PhD scholarship

 PhD positions in Bioinformatics, Genomics and Life Science:


Update 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.

Apply here


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.

Apply here


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

Apply here


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

Apply here


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

Apply here


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.

Apply here


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

Apply here


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


Graduate student: Single-molecule biophysics

Dr. Sabrina Leslie at UBC Michael Smith Laboratories is recruiting a Ph.D. student with interest in biophysics, nanoscience and biology. Our group develops and utilizes single-molecule fluorescence microscopy techniques to study interactions of biomolecules in cell-like environments. We’ve developed the Convex Lens-induced Confinement (CLiC) imaging platform, which makes it possible to watch individual, naturally fluctuating biomolecules as they search for and bind to each other, allowing us to make measurements that are not possible with other methods. This technique is applied both to basic biophysical research and development of drugs and therapeutics.

Project: Effects of topology on DNA structure and interactions

DNA supercoiling drives structural transitions within a DNA molecule. This project will study the dynamics of such transitions, how multiple transitions within the same molecule can compete with one another, and how such transitions affect protein-DNA interactions. The goal of the research project will be to better understand the role of these structural transitions in gene regulation and bridge the gap between in vitro and live cell studies.

Training: Graduate students in the Leslie Lab receive training in single-molecule microscopy, specializing in the CLiC imaging technique pioneered in our lab; bulk characterization techniques such as Dynamic Light Scattering, and fluorimetry; standard molecular biology techniques including cell transformation, and gel electrophoresis; and computational modelling, image processing and analysis. The training environment will include interactions with a start-up company, ScopeSys Inc., which is commercializing CLiC technology; as well as collaborators in pharmaceutical science, biochemistry and medicine.

We are looking for a well-organized, enthusiastic team player who enjoys lab work and troubleshooting scientific instrumentation. A successful candidate would have experience with or interest in DNA structure and function, fluorescence microscopy, statistical mechanics, mathematical modelling, and computer programming. Background in biophysics, molecular genetics, quantitative biology, or a related field is an asset. Proficiency with a musical instrument and/or dungeons and dragons are also assets. The successful candidates must have a passion for innovation and pushing scientific and engineering capabilities to the forefront of what is possible today.

To apply, please send a cover letter and CV to leslielab@msl.ubc.ca

Dr. Sabrina Leslie would consider supervising a MSc or PhD in any of the following programs as allowed by the program guidelines and admission committees.

  • MSc/PhD in Physics and Astronomy
  • MSc/PhD in Genome Science and Applied Technology
  • MSc/PhD in Bioinformatics
  • MSc/PhD in Biomedical Engineering

Reference Number

Please mention reference number GPS-55569 in all your correspondence about this Doctoral student position.

Apply here


Posted on September 15, 2022

Two PhD positions in Plant Genomics

UCD School of Biology and Environmental Science, Ireland, recruiting 2 PhD students to Unravel the sex determination system in Cannabis sativa.

Unlike many other plants, Cannabis sativa (hemp) produces male and female individuals. It is established that sex determination is genetic, but the exact molecular pathways involved remain elusive. In this project, we will use genomics and transcriptomics to identify genes controlling sex determination in Cannabis.

If you have a BSc or MSc in life sciences or bioinformatics and are interested in plants, this project is for you!

PhD student 1:

  • Analysis of a mapping population segregating for sex expression
  • Genome sequencing, assembly and annotation
  • Genetic analyses
  • 4 year fellowship, €18,500 per year

PhD student 2:

  • Analysis of the effect of plant hormones on sex expression
  • Transcriptomics
  • Plant growth and phenotyping
  • 4 year fellowship, €18,500 per year

To apply, send a letter of motivation, CV, your academic transcripts and contact details of 2 academic references in a single pdf file to rainer.melzer@ucd.ie

Deadline for applications: 30th September 2022

Apply here


PhD in Ocular Proteomics

The project focuses on the fundamental mechanistic study of ocular diseases, particularly dry eye disease and glaucoma employing the mass spectrometry-based proteomics and cell culture platforms. We are looking for highly motivated students to join our young research team to work on several projects funded by several grants from the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG).

The Experimental and Translational Ophthalmology Department of the University Medical Centre of the Johannes Gutenberg University Mainz is a leading eye research laboratory in Germany that focuses on the pathogenesis of various ophthalmic diseases. Our department features a well-equipped protein-biochemistry laboratory with conventional electrophoretic systems, as well as a state-of-the-art mass spectrometry system for protein profiling and biomarker identification.

Candidates should fulfill the following requirements:
• MSc degree in biochemistry, biology or related fields
• Self-financed throughout the course of study e.g. from the German Academic Exchange Service (DAAD) or other scholarships/ funding from home-country
• Proficient in English

Interested candidates are welcome to send your application to Dr. Perumal at nperumal@eye-research.org

Application Deadline 31 Dec 2022

Apply here


Posted on September 13, 2022

15 fully funded PhD fellowships in Quantitative Biology

The advent of large-throughput data is transforming life sciences into an increasingly quantitative discipline. The University of Lausanne (Switzerland) is at the forefront of this revolution, with quantitative research ramping up throughout the Faculty of Biology and Medicine, a dedicated department of Computational Biology, and interdisciplinary units such as the Center for Integrative Genomics. UNIL also hosts the headquarters of the Swiss Institute of Bioinformatics, to which many quantitative research groups are affiliated, and closely collaborates with EPFL on the same campus. Ideally situated along the lake of Geneva, near Lausanne's city center, UNIL brings together over 120 nationalities.

UNIL's Faculty of Biology and Medicine has recently launched a doctoral program entitled "Quantitative Biology". A wide range of research groups are recruiting PhD students, covering areas as diverse as Genetics, Cell biology, Metabolism, Computational biology, Oncology, Evolution, Microbiology, Imaging, Molecular biology, Neuroscience, Gene regulation, Radiobiology, Plant science, Ancient DNA, Population Genetics, Single-cell Genomics, Epi-lipidomics, Stem Cell Biology, Tissue Engineering and Biomaterials.

In 2022, hiring principal investigators include Francesca Amati, Sven Bergmann, Giovanni Ciriello, Christian Fankhauser, Maria C. Gambetta, Jérôme Goudet, Gilbert Greub , François Kuonen , Zoltán Kutalik, Alexandre Reymond, Marc Robinson-Rechavi.

Your qualifications

We are accepting applications from talented and enthusiastic candidates who are interested in a dynamic, well-supported lab at a top research institution. Candidates need to finish a Master’s degree in a relevant area before the start date of their doctoral studies.

We are looking for three main types of PhD students:

  • Students with a life science degree, interested in working in an experimental lab, but with a high degree of motivation to learn the fundamentals of computational biology, and to develop quantitative skills to analyze data more effectively
  • Students with a life science degree interested in working in a dry computational lab, keen to deepen their quantitative skills and broaden their horizon in terms of experimental and computational techniques
  • Students with a non-biological background (e.g. computer science, maths, physics), who are highly motivated to transition to Life Sciences

A high level of written and spoken English proficiency is required since most scientific activities are conducted in English.

Informal inquiries

Prof. Giovanni Ciriello, Co-director of the UNIL Doctoral Program in Quantitative Biology program

giovanni.ciriello@unil.ch

Your application Deadline: 15.10.2022

Apply here


PhD Student (f/m/d) Research group Molecular and Cellular Radiobiology

Through cutting-edge research in the fields of ENERGY, HEALTH and MATTER, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) solves some of the pressing societal and industrial challenges of our time. Join our 1.400 employees from more than 50 nations at one of our six research sites and help us moving research to the next level!

At the Institute of Radiooncology – OncoRay scientists (f/m/d) specializing in medicine, physics, biology and IT work together to crucially improve the treatment of cancer by administering radiation therapy that is biologically-personalized and technically-optimized.

As part of the Institute, the Department of Radiobiology invites applications as PhD Student (f/m/d) Research group Molecular and Cellular Radiobiology.

The position will be available from 1 December 2022. The employment contract is limited to three years.

Your tasks:

  • Handling of cell cultures, primary cell cultures/organoids/cancer stem cells
  • Methods of Cell and Molecular Biology
  • Bioinformatic analysis of omics data sets

Your profile:

  • Diploma or Master's degree in Biochemistry, Biology or Bioengineering with very good marks
  • Strong experience in handling cell cultures, primary cell cultures/organoids/cancer stem cells, cell and molecular biology, bioinformatic analysis of omics data sets (e.g. transcriptome, methylome, or similar)
  • Experience in histology and staining including the microscopic analysis of tissues
  • Goal oriented, capable of handling deadlines and highly motivated
  • Team player (f/m/d) who can also operate independently

Deadline: 7 October 2022

Apply here


Posted on September 12, 2022

2 PhD Candidates in Synthetic Biology/ Functional Metagenomics

NTNU is a broad-based university with a technical-scientific profile and a focus in professional education. The university is located in three cities with headquarters in Trondheim. At NTNU, 9,000 employees and 42,000 students work to create knowledge for a better world. You will find more information about working at NTNU and the application process here.

For a position as a PhD Candidate, the goal is a completed doctoral education up to an obtained doctoral degree. The Department of Biotechnology and Food Science is advertising two three-year PhD positions. The positions are funded by the Horizon Europe framework programme, and are specifically responsible for the project "Innovative Tools for Sustainable Exploration of Marine Microbiomes: Towards A Circular Blue Bioeconomy and Healthier Marine Environments (BlueTools)." The PhD candidates will join an interdisciplinary lab led by Rahmi Lale that uses microfluidics, single-cell arrays, artificial gene expression, and machine learning in the fields of biophysics, synthetic and computational biolog.

Required selection criteria

  • Hands-on wet-lab experience with DNA cloning, gene expression, and/or recombinant protein production;
  • Strong written and oral English skills;
  • You must have a professionally relevant background (MSc or equivalent) in applied microbiology, molecular bio(techno)logy, (bio)nanotechnology, bioengineering, or chemical biology;
  • Your education must correspond to a five-year Norwegian degree program, where 120 credits are obtained at master's level;
  • You must have a good academic background from previous studies, as well as an average grade from the master's degree programme, or equivalent education, of B or higher on the NTNU grading system. If you don't have letter grades from past studies, you must have a solid academic foundation. If you have a lower grade point average, you may be considered if you can demonstrate that you are especially qualified for a PhD education.

About the application

The application and supporting documentation to be used as the basis for the assessment must be in English. In the application letter, please specify which of the two PhD positions you are applying to, or both.

Publications and other scientific work must follow the application. Please note that your application will be considered based solely on information submitted by the application deadline. You must therefore ensure that your application clearly demonstrates how your skills and experience fulfil the criteria specified above.

The application must include:

  • Letter of application
  • CV and certificates
  • transcripts and diplomas for bachelor's and master's degrees. If you have not completed the master's degree, you must submit a confirmation that the master's thesis has been submitted
  • Name and contact information of two references

If all, or parts, of your education has been taken abroad, we also ask you to attach documentation of the scope and quality of your entire education, both bachelor's and master's education, in addition to other higher education. Description of the documentation required can be found here. If you already have a statement from NOKUT, please attach this as well.

Deadline 28th September 2022

Apply here


PhD Studentship: AI-based usage of retinal images with brain imaging

The GW4 BioMed2 MRC DTP operates across four research-intensive universities (Bath, Bristol, Cardiff and Exeter) providing students within our programme access to the combined research strengths, training expertise and resources of each institution. Many DTP projects are co-supervised across two or more of these universities, allowing students to join existing and emerging research partnerships.

The GW4 BioMed2 MRC DTP offers competitive, fully-funded studentships in one of our three research themes:

The studentship will be hosted in the University of Bristol, which is ranked 5th in the UK for research. The student will be supported by a comprehensive multi-disciplinary supervisory team who are embedded in a number of rich active research communities in the areas of genome bioinformatics, epidemiology, machine learning, AMR and public health in the Universities of Bristol (Prof Kristen Reyher, Prof Andrew Dowsey, Dr Sion Bayliss) and Bath (Dr Lauren Cowley).

Application deadline: 2nd November 2022

Additional guidance for students can be found here. Please contact  kristen.reyher@bristol.ac.uk or s.bayliss@bristol.ac.uk for more information.


