in computational omics analysis and proficiency in programming (in, e.g., Python)
  • at least basic to intermediate statistical and mathematical skills•   demonstrable experience in working with next-generation sequencing data (for position 1) or (mass spectrometry-based) metabolomics data analysis (position 2)
  • affinity with microbiology, metabolism and/or biosynthetic pathways
  • team player attitude, enjoying multidisciplinary science
  • a very good level of oral and written English.

For more content-related information about position 1, please contact Marnix Medema, Associate Professor Bioinformatics, by email (marnix.medema@wur.nl). For information about position 2, please contact Justin van der Hooft, Assistant Professor in Computational Metabolomics, by email (justin.vanderhooft@wur.nl).
For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.

For details visit here


Posted on November 22, 2022

EuReCa PhD Program- 8 PhD positions  at Institut Curie (COFUND)

Institut Curie is recruiting 8 PhD students through its international program called EuReCa (Europe, Research & Care). This program, part funded by the European Commission’s MSCA COFUND scheme, provides PhD students with a 3-year doctoral contract, a high level interdisciplinary, inter-sectorial, as well as international training and coaching sessions with personalized career development plans, secondments and mentoring.

PhD research projects in life sciences cover Institut Curie’s priority research themes:

 

·      Epigenetics, RNA and genome dynamics

·      Cell biology and developmental biology

·      Tumor biology and immunology

·      Radiobiology and molecular imaging

·      Physics of living systems and chemical biology

·      Computational and systems biology

 

Institut Curie brings together a world-class multidisciplinary cancer research center and a model hospital group in Paris and surroundings. By embracing cross-disciplinary approaches, it drives the discovery of more effective treatments and leads to improved patient care.

Open positions

Project 1

Histone variant H3.3 and cellular programs during development and cancer

Thesis supervisor(s): Geneviève Almouzni & Iva Simeonova

Research group: Chromatin Dynamics

Project 2

Optical Mapping on single chromosomes of DSB repair events by recombination in normal and cancer cells

Thesis supervisor(s): Valerie Borde

Research group: Chromosome dynamics and recombination

Project 3

Polymer modeling of local chromosome dynamics upon gene induction

Thesis supervisor(s): Antoine Coulon & Vittore Scolari

Research group: Genome Functions in Space and Time

Project 4

The role of mechano-chemical cues in vertebrate axial patterning and somite generation

Thesis supervisor(s): Karine Guevorkian and Benoit Sorre

Research group: Dynamic Control of Signaling and Gene Expression

Project 5

Temperature scaling of gene regulatory networks for C. elegans larval development

Thesis supervisor(s): Wolfgang Keil & Christopher M. Hammell

Research group: Quantitative Developmental Biology

Project 6

Investigating the role of Polycomb in epigenetic regulation and inheritance during mouse germline formation and embryogenesis: study of a new member of the PRC2 complex, EZHIP (Ezh2 Inhibitory Protein) using transgenic model

Thesis supervisor(s): Raphaël Margueron

Research group: Mechanisms of Repression by Polycomb Proteins

Project 7

Deciphering the dynamics of gene co-expression at the single cell level to understand patterning and epithelium-to-mesenchyme transition in development and cancer

Thesis supervisor(s): Anne-Hélène Monsoro-Burq

Research group: Signaling and Neural Crest Development

Project 8

Contribution of the roles of RNA species in the regulation of the human NHEJ-factor KU functions during DNA replication

Thesis supervisor(s): Vincent Pennaneach & Sarah Lambert

Research group: DNA Recombination, Replication and Genome Stability

 

Eligibility criteria

1.      Early-stage researchers (ESR) shall at the call deadline be in the first four years (full-time equivalent research experience) of their research careers and have not been awarded a doctoral degree.

Full-time equivalent research experience is measured from the date when a researcher obtained the degree which would formally entitle him or her to embark on a doctorate.

2.      Applicants may not have resided or carried out their main activity (work, studies, etc.) in France for more than 12 months in the 3 years prior to January 9th, 2023.

Time spent as part of a procedure for obtaining refugee status under the Geneva Convention, compulsory national service and/ or short stays such as holidays are not taken into account.

3.      Applicants must be in possession of a European master degree or equivalent master’s degree which would formally entitle them to embark on a doctorate.

Application deadline: January 9th, 2023 at 4:00pm (CET)

For details visit here


PhD position (4 years) at K.G. Jebsen Center for Parkinson’s Disease

The newly-established K.G. Jebsen Center for Parkinson’s Disease started in September 2022 and is hosted at the Department for Clinical Medicine at the University of Bergen (UiB), in collaboration with the Department of Biomedicine and the Neurology Department at Haukeland University Hospital. The Center is led by Professor Charalampos Tzoulis (Charalampos (Haris) Tzoulis | University of Bergen (uib.no)  and its main aims are to advance the mechanistic understanding of Parkinson’ s disease and to improve the diagnosis and treatment of patients.  The K.G. Jebsen Center laboratory is co-localized with the Neuro-SysMed laboratory, offering a flourishing transdisciplinary scientific environment and a unique opportunity for interaction between clinical and translational science.

PhD position

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

The position is part of the K.G. Jebsen Center for Parkinson’s Disease funded by the University of Bergen. This PhD position will be in molecular neuroscience to work on a project focusing on advancing the mechanistic understanding of Parkinson’s disease.

About the project/work tasks:

The main purpose of the PhD position is to complete a doctoral thesis, which qualifies for independent research and other forms of employment that demand specific competency. The position is for a period of four (4) years.

The applicant is expected to write a PhD dissertation related to the stratification of Parkinson’s disease using mitochondrial and other tissue-based molecular markers.

Parkinson’s disease (PD) is the fastest growing neurological disorder and represents one of the most urgent health and societal challenges of our time. The clinically and biologically heterogeneous nature of PD hampers efforts to uncover underlying disease mechanisms, which in turn impedes efforts to design effective treatments. This project aims to address the biological heterogeneity of PD, identify distinct molecular disease subtypes using primarily post-mortem brain tissue, and lay the foundations for developing biomarkers for patient classification in clinical practice.

Qualifications and personal qualities:

  • The applicant must hold a Master`s degree or equivalent in molecular biology, neuroscience, neuropsychology or similar disciplines, or a medical (MD) degree
  • In the hiring process, emphasis will be placed on professional strengths, possible research expertise and experience from similar projects, good collaboration skills and the ability and motivation to carry out a doctoral project. The following will be prioritized:
  • Basic knowledge of neurobiology, neuroanatomy and neuro-histology
  • Experience with histology and immunohistochemistry
  • Experience working with brain tissue (human or other animal) will be an advantage
  • The candidate should be able to work independently and in a structured manner, and have the ability to cooperate with others
  • The applicant must be fluent in oral and written English on a high technical and scientific level
  • The following qualities will be prioritized:
  • High scientific ambition, determination, and the desire for innovation and impact
  • In cases where ranked applicants have approximately equivalent qualifications, the centre’s strategic considerations, motivation, and the applicant’s personal eligibility will be considered

General information:

For further information please contact Professor Charalampos Tzoulis, E-mail: Charalampos.Tzoulis@uib.no

Deadline 27th November 2022

Apply here


Posted on November 18, 2022

PhD scholarship in Bioinformatics Applied to Pangenome Graphs

DTU Health Tech is looking for a qualified candidate for a PhD position in Bioinformatics applied to pangenome graphs.

Responsibilities and qualifications
In this position, you will develop algorithms and computational methods to deal with the analysis of large datasets from modern and ancient sources. More specifically, these algorithms will be aimed at developing novel methods using pangenomes graphs.

Traditionally, sequencing projects used a single linear reference genome to conduct analyses. Recently, groups have proposed replacing this single reference with a graph encompassing all known diversity within a species. While this approach has yielded exciting results, a lot of work remains to fully exploit the power of pangenomic graphs. The Modern and Ancient Genomes group at DTU are pioneers in terms of developing probabilistic inference methods on pangenome graphs. The position involves computational methods development which means that a large portion of time will be dedicated to algorithm development and coding, likely in C++.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree and a bacherlor's degree. Ideally, your degree should be in computer science, mathematics or biological science with a focus on quantitative and mathematical aspects.

More specifically you should ideally have the following qualifications:

  • Knowledge of a programming language like Python, Perl, C++ and/or Java
  • Ability to work in a UNIX environment, ideally in a high-performance computing environment
  • Thorough understanding of basic algorithms and data structures used in computer science
  • Knowledge of probabilities and statistics
  • Firm grasp of first-year university mathematics (differential calculus/linear algebra)
  • Experience in bioinformatics and knowledge of metagenomics are a plus
  • Expertise in next-generation sequencing data generation and processing are also a plus but not required

The language of communication at DTU is English.

Approval and Enrolment
The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see DTU's rules for the PhD education.   

Assessment
The assessment of the applicants will be made by  Prof. Gabriel Renaud.

We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.

Salary and appointment terms
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.

Starting date is as soon as possible (or according to mutual agreement). The position is a full-time position.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Prof. Gabriel Renaud (gabre [at sign here] dtu.dk). 

You can read more about DTU Health Tech at www.healthtech.dtu.dk/english.  

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark. Furthermore, you have the option of joining our monthly free seminar “PhD relocation to Denmark and startup “Zoom” seminar” for all questions regarding the practical matters of moving to Denmark and working as a PhD at DTU.

Application procedure
Your complete online application must be submitted no later than 27 November 2022 (Danish time)Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

  • A letter motivating the application (cover letter)
  • Curriculum vitae
  • Grade transcripts and BSc/MSc diploma (in English) including official description of grading scale
  • A link to a code portfolio like GitHub or GitLab.

Apply here


PhD Scholarship in Big Data and Analytics for Crop Genetics

Modern agriculture and biomedical research are driven by the availability of big data and the development of data science. The recent development in data analytics coupled with gene editing technology has transformed crop breeding and enabled a new frontier of de novo breeding. Through Murdoch University and Grain Research and Development Corporation (GRDC)’s initiative, multiple PhD Scholarship positions have been made available on developing new data analytics methods and modelling for grain research innovation and ensuring enduring profitability for Australian grain growers and breeders.

We are seeking a PhD student who is interested in performing PhD on applied bioinformatics. Scholarship of $70,000 AUD will be offered to successful candidate. The PhD project will focus on data analytics, data mining, and statistical modelling of complex biological system in crops. The project will have access to large volume of state-of-the-art Next Generation Sequencing-based genomics and pan-genomics data, large field trial data across multiple geographical sites, and environment data.

The PhD research will involve cutting-edge bioinformatics and data science technologies, and this is a perfect training opportunity for those who is interested in machine learning, data mining, artificial intelligence, and bioinformatics. High-performance computing may also be involved based on candidate’s experience and interests. Even if majority of the research will be computation based, the candidate will work with a team of bioinformatician, crop geneticist, field trail experts, and computational scientists. It is highly likely completion of PhD will lead to post-Doctorate research opportunities on data science and statistical modelling as either an extension or a spin-off of the PhD program.

Eligibility

  1. Education background in Computer Science, Statistics, Molecular Biology, or relevant areas.
  2. Knowledge in data analysis and preferably some experience in data handling.
  3. Preferably knowledge in database management.
  4. Good communication skills and teamwork spirit.
  5. Problem solving skills and be able to work under pressure.

How to Apply

Contact Dr Penghao Wang at p.wang@murdoch.edu.au or Prof Chengdao Li at c.li@murdoch.edu.au

Required Documents

Please provide the following:

  • A Current CV
  • A short response to the criteria
  • A list of publications (if any)
  • Any further supporting documents that may help your application

 

Payment Method

Stipend $33,000 per annum


PhD position in theoretical and computational modeling of gene regulatory networks and genome evolution

A PhD position is available in the group of Prof. Erik van Nimwegen at the Biozentrum of the University of Basel and Swiss Institute of Bioinformatics in theoretical and computational modeling of gene regulatory networks and genome evolution.

