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Bioinformatician position available, Medical University of Vienna

We are looking for a bioinformatician in the fields of epigenetics, gene regulation & proteomics. This position is embedded in the special research program (SFB) “Histone deacetylases (HDACs) as regulators of T cell-mediated immunity in health and disease”. The ideal candidate has knowledge in the analysis of NGS dataset and pathway analysis. The candidate will be responsible for the computational analysis of NGS data and for basic pathway and network analysis. Throughout the project, the candidate will work in close collaboration with the whole research network.

 
ABOUT THE RESEARCH PROGRAM
The special research program (SFB) “Histone deacetylases (HDACs) as regulators of T cell-mediated immunity in health and disease” constitutes a major strategic grant, consortium and research network newly funded by the Austrian Science Fund (FWF). The overall aim of this 8-year SFB research program and consortium is to provide a mechanistic molecular rationale for the development and application of isoform-selective HDAC inhibitors for the treatment of T cell-mediated diseases, and to test essential regulatory roles of reversible lysine acetylation beyond histone modifications and epigenetic gene regulation in T helper cells. It comprises an interdisciplinary team of eight research groups, of which seven are located in Vienna and one in Salzburg, Austria. The project started in March 2019.
 
APPLICATION: Candidates have to demonstrate a strong motivation to engage in the SFB network. Previous research experience in Systems Biology, Bioinformatics, or another relevant discipline is desired. Electronic applications must include the following documents in a single PDF file:
1.   Academic Curriculum Vitae of no more than 2 -3 pages
2.   List of peer-reviewed publications (submitted papers must include the submission confirmation)
3.   Motivation letter explaining why you wish to start / continue a career in the field (1-page)

The job offer is open until March 31, 2021. The position will be filled as soon as suitable candidates have been identified and selected. Two reference letters must be e-mailed by mentors of applicants to Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!. Short-listed candidates will be invited for Zoom interviews in April 2021. The position (initially for up to 2 years) is open immediately; the actual start date is flexible.
 
Links: www.meduniwien.ac.at/HIThttp://www.meduniwien.ac.at/HIT/contact.html,
 


PostDoc Biostatistik/Epidemiologie/Bioinformatik

Wir suchen eine*n Wissenschaftler*in bzw. Postdoktorand*in am Institut für Medizinische Biometrie und Statistik an der Universität zu Lübeck.

Das erwartet Sie:
• Eigenverantwortliche statistische Auswertungen in klinisch-experimentellen und genetisch-epidemiologischen Projekten
• Methodische Forschung zu genetisch-epidemiologischen und / oder bioinformatischen Methoden mit einem Schwerpunkt auf Methoden des maschinellen Lernens
• Beteiligung an der biometrischen Beratung sowie an der Lehre in den verschiedenen Studiengängen unserer Universität
• Publikationstätigkeit und Einwerbung von Drittmitteln

Das bringen Sie mit:
• Ein abgeschlossenes Hochschulstudium sowie eine Promotion in Mathematik, Statistik, Epidemiologie, (Bio-)Informatik oder in einem vergleichbaren Fachgebiet
• Ausgewiesene Kenntnisse in Methodenentwicklung und angewandter Statistik
• Grundlagen zu Verfahren des Maschinellen Lernens
• Praktische Erfahrungen in der Auswertung genetisch-epidemiologischer oder anderer molekularbiologischer Datensätze
• Fundierte Programmierkenntnisse in R (inkl. Implementierung von statistischen Methoden)
• Engagierte, selbständige Arbeitsweise, wissenschaftliche Kreativität und Freude am Arbeiten in einem interdisziplinären Team
• Idealerweise Erfahrungen in der Lehre und der biometrischen Beratung
• Kenntnisse in der Durchführung von Simulationsstudien sind gewünscht