Posted on September 09, 2022

PhD candidate in chronic kidney disease (medical image data analysis)

We are looking for a PhD candidate for our collaborative project on chronic kidney disease. The tasks will involve devising computational methods for automating nephropathology procedures using deep learning as well as quantification of information in images of kidney structures imaged with super-resolution microscopy in 3D. We are strongly interested in development of self-supervised learning methods for this project. Our collaboration partners include medical as well as microscopy experts located in Cologne, Freiburg, and Stockholm. We offer work in a stimulating, interdisciplinary environment in the heart of cosmopolitan, historical city.

We invite applicants to join our international and interdisciplinary scientific team in the heart of cosmopolitan, lively, historical city.

Requirements:

  • degree in computer science, physics, bioinformatics, or a related field,
  • good knowledge of programming (python),
  • experience with computation on cluster architectures,
  • experience with machine learning is preferred,
  • great communication skills, capacity of working in a team and in an interdisciplinary environment.

Responsibilities:

  • development of computational methods and processing pipelines dedicated to the project,
  • implementation of computational pipelines including existing machine learning methods,
  • communication with medical and experimental collaboration partners.

We offer:

  • opportunity to apply and develop cutting-edge machine learning and computational technologies to resolve timely medical and scientific problems,
  • lively, collaborative, and international multi-disciplinary working environment where colloquial and working language is English,
  • development and networking through participation in workshop and conferences both ML and biomedical

Please email your application including CV, cover letter, and contact to 2 references.

Apply here


12 Doctoral Researcher Positions in Antimicrobial Biomaterials

Friedrich Schiller University is a traditional university with a strong research profile rooted in the heart of Germany. As a university covering all disciplines, it offers a wide range of subjects. Its research is focused on the areas Light—Life—Liberty. It is closely networked with non-research institutions, research companies and renowned cultural institutions. With around 18,000 students and more than 8,600 employees, the university plays a key role in shaping Jena’s character as a cosmopolitan and future-oriented city.

The new DFG Research Training Group (RTG) 2723 Materials‐Microbes‐Microenvironments (M‐M‐M): Antimicrobial biomaterials with tailored structures and properties, at Friedrich Schiller University Jena, Germany, combines expertise in materials, life, medical, optical and computational sciences to develop ground-braking and highly innovative antimicrobial biomaterials for the prevention of biomaterial-associated infections (BAI).

The research groups of the RTG M-M-M invite applications for: 12 Doctoral Researcher (DR) Positions (m/f/d) to conduct research and training in the Development of novel antimicrobial materials and the biological/medical compatibility and reactions commencing on 1. February 2023 (fixed date). The positions are for 4 years. Six of the positions (materials science) are full time (100%), six of the positions (life sciences) are part time (65%). Each doctoral researcher will work in one of the following interdisciplinary tandem projects (materials science & life sciences):

• Project A: Switchable antimicrobial materials (Prof. Dr. K. D. Jandt (FSU) & Prof. Dr. B. Löffler (UKJ))

• Project B: Antimicrobial and bioactive nanoparticle functionalized protein coatings (Prof. Dr. K. D. Jandt (FSU) & Prof. Dr. B. Wildemann (UKJ))

• Project C: Antimicrobial bioactive glass for treatment of traumatic or pathological bone defects (Prof. Dr. D. Brauer (FSU) & Prof. Dr. G. Matziolis (UKJ))

• Project D: Graphene based antimicrobial biomaterials (Prof. Dr. A. Turchanin (FSU) & PD Dr. L. Tuchscherr (UKJ))

• Project E: Microbiological testing of materials (Prof. Dr. M. Pletz (UKJ) & Prof. Dr. C. Eggeling (FSU))

• Project F: Digitized antimicrobial biomaterials semantic knowledge base (Prof. Dr. M. Sierka (FSU) & Prof. Dr. T. Figge (FSU/HKI))

Your profile

• An outstanding master’s degree (MSc) in materials science or physics or chemistry or chemical science or materials engineering or closely related (for materials science DRs), or microbiology or cell biology, molecular biology, biochemistry, biotechnologies, medicine, computer science, bioinformatics or closely related (for life science DRs). Candidates in the final stages of obtaining their degree are also eligible to apply

• Desired methodological skills materials science (one or more): materials design and synthesis, materials characterization and testing, PVD, microscopy methods, handling of proteins and nanomaterials, organic and inorganic materials preparation, computational materials science, data base experience, materials engineering skills

Please submit your application via the JSMC Online Application Portal, under the vacancy ID 275/2022 by 10. October 2022:

Apply here


Posted on September 08, 2022

PhD Positions in Biosciences/ Microbiome

We are looking for one or two PhD students to join the lab in Fall 2023. We are seeking creative, collaborative, and innovative scholars from diverse backgrounds who are broadly interested in using synthetic microbial communities to identify how microbiomes assemble and function. We use fermented food microbiomes as our primary experimental systems, but we are happy to work with a range of microbial systems, from planarian worms to plant leaves.

We have many ongoing projects that could serve as the starting point for a dissertation (please see here for more info). Students can also create brand new projects for their PhD research. In helping students find a research project, our main goal is to make sure the student is developing a project that they are passionate about and aligns with their long-term career goals. Projects can focus on basic microbiology (e.g. mechanisms of microbial interactions, how microbes evolve in multi-species communities, linking microbial traits with microbiome assembly) or applied microbiology (e.g. how to predictably manipulate microbiomes to accomplish a goal, linking microbiome diversity with fermented food quality/safety).

Our group also loves using fermented foods to teach the public about microbes, and we encourage those interested in microbial outreach and education to consider our group. Examples include our outreach website MicrobialFoods.org and various public events detailed in our Open Lab page.

If you are interested in joining our lab as a graduate student, please consider the following:

  • Learn more about the graduate program in the Department of Biology.
  • Application deadlines and information about Tufts graduate programs can be found here.
  • Interested candidates should email Ben (benjamin.wolfe@tufts.edu) with a description of their research goals and a copy of their CV before applying to the program.

Apply here


PhD Studentship: BioSynth Trust: Developing understanding and confidence in flow cytometry

Flow Cytometry (FC) is a common biometrology tool for measuring the identity of cell populations. FC has three components that determine the metrological quality of the final answer – upstream preparation of cell samples, the FC instrument itself, and subsequent data processing. FC output data analysis is typically completed in two common manners – operator manual gating (still regarded as the “gold standard” for FC analysis), and, automated software gating solutions.

The aim of this new project is to develop enhanced confidence factors in synthetic cell cluster datasets, extending their performance capabilities and applicability. This project will be in collaboration with UK National External Quality Assessment Service for Leucocyte Immunophenotyping (UK NEQAS-LI) - part of the Sheffield Teaching Hospitals NHS Foundation Trust, providing live cell and database benchmarking resource.

ENTRY REQUIREMENTS

Entry requirements for United Kingdom Applicants should have or are expected to achieve a first or upper second class undergraduate degree in a bioscience, bioinformatics, computer science or engineering discipline. A postgraduate master’s degree and/or equivalent industry experience would be beneficial. A dynamic personality with excellent communication and teamwork skills is desirable. A background in one of the key areas may strengthen your application: flow cytometry, mass cytometry, bioinformatics, cell culture techniques, computational techniques, software and programming.

English language requirements: Applicants must meet the minimum English language requirements.

HOW TO APPLY

All applications should be made online.  Under programme name select 'Mechanical and Manufacturing Engineering'. Please quote reference: P2SAM22-19.

Application deadline 23 September 2022


Posted on September 06, 2022

International PhD Scholar Initiative

Our International PhD Scholar Initiative enables outstanding international students to join our Medical Biology PhD Program.

The International PhD Scholar Initiative (IPSI) recruits candidates who completed their latest degree outside of Australia to come to WEHI to undertake their PhD research. IPSI selects students on the basis of their academic record, relevant experience, research motivation, referees' reports and a video conference interview.

The next application round is now open, and will close on Friday 11 November 2022.

WEHI offers a number of dedicated scholarships to support International PhD Scholars. Our International PhD Scholarships provide a living allowance equivalent to the current Melbourne Research Scholarship rate. In addition, all international PhD students receive WEHI’s $2000 per annum scholarship top-up plus a relocation allowance (once-off lump sum of $3000), health insurance coverage and a university tuition fee offset.  International students who are in the final year of their current degree (expected to complete their current degree in mid-2023) are eligible to apply for this round of the International PhD Scholar Initiative.

Eligibility

To be eligible for the International PhD Scholar Initiative applicants must meet the following academic requirements:

  • Have a four-year undergraduate degree (with a substantial research component) or masters degree at an international university; or
  • be in the final academic year of their current degree due to complete in first semester of 2023.

This initiative is for applicants who will be enrolled as an international student in Australia.

  • Australian citizens, Australian permanent residents and New Zealand citizens qualify as domestic students with University of Melbourne and are not eligible to apply for the International PhD Scholar Initiative.
  • If your last degree of study was at an Australian university, you are also not eligible for the International PhD Scholar Initiative. These international students should please see the scholarships options available.

How to apply 

Applications for the 2022 International PhD Scholar Initiative are now open and will close on Friday 11 November 2022.  Apply here

PhD scholarship in Immunoinformatics and Machine Learning

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.

The Immunoinformatics and Machine Learning group at the section for Bioinformatics (DTU Health Tech) is looking for a highly talented and motivated student to pursue a PhD. If you want to develop state-of-the-art machine-learning algorithms in immunoinformatics, understand how the immune system discriminate among self and foreign proteins, and work on an international environment, this is the right place for you!

The immune system normally develops an immune response against foreign proteins. However, the recognition of what is self or foreign can go wrong developing autoimmune diseases. The cause of what makes this disruption of the tolerance is not yet known. The proposed project wants to learn which patterns autoimmune antigens drive this disruption by the use and development of tailored machine learning algorithms, protein features and immune predictors to move forward the field.

The perfect candidate will be a highly skilled MSc on Bioinformatics or Systems Biology with a strong background on machine learning algorithms and statistical analysis that is able to work independently and conduct a research project as a member of a team. In addition, an immunology, biology and/or chemistry is expected. Experience developing tools for immune prediction and good programming skills is required. Proven experience on projects using Deep-Learning, protein structure and statistics is a plus.

We provide an international, innovative and interdisciplinary work environment, with access to state-of-the-art computing servers as well as many other infrastructures within the university. We expect the ideal candidate to enjoy working in a team as teaching and supervision of BSc and MSc student projects will be expected. 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.

Further information
Further information may be obtained from Assistant Professor Carolina Barra, carolet@dtu.dk.

Application procedure
Your complete online application must be submitted no later than 19 September 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

Apply here


Posted on September 05, 2022

PhD student in Bioinformatics

The candidate will develop computational tools and analyze genomics, proteomics, and transcriptomics data. You will join an interdisciplinary team of life scientists and bioinformaticians who use the latest proteomic approaches and equipment to better understand plant biology.

Your qualifications: - A master degree in computational biology, bioinformatics, systems biology, computer science, or biology

  • Good knowledge of bioinformatics and biology
  • Familiarity with OMICS data analysis
  • Familiarity with machine learning and statistics
  • Strong programming skills (python, R)
  • Comfortable with the Linux/Unix environment, databases (MySQL)

Our offer: Salary is in accordance with the German public service salary scale: TVL E13 66% for 48 months. The position is available from October 1st, 2022.

Your application: Please send your CV and supporting documentation as one PDF file by e-mail to Prof. Dmitrij Frishman (d.frishman@wzw.tum.de).

When you apply for a position with the Technical University of Munich (TUM), you are submitting personal information. With regard to personal information, please take note of the Datenschutzhinweise gemäß Art. 13 Datenschutz-Grundverordnung (DSGVO) zur Erhebung und Verarbeitung von personenbezogenen Daten im Rahmen Ihrer Bewerbung. (data protection information on collecting and processing personal data contained in your application in accordance with Art. 13 of the General Data Protection Regulation (GDPR)). By submitting your application, you confirm that you have acknowledged the above data protection information of TUM.