The Biozentrum
The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 32 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birth place of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

Your position

Our research group
Our research group is highly interdisciplinary, involving both an experimental section where researchers with a background in molecular biology and biophysics are experimentally studying genome evolution and gene regulation at the single cell level in bacteria, and a theoretical section where researchers with backgrounds in theoretical physics, computer science, and applied mathematics are using techniques from Bayesian probability, evolutionary theory, dynamical systems theory, and stochastic processes, to study the function and evolution of genome-wide regulatory networks in cells. We are particularly interested in uncovering the principles by which genome-wide regulatory networks specify and maintain cell identity in multi-cellular organisms, how cells control and exploit the noise in gene regulatory processes, and how gene regulation evolves. A full list of our group's publications can be found here.

This PhD position is not tied to a specific project and a research project will be designed in collaboration with the candidate, choosing from the current interests of our group. Current interests include the role of noise in gene regulatory strategies at the single cell level in bacteria (publication link, publication link, publication link), the role of recombination in bacterial genome evolution (publication link), the evolution of gene regulation in bacteria, and development of methods for inferring genome-wide gene regulatory networks in multi-cellular organisms, with the aim of attaining a quantitative understanding how they specify cell states and cell types (publication link, publication link).

Your profile

For this position we are looking for candidates with strong mathematical and computational skills that are excited to work in the area of quantitative modeling of either gene regulatory networks at the single cell level or microbial genome evolution. Depending on the project, experience in areas such as next-generation sequencing data, stochastic processes, dynamical systems theory, population genetics, and Bayesian statistics will be desirable. Candidates do not necessarily have to have a biological background but should have a deep interest in the biological research questions and a strong desire to directly work with experimental data and (depending on the project) experimental collaborators. The candidates should have a good knowledge of English. German is helpful but not necessary. The salary is generous and is set according to the guidelines of the Swiss National Science Foundation. The start date will by mutual arrangement with the possibility to start immediately.

Application / Contact

To apply, please send a single PDF containing your application letter, your CV, and contact information of 3 references by email to: erik.vannimwegen@unibas.ch.
Review of applications will begin immediately and proceed until the position has been filled.
For further information, please contact Erik van Nimwegen directly at the email address above.

Posted on November 17, 2022

PhD Student Bioscience / Computational Science

The University Hospital of Münster is one of the leading hospitals in Germany. Such a position cannot be achieved by size and medical successes alone. The individual commitment counts above all. We need your commitment so that even with little things we can achieve great things for our patients. There are many possibilities open for you so that you may develop with them.

The Department of Pediatric Hematology and Oncology of the University Childrens Hospital Münster, Germany, invites applications for a position limited to 3 years.

The Kerl work group identifies mechanisms of pediatric tumor development and development of therapy resistance by using different single cell sequencing technics in complex in vitro systems (e.g. organoids) and in in vivo model systems. Bioinformatics analysis within the project will be done in collaboration with the Institute of Medical Informatics Münster.

In this project we aim to identify mechanisms of the early transformation process from the cells of origin to embryonal tumors. Here we use different single-cell technics including scRNA-seq and spatial transcriptomics in mouse models as well as in complex in vitro models.

Tasks:

  • You will be involved in planing, performing and analyzing experiments, with a specific focus on analyzing single cell data
  • You will work part-time in the wet lab and will part-time analyze single cell data

Requirements:

  • Highly motivated applicants are welcome: you should be team-minded and flexible as well as dedicated to science are welcome
  • Therefore PhD students with the background of or interest in computational science are welcome
  • Basic skills in programming language, specifically in R, are an advantage, but are not mandatory to have

We offer:

  • State-of-the-art scientific infrastructure in a highly dynamic work group
  • A Family-friendly environment, subsidized public transportation

If you have any questions, please contact Dr. Kornelius Kerl, kornelius.kerl@ukmuenster.de.

We are looking forward to your online application until 14.12.2022!

Job Id:  6909

(*gn= gender neutral)

PhD positions available at reNEW Copenhagen Node (Molecular Biology or Bioinformatics)

The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) at Faculty of Health & Medical Science at the University of Copenhagen is looking for research assistant/PhD students to join the Brickman group starting February 2022 or upon agreement. These positions will each explore one of two proposed projects, both exploiting their recent findings with respect to the nature of enhancer regulation. These projects can be approached both experimentally and computationally, and applications are encouraged from individuals with both wet and/or dry skills in Molecular Biology.

Our research
The Brickman group is interested in the transcriptional basis for cell fate choice, exploring both fundamental mechanisms of transcriptional regulation by signalling and how gene regulatory networks define cell potency and fate in development and differentiation.  We recently found that transcriptional exit from pluripotency was achieved independently of transcription factor (TF) binding to enhancers, but that TF was required both to guide differentiation and safeguard plasticity (Hamilton et al., Nature 2019). We have observed a similar form TF mediated enhancer priming during the expansion of human VFGs derived from pluripotent cells (Wong et al. BioXiv 2022).  In these projects we seek to exploit these findings to improve in vitro embryo models and differentiation.

Job description
We are looking for individuals interested in focusing on enhancer networks in early human development and human organ specific differentiation.  As a PhD student in the Brickman group, you will be working in the field of stem cell and developmental biology. You will be part of an international interdisciplinary team of scientists focusing on understanding the transcriptional basis for development and exploiting this to develop new technologies for cell type specification in culture.

Responsibilities

  • To test the impact new drugs and medias on synthetic embryo/organ development.
  • Develop new approaches to in vitro culture.
  • To collect NGS data and multiomics on synthetic embryo/organ systems.
  • To generate improved human blastoids or enhanced organoid cultures for liver and pancreas.
  • To analyze NGS data and develop new pipelines for bioinformatic analysis.

Qualifications

  • An equivalent of an MSc degree in Developmental, Stem Cell, Molecular Biology or Bioinformatics.
  • Experience with cell culture, where experience with stem cell culture would be an advantage.
  • Experience with NGS technologies, such as ChIP-seq, CUT&TAG, CAGE-seq etc. (for postdoctoral researcher positions) and/or bioinformatics skills.
  • Skills in routine molecular biology, including cloning, Western blots, RT-qPCR etc.
  • English communication skills, both oral and written are a must.

The deadline for applications is 1 December 2022.

For further information contact Professor Joshua Brickman joshua.brickman@sund.ku.dk

For details visit here


Posted on November 10, 2022

PhD position in Metagenomics

The Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute – (Leibniz-HKIwww.leibniz-hki.de) investigates the pathobiology of human-pathogenic fungi and identifies targets for the development of novel natural product-based antibiotics.

The research group Systems Biology and Bioinformatics invites talented and highly gifted candidates to apply as Doctoral Researcher (f/div/m) in Metagenomics for 3,5 years initially.

The research group Systems Biology and Bioinformatics (SBI) are seeking an excellent and enthusiastic PhD student for high risk-high reward research in the fields of metagenomics and big data integration. SBI is active participant of several national and international collaborative efforts to study the interplay between the host, symbiotic communities and pathogenic species. Together with renowned scientists and supported by an excellent infrastructure you will have the opportunity to make an important contribution for a healthier society. The objective of the PhD project is to develop AI models using clinical, biochemical and microbiome data for discovering novel disease biomarkers and designing therapeutic strategies in chronic non-communicable diseases.

Requirements:

  • 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 Systems Biology, Computational Biology, Bioinformatics, Biophysics, Computer Science or a related discipline
  • Knowledge and experience in the analysis of biological high-throughput data
  • Knowledge in statistical methods in the context of biological systems
  • Experience with programming (Python, Perl, C++, R)
  • Well-developed collaborative skills

Further information:

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

The deadline for the advertisement is December 15, 2022, but applications will be reviewed on a rolling basis.  online application system.


Three PhD Positions in Inflammatory Bowel Diseases

The iRTG is associated with the Collaborative Research Center TRR 241 “Immune-Epithelial Communication in Inflammatory Bowel Diseases”, funded by the German Research Foundation (DFG). TRR 241 is a comprehensive framework which aims to study the cross-talk between intestinal epithelial cells and immune cells in order to understand the mechanisms underlying IBD pathogenesis and develop new therapeutic targets. For more information on our research please visit: https://transregio241-en.webspace.rrze.de/our-research/

We offer the opportunity to be integrated into a dynamic Erlangen-Berlin research network and to perform research under the supervision of leading scientists in the field. The structured educational program provided by the iRTG will qualify the PhD researchers of the TRR 241 for a future scientific career at the interface between clinical and biological research.

Keywords:

Immunology, intestinal epithelial cells, inflammation, IBD, bioinformatics

Eligibility

Required qualification:

  • Master’s Degree (or equivalent) in Life Science and excellent academic performance
  • Practical and theoretic experience in the field of molecular biology, immunology, cell biology or bioinformatics
  • Very good knowledge of English
  • High level of motivation, ambition and scientific interest.

The documents are to be sent in digital form (one pdf document) under the reference “iRTG-TRR 241-PhD application” to:

C.Guenther@uk-erlangen.de for project A02 “Mechanisms linking IFN-mediated cell death with bile acid signaling in small intestinal inflammation”

Ahmed.Hegazy@charite.de for project A05 “Oncostatin M as modulator of pathogenic memory T cells in IBD”

Rocio.Lopez-Posadas@uk-erlangen.de for project A07 “The Mevalonate pathway as a checkpoint for regulation of prenylation within intestinal epithelial cells in the context of inflammation”

For details visit here


Posted on November 07, 2022

24 fully funded Ph.D. positions in Life sciences

The Medical University of Vienna invites applications for all currently open PhD positions in its PhD programs. We encourage ambitious and creative young scientists, who are interested in research in the areas of human-centered technologies and sciences, with an M.Sc. or equivalent degree in (Bio) Engineering, (Bio)Informatics, Cell/Molecular/RNA Biology, Biochemistry, Genetics, Neurology, Translational Medicine or a related field to develop their original research project with the support of our renowned and international scientist.

The Medical University of Vienna (briefly: MedUni Vienna) is today the largest international medical training institute in the German speaking area with about 8.000 students. Within its 30 university hospital departments, two clinical institutes, 12 theoretical medicine centers and numerous highly specialized laboratories, it is included among the most important cutting-edge research institutes of Europe in the area of biomedicine and biotechnology.

We offer 24 fully funded Ph.D. positions in one of the most livable cities in the world – Vienna! Our university is a leader in transnational medical science and has an excellent infrastructure that invites you to do research and network with your peers. Last but not least, our university is home to a dynamic international research community that is constantly growing. Austria as a research location also offers young scientists many opportunities after graduation.

Application deadline: 20.11.2022

How to apply:  Please use our online application tool

Information on our application tool and process

General requirements: Master degree, English level B2

Got questions, please contact us by Email: phdrecruitment@muv.ac.at


PhD Studentships at MRC Laboratory of Molecular Biology

The MRC Laboratory of Molecular Biology (LMB) is one of the birthplaces of modern molecular biology and it continues to be a prolific source of new ideas, discoveries and inventions. As a leading international research centre, the LMB attracts some of the world’s best scientists. To date, the LMB’s scientists have earned 12 Nobel Prizes, as well as numerous other prestigious scientific awards.

We are at the heart of the Cambridge Biomedical Campus, located within one of the largest and most internationally competitive concentrations of healthcare-related talent and enterprise in Europe. The LMB building with its stunning design provides a globally competitive research centre with state of the art facilities for making the discoveries of the 21st Century.