Das bieten wir Ihnen:
• Eingruppierung in die Entgeltgruppe E 13 TV-L, bei Erfüllung der tariflichen Voraussetzungen
• Eine Vollzeitbeschäftigung, zzt. 38,5 Stunden / Woche. Eine Teilzeittätigkeit kann im Rahmen bestimmter Arbeitszeitmodelle vereinbar sein.
• Ein attraktives Arbeitsumfeld
• Möglichkeit zur wissenschaftlichen Weiterqualifikation (z.B. Habilitation)
• Flexible Arbeitszeitgestaltung (Gleitzeit)
• Attraktive Fort- und Weiterbildungsmöglichkeiten

Auf ein Gespräch mit Ihnen über fachliche Details freuen sich Frau Prof. Inke König (0451-500 50601) und Frau Prof. Silke Szymczak (0451-500 50600).
Wir freuen uns auf Ihre Bewerbung bis zum 30.03.2021 unter Angabe der Ausschreibungsnummer 4459. Über diesen Link können Sie sich bewerben: https://jobs.uksh.de/job/L%C3%BCbeck-Schl-23538/656819901/

Links: https://jobs.uksh.de/job/L%C3%BCbeck-Schl-23538/656819901/

Leader (m/f/d) of our new junior research group “Artificial Intelligence-based image data analysis”

The Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V. is a research institute dedicated to the development and improvement of analytical methods and tools for health research and related fields. The ISAS is a member of the Leibniz Association and is publicly funded by the Federal Republic of Germany and its federal states.

A new project area in the institute is the development of advanced imaging, especially light-sheet fluorescence microscopy (LSFM), for the analysis of whole organs under physiological and pathological conditions. LSFM generates extremely large data sets. Modern machine learning and artificial intelligence provide approaches to fully exploit these data sets and translate their rich information into a better understanding of the underlying biological mechanisms. Innovative machine learning approaches, for example based on explainable deep learning approaches, promise to make hidden structures of human cognition accessible and thus guide further experimental investigation and new hypotheses.

In the department of Biospectroscopy at the ISAS (Dortmund, Germany) you will setup your own research group that focuses on the following tasks:

• Devise and carry out an interdisciplinary research agenda that advances the use of LSFM and other microscopy approaches in life science research through the development of innovative machine learning approaches

• Exploit the advantages of an in-house IT infrastructure involving a high-performance GPU- cluster and petabyte-sized data storage facilities

• Build up a research infrastructure including large scale ground truth data sets and annotations of healthy and diseased organs in close cooperation with the biomedical research groups at ISAS and supported by appropriate artificial data enhancement techniques

• Develop open scientific software accompanying the research agenda, supporting data analysis, image segmentations, annotations and visualizations for biomedical research studies

• Establish a visible landmark in the computational life science research community through high ranking publications and successful third-party funding initiatives, as well as a regional, national and international network of interdisciplinary collaborators.

Your profile

• A PhD degree in computer science/statistics/physics/computer visualistics/data science or a related field

• Alternatively, a career changer, e.g. with biomedical PhD, who has acquired specialized IT knowledge over the years

• An excellent track record in computational biomedical research, ideally with a focus on microscopic image analysis

• Publications at top tier conferences in computer vision and machine learning, like NeurIPS, CVPR, MICCAI and ISBI.

• Excellent skills as communicator and team leader

• Fluent English (spoken and written)

• Good German communication skills are a plus

We offer

• A superbly equipped group funded initially for 5 years

• Scientific development opportunities in an international cooperative, interdisciplinary re-search environment and an excellent working atmosphere in a very dynamic and professional team

• Access to a research and teaching community at many nearby universities

• Extensive state-of-the-art equipment and infrastructure for the desired project

• A wide range of activities in skill enhancement and further qualification

 

Links: https://www.isas.de/news/042021-leader-mfd-of-our-new-junior-research-group-artificial-intelligence-based-image-data

Post-doctoral position / Scientist (m/f/d) in Bioinformatics

Das Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V. ist ein Forschungsinstitut mit der Aufgabe der Entwicklung und Verbesserung von Analysemethoden und -instrumenten für die Gesundheitsforschung und angrenzende Bereiche. Das ISAS ist Mitglied der Leibniz-Gemeinschaft und wird durch die Bundesrepublik Deutschland und ihre Länder öffentlich gefördert.  Für die Abteilung Bioanalytics an unserem Standort in Dortmund suchen wir eine/n Post-doctoral position / Scientist (m/f/d) in Bioinformatics.