As part of your application, you provide personal data to the Technical University of Munich (TUM). Please view our privacy policy on collecting and processing personal data in the course of the application process pursuant to Art. 13 of the General Data Protection Regulation of the European Union (GDPR) at https://portal.mytum.de/kompass/datenschutz/Bewerbung/. By submitting your application you confirm to have read and understood the data protection information provided by TUM. Severely disabled persons are given preference in the case of essentially equal suitability and qualifications.

Apply here


PhD research fellowship in mathematical pharmacology

The Graduate Research Training Program PharMetrX: Pharmacometrics & Computational Disease Modelling is an interdisciplinary PhD program bridging pharmacy and mathematics. It aims at understanding the drug-patient-disease interaction by analysing data of drug concentration, effect & disease profiles of pre-/clinical trials and of therapeutic care by developing and using mathematical & statistical models.

PharMetrX is a joint program of Freie Universität Berlin and the Universität Potsdam, supported by a consortium of global, research-driven pharmaceutical companies.We are currently inviting applications to start the PharMetrX Research+ Program or the PharMetrX Training+ Program.

The PharMetrX Research+ Program (Research & Training & Network) comprises an excellent research environment in the vibrant Berlin/Potsdam area, fascinating and innovative research projects in a highly relevant field, truly transdisciplinary supervision, an individual mentorship from one of the industry partners, a specifically tailored training program of compact modules, a network of peers and a highly competitive 3.5 years fellowship.

The PharMetrX Training+ Program (Training & Network) offers a specifically tailored training program of compact modules that convey the foundations in pharmacokinetics & pharmacodynamics, systems biology, statistics etc. as well as a network of peers. It is open for PhD students who have already started their PhD in the field of pharmacometrics or will do so soon.

Apply here


Posted on September 02, 2022

PhD Student Machine-learning-driven Digital Twin of Virus Infected Cell Dynamics

Through cutting-edge research in the fields of ENERGY, HEALTH and MATTER, Helmholtz-Zentrum Dresden-Rossendorf (HZDR) solves some of the pressing societal and industrial challenges of our time. Join our 1.400 employees from more than 50 nations at one of our six research sites and help us moving research to the next level!

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

CASUS invites applications as PhD Student (f/m/d) Machine-learning-driven Digital Twin of Virus Infected Cell Dynamics.

The position will be available from 1 October 2022. The employment contract is limited to three years.

The Scope of Your Job:

The global SARS-CoV2 Pandemic has demonstrated the urgency to develop new tools for our arsenal against pathogens. If YOU are passionate about designing the next generation of mathematical models and machine learning algorithms in virology – we are looking for YOUR talent!

Viruses require host cells to procreate and spread their progeny. For this, they enter cells, replicate and egress in a stepwise process occurring through interactions between molecules of the host cell and the pathogen molecules. These are known as host-pathogen interactions, they include various host mechanisms exploitations by the pathogen. Synchronized with virus entry, uncoating, and replication through a virus genetic program, virus induce dramatic changes of cell morphology.

Your tasks:

  • Engage with our international collaborators (Dresden, London, Zurich, Taipei etc.) to understand existing approaches and datasets
  • Develop novel mathematical models and data-efficient algorithms for continuum modelling of host-pathogen interactions
  • Design novel physics-informed deep learning architectures suitable for time-lapse microscopy data
  • Publish high-impact peer-reviewed research

Your profile:

  • Master’s degree in Computer Science, Data Science, Machine Learning, or Physics, Bioinformatics, Computational Biology, or relevant discipline
  • A solid background in Physics, Mathematics, Software Engineering, Machine Learning, or in a related subject
  • Excellent programming skills in languages such as Matlab and Python
  • Familiarity with modern deep learning frameworks like Numpy, Tensorflow 2.x.x, PyTorch
  • Previous experience or interest in Matlab to Python codebase conversion, Computer Vision, Deep Learning and Slurm cluster environments is a plus
  • Strong motivation to work in a collaborative environment
  • Excellent communication skills in English in a professional context (presentation of research results at scientific meetings, colloquial discussions, writing of manuscripts)

Deadline: 27 October 2022

Apply here


PhD position- Phage-host interaction / Microbiology

As a leading research institution for microbial biotechnology the Institute of Bio- and Geosciences - Biotechnology (IBG-1) at the Forschungszentrum Jülich focuses on molecular and applied microbiology. Current projects of the group of Prof. Dr. Julia Frunzke (Head of Bacterial Networks and Interactions) focus on the regulatory interaction of (pro-)phages and their host and on novel anti-viral defense mechanisms. The fundamental understanding of phage-host interaction bears a high potential for applications in medicine, agriculture and biotechnology. The employment of doctoral researchers at Jülich is governed by a doctoral contract, which usually has a term of three years.

Your Job:

  • Your PhD project will focus on novel antiviral (antiphage) strategies of bacteria. In particular, you will study the role of secondary metabolites and their mode of action in the defense against viruses infecting actinobacteria (Streptomyces).
  • You will benefit from annual SPP meetings, workshops and trainings organized at the Forschungszentrum and within the frame of the priority program.
  • Your methodological focus will be on genetic engineering, next-generation sequencing (NGS, RNA-seq and ChIP-seq), LC-MS/MS, and single-cell analysis (microscopy and flow cytometry).

Your Profile:

  • MSc degree in Biology, Biochemistry, Biotechnology, or similar disciplines
  • Experience in and enthusiasm for Microbiology, Molecular Biology and Virology/Phage Biology
  • Fluent command of written and spoken English
  • High degree of independence and commitment
  • Reliable and conscientious style of working and excellent ability to cooperate and work in a team

We look forward to receiving your application by 30.9.2022

Apply here


Posted on September 01, 2022

PhD students in Bioinformatics

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

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

Protein structure is essential for understanding their function as well as for developing drugs targeting proteins. Recently, a deep learning method that can predict the structure of most proteins was made freely available, and a database with predicted structure was released. However, proteins do not act alone - they act together with other proteins. Therefore, the next major challenge is to use these types of methods for predicting protein-protein interactions. Initial studies from us have shown that it is possible to predict accurate structures of a large part of dimeric proteins using either a modified version of AlphaFold2 or AlphaFold-multimer.

The Elofsson group is located at the Science for Life Laboratory. Elofsson has worked on protein structure predictions for more than two decades. He has worked on various techniques, both using machine learning and other computational techniques. His most important contributions for this work are the methods he has developed to identify the quality of protein models, Pcons and various versions of ProQ. The group consists currently of five PhD students and one senior researcher.

Qualification requirements:

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

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

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

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

Closing date: 21/09/2022

Apply here


PhD in Biophysics

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society.

Proteins are the workhorses in all living cells and, as such, form the basis of all living systems. In order to fully understand biological processes, it is critical to be able to identify and quantify the proteins in cells at any given time in the cell cycle. This can be done by sequencing since each protein has a unique amino acid sequence. However, practical realization of protein sequencing remains an enormous challenge. Small sample size, in which the numbers of specific proteins can differ by orders of magnitude, and the necessity to distinguish 20 different amino acids are only a few of the obstacles currently limiting our ability to sequence proteins.

We are looking for a highly motivated student with significant physics or engineering research experience to develop a novel sequencing technique that probes the protein profile using aptamers with sub-nanometre resolution. This high-resolution method, combined with nanotechnology, will be used for analysing proteoforms, particularly, splicing isoforms and post-translational modifications. We will be able to sequence single proteins and their proteoforms and therefore create the opportunity for single-cell proteomics and screening for on-site medical diagnostics. It will lead to a revolution in biophysics, biotechnology, and healthcare.

Requirements:

The candidate should have an MSc degree in the field of physics or engineering. An application from a candidate who is experienced in biochemistry will be favorably treated, but this is not a requirement. Doing a PhD at TU Delft requires English proficiency at a certain level to ensure that the candidate is able to communicate and interact well, participate in English-taught Doctoral Education courses, and write scientific articles and a final thesis.

Additional information For information about this vacancy, you can contact Chirlmin Joo (group leader) via bionanoscience.delft@gmail.com.

Please apply before 15 September 2022 via the application button, Apply here


Posted on August 31, 2022

PhD student in Pharmacokinetic-Pharmacodynamic modelling

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 Pharmacy at Uppsala University has an interdisciplinary environment at the center of the pharmaceutical arena. With frontline research, first-rate education and extensive collaborations we constitute an important driving force in the development of our academic field. In this inspiring environment our rich diversity of research groups, several of international prominence, develop and conduct work of great scientific importance. Among our core competences are computational modelling and simulations, PKPD, in vitro ADME models, advanced in vivo methods, as well as patient and societal aspects, from optimizing the use of drugs in individuals to societal pharmaceutical policies.

Duties:

A doctoral position focusing on the characterization of pharmacokinetic and pharmacodynamic relationships for antibiotic therapy is available within the research area of ​​pharmacokinetics-pharmacodynamics, focusing on antibiotics, at the Department of Pharmacy.

Requirements:

The applicant should have an MSc degree in a relevant area, such as pharmaceutical sciences, medicine, engineering with minimum 240 credits or alternatively a Master in pharmaceutical modelling or in Drug development, including courses in pharmacokinetics, physiology, pharmacology, modelling and programming (e.g. in R).

For further information about the position, please contact: Professor Lena Friberg, lena.friberg@farmaci.uu.se.

Please submit your application by 12 September 2022, UFV-PA 2022/3084.

Apply here


PhD position in applied immunology

A PhD position is available in the laboratory of Professor Susan Treves at the Department of Biomedicine (DBM) in Basel, Switzerland. The successful candidate will investigate whether carriers of gain of function RYR1 mutations have a more efficient immune system, altered levels of circulating antibodies and cytokines at rest or after vaccination.

Selected publications from our laboratory relevant to this project:

(i) Ca2+ signaling through ryanodine receptor 1 enhances maturation and activation of human dendritic cells. Bracci et al. (2007) J. Cell Sci. 120:2232-2240.

(ii) Ryanodine receptor activation by Cav1.2 is involved in dendritic cell MHC class II surface expression. Vukcevic et al. (2008). J. Biol. Chem. 283:34913-34922.

(iii) Frequent calcium oscillations lead to NFAT activation in human immature dendritic cells. Vukcevic et al. (2010). J. Biol. Chem 285:16003-16011.

(iv) Gain of function of the immune system caused by a ryanodine receptor 1 mutation. Vukcevic et al. (2013). J. Cell Sci. 126:3485-3492.

(v) Functional characterization of endogenously expressed human RYR1 variants.Z orzato, et al. (2021). J. Vis. Exp. (172), e62196.

Your position

a) Manage and functionally characterize EBV-immortalized human B-lymphocyte cell lines from patients with RYR1 mutations and non-mutant family members.
b) Compare the functional effect of novel RYR1 mutations in muscle cells and EBVimmortalized human B-lymphocytes.
c) Profile sera from RYR1 mutation carriers and non-mutant family members for cytokine content at rest and after vaccination.
d) Assess the functional parameters of the innate and adaptive immune system of patients with RYR1 mutations compared to non-mutant family members.

Your profile

A strong experience in cell culture and imaging. The candidate should be well-organized, highly motivated and must be fluent in English.

Application / Contact

Please send your CV, a summary of your research experience and interests, techniques that you are competent in, and the contact details of two referees to Prof. Susan Treves: susan.treves@unibas.ch
Application deadline: applications will be reviewed as they arrive. For details visit here


Posted on August 30, 2022

PhD position in Biostatistics/ Demography

The Department of Medical Epidemiology and Biostatistics (MEB), Stockholm is among the largest departments of epidemiology in Europe with special focus on increasing our knowledge of the aetiology of different diseases. Our department consists of researchers, doctoral students, biostatisticians, data collectors and database administrators as well as administrative personnel, in total some 250 staff. The department is situated at campus Solna.

A doctoral student position is available within the biostatistics group at the Department of Medical Epidemiology and Biostatistics (MEB) at Karolinska Institutet (https://ki.se/meb), Stockholm. The biostatistics group at MEB, KI comprises 5 professors, 3 senior lecturers, 9 PhD-level statisticians, 4 masters-level statisticians, and 10 doctoral students. The group is involved in a wide variety of research projects, including population-based cohort and case-control studies, twin and family studies, survival analyses, predictive modeling, genetic epidemiology and bioinformatics.