Every year the LMB International PhD Programme gives 20-30 new graduate students from universities all over the world the opportunity to do cutting-edge research. At the LMB, we aim to train the scientific leaders of the future: we seek the best students, give them rewarding research projects and provide a supportive environment with access to world-class facilities and experts.

Graduate students register for their PhD with the University of Cambridge and belong to one of its Colleges.

Areas of study include:
• Structures of biological “machines” by X-ray crystallography and cryo-EM
•  Computational biology
•  Biology of immunity and DNA repair
•  Intercellular signalling, membrane trafficking and advanced optical microscopy of live cells
•  Cellular neurobiology and genetic analysis of behaviour
•  Genetic, optical and electrophysiological analysis of neural circuits
•  Molecular origins of neurodegenerative diseases
• – Chemical and synthetic biology

Competitively awarded fully-funded UK and international studentships available for PhDs commencing in October 2023

Application deadline: UK and overseas applicants – 1 December 2022

Apply here


Posted on November 03, 2022

Doctoral researcher in Machine Learning / Bioinformatics

The University of Luxembourg is an international research university with a distinctly multilingual and interdisciplinary character. The University was founded in 2003 and counts more than 6,700 students and more than 2,000 employees from around the world. The University’s faculties and interdisciplinary centres focus on research in the areas of Computer Science and ICT Security, Materials Science, European and International Law, Finance and Financial Innovation, Education, Contemporary and Digital History. In addition, the University focuses on cross-disciplinary research in the areas of Data Modelling and Simulation as well as Health and System Biomedicine. Times Higher Education ranks the University of Luxembourg #3 worldwide for its “international outlook,” #20 in the Young University Ranking 2021 and among the top 250 universities worldwide.

Within the University, the Luxembourg Centre for Systems Biomedicine (LCSB) is a highly interdisciplinary research centre (IC), integrating experimental biology and computational biology approaches in order to develop the foundation of a future predictive, preventive and personalized medicine.

Your Role:

We seek a highly motivated machine learning scientist / computational biologist / bioinformatician (MSc level) who is experienced in applying statistical learning algorithms to large-scale biomedical datasets and optimizing and evaluating prediction models. The candidate will conduct integrative machine learning analyses of cellular imaging datasets, with a focus on applications in neurodegenerative disease research. This will include the development of new structured machine learning approaches, the application of learning algorithms to complex biomedical data, and the joint interpretation of the data together with experimental collaborators.

The project will use new high-throughput data from patients, healthy controls, as well as in-vitro and in-vivo disease models. The goal is to build models with improved predictivity for sample classification and improved interpretability to better understand molecular and cellular perturbations in common neurological disorders. This project will be jointly conduced between groups from the computational field and the biomedical field.

What we expect from you…
* The candidate will have a MSc or equivalent degree in biostatistics / machine learning, computational biology or bioinformatics
* Prior experience in large-scale data processing and statistics / machine learning is required, ideally with experience in the area of biomedical
imaging analysis
* Excellent communication and organization capabilities to facilitate the exchange between groups from different disciplines are essential
* A track record of previously completed courses and/or publications involving statistical and machine learning analyses of large-scale data (e.g.,
imaging data, omics) should be outlined in the CV
* Demonstrated skills and knowledge in biostatistics and biomedical data processing are highly advantageous
* The candidate should have a cross-disciplinary aptitude, strong organizational and interpersonal skills, and a keen interest in collaborative
biomedical research
* Fluency in oral and written English

Job Number: UOL05366

Application deadline: January 02, 2023

Apply here


PhD position: Epitranscriptomic regulation

Our research is focused on understanding the mechanisms of dynamic histone; DNA and RNA modifications in embryo development and cancer. These mechanisms, also known as epigenetic and epitranscriptomic regulation, have profound effect on the development of an organism and the differentiation of normal cells to cancer cells. In particular, recent pioneering work in the field of RNA regulation and novel methodology for analysing single cells enables novel studies on valuable biological material.

Oslo University Hospital is a workplace with great diversity. We believe this is absolutely crucial to solving the tasks required of us. We therefore want this diversity to be reflected among the applicants for our positions and encourage everyone to apply regardless of who you are and what background you have.

 

Qualifications

  • Knowledge of basic methods in molecular biology (cell culture) and/or embryology are essential.
  • Also required is experience with at least one of the following research areas: Histone modifications, RNA biochemistry methods (including PAR-CLIP, RIP-seq, and RNA-seq), RNA biology, genome stability, knock-down/overexpression systems, Crispr-Cas9 based engineering, embryology and bioinformatics.
  • Potential candidates have recently completed a Master degree in molecular biology using methodology relevant for the techniques described above. Interested persons should submit the following documents:
  • 1) A concise application letter explaining your motivation for this position (up to one page).
  • 2) Curriculum vitae including a list of any peer-reviewed publications.
  • 3) Contact information of three relevant references.

Deadline: November 30, 2022

Apply here


Fully-funded PhD positions in Biology, Neuroscience & Data Science

Fully-funded PhD positions in Biology, Computer Science, Chemistry & Materials, Data Science & Scientific Computing, Mathematics, Neuroscience, and Physics

The Institute of Science and Technology Austria - ISTA is looking for highly qualified candidates with Bachelor’s or Master’s degrees to apply for the PhD program. We offer fully-funded PhD positions in Biology, Computer Science, Chemistry & Materials, Data Science & Scientific Computing, Mathematics, Neuroscience, and Physics, in a world-class research environment on the outskirts of Vienna.

 In 2019, ISTA was ranked #3 in the world-wide Nature Index ranking (normalized). In 2018, ISTA was ranked within the top ten of Nature Index Rising Stars “Top 30 academic institutions under 30” list and was featured in this article in Nature Index.

All students are offered 5-year contracts, they receive internationally competitive salaries, and full social security coverage. There is also financial support for students for attending scientific conferences and workshops.

The application deadline is January 8, 2023 for a Ph.D. start date in September 2023

Apply here


Posted on October 30, 2022

PhD Student Microbial Genome Plasticity

The University Hospital of Münster is one of the leading hospitals in Germany. Such a position cannot be achieved by size and medical successes alone. The individual commitment counts above all. We need your commitment so that even with little things we can achieve great things for our patients. There are many possibilities open for you so that you may develop with them.

Our group focuses on the characterization of virulence, fitness and resistance properties in Escherichia coli and related enterobacteria. In this context, we also use comparative and functional genome-based approaches to study the interaction between bacteriophages and bacteria.

We want to study the specific interaction between lytic bacteriophages and multidrug-resistant E. coli variants. The focus is on (i) characterizing specific interactions between bacteriophages and bacterial pathogens and phage-recognized receptors, and (ii) testing different bacteriophage isolates for their effect in complex bacterial communities.

Your responsibilities:

  • Microbiological and molecular biological studies on the specificity of different bacteriophage isolates on selected clinical bacterial isolates in vitro and in an artificial intestinal model.
  • Characterization of the role of selected bacteriophages for horizontal gene transfer between bacteria, characterization of plasmid-encoded phage receptors
  • Analysis of the influence of bacteriophage (cocktails) on the intestinal microbiome composition (16S rDNA-based amplicon as well as shotgun metagenome sequencing)
  • Interpretation of results, statistical analysis of data
  • First drafting of scientific texts in connection with the dissertation project

We are looking forward to applicants with:

  • Master's degree in biology, biochemistry, life sciences, biotechnology or molecular biomedicine.
  • Very good knowledge in micro- and molecular biology, bacterial genome analyses
  • Willingness to work with NGS datasets (ideally, previous experience in Linux and comparative DNA sequence data analysis)
  • High motivation and a keenness to develop an independent working style
  • Ability to work in a team and social competence

Applications of women are specifically invited. In the case of similar qualifications, competence, and specific achievements, women will be considered on preferential terms within the framework of the legal possibilities. Handicapped candidates with equivalent qualifications will be given preference.

Please aplly online including a short letter of motivation, a brief statement of research experience, CV and publication list as a single PDF-file until 01.12.2022.

Please direct any questions to Professor Dr. Ulrich Dobrindt, Institute of Hygiene, University of Münster, Germany, +49 251 83-35406 or dobrindt@uni-muenster.de.

Apply here


PhD candidate - Machine learning and multi-omics

The Institute of Translational Genomics (ITG) translates insights from genomics and multi-omics into mechanisms of complex disease development and progression. The objective of this PhD will be methodological development using machine learning approaches for the analysis of multi-omics data in order to improve type 2 diabetes (T2D) prognosis and prevention approaches, achieve better patient stratification and identify potential new drug targets.

The successful candidate will join a dynamic and international team of researchers and analysts in a collaboration funded through the EU Horizon2020 framework, which brings  together both private  and public researchers  to  achieve a paradigm shift  in T2D healthcare. The project will provide a unique opportunity to gain experience with diverse omics datasets as well as  a wide spectrum of translational genomics analyses.

Your mission

  • Development of new methods for the analysis of multi-omics data (genotyping data, proteins, metabolites, imaging traits) using machine learning approaches
  • Performing exploratory data analysis, quality control and statistical mining on large datasets containing T2D-related data
  • Developing new pipelines and software, quality control
  • Identification and validation of novel drug targets and drug repositioning opportunities
  • Development and validation of integrated prediction score combining metabolomics, proteomics, genetics and imaging measurements

Your qualifications

  • A Master’s degree in Computer Sciences or a related field
  • Practical experience with machine learning approaches
  • Familiarity with *NIX environments and the bash scripting language
  • Familiarity with high-performance computing environments
  • Spoken and written fluency in English

Desired Qualifications:

  • Knowledge of human genetics, GWAS and basic bioinformatics resources (Ensembl, the GWAS Catalog, genome annotation and expression databases…)
  • Practical experience with omics data analysis
  • Familiarity with common statistical genetics tools (e.g. plink, bcftools)

Apply here


Posted on October 27, 2022

PhD candidate- Spatial and Single Cell Transcriptomics

Our mission as research center: Discover personalized medical solutions for environmentally triggered diseases to promote a healthier society in a rapidly changing world.

The (HPC) founded and funded by Helmholtz Munich stands for the intelligent fusion of biomedical sciences, engineering and digitization. At HPC, top scientific talents from across the globe work together on the development of novel solutions that make a difference in the prevention, diagnosis and treatment of diseases.

Our research group aims to develop and use microfluidic chip technologies for analyzing tissues of metabolic diseases. For this we are searching a PhD candidate to investigate spatial transcriptomic changes occurring during manifestation of the liver and pancreas disease. The envisaged tissue technology is applied for revealing cell-cell communication events during the progression of fatty acid liver diseases and pancreatic cancer.

Your mission

    • Establish bioanalytical workflow to measure spatial transcriptomic signals in the liver and pancreas
    • Extend an existing microfluidic chip platform for spatial signal retrieval
    • Investigate cell-cell communication

Your qualifications

  • Very good skills in spoken and written English
  • You are highly organized, and can work on complex problems at the interface of bioengineering and cell biology
  • You are willing to work in an international team
  • You have the interest to acquire the capability to produce microfluidic chip technologies
  • Knowledge of a computer programming language (e.g. python or R) is a plus. In case you do not have any bioinformatic qualification you will have to learn this within the first year of the PhD.