Nähere Informationen zur Stelle finden Sie unter www./isas.de/karriere.

Postdoctoral Researcher (f/m/n) Metagenomics & Soil Biodiversity

Project "Diversity and scenario modelling of molecular markers of plant pathogens in plant, litter and soil metagenomes" at theGerman  Centre  for  Integrative  Biodiversity  Research (Div)Halle-Jena-Leipzig: Soils  host  one  quarter  of  all species  on  Earth,  providing  critical  services  to  mankind. This  project asks how soil microorganism communities respond to global change and which changes in soil functions will occur. We will generate answers by mining metagenomics data covering large environmental gradients, available   in   our   consortium   and the   public   domain,   for molecular   markers   of   microbial plant pathogenicity.  On  this  basis  we  will model  global distribution of  microbial  plant  pathogens under climate  and land-use  change scenarios. We will integrate local experimental data to establish causality informing scenario modelling. The project is supervised by François Buscot at the Helmholtz-Centre for Environmental Research (UFZ) in Halle, together with Anna Heintz-Buschart (UFZ/iDiv), Nico Eisenhauer (iDiv), Carlos Guerra (iDiv), and Kirsten Küsel (Friedrich Schiller University of Jena).

Links: https://www.idiv.de/fileadmin/content/Vacancies_PDF/Vacancies_2021/Postdoc_flexpool_UFZ_04_Buscot_2021_final.pdf https://apply.idiv.de

Phd project in “Single cell genomic approaches to study mitochondrial genetics and disorders”

Project description

Mitochondria are central to numerous physiological processes and are unique organelles that carry their own genome, often in high copy number, encoding a subset of proteins, transfer RNAs, and ribosomal RNAs essential to their function. Germline inherited mitochondrial DNA (mtDNA) mutations are a major cause of human disease and hundreds of point mutations and deletions have been associated with a variety of overlapping phenotypes, estimated to affect ~1 in 4,300 individuals, placing them among the most common inherited metabolic disorders. Mitochondrial diseases are characterized by remarkable heterogeneity and while variable heteroplasmy (fraction of mitochondrial genomes carrying a variant) of associated pathogenic mutations/deletions may present a natural modulator of disease severity, many syndromes include cell-type specific phenotypes. Moreover, the accumulation of somatic mtDNA mutations has been associated with ageing phenotypes and malignancies. However, establishing genotype-phenotype correlations on a cellular and molecular level has been challenging due to the unique nature of mitochondrial genetics that include variant heteroplasmy as a dynamic variable, but also tissue-dependent differences in mtDNA copy number, its cell cycle-independent turnover and the uncertainty about rates and mechanisms underlying accumulation of somatic variants. To bridge this gap, we develop and apply single cell multi-omic technologies to enable the linkage of an individual cells’ mtDNA genotype to its phenotype, such as its gene expression, protein expression and/or chromatin accessibility profile to enhance our understanding of mitochondrial genetics and underlying human disease. In particular, we are interested to understand adaptive genomic and cellular responses to high levels of pathogenic mtDNA or an increased mutational burden in cellular and animal models, including primary patient specimens.