The aims of this doctoral project are to (a) describe the variation of prostate-specific antigen (PSA) testing by small areas and socio-economic status and (b) investigate potential biases in using small area estimates of exposure for family-based studies. These analyses will use the large-scale Swedish health and population registers, including the Stockholm PSA and Biopsy Register and the Swedish Multi-generation Register.

Reference number: STÖD 2-3320/2022

Last application date 15.Sep.2022 11:59 PM CEST

Apply here


12 Doctoral Researcher Positions in antimicrobial biomaterials/ Biological sciences

The DFG Research Training Group (RTG) 2723 “Materials‐Microbes‐Microenvironments (M‐M‐M): Antimicrobial biomaterials with tailored structures and properties” at Friedrich Schiller University Jena and Jena University Hospital (UKJ), Germany, combines expertise in materials, life, optical and computational sciences to research and develop completely new antimicrobial biomaterials. Our core mission is to elucidate fundamental principles of the interactions of materials, microbes and bone cells. We aim to design and create novel antimicrobial biomaterials that reduce the number of biomaterials associated infections (BAI) by using physical materials properties. This will allow the development of novel antimicrobial biomaterials with tailored structures and properties.

How can novel antibiotic free antimicrobial biomaterials based on physical principles be designed? What is their working principle? Can materials be designed in a way that suppresses microbes and promote bone cells? Are the current biological test methods for antimicrobial biomaterials sufficient or do they require new materials new test methods? How can we use advanced microscopy methods to understand the material- microbe-cell interactions in depth? Can computational materials science and advanced image analysis help to develop these new materials?

Answering these questions requires that we come together as a scientific community to which we contribute
expertise as well as a curiosity about unfamiliar subjects.
We expect:
• An outstanding MSc. in natural sciences (material sciences, physics, chemisty, materials engineering, microbiology, cell biology, molecular biology, biochemistry or closely related fields). Candidates in the final stages of obtaining their degree are eligible to apply
• Desirable methodological skills: materials creation and synthesis, materials characterization and testing, PVD, microscopy methods, handling of proteins and nanomaterials, organic and inorganic materials preparation, computational materials science, data base experience, materials engineering skills (materials science) or basic training in microbiology and bacterial culture; experience in cell culture and infection experiments; basic knowledge in molecular biology, FACS-analysis, advanced automated image data analysis, programming skills (life sciences)
• Highly motivated individuals with an interest in joining one of the interdisciplinary research areas of the RTG
• The abililty to work creatively and independently towards developing your own research project
• A collaborative personality with enthusiasm for actively participating in the dynamic RTG community
• Excellent English communication skills, both written and spoken
We offer:
• Research in a clinically highly relevant topic
• A highly communicative atmosphere within a scientific network providing top-level research facilities
• An international competitive interdisciplinary training program in materials science and life science
• A competitive theoretical and hands on training in antimicrobial biomaterials
• A comprehensive mentoring program and soft skill courses for early career researchers
• Jena – City of Science: a young and lively town with a vibrant local cultural agenda

Applications are exclusively accepted via the JSMC Online Application Portal:  Please familiarize yourself with the currently available projects (https://www.jsmc-phd.de/vacant- positions.html) and the application process as described in the Online Application Portal. Selected applicants will be invited to a recruitment meeting taking place in Jena on 1. December 2022. Awarding decisions will be announced shortly thereafter, and candidates are expected to be available to start their projects on 1. February 2023.

Application deadline: 10. October 2022


Posted on August 29, 2022

PhD Position: Combining Machine Learning and Symbolic Reasoning for Drug Safety

Are you an excellent Artificial Intelligence researcher with a Msc diploma in AI or Computer Science, do you want to work on combining machine learning and symbolic reasoning techniques for the benefit of patients? Then please apply at Vrije Universiteit Amsterdam (VU)

We seek an excellent and motivated PhD candidate in a multidisciplinary project using techniques from Artificial Intelligence to improve medication safety in patients with chronic kidney diseases. The LEAPfROG project (“Leveraging real-world data to optimize pharmacotherapy outcomes in multimorbid patients by using machine learning and knowledge representation methods”) develops methods, tools and algorithms to:

1) create high quality real-world data from electronic health records of patients;

2) create computer-interpretable medical domain knowledge;

3) combining learning from real-world patient data and reasoning with medical domain knowledge sources (included topics: prediction models, causal inference, explainability, interpretability), and lastly

4) create a prototype for a clinical decision support system for physicians, pharmacists and patients in which the developed methods, tools and algorithms are integrated to support decisions making at-the-bedside.

Your duties

  • conduct research and publish results at conferences and in academic journals, leading to a PhD thesis
  • collaborate within the team at the VU, the wider LeapFrog project team and with experts in the field
  • contribute to teaching, by supervising MSc and BSc thesis projects and some teaching assistant tasks

Requirements

  • Msc degree in Artificial Intelligence or Computer Science and an interest in the medical domain.
  • Good knowledge in either symbolic AI techniques (e.g data modelling, semantic technologies) Machine Learning is required. Knowledge of both is a plus.
  • Good communication and presentation skills in English are required. Due to the use of medical data, language skills in Dutch is a plus.
  • The ability to work in a multidisciplinary team.

Application Are you interested in this position? Please apply via the application button and upload your curriculum vitae and cover letter until 01/09/2022.

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

Name: Prof. Anette ten Teije or Prof. Frank van Harmelen
E-mail: annette.ten.teije@vu.nl or frank.van.harmelen@vu.nl

Apply here


PhD position in computational genetics and machine learning

Aarhus University’s ambition is to be an attractive and inspiring workplace for all and to foster a culture in which each individual has opportunities to thrive, achieve and develop. We view equality and diversity as assets, and we welcome all applicants.

Applicants are invited for a PhD fellowship/scholarship at Graduate School of Technical Sciences, Aarhus University, Denmark, within the Quantitative Genetics and Genomics programme. The position is available from 2 January 2023 or later.

Title:
Re-advertisement: PhD position in computational genetics and machine learning: analysis of multi-omics biological data in novel populations of Brachypodium

Research area and project description:
We are looking for a talented and creative PhD student to contribute to the SIEVE project (“Selection of mutations by in silico and experimental variant effects: a new strategy to improve fitness in cool-season grasses”). The SIEVE project is supported by an Emerging Investigator grant by the Novo Nordisk Foundation, which funds groundbreaking research with promising applications in data science and the green transition in Europe.

The PhD student will be involved in an innovative research project in computational genetics and machine learning applied to a model species (Brachypodium). She/he will evaluate the impact of mutations by analyzing multi-omics data in mutant populations: (i) whole-genome sequencing; (ii) RNA expression; (iii) metabolomics; and (iv) physiological measurements. These analyses will benefit from expertise in machine learning (applied statistics, deep learning, network analysis) and computational genetics (quantitative genetics, evolutionary genomics, bioinformatics).

Qualifications and specific competences:
Candidates must hold (or be expected to hold) a Master’s degree in a field related to computational genetics (e.g., quantitative genetics, evolutionary genomics, bioinformatics) or machine learning (e.g., applied statistics, deep learning, network analysis).

The ideal candidate will also demonstrate some knowledge of scripting/programming languages (e.g., in R, Python, Java or Shell), previous research experience in relevant fields, and good communication skills in English.

How to apply:
Please follow this link to submit your application. Application deadline is 30 September 23:59 CEST. Preferred starting date is 2 January 2023.

For information about application requirements and mandatory attachments, please see visit here


Posted on August 26, 2022

PhD position in Computational Structural Biology of Antibiotic Mechanisms

Utrecht University is a friendly and ambitious university at the heart of an ancient city. We love to welcome new scientists to our city – a thriving cultural hub that is consistently rated as one of the world’s happiest cities. We are renowned for our innovative interdisciplinary research and our emphasis on inspirational research and excellent education.

Many antibiotics, including clinical used ones, kill bacteria by destroying their cell membranes (e.g., see our recent work Shukla et al., Nature 2022 . These mechanisms are complex, often require the formation of large supramolecular structures, and are heavily modulated by the complex composition of the cell membrane.

You as PhD candidate will work in a multidisciplinary team that uses a variety of biochemical, structural biology (solid-state NMR, microscopy) and computational tools to study membrane-active antibiotics.

During this PhD you will be focusing on 2 research topics. Firstly, you will focus on simulating complex ‘cell’ membranes & integrate this with our experimental data to rationalize the mode of action of antibiotics (‘computational microscopy’). Secondly, you will focus on structure determination by using experimental data to calculate drug-target structures in membranes. Projects are embedded with academic & industrial collaborators that strive to bring new antibiotics to the clinics.

Profile

We are looking for a recently graduated or soon to graduate Master's student who is excited and motivated to join us as PhD candidate. You find yourself in the following qualifications: motivated, focused, social and a team player. You will bring the following:

  • a Master’s degree in Life Sciences or a related field;
  • proficiency in writing and speaking English;
  • willingness to work on multiple projects.

Deadline: 20 september 2022.

Apply here


PhD-position in Cancer Biology

At the Faculty of Medicine, Department of Biomedicine in Professor Martha Chekenya Enger´s research group, a PhD-position (100 %) is available for a period of four (4) years. 25 % of the PhD student´s time will be dedicated to obligatory duties such as teaching assistance, exam work or supervision, depending on the demands at the department.

The position is part of the “Developing novel small molecule inhibitors of Chondroitin sulfate proteoglycan 4 (CSPG4) function: approaching new therapy for glioblastoma” project, funded by the University of Bergen.

Glioblastoma is the most malignant primary brain cancer, where no effective treatments are currently available. The focus of the project is to develop novel small molecules that inhibit the function of Chondroitin sulfate proteoglycan 4 (CSPG4), an important biomarker for aggressive disease course in brain cancer patients. Preliminary finding from RNAseq CSPG4 mutant cells revealed distinct gene profiles.

The project will validate this aberrant signalling cascade using high dimensional cytometry (CYTOF/Hyperion analysis). Integrative structure-based drug discovery and computational approaches will be used to identify drug candidates with similar effect of the CSPG4 mutations. As a foundation for drug discovery, the structure of CSPG4 will be determined and small molecule ligands will be designed. The hits will be validated as future drug candidates to target glioblastoma cells using diverse molecular and cell biology techniques in vitro and in vivo.

Qualifications and personal qualities:

  • The applicant must hold a master`s degree or equivalent in the field of biochemistry, structural biology, or molecular biology
  • Applicants must demonstrate theoretical knowledge and competence in biochemistry, and molecular biology methods
  • Documented experience in high dimensional flow cytometry (CyTOF/Hyperion) will be strongly merited
  • The successful candidate must have experience in related molecular and cellular biology techniques (molecular cloning, recombinant protein expression, purification, characterisation). Experience with structure analysis (x-ray crystallography/Cryo-EM) and structure-based drug design is an advantage
  • Documented experience from relevant research projects using various growth and reporter assays, flow cytometry, immunofluorescence, CRISPR, cell culture generation of stable cell lines and single clone derivation using mammalian tumour cells is a plus

For further information about the position, please contact Professor Martha Chekenya Enger, e-mail: martha.enger@uib.no

Deadline: 14th September 2022

Apply here


PhD  in Life science (Plant Defence Plasticity to Insect Attack)

Wageningen University & Research :The mission of Wageningen University and Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment.

As PhD student you will unravel how plant species in the family Brassicaceae differ in their defence strategies to deal with attack by multiple insect species. Plants respond to insect attack by mobilizing defences that specifically target the current attacker. How this response limits or provides opportunities to deal with future attack and how plants account for future risks will be the focus of your research.

In controlled greenhouse studies you will challenge plants with various patterns of herbivore attack to identify how plant responses to current attack are influenced by previous attack. You will directly collaborate with other PhDs and post-docs. The team links plant physiological adaptations to attack by multiple herbivores in a plant phylogenetic context (your work) to plant growth-defence strategies and patterns of plant-insect interactions in the field.