Quote Reference: 15167954

Expires on December 25, 2022

Apply here


Cancer Research UK 4 Year PhD Studentships

The CRUK Manchester Institute is currently located over two sites at the Oglesby Cancer Research Building, Manchester Cancer Research Centre and our temporary site at Alderley Park, Cheshire until our new research facilities are re-established on our former site in Withington, South Manchester next to the The Christie NHS Foundation Trust.  The rebuilding of our world-class Paterson research facilities is well underway, and we anticipate returning to our original site in Withington, Manchester in 2023.
We welcome applications from enthusiastic and ambitious candidates with a strong academic track record to our PhD programme.  Applicants should hold or expect to graduate with a First or minimum upper-second class undergraduate honours degree (or equivalent from a non-UK university) in a relevant subject and Masters-level and/or other laboratory research experience in cancer.   Laboratory research experience as part of, or outside of a university degree course or a Master-level degree in a relevant subject is advantageous but is not a conditional requirement in making an application.
The Cancer Research UK Manchester Institute is proud to be a diverse, open and global Institute.  Our priority, and that of the University of Manchester, is to support our current students and welcome new ones from Europe and other continents, we therefore encourage students of all nationalities to apply for the programme.
Cancer Inflammation and Immunity Research Group
All applications will be considered equally irrespective of ethnicity, disability, sexual orientation, gender, religion/belief, age and nationality.  To help us monitor equality, diversity and inclusion within the Institute, you will be asked to complete and submit an EDI monitoring form during the application process.  Equal opportunities information will not be shared and will not form any part of the selection process or divulged to members of the selection, recruiting or interview panels.
Successful applicants will receive a non-taxable annual stipend (living allowance) of £21,000 GBP per annum, fully funded bench and tuition fees (home and international) for 4 years.  Registration and graduation will be affiliated to the University of Manchester, UK.

Application deadline: Friday 9 December 2022, 1700 hrs (GMT).

Interview date: Tuesday 17 January 2023, Alderley Park, Cheshire, UK.


Posted on October 25, 2022

PhD Student (gn) Computational Biology

The University Hospital of Münster is one of the leading hospitals in Germany. Such a position cannot be achieved by size and medical successes alone. The individual commitment counts above all. We need your commitment so that even with little things we can achieve great things for our patients. There are many possibilities open for you so that you may develop with them.

The the lab for Functional Genomics in Psychiatry at the Department of Mental Health, WWU Muenster, Germany offers a position, limited to initially 3 years.

The mission of the Ziller lab is to develop and apply novel strategies to dissect the genetic and epigenetic basis of complex diseases, with particular focus on psychiatric disorders. Our research is focused on the question how many genetic and environmental risk factors act in concert to create a permissive molecular environment that fosters the emergence of psychiatric disorders such as schizophrenia and bipolar disorder and lead to treatment resistance.

In order to address this problem, we employ a highly interdisciplinary, integrative biology approach that utilizes human pluripotent stem cell based model systems, high throughput functional genomic screening and big data based machine learning, bridging the scales from genetics to patient level traits. The Ziller lab is part of the Department for Mental Health of the Medical Faculty, WWU Muenster.

The overall goal of the Department is to dissect the molecular mechanisms underlying psychiatric diseases and treatment resistance, rapidly utilizing these insights to develop new patient tailored therapeutic approaches in a knowledge driven fashion.

We are looking for a motivated individual highly skilled in computational biology/ bioinformatics with the desire to make a difference for people suffering from mental health problems. A Masters Degree in (Bio)Informatics/Data Science or related disciplines is desirable. The position focuses on the integration of multi-omic datasets and clinical information to develop and implement new methods to predict likelihood of treatment resistance and support the selection of adequate treatment strategies in an evidence based fashion.

Ref. Nr. 6850

(*gn=gender neutral)

Please apply (including the above reference number) with all relevant information (a cover letter expressing research interests, along with a brief summary of your previous projects, including applied techniques and a complete CV) until 16.11.2022 electronically via our online application form.

Apply here


PhD in Neurodegeneration/ Inflammation

The University of Luxembourg is an international research university with a distinctly multilingual and interdisciplinary character. The University was founded in 2003 and counts more than 6,700 students and more than 2,000 employees from around the world. The University’s faculties and interdisciplinary centres ;focus on research in the areas of Computer Science and ICT Security, Materials Science, European and International Law, Finance and Financial Innovation, Education, Contemporary and Digital History.

Your Role…
* A particular focus will be the characterization of the role of the metalloproteinase/disintegrin ADAM17 in neurodegeneration and neuroinflammation
* Develop cellular models including differentiation of iPS cells as well as use of immortal and primary cell lines to experimentally approach the
hypotheses
* Design and apply biochemical assays to test the functional role of ADAM17 in the above mentioned in vitro cell systems and eventually also involving
animal models
* Analyze and interpret results and data obtained, liaise with computational biology experts and prepare result report documentation
* Write regularly progress reports, prepare document research projects, contribute to manuscripts from scientific results, prepare presentations for
internal and external scientific meetings and eventually grant proposals

What we expect from you…
* MSc, MD or equivalent diploma in natural sciences (preferably medicine, human biology, biochemistry)
* Knowledge of molecular biology and medical (patho)physiology
* Good self-organisational and communication skills for a small team
* Flexibility and ability to travel to cooperation partner within the greater region (UniGR)
* Basics in laboratory research including handling/experimentation with laboratory animals desirable
* Experience in or previous Exposure to bioinformatics would be an asset
* Fluency in English mandatory, and good level of French and German is desired

 

For further information and application details, please contact Dr. Jochen Schneider via email: jochen.schneider@uni.lu

Apply here


Posted on October 19, 2022

PhD positions on integrative omics and phylogenomics

Would you like to participate in an exciting interdisciplinary research project to discover the hidden chemistry of plants and its evolution using computational omics approaches? Do you enjoy collaboration and teamwork while being at the cutting edge of scientific progress? We are looking for two PhD candidates with complementary skills to pioneer new technologies to analyze, explore and leverage the diversity of plant chemistry hidden in plant genomes.

Plants represent an untapped resource of natural bioactive compounds that significantly contribute to plant resilience to pathogens, herbivores, and abiotic stresses, and may be applied for medicine or crop protection. In this project, you will design and/or apply innovative omics integration strategies for genomics, transcriptomics, and metabolomics data, to discover plant specialized metabolite biosynthetic pathways and study their evolution. You will work together with the other PhD candidate in this project, which will entail a combination of algorithm development, greenhouse experiments, integrative omics analysis, and evolutionary genomics. Extensive local and international collaboration is foreseen, including possibilities for a foreign research visit as part of your PhD project.

The research is embedded within the chairs of Bioinformatics and Biosystematics. The projects will be (co-)supervised by Dr. Marnix Medema, Dr. Justin van der Hooft, Dr. Klaas Bouwmeester and Prof. Dr. Eric Schranz.

We ask

We are looking for two enthusiastic and complementary team players with all or a subset of the following skills:

  • a solid academic record (MSc) in bioinformatics, biology, or biotechnology
  • experience in computational omics analysis and proficiency in programming (in, e.g., Python)
  • at least basic to intermediate statistical and mathematical skills
  • demonstrable experience in working with next-generation sequencing data or with greenhouse experiments with plants
  • affinity with plant science, metabolism and/or biosynthetic pathways
  • you meet all the entry requirements of the  WUR PhD programme.

More information

For more information about this position, please contact Marnix Medema, Associate Professor Bioinformatics, by email (marnix.medema@wur.nl).
For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl.


Posted on October 18, 2022

PhD positions in Data Science

The Munich School for Data Science (MUDS) has open PhD positions for students with a background in computer science, data science or similar, or one of the domain sciences biomedicine, plasma physics, earth observation and robotics with a very strong focus in computer science, data science or similar, or interdisciplinary study programs combining both (e.g. geoinformatics, bioinformatics).

 

MUDS is a joint initiative of research centers and universities in the Munich area: Helmholtz Munich, Max Planck Institute of Plasma Physics, and the German Aerospace Center, with the Ludwig-Maximilians-University Munich and the Technical University of Munich, as well as with the Leibniz Supercomputing Center and the Max Planck Computing and Data Facility, together with an increasing number of industrial partners.

 

The aim of MUDS is to train candidates at the interface of data science and the scientific domains pursued at the participating centers. Methodologically, it covers a broad range of topics, from large-scale data management to data mining and data analytics (including machine learning and deep learning), from high-performance computing to high-performance analytics; from data integration to data-related topics such as uncertainty quantification, model-order reduction, or multi-fidelity methods. The primary fields of application are biomedicine, plasma physics, earth observation and robotics. Consequently, a MUDS student will learn to

(i) develop and adapt state-of-the-art methods from data science and
(ii) apply the acquired knowledge to the research domains of the respective Helmholtz centers.

The goal of MUDS is to attract excellent candidates who are interested in interdisciplinary training specifically tailored to the needs of their individual projects. Their research will be accompanied by scientific and transferable skills workshops, summer schools and events, as well as an optional international lab research stay, thus enabling the PhD candidates to become the outstanding data scientists of tomorrow.

Deadline for applications is November 15, 2022. 

For details visit here


PhD position in tree epigenomics

A PhD position in tree epigenomics is available at the Technical University of Munich (TUM), Germany (www.johanneslab.org). The position is part of a government-funded collaborative project between the TUM (Plant epigenomics, Forest growth and yield science), University of Freiburg (Forest Genetics) and the University of Marburg (Plant Ecology and Geobotany).

Description: DNA methylation is an important epigenetic mark with fundamental roles in gene regulation and transposable element silencing. In plant genomes, aberrant DNA methylation changes (i.e. epimutations) can arise spontaneously, similar to DNA sequence mutations. Unlike in animals, these epimutations are often transmitted across many generations and have been shown to contribute to the heritability of important plant traits. It remains unclear if and how epimutations shape the course of plant evolution, and whether they are exploitable in agricultural breeding programs. In this project, we investigate how past environmental conditions and growth histories of forest trees have affected epimutational processes within the 3D topology of a tree, and the extent to which somatically-acquired methylation changes affect seedling fitness in the next generation. The project will contribute to the knowledge about the adaptability of tree species to changing environmental conditions.

What are we looking for: We are looking for a talented PhD student who will take charge of the analysis and interpretation of genome-wide methylation data in trees. The applicant would make use of and combine several in-house computational algorithms into a single analysis pipeline. We have a strong preference for bioinformaticians/computational biologists with a deep appreciation for biological phenomena or, alternatively, experimentalists with a solid background in bioinformatics/computational biology. For specific inquiries regarding this position contact Frank Johannes at work@johanneslab.org.

Location: The Johannes lab is embedded in TUM School of Life Sciences. The TUM is rated among the best in Germany and ranks well internationally. The TUM Life Sciences campus is located about 30 minutes from the city center of Munich and 15 minutes from the Munich international airport. The Campus houses state of the art facilities for plant phenotyping, computing and bioinformatics.

Application: Send your application directly to susanna.fink@tum.de. The application should include: 1) a full CV, 2) a short statement of research interests and experience, and 3) contact information for two references (preferably everything in a single pdf file).

The application deadline is October 22, 2022. Starting date is as soon as possible.

Apply here


Posted on October 15, 2022

PhD candidate:  In-cell structural biology and biophysics

Our mission as research center: Discover personalized medical solutions for environmentally triggered diseases to promote a healthier society in a rapidly changing world.

The Helmholtz Pioneer Campus (HPC) founded and funded by Helmholtz Munich stands for the intelligent fusion of biomedical sciences, engineering and digitization. At HPC, top scientific talents from across the globe work together on the development of novel solutions that make a difference in the prevention, diagnosis and treatment of diseases.

The Jasnin Lab uses in situ cryo-electron tomography to explore the molecular architecture of actin systems within unperturbed cellular environments, and elucidate the structural principles governing actin functions across scales.

We are looking for a highly motivated PhD candidate – In-cell structural biology and biophysics (f/m/x) .