We ask

  • A successfully completed MSc degree in life sciences, plant sciences or biology.
  • You are an enthusiastic and team-oriented plant physiologist or molecular ecologist.
  • You enjoy puzzling on experimental designs to find a feasible solution to test challenging hypotheses on how plants deal with attack by multiple herbivores.
  • In collaboration with other young scientists, you are reliable, communicative, and supportive.
  • Your knowledge and experience has a strong basis in plant physiological responses to stress, and you enjoy to combine molecular and physiological profiling of plant responses to insect attack with measurements on plant and insect performance.
  • Hands on experience in basic molecular techniques such as sample preparation and qPCR is expected.
  • Affinity with bioinformatics in RNA-seq transcriptome analysis is considered a pre.

For more information about this position, please contact Dr. Erik H. Poelman, erik.poelman@wur.nl
For more information about the procedure, please contact vacaturemeldingen.psg@wur.nl

This vacancy will be listed up to and including 18th September 2022.

Apply here


Posted on August 25, 2022

PhD scholarship in molecular biology

Senior researcher Carsten Jers advertises a PhD position in the Bacterial Signal Transduction group at the DTU Biosustain. The research group, headed by Professor Ivan Mijakovic, consists of a multidisciplinary team of researchers working on a broad range of topics incl. bacterial post-translational modifications, development of cell factories and nanotechnology.

This PhD position will provide a great opportunity to conduct research in metabolic engineering in collaboration with other researchers in our group and an international partner with the opportunity for international research stays and visits.

Responsibilities and qualifications

The PhD student will work on the development of an enzymatic bioconversion process. This will initially entail the design and construction of Bacillus subtilis strains that display a particular enzyme on the surface. These strains will subsequently be evaluated to establish whether the enzyme is displayed in an active form using various analytical methodologies (e.g. mass spectrometry and HPLC). The candidate will conduct the experimental work.

Thus, we are looking for a researcher with the following competences:

  • A Master’s degree in biotechnology, molecular biology (or related).
  • Hands-on experience with bacterial cell culturing and molecular biology assays (vector and strain construction).
  • Fluency in spoken and written English

Practical or theoretical experience with metabolic engineering is desired. Hands-on experience with B. subtilis would be a plus but is not required.

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.

Your complete online application must be submitted no later than 5 October 2022 (Danish time).

Further information
Further information may be obtained from Carsten Jers (cjer@biosustain.dtu.dk). Apply here


PhD position in molecular biology and functional genomics of erythropoiesis

IGMM (Institute of Molecular Genetics of Montpellier) is a multidisciplinary research institute at the forefront of several research fields including genomics, cancer biology, hematopoiesis, and virology. It gathers 200 people working in 18 research groups, combined with18 technological platforms. IGMM is an internationally recognized leading institute in basic science and works at the interface with several clinical centers.

Erythropoiesis is the major cellular output of the hematopoietic system. It is a complex and continuous differentiation process controlled by a vast array of transcription factors regulating chromatin structure and cellular functions. We recently identified novel erythroid regulators (transcription factors and chromatin regulators) and will undertake an in-depth analysis of their functions in the context of normal and pathological erythroid differentiation.

The project will combine state of the art genomic approaches, biochemical/proteomics analyses and cell biology studies to unravel the role and intracellular dynamics of these novel factors, with the long-term goal of identifying new leads for targeted control of erythropoiesis in clinical settings. This exciting and ambitious project will take place in Eric Soler's team (IGMM, Montpellier), and will be part of a collaboration with the labs of Naomi Taylor (IGMM) and Olivier Hermine (Necker hospital/IMAGINE, Paris).

The PhD candidate will work in Dr. Eric SOLER's team "Chromatin Dynamics in Hematopoiesis". The multidisciplinary work will be carried out in the frame of a collaboration between basic research and clinical laboratories.

Application Deadline : 09 September 2022

Reference : UMR5535-ERISOL-003
Workplace : MONTPELLIER

Apply here


Posted on August 24, 2022

PhD position in Computational Biology

The Kim lab in the Department of Computational Biology at Cornell Universityseeking new members at the graduate and undergraduate levels. Potential members of the lab are expected to have a strong background in quantitative sciences, and to be interested in research in biology and genetics that incorporates mathematical, statistical, and computational approaches. Please send all inquiries and applications to Jaehee Kim.

Graduate Students

  • Prospective graduate students can apply to the graduate program of the Department of Computational Biology at Cornell. For students specifically interested in the lab, please notify me in advance about your application.
  • For current graduate students at Cornell interested in the lab, please send me CV and a short description of research interest.

Undergraduate Students

Highly motivated undergraduate students with strong mathematical or computational backgrounds interested in the lab should email an inquiry to Jaehee with a transcript (unofficial is fine), CV, and a short description of research interest.


PhD Assistantship in Wildlife Genomics

I am looking to fill a fully funded PhD assistantship in the College of Forestry, Wildlife, and Environment at Auburn University, starting Fall/Spring of 2022/2023. Research in the lab is broadly focused on conservation and ecological genetics and typically relies on whole genome sequencing data and bioinformatic tools. Current research in the lab includes investigation of the genomic determinants of fitness, understanding the complexities of population recovery from recent crashes, and developing methods for efficiently tracking individual movement in large populations.

The applicant hired to fill this position will focus on the genomics of an emerging fungal pathogen of pine, a critical timber resource in the southeastern U.S. In particular, the student hired for this work will develop a project to understand the evolutionary history and origins of this pathogen in this new host species with an emphasis on understanding the phylogeography of this species across the southeastern U.S. landscape. Current plans involve collection of ~250 fungal samples from each of 5 southeastern U.S. states and generation of sequencing data using the MinION platform, but this could be expanded to suit student interests.

This project is part of a large, interdisciplinary and multi-institutional collaboration that includes graduate students, postdocs, and scientists from Auburn and the Forest Service. Because of this, the ability to communicate across disciplines is a critical skill needed to complete this project. Although familiarity with bioinformatics and molecular techniques is desirable for this position, previous experience in this area is not required.

Please do not self-select yourself out of applying as there are many ways to acquire skills that will set you up for a successful graduate experience. Diversity and inclusion are a high priority of this lab group; all interested applicants are encouraged to get in touch with me directly prior to applying to the graduate program. To do so, please send me an email (janna.willoughby@gmail.com) with your background and interests and a pdf of your CV. Applications will be evaluated on a rolling basis.

For more information visit here


Posted on August 23, 2022

PhD scholarship: In-silico simulation of upper extremity biomechanics

A PhD scholarship is available at Queensland University of Technology (QUT), Brisbane, Australia on understanding the biomechanics of the shoulder after joint replacement with a focus on better understanding causes of implant loosening and enabling quantitative selection of implant design and position using computational models.

The project is part of an Industrial Transformation Training Centre (ITTC) for Joint Biomechanics funded by the Australian Research Council and led by researchers at Queensland University of Technology. The ITTC is a collaboration between Queensland University of Technology, University of Queensland (UQ) and University of New South Wales (UNSW) and our researchers and students engage with industry partners in the medical device and technology sector.

Eligibility

  • meet QUT academic and English language entry requirements for the Doctor of Philosophy or Professional Doctorate
  • undergraduate degree in biomechanics, mechanical engineering, or related discipline
  • first-class honours (H1) or equivalent
  • both domestic and international applicants are welcome to apply.

Essential criteria:

  • an undergraduate degree with first or second class division 1 Honours in biomechanics, mechanical engineering biomedical engineering, or a related discipline
  • eligibility for admission to the PhD program at Queensland University of Technology
  • knowledge of 3D computational simulations of musculoskeletal tissues and analysis
  • excellent communication skills (written and verbal) in English, including meeting the QUT English language requirements (no exceptions can be made to the latter).
  • this project requires a background in biomechanics, mechanical engineering, biomedical engineering, or a related discipline. Experience in 3D computational modeling using FEA modeling approaches is highly desirable.

How to apply

Contact Associate Professor Saulo Martelli via email saulo.martelli@qut.edu.au for more details.

Send your application with your curriculum vitae to Associate Professor Martelli.

Applications will be accepted until 15th September 2022, but applications will be assessed starting 1 September 2022.

For details click here


PhD Position - Investigating Tumor Heterogeneity

The German Cancer Research Center is the largest biomedical research institution in Germany. With more than 3,000 employees, we operate an extensive scientific program in the field of cancer research. The Precision Sarcoma Research Group (Leader: Dr. Priya Chudasama) at the German Cancer Research Center offers a PhD position in an interdisciplinary and collaborative research project within the ‘Heterogeneity, Evolution, and Resistance in Oncogenic fusion gene-Expressing Sarcomas affecting Adolescents and Young Adults (HEROES-AYA)’ consortium, a multi-institutional effort funded by Federal Ministry of Education and Research (BMBF).

Job description: Sarcomas, or malignant tumors of soft tissue and bone (World Health Organization classification), are a heterogeneous group of more than 200 cancer subtypes that arise from primitive mesenchymal tissue, such as bone, cartilage, muscle, peripheral nerves, and fat. About one third of sarcomas are characterized by recurrent genetic changes known as oncogenic fusions created by structural rearrangements such as chromosomal translocations. This project focuses on functional characterization of intra-tumoral heterogeneity (ITH) - associated events, such as mutations, in fusion-driven sarcoma tumor samples that will be identified by integrative bulk, single-cell and spatial multi-omics approaches.

Requirements:

  • Master's degree in molecular biology, biochemistry, biotechnology or a related field
  • Profound knowledge of cancer biology and immuno-oncology
  • Proficiency in the programming languages Python and/or R
  • Track record of working with cancer genomics datasets, single-cell and spatial technologies will be considered a plus
  • Ability to work independently in a highly collaborative environment and with proactive work attitude and team spirit, ability to drive the projects by own initiative and creativity
  • Excellent writing and presentation skills in English, enthusiasm to communicate scientific findings in meetings and conferences

Application Deadline: 09.09.2022

Apply here


Posted on August 22, 2022

PhD positions in Genetics

The Laboratory of Genetics (University of Wisconsin – Madison) is the oldest and one of the finest centers of genetics in the nation. It is highly regarded for its research contributions in the areas of disease genetics, cell biology, neurogenetics, developmental genetics, gene expression, genomics, evolutionary and population genetics, and computational biology. The laboratory consists of two departments: Genetics, in the College of Agricultural and Life Sciences; and Medical Genetics, in the School of Medicine and Public Health. Although administratively distinct, these two departments function as one at both the faculty and student levels.

The strength of genetics research at Wisconsin derives in large part from the Laboratory of Genetics, but state-of-the-art genetics research is conducted in many campus departments and centers. Mentoring faculty of the genetics Ph.D. program includes over 80 mentors selected from 22 campus departments and schools based on the strength of their scholarly genetics research. A key feature of the mentors is that they conduct genetic research, using any number of tools, and can therefore provide students with a solid foundation of genetic knowledge and experiences. The genetics research pursued on campus provides an exceptional community.

Genetics Ph.D. students choose one of the mentoring faculty as the graduate thesis advisor and mentor. Genetics graduate students spend time during the first semester of graduate school rotating in the laboratories of three or four faculty mentors, selected by the student. Following rotations, a graduate thesis advisor is chosen by mutual consent of both student and mentor.

Graduate training in genetics emphasizes study and research leading to a Ph.D. degree in genetics. The goal of the genetics graduate training program is to train the next generation of professional geneticists. This includes selecting the most promising university graduates for admission to the program and training those students in the methods and logic of genetic analysis. Such analyses are increasingly important in contemporary biological and biomedical research.

The curriculum includes:

  1. coursework on the principles of genetics and on the methods of genetic and genomic analyses, and
  2. original research in a specialized area, which culminates in the writing and defense of a doctoral thesis.

The genetics graduate program is supported by the oldest and one of the largest NIH-funded genetics training grants in the country.

The application deadline is December 1.

For details visit here


Doctoral scholarship holder Lung cancer screening

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

To improve lesion detection, computer-aided detection (CAD) algorithms are increasingly being used. Existing CAD systems have a wide performance variability and the current development speed of computerized tools to support reading and classification of lung lesions is so fast that more research in this area is needed. Furthermore, data of the performance of these algorithms on CT-studies using new techniques in the field of dose-reduction (e.g. denoising algorithms, photon-counting CT) is lacking.