Your mission

 

  • Have a keen interest in electron microscopy (EM), fluorescence microscopy and actin structure and function
  • Have a keen interest in learning cryo-electron tomography (cryo-ET), correlative cryo-focused ion beam milling (cryo-FIB) sample preparation and image processing
  • Study actin-based processes critical for health and disease using the cryo-ET workflow, from cell sample preparation and optimization to imaging and data analysis
  • Use computational tools for in-cell structural analysis of actin assembly and force generation

Your qualifications

 

  • Excellent MSc in biology, physics, biochemistry, bioinformatics, or related field of science
  • Knowledge/experience with EM or other structural biology techniques
  • Ability to work in an interdisciplinary (combining structural, molecular, cellular and theoretical approaches) and international team of researchers
  • Fluency in English

Desirable qualifications

  • Experience with cell culture
  • Experience with cryo-EM/ET
  • Experience with (cryo-)FIB/SEM sample preparation
  • Experience with fluorescence microscopy
  • Experience with scientific scripting languages (Python and Matlab)

Quote Reference: 15167627

Apply here


PhD: Nutrient Bio-Accessibility Effects on the Gut Microbiota

The project will explore the bioaccessibility of prebiotic fibres from natural matrices. Most of the evidence on the efficacy of prebiotics (fructo-oligosaccharides (FOS), galacto-oligosaccharides (GOS), arabinoxylan-oligosaccharides (AXOS)) has been collated using the extracted and highly refined oligomers. There is an increasing emphasis on minimally processed foods and moves away from highly refined materials would meet this need.

Such minimal processing of natural plant-based starting materials which control the accessibility of the constituent oligomers might include fermentation, the use of enzymes, technologies such as pulse electric fields and thermo/physico mechanical preprocessing and the degree of ripening of the starting material. These processes will create changes in both the degree of polymerization of the ‘parent’ polysaccharide and the diffusivity of the oligosaccharides from the natural matrices – which both in turn will affect the fermentation kinetics and gut microbiota composition in the small-to-large bowel. Such natural matrices may also be dried to be used in ‘model’ food products (such as baked crackers) where the amount of prebiotic (parent molecule to soluble oligosaccharides) can be controlled.

The project therefore sits at the interface between physical sciences and digestive science and will form an innovative and full comparison of prebiotic sources and the extent to which they can be controlled through pre-processing, to measure the effect on in gut fermentation, and subsequent effects on the gut microbiota and metabolic markers. The student will develop a range of skills including microbiome analysis with shotgun metagenomic and bioinformatic approaches, metabolomics analysis and food structure and processing with an industrial element through Campden BRI, the industrial partner for this project.

Work will primarily be carried out at the Quadram Institute, but access to laboratory and process facilities at Campden BRI will be available. A minimum of a 3-month placement at Campden BRI will be part of the 4-year PhD study.

This project is part of a BBSRC-funded Collaborative Training Partnership (CTP) with The Food Consortium CTP. The student undertaking this project would be based at the Quadram Institute Bioscience.

For further information and to apply, please visit our website.

Application Deadline: 27/10/2022

Apply here


Posted on October 12, 2022

19 PhD student positions in Cancer Biology focusing on the Tumor Ecosystem - DTU Canbio2

CANBIO2, standing for doctoral training in “Cancer Biology 2”, is the second edition of our competitive PhD training program, supported by the doctoral research funding scheme PRIDE of the Luxembourg National Research Fund (FNR). Focused on the multiple distinct facets of the tumour ecosystem, the scientific program comprises the following three aspects: (i) advanced cancer models, (ii) cancer metabolism and (iii) novel treatment strategies integrating various aspects of the tumour environment. CANBIO2 will make use of advanced high throughput technologies and apply systems biology approaches to unravel novel targets for treatment.

 

The role of the ecosystem in cancer growth and progression is increasingly recognized. This tumor ecosystem (TE) includes multiple factors within the local tumor microenvironment such as tumor-associated fibroblasts, endothelial cells, tumor-infiltrated immune cells, skewed nutrient supply, hypoxia, as well as more distant players such as systemic immunity, cytokines and the microbiome. Together these conditions shape a supportive tumor milieu fostering growth, progression and metastasis.

To address this complex crosstalk and to eventually exploit it for novel therapeutic concepts, CANBIO2 sets out to train the next generation of cancer biologists and data scientists in a stimulating interdisciplinary environment. Individual projects will focus on a molecular, cellular and/or systems approach. Several projects require a data science background and will allow to develop advanced bioinformatics skills.

 

The program includes transferable skills training, support in career development, keynote lectures and annual PhD retreats. PhD candidates will conduct their research projects either at LIH (Department of Cancer Research, Department of Infection and Immunity) or at the University of Luxembourg (Luxembourg Centre for Systems Biomedicine, the Department of Life Sciences and Medicine, or the Department of Physics and Material Science). All PhD candidates will be enrolled at the University of Luxembourg in the Doctoral School in Science and Engineering of the University of Luxembourg for PhD studies in the discipline of Natural Sciences.

HOW TO APPLY

Applications including the following mandatory documents:
1.    Cover letter stating up to 3 project preferences (please write the project numbers in the title of the cover letter)
2.    A full curriculum vitae with at least 2 references (contact details only)
3.    The relevant diplomas showing marks  (MSc, MD or equivalent)

should be submitted by 6 November 2022 through the "apply button" below ONLY.

Apply here


Posted on October 07, 2022

PhD fellowship in Precision Health in Metabolism

We are offering a PhD fellowship in Precision Health in Metabolism commencing January 1, 2023, or after agreement.

Background
The vision of the Novo Nordisk Foundation Center for Basic Metabolic Research is to strengthen interdisciplinary research that transforms our understanding of the mechanisms underlying metabolic health and disease and then apply this knowledge to new prevention and treatment strategies. Established in 2010, we moved into new laboratories, offices, and meeting spaces in the Maersk Tower in 2017.

 

The Center has approximately 240 employees working across a wide range of biomedical disciplines in a highly collaborative, international research environment. You can read more about us here www.cbmr.ku.dk.

 

Our research
The Loos Group aims to identify the key genetic and non-genetic determinants of body weight regulation to gain insight into the deeper layers of biology that underlie obesity and metabolism. Additionally, we aim to improve prediction, prevention, and treatment through implementation of precision health strategies. You can read more about the Loos Group here.

Project description
We seek an enthusiastic, passionate researcher to carry out a PhD project in genomics of metabolic disease. The project will focus on multi-trait analyses to identify genetic variants that show distinct patterns of association with adiposity and metabolic traits and integration of multi-omics data to identify subtypes among individuals with obesity. In addition, by applying a range of bioinformatics methods and tools, the student will seek to identify the causative variants and genes, the relevant cell types and the states, and the physiological mechanisms by which the genetic variants may alter the phenotypic traits.

Principal supervisor is Professor Ruth Loos, Novo Nordisk Foundation Center for Basic Metabolic Research, e-mail ruth.loos@sund.ku.dk

 

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., bioinformatics, biostatistics, human genetics, genetic epidemiology, computational biology, etc.

Other important criteria are:

  • Experience with population genetic and association analyses of human complex traits
  • Experience in managing and analysing genome-wide genotype data
  • Basic understanding of the biology of obesity and metabolic disorders
  • Pronounced experience in the programming languages R and/or python
  • Experience from Linux/UNIX environment and high-performance computing
  • Familiarity with bioinformatics approaches to integrate human genetic associations with biological information
  • Experience of multi-trait genetic association analysis, polygenic risk scores, and/or Mendelian randomization is an advantage
  • Demonstrated scientific productivity, such as previous research publications
  • Excellent written and spoken English language skills

Application deadline: October 19, 2022, at 23.59pm CET.

Apply here


PhD Studentship: Genomic Signatures of Pathogen Evolution in Acinetobacter

UEA research is making real-world impact. That’s why 91 per cent of UEA research has been rated 'world-leading' or 'internationally excellent' by the Research Excellence Framework (REF2021). We’re also in the UK top 20 for research quality.

Some species in the bacterial genus Acinetobacter are responsible for causing serious infections that can be difficult to treat due to high levels of antibiotic resistance. Understanding how these pathogens have evolved will provide insights into how we can combat them in the future. This project will take two approaches to studying Acinetobacter evolution. Firstly, it is thought that one way that bacteria can adapt quickly to a changing environment is through large-scale genome rearrangements, which impact how much different genes are expressed. You will characterise these different arrangements in this project. Secondly, comparison of genome sequences can be used to identify signs of natural selection through differences in substitution patterns. You will characterise these patterns in the species analysed in this project.

 

Your supervisory team (Dr Ben Evans, UEA, UK; Prof Dan Brewer, UEA, UK; Dr Louis-Patrick Hararoui, Sherbrooke, Canada; Dr Santiago Castillo-Ramirez, UNAM, Mexico) will provide specific expertise in Acinetobacter, evolutionary genomics, and bioinformatics. In addition to training provided by the supervisory team, you will have the opportunity to attend internal and external training courses, such as in microbial genomics, evolution and programming, and to present your work at lab meetings, national and international conferences. You will develop skills in programming (e.g. Python), data analyses and presentation (e.g. using R), and scientific communication. You will have the opportunity to apply for funds from the Turing Scheme to visit the members of the supervisory team based outside of the UK.

Qualification:

Minimum 2:1 in an undergraduate degree with experience of bioinformatics or computer science. Knowledge in microbiology or evolutionary biology, as well as programming skills, would be beneficial.

Apply here


Posted on October 06, 2022

Fully funded PhD positions at EpiCrossBorders: the International Helmholtz Edinburgh Research School for Epigenetics

EpiCrossBorders is an international and interdisciplinary PhD training program centered on epigenetics research at the Helmholtz Munich, Germany, and the University of Edinburgh, UK. We are looking for PhD students to join the Epigenetics@HMGU research groups based at Helmholtz Munich. We invite highly talented and motivated students from all over the world to apply to our international program centered on Epigenetics research.

We are all connected! Not just people, but all organisms and their environment! For example, disruptions in environmental conditions and habitats can have great influence on species composition, the spread of diseases or food production. Thus to obtain optimal health outcomes we need a collaborative, multisectoral and transdisciplinary approach and multiple scales that recognizes the interconnections between all species: the ‘One Health’ approach.

 

EpiCrossBorders is currently looking for PhD students to join the Epigenetics@HMGU research groups based at Helmholtz Munich. We invite highly talented and motivated students from all over the world to apply to our international program centered on Epigenetics research. Together we will bridge national and disciplinary borders to achieve major discoveries!

 

PhD projects within the call aim for major discoveries in:

 

  • Chromatin-Biochemistry
  • Computational Biology & AI
  • Epitranscriptomics
  • Epimutations
  • Single cell and systems biology
  • Mathematical modelling
  • Statistical methods for spatial ‘-omics’
  • High throughput ‘-omics’ methods

Application deadline is November 12th, 2022.

Applicants should have obtained their degree latest before the start of the PhD. Applicants with a four-year BSc and without an MSc, please contact the research school office directly (epig‑rs@helmholtz‑muenchen.de).

Apply here


Two PhD candidate positions in Virology

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major societal themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Sustainability.

The Virology Section of the Department of Biomolecular Health Sciences of the Faculty of Veterinary Medicine studies the interaction between viruses and their hosts at the molecular/cell biological level as well as at the level of the organism. Ultimately, we strive to translate obtained knowledge into the development of novel vaccines, antiviral therapies, and diagnostic tools.

Would you like to know more about this vacancy? Please feel free to contact: Prof. dr. Frank van Kuppeveld, via f.j.m.vankuppeveld@uu.nl.