With this project, we want to address how computer algorithms for detecting and measuring of lung nodules are performing. The greatest challenge is to develop new test methods in a world with rapidly changing technology - including between others also artificial intelligence. We will mainly focus on the performance of CAD algorithms using low-dose chest CT protocols. The ultimate goal is to find vendor independent targets that ensure small lung nodules can be detected and adequately measured. We will work with anthropomorphic phantoms, mimicking the patient’s chest. In these phantoms, 3D printed simulated lung lesions can be inserted. What is the behavior of different available CAD algorithms? How do they react to radiation dose reduction and more noise in the images? In a next phase, a database consisting of clinical chest CT images will be established and used for further testing of existing CAD algorithms.

Position

  • You will work actively on the preparation and defence of a PhD thesis in the field of low dose chest CT. The research is situated within a multicenter project, in close collaboration with other PhD students from the department of medical physics at KU Leuven (Prof. dr. ir. Hilde Bosmans) and Ghent University (Prof. dr. ir. Klaus Bacher).
  • You will publish scientific articles related to the research project.

Profile

  • You hold a Master degree in biomedical sciences, biomedical engineering, biomedical physics, medicine, or related disciplines.
  • Your research qualities are in line with the faculty and university research policies.
  • You are a motivated person, willing to show commitment for a doctoral project, and to apply for an external fellowship (e.g., FWO strategic research fellowships 2023).
  • You are prepared for the interface between physics and medicine.
  • You can communicate fluently in English.
  • You act with attention to quality, integrity, creativity and cooperation.

Want to apply?

  • You can apply for this vacancy through the University of Antwerp’s online job application platform up to and including 25 September 2022 (by midnight Brussels time). Click on the 'Apply' button, complete the online application form and be sure to include the following attachments: a motivation letter, your academic CV.
  • The selection committee will review all of the applications as soon as possible after the application deadline. As soon as a decision has been made, we will inform you about the next steps in the selection procedure.
  • If you have any questions about the online application form, please check the frequently asked questions or send an email to jobs@uantwerpen.be. If you have any questions about the job itself, please contact Prof. ir. Caro Franck, tel. 03/821.36.13, caro.franck@uantwerpen.be.

PhD in Microbiology, Microscopy and Bioinformatics

Are you looking for a PhD position at the intersection between microbiology, fluorescence microscopy and bioinformatics? Do you enjoy developing new methods and performing microscopy, quantitative biology and modelling? The Tutucci group (A-Life & AIMMS, VU Amsterdam) in Amsterdam NL, is accepting applications for a 4 years fully-funded PhD position starting no later than February 1st 2023. Please apply at Vrije Universiteit Amsterdam (VU).

Candida albicans is an opportunistic fungal pathogen estimated to be present in 40-60% of healthy adults. However, in subjects with underlying disease, C. albicans increases its virulence, multiplies and causes deadly systemic infections. C. albicans virulence is linked to its ability to change morphology and to switch from a single cell yeast form to a filamentous pseudohyphal or hyphal form that can result in adhesive multicellular drug-resistant structures called biofilms.

The aim of this project is, therefore, to advance our understanding of C. albicans morphogenesis and biofilm development. Unlike previous studies, we use single cell technologies that allow us to characterize yeast, pseudohyphae and hyphae with high spatial and temporal resolution. To do so, we adapt the quantitative molecular imaging toolbox that we previously developed for the fungus S. cerevisiae and we develop single-cell approaches specific for C. albicans, to unravel the heterogeneity, organization and functioning of biofilms.

Your duties
  • you develop methods for multiplexed single molecule RNA FISH for C. albicans and study C. albicans differentiation
  • you develop fluorescence-based reporters to investigate cell signaling in single C. albicans cells
  • you develop imaging analysis and modelling approaches to study the spatial organization of gene expression in C. albicans yeast, pseudohyphae and hyphae
  • you communicate your research at local and international conferences
  • you are actively involved in both experimental and bioinformatic research
  • you publish your results in peer-reviewed journals and in a PhD dissertation

Requirements

  • you have a MSc or equivalent degree in Molecular biology, Biophysics, Bioinformatics, Systems Biology, Microbiology or a related field, with a strong interest in microscopy and data analysis
  • you have experience with imaging analysis and programming software such as Python/R studio/MATLAB
  • you have excellent communication skills in both written and spoken English

Are you interested in this position? Please apply via the application button and upload your curriculum vitae and cover letter until 31/08/2022.

Apply here


Posted on August 19, 2022

PhD candidate for the project “Targeting immunosenescence in atherosclerosis”

The Division of BioTherapeutics at the Leiden Academic Centre for Drug Research (LACDR) is looking for a: PhD candidate for the project “Targeting immunosenescence in atherosclerosis”.

Atherosclerotic cardiovascular disease is the leading cause of mortality and morbidity worldwide. An acute cardiovascular event, such as a myocardial infarction or stroke, is often triggered by rupture of an atherosclerotic lesion at advanced age. As we age, our immune system undergoes a gradual functional decline, also called immunosenescence, strongly affecting our adaptive immunity. Both T- and B cells are crucially involved in the pathophysiology of atherosclerosis, but it is unknown how immunosenescence affects their contribution to disease progression.

The PhD student will join our enthusiastic team studying the different immune aspects of atherosclerotic lesion development to discover new therapeutic targets and strategies for the treatment of atherosclerosis.

Key responsibilities      
The aim of your PhD project is to provide fundamental knowledge regarding the contribution of aged adaptive immunity to cardiovascular disease. You will search for new targets to dampen pro-atherogenic T- and B cell immunity to extend health span and inhibit progression of atherosclerosis. The project will involve in vitro and in vivo experiments in which you will modulate T- and B cells and identify novel druggable targets to inhibit atherosclerosis. You will perform flow cytometry and transcriptomics (single cell RNA-sequencing, TCR/BCR sequencing) to characterize aged adaptive immunity in both experimental mouse models and samples obtained from cardiovascular disease patients.

Selection criteria
We are looking for an enthusiastic, bright, well-motivated, and ambitious scientist:

  • With a recent Master degree in Biopharmaceutical Sciences, Biomedical Sciences, Biology, Medical Biology, or equivalent
  • With a strong interest in and experienced with immunological research
  • With experience with in vivo studies (artikel 9, proefdierkunde), flow cytometry, single cell technology (working in R), microscopical techniques and molecular biology is an advantage
  • With proficiency in English, both verbally and in writing
  • Who is an independent and creative team player with good communicative skills

Applications
To apply for this vacancy, please send an email to a.c.foks@lacdr.leidenuniv.nl quoting the vacancy number and including the following documents:

  • Motivation letter;
  • An updated CV;
  • Copy of master’s thesis or any other publication (if available);
  • The transcripts of your MSc studies and copy of your degree;
  • Written letters of recommendation by at least two former supervisors.

Only applications received before September 19th 2022 can be considered.

For more information


Ph.D. Student  in Bioinformatics

The Hospital of the University of Munich, Germany, is one of the largest and most competitive university hospitals in Germany and Europe. 48 specialized hospitals, departments and institutions harbouring excellent research and education provide patient care at the highest medical level with around 11.000 employees.

Scope of duties

  • You will work in the context of complex human diseases, within the DFG CRC 1123 and 914 on translational mechanisms and networks of novel therapeutic as well as diagnostic immune targets in cardiogascular diseases by single-cell based multi-omics approaches
  • You will work in close collaboration with clinicians and will conduct targeted multi-omics analyses of clinical high-throughput data (bulk RNA-seq, scRNA-seq, proteomics, flow cytometry in combination with clinical data on patient outcome)
  • You will contribute on the development of integrative bioinformatics methods for answering complex biological questions, particularly in the domain of network integrative methods
  • You will present the results at project meetings and publish them in high-ranking scientific journals

Our requirements

  • The applicant should have a major interest in cardiovascular immunology
  • Good knowledge of scripting in scientific scripting and programming languages like python3 or R. Good knowledge in C/C++ and/or Java is beneficial
  • Experience with the analysis of experimental data and high-throughput data ((sc)RNA-seq, proteomics, etc.) is a plus
  • Further we expect strong communication and teamwork skills
  • Mandatory vaccination in healthcare: Since 16.03.2022, all employees in hospitals will be subject to mandatory vaccination against SARS-CoV-2)

Reference Number 2022-K-0536

Apply here


Posted on August 18, 2022

PhD position in Animal Genomics

Established in 2007 at the University of Liège, GIGA is an interdisciplinary research center in biomedical sciences whose mission is advanced medical innovation. The institute encompasses more than 500 members (PI, senior researchers, post-doctoral scientists, thesis students, technicians) with expertise in medical genomics, in silico medicine, neuroscience, oncology, infection and immunity, and cardiovascular sciences.

GIGA provides its members access to a broad range of state-of-the-art technologies through core facilities, including the genomics platform (http://www.giga.uliege.be/). GIGA is the only Belgian research center directly integrated within a university hospital, making it a major player in translational research where links between researchers and doctors are at the heart of the research activity.

The Laboratory of ANIMAL GENOMICS (www.giga.uliege.be/cms/c_20639/fr/unit-of- animal-genomics-home) of the GIGA-MEDICAL GENOMICS (http://www.giga.uliege.be/cms/c_17588/fr/giga-medical-genomics-accueil) is seeking to hire an enthusiastic Post-Doc and a PhD candidate to work in the field of inflammatory bowel disease (IBD) genetics.

The IBD team in the Animal Genomics lab seeks energetic and highly motivated PhD student with a master’s degree or equivalent in Genetics, Bioinformatics, veterinary/human medicine, or related disciplines.

The project aims to uncover peripheral blood and gut cell-type specific cis-eQTL driving inherited predisposition to IBD. The project is built on prior investments particularly with regards to the establishment of new cohorts and the "pre-collection" of many samples (over 10.000 samples), which have laid the foundation of what has the potential to be an important contribution to the scientific community. Furthermore, through an H2020 (SYSCID), FNRS and Welbio funded projects, we have built a network of top-notch Belgian and International laboratories with complementary expertise in genomics, immunology, and cell biology to jointly develop a pipeline to systematically interrogate IBD-relevant functions of GWAS-identified candidate genes to select promising new drug targets.

The candidate must have:
- Strong expertise in molecular biology. Expertise in single cell biology and NSG
are assets.
- Proficiency in using R/Bioconductor packages as well as
scripting/programming languages (Bash, Perl, Python ...). Familiar with Linux
environment and computing clusters
- Good spoken and written English
- Determined to work independently and as part of a team, good
communication and organizational skills.

How to apply? Please provide a cover letter in which you describe yourself and explain your interest in the position and your long-term career perspectives, a CV including information about your education, previous work experience and expertise, and two references with contact information. Documents should be sent to srahmouni@uliege.be.

For details visit here


Doctoral student in Biology (Neuroscience)

Lund University was founded in 1666 and is repeatedly ranked among the world’s top 100 universities. The University has around 44 000 students and more than 8 000 staff based in Lund, Helsingborg and Malmö. We are united in our efforts to understand, explain and improve our world and the human condition. Lund University welcomes applicants with diverse backgrounds and experiences. We regard gender equality and diversity as a strength and an asset.

Biology is the broad subject about all living things. It encompasses everything from processes at the molecular and cellular level to global processes at ecosystem level. The subject is divided into a range of sub-disciplines and specialisations. The PhD programme at the Department of Biology includes many of these specialisations, from molecular biology to applied ecology, from viruses and individual cells to evolutionary biology and global biodiversity. Taking on research studies at the Department of Biology generally means focusing on a delimited part of the research area of biology and may include field studies, experiments, theoretical studies, or a combination of these.

The PhD candidate will be part of an interdisciplinary team at Lund University (7 PIs and 4 new PhD students) who over the next 6 years will collaborate to investigate the sublethal effects of commonly used pesticides in different species of insects. The project is highly interdisciplinary, involving research in fields such as analytical chemistry, genetics, metabolomics, ecology, and physiology, including collaborative laboratory, field and semi-field studies. Chemical insecticides play an integral role in controlling agricultural pests, however, their sublethal consequences for non-target species are often overlooked. Most of these pesticides are neurotoxins, yet how they affect the brain and its function in diverse insect species is poorly understood.