Would you like to contribute to our understanding of the enteroviral life cycle? Are you looking for a PhD candidate position? We have two openings at the Virology Section of the Faculty of Veterinary Medicine of Utrecht University where we are building a team of PhD candidates and Postdoctoral researchers for the ERC Advanced project of Prof. dr. Frank van Kuppeveld.

Enteroviruses are highly prevalent human and animal pathogens that cause a broad variety of diseases. Well-known human pathogens are poliovirus, coxsackievirus, enterovirus-A71, enterovirus-D68, and rhinovirus. Although valuable insights have already been obtained in the enteroviral life cycle, many important questions cannot be answered due to shortcomings of current methodologies. The laboratory of Prof. dr. Frank van Kuppeveld has contributed many important molecular insights into the enteroviral life cycle. Recently, a novel high-resolution imaging technology, VIRIM, was developed which allowed us for the first time to visualize translation of single (entero)viral RNAs in living cells (Boersma et al, 2020, Cell).

The overarching goal of this ERC project is to visualize and dissect the spatial and temporal regulation of the different phases of the enterovirus life cycle and to elucidate the underlying molecular mechanisms. To further our understanding, the newly established ERC Advanced team will develop and use novel methodologies to study this process.

Qualifications

To be successful in this role you:

  • have received a MSc degree in virology, molecular biology, or biochemistry;
  • have hands-on and proven interest and experience in molecular biology, biochemistry, microscopy, and/or virology;
  • have affinity and experience with at least one of the technical profiles in the job description;
  • are a team player who is enthusiastic to collaborate with other team members and research groups;
  • communicate clearly and effectively and have proven English skills in presenting and writing.

 

The application deadline is 17/10/2022

Apply here


Posted on October 05, 2022

PhD position: Virus bioinformatics

The Computational Biology Group at the Department of Biosystems Science and Engineering of ETH Zurich in Basel works at the interface of mathematics, statistics, and computer science with biology and medicine. We develop statistical and evolutionary models and efficient algorithms for high-throughput molecular profiling data, with applications in oncology and infectious diseases. Applications are encouraged for a position as a PhD student.

 

Project background

The open position is in the field of computational virology and analyzing viral sequencing data to improve HIV diagnostics. The goal is to develop computational methods for viral next-generation sequencing data that enable DNA-based HIV drug resistance testing, to test the method on a large clinical dataset, and to devise a novel genotypic HIV-1 DNA drug resistance test.

 

Job description

The position involves:

  • design and implementation of novel statistical and machine learning methods for next-generation sequencing data
  • validation, testing, and application of the models to large clinical datasets comprising NGS data from integrated HIV proviruses
  • integration of the models into computational viral NGS data analysis workflows
  • development of a novel genotypic HIV-1 DNA drug resistance test

 

Your profile:

You have a strong quantitative background in computational biology, statistics, machine learning, computer science, physics, mathematics, or a related field. Exposure to modelling biological systems and experience in developing software for their analysis are also advantageous. You are expected to engage in an interdisciplinary research team and foster collaboration across computational sciences, virology, and clinical diagnostics.

 

For further information please visit our website at www.cbg.ethz.ch. Questions regarding the position should be directed to Prof. Dr Niko Beerenwinkel (by email at niko.beerenwinkel@bsse.ethz.ch).

Apply here


PhD student in Cancer and Vascular Biology

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

 

The Department of Immunology, Genetics and Pathology at Uppsala University has a broad research profile with strong research groups focused on, among other things, cancer, autoimmune and genetic diseases. One of the basic ideas at the department is to stimulate translational research and thus a closer collaboration between medical research and healthcare. Research is conducted in medical and clinical genetics, clinical immunology, pathology, neuro-oncology, vascular biology, radiation science and molecular tools. Parts of the business are also integrated with the departments of oncology, clinical genetics, clinical immunology, clinical pathology and hospital physics at the University Hospital.

 

Duties
The candidate will perform research studies in the cancer and vascular biology field in Anna Dimberg´s research group. The project is focused on understanding how the tumor microenvironment affects cancer progression and response to therapy in brain tumors. Cell culture models, experimental tumor models and analysis of tumor tissue from patients will be used to identify and explore new targets for cancer therapy. The work includes molecular characterization of the microenvironment in human brain tumors and experimental models through wet lab experiments and also bioinformatic analysis of internal and external data sets.

The PhD position full time research studies for 4 years.  The recipient of the PhD position will mainly perform research studies, but other tasks such as teaching and administrative work can be included up to 20 percent. The position will be extended with the time spent at teaching to ensure that 4 years are spent on research studies.

Requirements

  • Master degree in medical science
  • Ability to work in interdisciplinary projects
  • Ability to work independently and jointly in a group
  • Solid experience in neuroscience
  • Experience in laboratory work
  • Experience in bioinformatics analysis of large scale dataset
  • Experience in analysing single cell RNAseq data, from raw sequence data processing to downstream analysis
  • Expertise in the R programming language, and experience in working in a Linux/Unix computer environment

 

For further information about the position, please contact: Anna Dimberg, 0702-166496, anna.dimberg@igp.uu.se

Please submit your application by 12 October 2022, UFV-PA 2022/2835.

Apply here


Posted on October 03, 2022

Pasteur-Paris University International Doctoral Program (PPU) IN LIFE SCIENCES AND BIOMEDICINE

An exceptional PhD program in the exciting, dynamic and interactive research environment of the Institut Pasteur in collaboration with Parisian universities. The PPU PhD program is for students holding a Master’s degree (or equivalent) in science, medicine or related fields from a non-French university.

 

Program philosophy and resources

• Improving public health and welfare through scientific discovery

• intensive research experience in a dynamic and supportive learning environment

• nurturing scientific curiosity while fostering creativity and independence

• stimulating discipline-specific and cross- disciplinary coursework

• mentorship from world-class faculty and a personalized thesis advisory committee

• extensive cutting-edge resources and state-of-the-art technology platforms on site

• a three-year salary covering living expenses and social benefits

• assistance with housing and visas

• dedicated student club for science and social activities

 

Application process There are 3 steps in the selection process

• First step: being selected by a host laboratory. Available labs and their projects will be on the website from September 19 to November 2, 2022. Contact the lab of interest as early as possible after September 19 to be interviewed by the supervisor.

• Second step: submit complete application in collaboration with host lab by November 15, 2022.

• Third step: short-listed candidates will be invited for an interview at the Institut Pasteur early February 2023, with decision shortly thereafter.

Deadline for application: Nov. 2, 2022
Contact: phd@pasteur.fr

 

For details visit here


Graduate Study Positions in Life sciences

The Interdisciplinary Graduate Program in Biomedical Sciences (IGPBS) admits pre-doctoral students with interests in all areas of basic biomedical research. The first year of the program involves coursework in molecular and cellular biology and rotations in three laboratories. At the end of the first year, students who select an advisor with a primary appointment in Microbiology become members of the Ph.D. program of the Department of Microbiology, Molecular Genetics and Immunology.

Graduate Study Positions are available immediately in the Ph.D. program of the Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA. The program provides outstanding scientific training for exceptional degree candidates in Bacteriology, Virology, and Immunology. Independent dissertation research ranges from basic bacterial and viral genetics, molecular mechanisms underlying human infectious and immunological diseases, and human translational studies. The program is designed to prepare individuals for careers in academic, governmental or industrial settings.

 

Applicants should hold a minimum of a baccalaureate degree in life or biological sciences, microbiology, molecular biology, or a related discipline. For detailed information about the program and application process visit here


Posted on September 30, 2022

PhD Candidate Clinical Epidemiology

The LUMC, situated in Leiden, the Netherlands, is an academic medical centre for patient care, research and education, aiming to meet the challenges of tomorrow’s health care. It has a strong focus on research, connecting and combining fundamental research into disease-causing mechanisms with patient-focused studies in areas like oncology, regenerative medicine, and population health. The LUMC has research facilities that include capabilities for multiple appliances. The combination with clinical and societal outreach programmes allows for ground-breaking research and innovation in basic and applied science.

 

Are you enthusiastic about epidemiological research? Would you like to contribute to unraveling the link between obesity and thrombosis via inflammatory processes and to study blood clotting? And would you like to follow the training to become a registered clinical epidemiologist (epidemiologist B) in addition to your PhD research and become proficient in all aspects involved in conducting strong scientific and clinically relevant research? Then you are the PhD candidate in Clinical Epidemiology we are looking for!

 

We are looking for an enthusiastic researcher with the ambition to develop scientifically and obtain a PhD. You are analytical and can work well independently as well as in a team. You also have an oral and written command of the English language at a scientific level. Some experience with -or enthusiasm for- epidemiology is desirable. You have an MSc in Biomedical Sciences, Health Sciences, Epidemiology, Medical Statistics, (Molecular) Biology, or a related field. In addition to your PhD research, you can also follow the training to become a clinical epidemiologist B in our department.

 

Profile:

• You have an MSc in Biomedical Sciences, Health Sciences, Epidemiology, Medical Statistics, (Molecular) Biology or a related field
• You will work with large epidemiological datasets and you will conduct research into different types of body fat distribution and the relationship with inflammatory processes, blood clotting and thrombosis.
• You will collaborate with various (national and international) research groups with expertise in the field of obesity, body fat distribution, and thrombosis
• Some experience with -or enthusiasm for- epidemiology is required
• In addition to your PhD research, you can follow the training to become a registered clinical epidemiologist (Epidemiologist B) in our department

Your workplace

You will work at the department of Clinical Epidemiology of the LUMC. The Department of Clinical Epidemiology focuses on scientific research and education. The department consists of various research groups (thrombosis, obesity, hemophilia, kidney failure, osteoarthritis, transfusion), each with a team of professors, senior researchers, postdocs, PhD students, and students. At the department there is a positive and open working environment which results in important knowledge exchange between the different research fields.

Contact: Ms. Astrid van Hylckama Vlieg, Assistant Professor, Clinical Epidemiology
071 526 1562
Email:     a.van_hylckama_vlieg@lumc.nl

Closing date 2 October 2022

Apply here


Two Phd Positions in Microbiology/ biomedical science

We are offering at the Max von Pettenkofer Institute – Institute for Medical Microbiology and Hygiene – of Ludwig-Maximilians-Universität München, two positions as Doctoral scientist/Ph.D. student (m/f/d) TV-L E13 (65%) The positions will be available from November 2022 at the Max von Pettenkofer Institute (located in Munich city center), within the postgraduate program Infection Research on Human Pathogens.

The projects for the successful candidates will be available in the scientific groups of Prof. Dr. Christine Josenhans (1) or Prof. Dr. Sebastian Suerbaum (2).

Project (1) will be on functional and evolutionary aspects of membrane proteins of Helicobacter pylori and

Project (2) on pathogenic bacteria genome evolution and epigenetics.

We are seeking highly motivated individuals with a drive for science and discovery, who would like to perform their Ph.D. thesis in an interdisciplinary and international environment. We anticipate applicants with an excellent previous scientific training, very good communication skills, and the ability to work independently and as part of a team. We offer an excellent research environment, access to a wide variety of techniques, and the possibility to participate in the structured graduate program of MvPI and LMU, including focused lectures, seminars, and skills courses.

Applicants with a completed undergraduate degree (Master or equivalent) in the life sciences, biomedical or natural sciences will be considered. Experience in microbiology, safe handling of human pathogens, cellular biology or biochemical methods will be beneficial for successfully conducting the project.

Please email your complete application documents, including your CV and complete transcripts of records, letter of motivation, and two references, until 15th of October, 2022, to: PhD.infection@mvp.lmu.de

For details visit here


Posted on September 28, 2022

10 PhD positions in Bioscience

10 PhD positions in infection biology, immunology, molecular/cell biology, genetics, microbiology, parasitology, seasonal epidemiology and evolutionary pathogenomics.

The International Max Planck Research School for Infectious Diseases and Immunology (IMPRS-IDI) is recruiting up to 10 PhD students for projects at the Max Planck Institute for Infection Biology, the Charité-Universitätsmedizin Berlin, the Freie Universtität, the Technische Universität and the German Rheumatism Research Centre in Berlin.

We offer:

    • outstanding research and training opportunities with access to state-of-the-art facilities
    • an excellent scientific network – our faculty members are internationally recognized scientists affiliated with renowned research institutes and universities in Berlin and around the world
    • a prestigious graduate school program with a project-adapted curriculum (training courses, lectures etc on scientific, technical and complementary skill topics) and a strong PhD student community
    • a stimulating international and multi-disciplinary research environment on thriving campus locations in Berlin

The following PhD projects are available and will start between May and December 2023:

  • Innate immune recognition in the gastrointestinal epithelium – Organoids as host model
    (Bartfeld lab)
  • Role of ILC3 and ILC3-derived effector molecules for metabolic adaptation during pregnancy (Diefenbach lab)
  • Elucidating the impact of climate on the seasonal dynamics of respiratory viruses
    (Domenech de Cellès lab)
  • Deciphering the mechanisms of innate immune responses using Drosophila melanogaster as a model (Iatsenko lab)
  • Within-person evolution of the human microbiome (Key lab)
  • How endomembrane remodeling controls immune signaling from endosomes. (Majer lab)
  • Mechanisms of adaptation in proofreading impaired large DNA viruses (Osterrieder lab)
  • Plasmodium falciparum variant surface antigens (VSAs), antibodies and poor cytoadhesion promoting asymptomatic persistence of malaria parasites. (Portugal lab)
  • Adaptive NK cell responses in infection and tumours (Romagnani lab)
  • Molecular dynamics of Innate Immune protein condensates (Taylor lab)

We are looking for:

  • creative, highly motivated and talented candidates of all nationalities and backgrounds who are truly committed to research
  • applicants must have an excellent M.Sc. or equivalent degree
  • candidates from biological disciplines including biophysics, biochemistry, molecular and cell biology, infection biology, immunology, microbiology, genetics, genomics, evolutionary biology, medical biotechnology, bioinformatics or closely related disciplines are encouraged to apply. For some projects, candidates with a strong background in a quantitative discipline (e.g. mathematics, statistics, physics) or computer science are sought – please check the project descriptions for individual skill requirements on our website

Interested in joining us?

To apply, please submit your application via our online application platform until October 31st 2022.

Contact: IMPRS-IDI Coordination Office (imprs-office@mpiib-berlin.mpg.de)


Posted on September 27, 2022

PhD fellowship in Functional Genomics

We are offering a PhD fellowship in Functional Genomics commencing January 1, 2023, or after agreement.

About us
The Novo Nordisk Foundation Center for Basic Metabolic Research’s vision is to strengthen interdisciplinary research that transforms our basic understanding of the mechanisms that underlie metabolic health and disease, and to accelerate this knowledge toward new prevention and treatment strategies. We were established in 2010 and in 2017, we moved into new laboratories, offices, and meeting rooms in the Maersk Tower www.maersktower.ku.dk.

The Center has around 260 employees who work in an international, highly collaborative research environment across a range of biomedical disciplines. You can read more about us here www.cbmr.ku.dk.

The Kilpeläinen Group uses genomic, molecular and health data to understand how genetic variants contribute to the risk of cardiometabolic disease. Through in-depth understanding of disease mechanisms, particularly in the adipose tissue, the group seeks to open avenues for new treatments. The group’s research strategy starts from human genetic association data, followed by bioinformatic prioritization of the causal variants, genes, and cell types.

We seek an enthusiastic, passionate researcher to perform a PhD project in Functional Genomics. The main objective of the PhD project is to identify gene regulatory effects in human adipose tissue that connect non-coding genetic variants to an increased risk of obesity and cardiometabolic disease. The project will propel understanding of how genetic risk variants may contribute to obesity and cardiometabolic disease by regulating gene expression in adipose tissue.

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., bioinformatics, biostatistics, computational biology, etc.

Other important criteria are:

  • Pronounced experience in the programming languages R and/or Python
  • Experience from Linux/UNIX environment and high-performance computing
  • Experience in analysing genetic association data
  • Experience in analysing RNA sequencing data
  • Experience in mapping gene enhancers using data on e.g., chromatin accessibility and histone modifications
  • Excellent academic track record and demonstrated scientific productivity, such as previous research publications
  • Excellent communication skills in both written and spoken English
  • Some hands-on experience of wet lab research is an advantage

Application deadline: October 9, 2022, at 23.59pm CET.

Apply here


PhD studentsin Amphibian Conservation, Genomics,and Synthetic Biology

Want to help save frogs declining from a pandemic disease?Interested in studying functional genomicsand using the latest methods in synthetic biology?

The One Health Research Group at the University of Melbourne is recruiting PhD students to studythe genetic basis of immunity tothe disease chytridiomycosis anddevelop targeted genetic interventionmethodsto increase disease resistance in declining frogs.

Our research includes quantitative genetics, comparative genomics, transcriptomics, and developing synthetic biologyapproachesin frogs.The projects are funded through the Australian Research Council,and PhD scholarswill be advised by Drs Lee Skerratt, Tiffany Kosch, Lee Berger and members of the One Health Research Groupand collaborators including Zoos Victoria. The project will be based at the Melbourne Veterinary School at the Werribee campus.

Qualifications Expertise needed: Applicants must have experience with molecular biological, immunological, or genetics research such as genomics, quantitative genetics, synthetic biology, microbiology, or immunogenetics. Skills or interest in population genetics, functional genetics, conservation genetics, disease ecology, HPC computing, bioinformatics, statistical analyses, and animal husbandry are an advantage.

Please submit a CV, cover letter, transcripts,a nd contact information for two referees to Dr Tiffany Kosch tiffany.kosch@unimelb.edu.au by 30 September2022.

Apply here


Posted on September 26, 2022

PhD student to study the impact of RadioGenomics

The Barcelona Institute for Global Health (ISGlobal) is a cutting-edge institute addressing global public health challenges through research, translation into policy and education. ISGlobal has a broad portfolio in communicable and non-communicable diseases including environmental and climate determinants, and applies a multidisciplinary scientific approach ranging from the molecular to the population level. Research is organized in three main areas, Malaria and other Infectious Diseases, Child and Maternal Health, and Urban Health, Climate & Non-Communicable Diseases. ISGlobal is accredited with the Severo Ochoa distinction, a seal of excellence of the Spanish Science Ministry.

ISGlobal is seeking a motivated student to join the Bioinformatics Research Group of Dr. Juan R Gonzalez at ISGlobal with the vision of leveraging omics and imaging data analytics through federated data analysis to improve health care outcomes. This is a unique opportunity for a motivated data scientist to contribute to the digital transformation of biomedicine and carry out research that has social impact and responds to unmet medical needs.

The doctoral candidate will develop novel research that applies advanced data modelling of clinical, genomic and transcriptomic data and deep learning to various different imaging modalities. An ambition of this team is to implement predictive modelling to understand disease drivers leading to early disease diagnosis and the discovery of novel digital biomarkers. This will be achieved by analysing extensive amount of data of chronic obstructive pulmonary disease (COPD) from different hospitals and cohorts from Spain and Europe. The candidate will also work on developing a DataSHIELD infrastructure to analyse available data using a federated system where all the information will be harmonize using OMOP.

Training and experience /Qualifications

Candidates are expected to:

  • Have a completed, or close to completion, Master Degree with strong analytics expertise in any of the following areas: Biomedical Sciences, Computer Science, Engineering, Mathematics, Statistics, Physics or related fields with focus on data analytics. Additional profiles will be considered if highly motivated researchers in other related disciplines decide to apply
  • Programming experience in one or more general purpose programming language: Python and/or R
  • Experience using one of the following deep learning libraries: Tensorflow, PyTorch or similar is desirable
  • Be familiar with OMOP
  • Be willing to work in an interdisciplinary team within a highly collaborative research institute
  • Be fluent in spoken and written English

Specific Requirements

We are looking for a person with high organizational and teamwork skills, capable of working autonomously, proactively and motivated, with good verbal and written communication. Flexibility of schedules will be valued.

How to apply

Applicants must fill in the request form and include the following code reference position: PREDOC_COPD_BRGE_Sep22, attach the CV and a Cover Letter. Each attached document must be named with the candidate name and surname.

The receipt of applications will be open until 5 October 2022

Applications will be accepted until 17.00 CET of the closing date.

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PhD Position for Developing a Federated Metadata Repository for Clinical Data

The Department of Mathematics and Computer Science at the University of Southern Denmark for the Computational Biology group chaired by Associate Professor Richard Röttger and Novo Nordisk jointly invite applications for a PhD position for the creation of a federated metadata platform for sensitive clinical data to be filled as soon as possible.

A large roadblock of medical research is the difficult access to sensitive data which hinders the training of complex and powerful machine learning concepts. This issue is amplified when considering rare diseases with low incidence numbers per hospital. To enable the identification of suitable patients for clinical studies amenable to machine learning, a privacy-preserving metadata platform is required. Here, the actual patient data remains at the site of storage, but virtual cohorts can be identified according to clinical phenotypes, symptoms and diagnoses and later used for federated machine learning approaches without breaching patient privacy.

We are seeking outstanding candidates with strong analytical and problem solving skills, who are strong in written and oral communication (in English), and have documented experience in the development of complex compute systems. The applicant should be fluent in the state-of-the-art web-development frameworks, virtualization techniques as well as database technologies. Expertise in clinical data science and machine learning, as well as computer security and data privacy are welcome.

Place of work:
Computational Biology Group  (Associate Professor Richard Röttger, roettger@imada.sdu.dk), Department of Mathematics and Computer Science, located at the main campus of the University of Southern Denmark, Odense, Denmark.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

Application deadline: 19 October 2022.

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Posted on September 23, 2022

Doctoral (PhD) student position in next generation sequencing

The Department of Biosciences and Nutrition performs research and education in several areas of medical science including aging, Alzheimer, bioorganic chemistry, biomaterial, molecular endocrinology, cancer biology, functional genomics, systems biology, epigenetics, structural biochemistry, immunology, and nutrition. It offers an excellent international research and working environment, including around 250 scientists, students, administrative and technical personnel. The Department resides in Neo at Campus Flemingsberg, a biomedical research building, aimed at being a creative and open environment that enables meetings, synergies, and exploration of areas of mutual interest across disciplines.

Our group has developed the first biomimetic method to spin artificial spider silk fibers and succeeded in establishing a production and purification method of recombinant silk proteins that results in unprecedented protein yields (Andersson et al. Nat Chem Biol. 2017; Schmuck et al. Mater Today. 2021). Furthermore, we have sequenced a whole spider genome of outstanding quality and have analyzed the transcriptome of the silk glands. Our research group consists of three PhD students, two technicians, four post docs and a bioinformatician, and is funded by the European Research Council, Swedish Research Council, FORMAS and Center for Innovative Medicine. The research group is located at Karolinska Institutet, campus Flemingsberg, and at SLU in Uppsala.

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.

The applicant must have theoretical knowledge of biology and bioinformatics (transcriptomics analysis by bioinformatics tools, as well as be able to write scripts in R. It is meritous if the applicant has previous experience of image analysis and microscopy. The applicant must be fluent in both written and spoken English. A positive attitude and strong drive to pursue research is desirable. Emphasis will be put on personal qualities in the selection process.