Admission requirements 

A person meets the general admission requirements for third-cycle courses and study programmes if he or she by the time of appointment:

•     has been awarded a second-cycle qualification, or

•     has satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second cycle, or

•     has acquired substantially equivalent knowledge in some other way in Sweden or abroad.

A person meets the specific admission requirements for third cycle studies in Biology if he or she has passed an independent project (for example a degree project) of at least 30 credits in a relevant subject and have good oral and written proficiency in English.

Additional requirements

•     A MSC in a relevant topic, such as neurobiology, ecology, behavioural science, computer science, neuroscience, engineering

•     Very good oral and written proficiency in English.

In addition to the mandatory requirements, documented experience in the following areas will be considered as strong merits:

•     Tracking animal behaviour in lab, semifield or field conditions;

•     Data processing, statistical computing, and scripting in Matlab or other programming languages;

•     Insect neurobiology,  e.g. brain dissections, electrophysiological recordings, brain imaging.

•     Ecotoxicology

Reference number PA2022/2326

Last application date 01.Sep.2022 11:59 PM CEST

Apply here


Posted on August 17, 2022

12 fully funded PhD Positions | Ageing Research (Biology, Bioengineering, Bioinformatics, Biophysics)

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

The structured Ph.D. training programme within a cutting-edge research environment will start on an individual basis between July 1 and October 1, 2023. The initial contract is limited to three years. Payment is based on the German TV-L E13 scale, 65% if terms and conditions under collective bargaining law are fulfilled or on an equivalently remunerated Ph.D. support contract of the Max Planck Society.

We offer

  • An outstanding international research environment at on of the most prestigious ageing research clusters in Europe
  • Excellent infrastructure for training and research by internationally recognized scientists in facilities with state-of-the-art technologies
  • Ph.D. projects that can be carried out in up to 49 participating research groups of the above mentioned institutes
  • An interdisciplinary and structured Ph.D. programme in the vibrant city of Cologne, Germany, completely conducted in English
  • An individual career mentoring programme, extensive methods courses and soft skill workshops
  • Intensive support and guidance for international students in all administrative matters

We are looking for

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

Application period: Aug 15 - Nov 7, 2022

Contact:

Application details


Phd Student: Epigenetics

The DNA Repair and Chemoresistance Group headed by Dr. Eric Van Dyck (Department of Cancer Research (DoCR, Luxembourg)) carries out fundamental and translational research on the molecular mechanisms governing DNA repair, chromatin dynamics and chemoresistance in cancer. Our main research interest resides in the identification & validation of novel strategies to improve cancer treatment, with a particular focus on gliomas.

We have received funds from Télévie/FNRS to undertake a collaborative project with Dr. Sabrina Fritah (NORLUX Neuro-Oncology Laboratory, DoCR). The goal of this project is to investigate the molecular mechanisms governing the epigenetic reading of DNA methylation marks by members of the Methyl-CpG Binding Domain Protein 1 (MBD1) family in wild-type and mutant IDH1 gliomas.

Key responsIbilities

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

KEY SKILLS, EXPERIENCE AND QUALIFICATIONS

  •  Master’s degree (or equivalent degree) in biochemistry or molecular biology, with a solid background and research experience in cancer biology and epigenetics
  • Wet laboratory and analytical skills, demonstrated experience in cell culture, nucleic-acids and protein characterization (including  the expression/purification of recombinant protein, DNA binding assays, chromatin immunoprecipitations (ChIPs)), as well as in the CRISPR-cas9 technology and bioinformatics will be considered as strong assets
  • Excellent time management, rigour, perseverance, scientific creativity and originality, writing skills, conciseness, sense of priority and ability to work with others
  • Language skills: fluent command of English, knowledge of other languages of the European Union is an asset

Ref: JA/PHDEG0822/EVD/DRC

SCIENTIFIC Contacts Dr. Eric Van Dyck & Dr. Sabrina Fritah eric.vandyck@lih.lu ; sabrina.fritah@lih.lu

Applications including a cover letter and a curriculum vitae should be sent through our website before 15 September 2022 via the apply button below.

For details click here


PhD on engineering plant circadian clocks for climate adaptation( Biology, Bioinformatics , System Biology)

The lab of Prof. Devang Mehta (https://mehta-lab.com) conducts research in experimental plant systems biology in the Division of Crop Biotechnics (Department of Biosystems) at KU Leuven (Belgium). We have an open full-time PhD position in Bioscience Engineering to study and engineer the plant circadian clock for enhanced latitudinal adaptation due to climate change.

The Division of Crop Biotechnics performs cutting-edge research on crop and model plant species, integrating knowledge at the cellular, tissue, plant, environment, and agro-systems level. The Division consists of several research groups developing various molecular tools and having a strong expertise in molecular biology, plant pathology, tropical crops, genomics, plant hormones, plant nutrition and soil. The Laboratory for Experimental Plant Systems Biology is the newest lab in the Division and specializes in developing and applying genomics and proteomics technologies in plant systems for a variety of different problems.

The project will involve experiments using specialised growth environments with advanced LED optics as well as genetic tools such as CRISPR-mediated mutagenesis and high-throughput transcriptomics and proteomics. As a result, the successful candidate will have the opportunity to acquire a range of skills suitable for both academic and industrial careers. Further, you will be given the freedom to shape the project as you develop scientifically and use the excellent research environment at KU Leuven to realise your own ideas within the project’s context.

Profile

We seek a candidate with a Master’s degree (European or equivalent) in Biology, Bioinformatics, Biotechnology, Biochemistry, Synthetic Biology, Bioengineering or other relevant degree for the project described above.
A successful candidate will ideally:
• Have some experience in molecular biology or biochemistry labs (any model system)
• Intermediate programming or data-analysis skills or an interest in developing such skills
• Be creative with a strong interest in fundamental and applied scientific research
• Be able to work well in a multi-disciplinary team
• Have good academic performance at the MSc and BSc levels
• Demonstrate an ability to write and communicate in English
• Be eager to learn new techniques
• Be able to integrate in an international and diverse working environment
For more information, please contact Prof. dr. Devang Mehta (mail: mdevang@ualberta.ca). You can apply for this job no later than October 1st, 2022 via the online application tool.

Posted on August 16, 2022

EMBL - Life Sciences International PhD Programme 2023 Winter Recruitment

The EMBL International PhD Programme (EIPP), originally established in 1983, provides PhD students with an excellent starting platform for a successful career in science by fostering early independence and interdisciplinary research. EMBL is dedicated to promoting excellence in the molecular life sciences throughout Europe.

To achieve this goal, we inspire and train talented young scientists to become skilled and creative future leaders in academia, industry and other sectors. The EIPP provides comprehensive interdisciplinary training, maintaining a careful balance between theory and practice, close mentoring and creative freedom, collaborative teamwork and independence.

These key characteristics make the EIPP a role model, which has inspired similar programmes at research institutions throughout Europe and the world. The enriching encounter of different nationalities, the friendly and collaborative atmosphere, and the passion for science is what unites EMBL’s diverse staff and provides the ideal setting to forge long-lasting connections and make studying at EMBL a unique formative experience.

Two recruitment rounds are organised each year across all EMBL sites. The application deadlines and all relevant information are published well in advance. Watch a webinar to learn everything you need to know about preparing and submitting your application, and read more in detail about the full application process.

Application opens August 2022
Application submission deadline 04 October 2022, 23:59 CET
Reference deadline 06 October 2022, 23:59 CET
Interview dates To be confirmed
Written application results will be announced in November 2022
Expected start date flexible; by October 2023 at the latest

Application details


PhD position in reverse translational breast cancer research

A PhD position is available in the laboratory of Professor Momo Bentires-Alj (https://bentireslab.org/) at the Department of Biomedicine (DBM) in Basel, Switzerland. The successful candidate will work on primary patient breast cancer organoid cultures, proteomics, and image-based drug screening.

Selected publications of our lab include: 1- PIK3CAH1047R induces multipotency and multi-lineage mammary tumors. Koren S, et al., Nature 2015. 2- Hippo kinases LATS1/2 control human breast cell fate via crosstalk with ERα. Britschgi A, et al., Nature 2017. 3. Glucocorticoids promote breast cancer metastasis. Obradović MMS, et al. Nature 2019. 4. Hepatic stellate cells suppress NK cell sustained breast cancer dormancy. Correia AL, et al., Nature 2021.

Your position
The tasks include: a) Manage and characterize breast cancer patient-derived organoid samples, b) Assess their response to single or combination therapy using image-based drug screening (Pharmacoscopy); c) Validate the findings in vivo

Your profile
A strong experience in primary cell culture and imaging. Expertise in drug screening, and/or mouse work is a plus. The candidate should be well-organized, highly motivated, a team player, and must be fluent in English.

We offer you
A stimulating, challenging and interdisciplinary translational research environment, state-of-the-art technologies and core facilities, and attractive employment conditions. The DBM is an international institute pursuing basic, translational and clinical research, with access to cutting-edge core facilities.

Application / Contact

Please send your CV, a summary of your research experience and interests, techniques that you are competent in, and the contact details of three referees. to Nathalie Laschet: Nathalie.laschet@unibas.ch

Application deadline: applications will be reviewed as they arrive.

Lab website


PhD fellowship in Breast Cancer Research

We are offering a PhD fellowship in breast cancer commencing 1 November 2022 or as soon as possible hereafter. Our group and research The Petersen/Villadsen Group is part of the Morphogenesis and Differentiation program at the Department of Cellular and Molecular Medicine (ICMM), University of Copenhagen (ku.dk).

A focus of the laboratory is to understand how the cellular differentiation hierarchy in the human breast gland contributes to the development of breast cancer. It has been discovered that many cancers, including breast cancer, retain a differentiation hierarchy resembling what is found in the corresponding normal tissue. Currently, we are beginning to obtain a highly detailed resolution of the spatial pattern of cellular subtypes within the normal breast gland.

Project description

The project will focus on deepening the understanding of how cellular differentiation states in the normal breast gland and breast cancers resemble one another and how they may differ. Our lab has developed several breast-derived cell culture models of epithelial, stromal and cancer origin that can act as a platform for examining the consequence of malignant transformation with regard to cell of origin as well as concurrent differentiation state transitions within a hierarchy.

The PhD candidate will be involved in establishing and characterizing cell culture models with the purpose of examining to which extend the initial cellular differentiation state imposes certain phenotypes upon transformation, and to which extend state transitioning can be modulated.

Your key tasks as a PhD fellow at the Faculty are:

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

Key criteria for the assessment of applicants Applicants must have qualifications corresponding to a master’s degree Biochemistry, Biology, Biomedicine or similar (equivalent of the Danish candidate, 3 + 2 years) related to the subject area of the project.

Application deadline: Sunday 28 August 2022, 23:59 p.m. CET.

Application details


Posted on August 15, 2022

PhD scholarship -Biomedical sciences (Liver Cell Biology)

For already 50 years, the Vrije Universiteit Brussel has stood for freedom, equality and connectedness. These values are strongly present on our campuses, in our students as well as our staff. At the VUB, you’ll find a diverse collection of personalities: pure innovators and especially people who are 100% their authentic selves. With about 3.500 employees, we are the largest Dutch-speaking employer in Brussels, an international city with which we are all too happy to be connected, and around which our four campuses are located.

The Faculteit Geneeskunde en Farmacie, Department Basis (bio)-medische wetenschappen, is looking for a PhD-student with a doctoral grant. More concretely your work package, for the preparation of a doctorate, contains: PhD research on the intitiation of liver fibrosis, as a member of the Liver Cell Biology research group of Prof. Leo van Grunsven, Brussels Health Campus of the VUB (Jette).

The lab studies molecular mechanism involved in liver disease and liver regeneration, thereby making use of several mouse models as well as in vitro models of liver disease (for more information please visit https://livr.research.vub.be/). The general aim of the PhD project is to increase our understanding of the initiating events of hepatic stellate cell activation that take place when a liver is damaged due to an acute or even a chronic liver insult.

You will study liver fibrosis initiation and hepatic stellate cell activation in mouse livers and in advanced in vitro 3D spheroid cultures.