Reference number STÖD 2-3674/2022

Last application date 13.Oct.2022 11:59 PM CEST

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Graduate Students (Machine learning/ Computational Biology/)

About the lab: the Gerber Lab develops novel statistical machine learning models and high-throughput experimental systems to understand the role of the microbiota in human diseases, and applies these findings to develop new diagnostic tests and therapies. A particular focus of the Gerber Lab is understanding dynamic behaviors of host-microbial ecosystems. Our work in this area includes Bayesian statistical machine learning methods for discovering temporal patterns in microbiome data, inferring dynamical systems models from microbiome time-series data, or predicting host status from microbiome time-series data with human interpretable rules.

Environment:  the Gerber Lab is located in the Division of Computational Pathology, which Dr. Gerber heads, at Brigham and Women’s Hospital (BWH) at Harvard Medical School (HMS), and the Massachusetts Host-Microbiome Center, which Dr. Gerber co-directs. BWH, an HMS affiliated teaching hospital is adjacent to the HMS main quad and is the second largest non-university recipient of NIH research funding.

I am always excited to work with talented graduate students with interests relevant to my lab, which focuses on developing novel machine learning/computational biology/wet lab approaches to further understanding of the microbiome–the trillions of microbes living on and within us. This fascinating, complex and dynamic ecosystem is crucial for human health, and when disrupted may contribute to a variety of diseases including infections, arthritis, allergies, cancer, heart and bowel disorders.

In general, I can only be a primary advisor (and provide financial support) for students enrolled at Harvard or MIT. However, I am open to co-advising students at other institutions.

If you’re interested, email me at ggerber@bwh.harvard.edu. Please include your CV and a brief description of your research interests.

Students should have a high level of interest in:

  • Developing and applying new technologies to biomedical problems.
  • Advancing knowledge of the microbiome and its role in human health and disease.
  • Having your work make an impact on healthcare outcomes.
  • Working on an interdisciplinary team and collaborating with computational, wet lab and clinical scientists.

Posted on September 22, 2022

PhD position in Lung Cancer

At the Department for Health Evidence, we are looking for an enthusiastic PhD candidate for our KWF-project 'Towards risk-stratified follow-up care in lung cancer patients.' You will coordinate the project, interview physicians and patients and develop the dynamic AI model. For this, you will use both qualitative and quantitative research methods, write scientific papers and present the results at international conferences. Will you join our team?

In the Netherlands, routine follow-up of lung cancer patients consists of chest computed tomography (CT) scans every 3-6 months for the first 2 years and then yearly CT scans until 5 years of follow-up. With this one-size-fits-all approach, local recurrences can be detected but the risk of distant recurrence is much higher. Therefore, metastases often develop outside the scope of the scan. Furthermore, this approach was introduced before potentially survival prolonging treatments in oligometastatic (up to 5-10 metastases) patients became available. This routine follow-up is also a source of anxiety for patients, which often already starts several weeks before the planned imaging.Moreover, routine follow-up can delay diagnosis and treatment if a recurrence occurs between planned visits.

Therefore, improvement of follow-up care, by depicting the right follow-up frequency and the most optimal imaging modality per patient, is necessary to timely detect (oligometastatic) disease recurrence at a stage where effective and even curative-intent treatment is still possible. The presence of (PRO) symptoms prior to the detection of disease recurrence offers opportunities for patient participation and thus personalized follow-up strategies.

This project aims at developing a risk-stratified follow-up care approach in lung cancer patients. For this, we will develop and validate a dynamic AI model to estimate the individual risk of both local and distant recurrence in lung cancer survivors. Furthermore, a mixed-methods study will be performed amongst end users (patients and healthcare practitioners (HCPs)) to identify needs and preferences for adopting and implementing a risk-stratified follow-up care approach.

Tasks and responsibilities

  • Develop and validate a dynamic AI model to estimate the individual risk of recurrence in lung cancer patients.
  • Identify needs and preferences for adopting and implementing risk-stratified follow-up.
  • Publish the results in international journals.
  • Present the results at national and international conferences.
  • Write a PhD thesis for defence at Radboudumc.

Apply before 10 October 2022

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PhD fellowship in Metabolite Receptology

We are offering a PhD fellowship in Metabolite Receptology, SUNCR1 and Liver Pathology commencing 1 January 2023 or after agreement.

About us
The Novo Nordisk Foundation Center for Basic Metabolic Research’s vision is to strengthen interdisciplinary research that transforms our basic understanding of the mechanisms that underlie metabolic health and disease, and to accelerate this knowledge toward new prevention and treatment strategies. We were established in 2010 and in 2017, we moved into new laboratories, offices, and meeting rooms in the Maersk Tower www.maersktower.ku.dk.

The Group
The aim of the Schwartz Group is to characterize and understand how signaling metabolites and their specific GPCR sensors interact with hormonal and neuronal mechanisms to control endocrine and metabolic functions as the basis for developing novel means to prevent and treat obesity and diabetes and related diseases. More information about the group can be found here.

Project description
We are seeking an enthusiastic, passionate PhD fellow to investigate the role of metabolite receptors - in particular the succinate receptor SUCNR1 - in hepatic response to metabolic stress and how this is a balance between protective repair and damaging inflammation. A special focus will be on characterizing the development of hepatic crown-like structures and their role in these processes.

Key criteria for the assessment of applicants

  • Must have a master degree in Human Biology, Molecular Biomedicine or equivalent
  • Expertise within GPCRs is a must and extensive experience with metabolic stress liver diseases preferable
  • Professional qualifications relevant to the PhD program including hands-on experience with histology, IHC, RNAscope technology, tissue clarity, microscopy and image analysis
  • Hands-on experience with western blotting, RT-qPCR, etc.
  • Practical skills in performing of animal experiments
  • FELASA ABD Certificate for in vivo mouse work
  • Ability and enthusiasm to learn new methods and techniques
  • Good communication skills in English, both oral and written (Danish is also preferred)
  • Highly ambitious and self-driven
  • Strong work ethics and team player mentality
  • Previously demonstrated a capacity for excellence, either during master’s degree or publications

Application deadline: 3 October 2022, 23.59pm CET

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Posted on September 19, 2022

24 Interdisciplinary PhD projects in Ultrafast Science – IMPRS UFAST

 The International Max Planck Research School for Ultrafast Imaging & Structural Dynamics (IMPRS UFAST) is a joint venture of the Max Planck Institute for the Structure and Dynamics of Matter, Deutsches Elektronen-Synchrotron DESY, University of Hamburg and European XFEL GmbH. The International Max Planck Research School for Ultrafast Imaging and Structural Dynamics in Hamburg, Germany, offers a structured PhD program focusing on ultra-fast phenomena, X-ray physics and dynamical imaging in all areas of science covering physics, chemistry and biology.

The program offers exciting research opportunities at ultra-intense electron and X-ray sources to directly observe atomic motions during primary events. The use of ultrafast imaging over the relevant length and time scales generates new levels of understanding of the interplay between structure and dynamics. Specific areas include the theoretical and experimental aspects of condensed matter and atomically resolved dynamics, fundamental light-matter interaction, accelerator-based light sources, coherent imaging, coherent controlled molecular and solid state dynamics, molecular imaging, extreme timescale spectroscopy, ultrafast optics and X-ray science, and their relevance and applications in chemistry, biology and medicine.

Requirements:

We seek applicants with an excellent academic background. You hold (or are about to complete) an MSc degree or equivalent in physics, chemistry or related areas. You need to be passionate about research in ultrafast phenomena and motivated to conduct rigorous scientific work over the full degree period.

Apply:

The application deadline is 15th November 2022. PhD projects start in summer/autumn 2023. In exceptional cases, it may be possible to start on the research project earlier. For any further questions or problems regarding the application process or the online system, please contact the IMPRS UFAST coordinator on IMPRS.UFAST@mpsd.mpg.de.

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PhD Fellowship in Intestinal Microbiology

The University of Stavanger invites applicants for a PhD Fellowship in Intestinal Microbiology at the Faculty of Science and Technology, Department of Chemistry, Bioscience and Environmental Engineering. The position is vacant from January 2023.

In the clinic, microbial eukaryotes are usually treated as parasites. However, recent data suggest a possible beneficial and/or commensal role for intestinal eukaryotes such as Blastocystis. Given the widespread distribution of Blastocystis in the general population and our preliminary data, we hypothesise that this intestinal microbe plays a beneficial role in human intestinal health and inflammatory bowel disease (IBD) in particular.

Qualification requirements:

We are looking for applicants with a strong academic background who have completed a five-year master degree (3+2) within Biological Sciences, preferably molecular biology or microbiology, and ideally acquired recently; or possess corresponding qualifications that could provide a basis for successfully completing a doctorate.

Requirements for competence in English

A good proficiency in English is required for anyone attending the PhD program. International applicants must document this by taking one of the following tests with the following results:

  • TOEFL – Test of English as a Foreign Language, Internet-Based Test (IBT). Minimum result: 90
  • IELTS – International English Language Testing Service. Minimum result: 6.5
  • Certificate in Advanced English (CAE) or Certificate of Proficiency in English (CPE) from the University of Cambridge
  • PTE Academic – Pearson Test of English Academic. Minimum result: 62

Contact information

More information on the position (and project description) can be obtained from Head of Department Ingunn W. Jolma, e-mail: ingunn.w.jolma@uis.no or Professor Mark van der Giezen, tel: +47 51 83 44 93, e-mail: mark.vandergiezen@uis.no.

Information about the appointment procedure can be obtained from HR advisor Rosa Andrade, tel: +47 51 83 11 91, e-mail: rekruttering@uis.no.

Deadline 9th October 2022

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Posted on September 16, 2022

International PhD Programme on Gene Regulation, Epigenetics & Genome Stability

Are you a talented and enthusiastic student seeking an opportunity to work on research projects at the cutting edge of modern biology? Then you should consider joining our International PhD Programme (IPP). As an IPP PhD student, you address key questions related to the overarching theme of Gene Regulation, Epigenetics & Genome Stability while becoming part of our lively IPP community with more than 150 IPP students from more than 40 countries. For an overview of the IPP, have a look at IPP at a Glance, if you want to find out more about the benefits of being an IPP PhD student, check out What the IPP offers.

The programme is coordinated by the Institute of Molecular Biology (IMB) — a modern research centre located on the bustling campus of Mainz University in Germany.

About the IP:

Our research groups cover a broad range of expertise in genomics, biochemistry, proteomics, cell and developmental biology, bioinformatics, systems biology, and applied physics. For a better overview, browse through our research topics. In the IPP, you will have the chance to get insights into techniques like CRISPR/Cas genome editing, next-generation sequencing, modeling of gene networks, mass spectrometry or super-resolution microscopy. Our scientific and social events and the open and vibrant atmosphere in the IPP ensure high levels of exchange and collaboration between the participating groups.

Following topics:

  • Ageing & Disease
  • Epigenetics & Nuclear Dynamics
  • DNA Repair & Genome Stability
  • Bioinformatics & Computational Biology
  • Gene Regulation & Evolution
  • RNA Biology
Eligibility Criteria

To apply to the IPP you must provide the following:

  • Fully completed application form submitted before the relevant deadline
  • A Master degree or equivalent (1st Class BA Hons or BSc Hons) or anticipate receiving before enrolment
  • Full details of two referees, at least one of them should have supervised you in a research project
  • High level of both spoken and written English

If you have any questions that are not answered here or in the FAQs, you can contact us via email.

Application & Reference deadline: 19 November 2022 (12:00 noon CET)

For details visit here

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