You will determine the chromatin landscape and dynamics of quiescent, activated and inactivated HSCs.

You will be trained in RNAseq analysis, multicellular 3D tissue culture and all standard RNA and protein techniques.

You’ll have the opportunity to participate in local and international conferences, in order to expand your scientific network.

You will enroll in the Doctoral School of Life Sciences and Medicine to benefit from workshops on domain specific skills as well as transferable skills.

What do we expect from you?

  • Master diploma biomedical sciences, biology, biochemistry, bio-engineer or a related biomedical diploma.
  • A candidate should:· hold a diploma or Master degree in biomedical sciences, biology, biochemistry or bioengineering or related biomedical field, with excellent marks.· show interest or have lab experience in molecular biology and tissue culture.· show interest or have experience in (single cell) RNAseq analysis using Python or R.· be structured and responsible and contribute with enthusiasm to an ambitious and interdisciplinary team.· be fluent in written and spoken English.

Send us ONLINE and at the latest on 15/09/2022 your CV, letter of motivation and the highest degree you’ve attained (not applicable for VUB alumni).

Apply here


PhD Student in Infectious disease research

We seek a highly motivated PhD candidate who will enjoy working in a multinational environment on projects related to infectious diseases in the framework of the “Luxembourg-Laos Partnership for Research and Capacity Building in Infectious Disease Surveillance – PaReCIDS”. The PaReCIDS project was established in 2011 with the goal to develop research and laboratory capacity in Lao People’s Democratic Republic (PDR). In the past years, multiple research studies on hepatitis viruses, measles, rubella and other infectious diseases in the Lao PDR were conducted in close collaboration with staff of the Lao Luxembourg Laboratory at the Institut Pasteur du Laos.

Our team focuses on applied infectious disease research, in particular on vaccine-preventable diseases in the Lao PDR. Selected candidates will be expected to contribute to study design and implementation including sample and data collection, result analysis and interpretation as well as training of local staff in the framework of PaReCIDS. The presentation of results at national and international conferences and the writing of scientific manuscripts are also part of the assignments.

KEY SKILLS, EXPERIENCE AND QUALIFICATIONS

  • Master’s degree in Biomedical Sciences, Biology, Medicine, Epidemiology or other related fields
  • Keen interest in applied infectious disease and public health research
  • Strong motivation for international travel and working within the Luxembourg and Lao environments
  • Fluency in English is mandatory
  • Good information seeking and assimilation skills, motivation to read and critically discuss scientific articles
  • Strong analysis and problem-solving capacities
  • Determination to overcome hurdles and successfully conclude research studies (perseverance)
  • Open to constructive criticism
  • Good time management, rigour, scientific creativity, writing and presentation skills
  • Sense of priority and ability to work with people with different background and culture
  • Experience in standard laboratory methods (for example ELISA, PCR, sequencing…) and in the analysis of epidemiological data, statistics, R, python or Stata is considered an asset
  • Location:                  Esch-sur-Alzette
  • Start date:               January 2023
  • Ref:                           VD/PHDID0822/JH/DII INF3

Applications including a cover letter and a curriculum vitae should be sent before 15 september 2022 through our website


PhD in Cancer Biology/ Biosciences

This PhD project will explore the role of transport proteins in Breast Cancer. (Newcastle University, UK)

Transporter proteins confer on cells the ability to uptake and efflux different molecules. These include the solute carrier (SLC) superfamily (incorporating the SLCO and the SLC22A families), which mediate solute uptake into cells, and the ABC family, which mediates efflux out of cells. These transporter families are important in breast cancer (BC) and in breast imaging, because certain members of these families transport estrogens, anticancer drugs, and MRI contrast agents. Thus transporters conceivably play a role in BC pathogenesis, treatment, and radiological diagnosis.

Our previous work on ABC transporters has shown upregulated expression of members of the ABC family in hormonally-regulated breast and ovarian cancer. We have shown partial reversal of paclitaxel resistance in ovarian cancer cells via inhibition of ABCB1-expressing cancer stem cell population known as side population (SP) cells. We have reported that MCF7 (hormone responsive) and MDA-MB-231 (hormone non-responsive) BC cell lines contain SP cells, the MCF7 SP cells having increased expression of ABCG2 and increased resistance to the chemotherapeutic drug mitoxantrone, compared to the MCF7 non-SP cells (NSP).

Eligibility Criteria

You must have, or expect to achieve, at least a 2:1 honours degree or international equivalent, in a subject relating to cancer biology, including cell biology and human genetics. Further qualification such as an MRes is advantageous. This award is available to home and international applicants. Successful international candidates will be required to make up the difference between the home fees and international fees. English Language requirements: IELTS 6.5 overall, with 5.5 or more in each sub-skill.

Application Closing Date 20 August 2022

Contact Details simon.lowes@nhs.net

Apply here


Posted on August 12, 2022

NKI PhD Program 2022 (Molecular Life Sciences & Cancer Biology)

The Netherlands Cancer Institute (NKI) comprises an internationally acclaimed research institute as well as a dedicated cancer clinic. This combination ensures rapid translation of basic research into clinical applications: today’s research for tomorrow’s cure. As a researcher in our team you can also make an important scientific contribution to realizing our common goal.

The NKI PhD recruitment program in molecular life sciences and cancer biology aims to recruit outstanding, national and international PhD students, and provide them with excellent research training in a vibrant scientific environment. The main priorities of this program are the effective mentoring of PhD students and ensuring that all candidates have the support and resources they need to perform high-quality research. PhD students at the NKI enjoy access to top-level research facilities and receive training in science and career related aspects. Lecture series and weekly seminars provide PhD students with immediate access to many of the world’s most renowned scientists.

What we have to offer

  • A four-year funded PhD on a wide range of topics in Molecular Life Sciences and Cancer Biology
  • An excellent scientific, international and collaborative learning environment
  • Individualized PhD supervision & mentoring
  • Training in science and career related aspects
  • Access to state-of-the-art infrastructure & core facilities
  • Regular lectures, journal clubs & seminar series
  • Participation in PhD symposia, retreats, social activities
  • Vibrant living environment

What we are looking for

  • Master’s degree or equivalent in (medical) biology, medicine, physics, chemistry, artificial intelligence or a related topic to be obtained within 3 months after the call deadline
  • Motivation and interest to do high-quality science
  • Relevant research experience
  • Outstanding academic results
  • Fluent in spoken and written English

Call open: 1st of July - 30th of September

Apply here


PhD position in antimicrobial resistance

Applications are invited to undertake a PhD project investigating Helicobacter pylori antimicrobial resistance. H. pylori is a bacterial pathogen that causes stomach inflammation and increases the risk of developing ulcers and stomach cancers. Treatment of H. pylori infection has become a challenge due to antimicrobial resistance. The successful candidate will join a multidisciplinary team on an exciting collaborative project characterising mechanisms of H. pylori antimicrobial resistance, with a view to developing more accurate diagnostics. The postgraduate student will be supervised by Dr Sinead Smith, Ussher Assistant Professor in Applied & Translational Medicine (Trinity college ireland).

Standard Duties and Responsibilities of the Post
  • Carry out an original body of high-quality research as part of the requirements for a PhD at Trinity College.
  • Complete taught modules (a minimum of 10 ECTS and a maximum 30 ECTS) as part of the structured PhD program at Trinity College.
  • Assist in the recruitment of patients and collection of clinical samples for isolation of H. pylori and analysis of resistance mechanisms by culture-based assays and molecular methods (PCR and DNA sequencing).
  • Maintain accurate research records.
  • Analyse data.
  • The student will be required to regularly meet with their supervisor and submit reports, attend and contribute to lab group meetings, communicate research findings at national and international conferences and liaise with other members of our multidisciplinary research and clinical staff.
  •  Contribute to the preparation of articles for publication in biomedical journals.
Person Specification: Essential
  • A minimum of a 2:1 honours degree or equivalent in a biological science or related field.
  • Proficiency in the English language.
  • Excellent written and communication skills.
  • Highly motivated.
  • Ability to work independently and as part of a multidisciplinary team.
  • Ability to meet deadlines.
  • Flexibility with regard to the research environment.
Desirable
  • Previous experience of working in a research laboratory environment.
  • MSc in a biological science or related field.
  • While training in the required techniques will be provided, practical experience in microbiology and/or molecular biology would be advantageous.
Application Procedure
Applicants should submit a full Curriculum Vitae to include the names and contact details of 2 referees (including email addresses), to: Dr Sinead Smith
smithsi@tcd.ie
Closing Date : 14-Sep-2022 12:00

PhD Positions in: Single-molecule Protein Sequencing and enzymology

Founded in 1614, the University of Groningen enjoys an international reputation as a dynamic and innovative institution of higher education offering high-quality teaching and research. Flexible study programmes and academic career opportunities in a wide variety of disciplines encourage the 36,000 students and researchers alike to develop their own individual talents. As one of the best research universities in Europe, the University of Groningen has joined forces with other top universities and networks worldwide to become a truly global center of knowledge.

Several PhD and post-doctoral positions are available in the group of Giovanni Maglia at the University of Groningen in the field of single-molecule protein sequencing and single-molecule enzymology using nanopores. Biological nanopores are an exciting new class of biosensors, which found practical application is in single-molecule DNA sequencing and single-molecule analysis. We will focus on designing and engineering biological nanopores to recognize either peptides or individual amino acids in proteins. A wide variety of problems will be tackled, which will require designing nanopore, model protein substrates, engineering unfoldases and proteases. The nanopores will be tested using single-molecule electrophysiology techniques.

Qualifications

The successful applicant has:

  • a Master degree in one of the following expertise: molecular biology, biochemistry, chemistry, physics, Engineering, or related disciplines
  • a good command of English (oral and written)
  • enthusiastic and a team player.

Proficiency in complex data analysis will be an advantage but it is not a requirement.

For information you can contact: Dr. Giovanni Maglia,   giovanni.maglia@rug.nl

Posted on August 11, 2022

PhD position in computational genetics and machine learning: analysis of multi-omics biological data

Aarhus University’s ambition is to be an attractive and inspiring workplace for all and to foster a culture in which each individual has opportunities to thrive, achieve and develop.

Applicants are invited for a PhD fellowship/scholarship at Graduate School of Technical Sciences, Aarhus University, Denmark, within the Quantitative Genetics and Genomics programme. The position is available from 2 January 2023 or later.
Title:
Re-advertisement: PhD position in computational genetics and machine learning: analysis of multi-omics biological data in novel populations of Brachypodium

Research area and project description:
We are looking for a talented and creative PhD student to contribute to the SIEVE project (“Selection of mutations by in silico and experimental variant effects: a new strategy to improve fitness in cool-season grasses”). The SIEVE project is supported by an Emerging Investigator grant by the Novo Nordisk Foundation, which funds groundbreaking research with promising applications in data science and the green transition in Europe.

The PhD student will be involved in an innovative research project in computational genetics and machine learning applied to a model species (Brachypodium). She/he will evaluate the impact of mutations by analyzing multi-omics data in mutant populations: (i) whole-genome sequencing; (ii) RNA expression; (iii) metabolomics; and (iv) physiological measurements. These analyses will benefit from expertise in machine learning (applied statistics, deep learning, network analysis) and computational genetics (quantitative genetics, evolutionary genomics, bioinformatics).

Qualifications and specific competences:
Candidates must hold (or be expected to hold) a Master’s degree in a field related to computational genetics (e.g., quantitative genetics, evolutionary genomics, bioinformatics) or machine learning (e.g., applied statistics, deep learning, network analysis).

The ideal candidate will also demonstrate some knowledge of scripting/programming languages (e.g., in R, Python, Java or Shell), previous research experience in relevant fields, and good communication skills in English.

Place of employment and place of work:
Center for Quantitative Genetics and Genomics, Aarhus University, Ole Worms Allé 3, Building 1171, 8000 Aarhus, Denmark

Contacts:
Applicants seeking further information are invited to contact:
Guillaume Ramstein (ramstein@qgg.au.dk) for information about the SIEVE project or this PhD position.

How to apply:
Please follow this link to submit your application. Application deadline is 30 September 23:59 CEST. Preferred starting date is 2 January 2023.


Posted on August 01, 2022

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