Keywords

Single cell multi-omics, mitochondrial genetics, mitochondrial disease, hematology, immunology

Entry requirements

Strong interest in life sciences, computational biology, method development and/or translational research. Master’s degree in computer science, bioinformatics, biotechnology, biochemistry, engineering, mathematics, physics, biology, (molecular) medicine or a related field. Expertise and interest to work computationally and/or experimentally, in particular with (single cell) sequencing data. Projects can be tailored accordingly. We in particular encourage applications from students with a computational background. Strong motivation to work independently as well as in an interdisciplinary research team. Very good language and communication skills in English.

Lab Location

Berlin Institute of Medical Systems Biology, Hannoversche Str. 28, 10115 Berlin

Starting date

Between August and December 2021

Funding

Limited to 3 years

How to apply

Please apply via the HFA application portal. The Hector Research Career Development Awardees will arrange interviews (via skype or if feasible in-person) with the most promising applicants. The final candidates will be invited for a personal presentation on July 8, 2021 in Bremen (Germany). The final decisions will be announced by August 2021.

Application Deadline

April 15th, 2021

Enquiries

For questions related to making your application, please contact Hector Fellow Academy Office: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! or www.hector-fellow-academy.de

 

Carry out your own PhD project! - In Single Cell Genomics and Mitochondrial Genetics supervised by Dr. Dr. Leif S. Ludwig (Berlin Institute of Health, Charité, Berlin Institute of Medical Systems Biology)

The Hector Fellow Academy offers you the opportunity to realize a self-developed research project under supervision of Dr. Dr. Leif S. Ludwig. He is a Hector Research Career Development Awardee working at the interface of biology and medicine. He specializes in the development and application of single cell multi-omic applications to study stem cells in hematology, immunology and oncology and how genetic variation and mutations in our mitochondrial genomes contribute to human diseases.

Keywords

Single cell multi-omics, mitochondrial genetics, mitochondrial disease, hematology, immunology

Entry requirements

Strong interest in life sciences, computational biology, method development and/or translational research. Master degree in computer science, bioinformatics, biotechnology, biochemistry, engineering, mathematics, physics, biology, (molecular) medicine or a related field. Expertise and interest to work computationally and/or experimentally, in particular with (single cell) sequencing data. Projects can be tailored accordingly. We in particular encourage applications from students with a computational background. Strong motivation to work independently as well as in an interdisciplinary research team. Very good language and communication skills in English.

Lab Location

Berlin Institute of Medical Systems Biology, Hannoversche Str. 28, 10115 Berlin

Starting date

Between August and December 2021

Funding

Limited to 3 years

How to apply

Please apply via the HFA application portal. The Hector Research Career Development Awardees will arrange interviews (via skype or if feasible in-person) with the most promising applicants. The final candidates will be invited for a personal presentation on July 8, 2021 in Bremen (Germany). The final decisions will be announced by August 2021.

Application Deadline

April 15th, 2021

Enquiries

For questions related to making your application, please contact Hector Fellow Academy Office: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! or www.hector-fellow-academy.de

PhD project in “Systems biology approach for elucidating bacterial revival after antibiotic treatment”

Project description

Resistance of bacterial pathogens to antibiotics is a serious threat to global health, with a predicted death toll of at least 2.4 billion people worldwide in the next 30 years, and costs up to $US3.5 billion per year. New solutions to fight antimicrobial resistance are imperative, both to rescue old antibiotics and also to undermine resistance development to newly discovered ones. Antibiotic tolerance – a transient physiological state where bacteria can tolerate antibiotics without being resistant – is increasingly associated with the raise of resistance. Tolerant bacteria survive antibiotic treatment, and once the antibiotic is removed they are able to resume growth, thus leading to relapsing infections. The aim of this project is to elucidate molecular mechanisms of bacterial revival of the enteric pathogen Salmonella Typhimurium after antibiotic treatment using systems biology approaches. This project is an excellent opportunity for students who want to develop their computational skills in tight combinabion with experiments in bacterial genetics and physiology. We are a dynamic, highly collaborative, multidisciplinary team with access to cutting-edge robotic platforms, thus our lab offers the perfect environment for such projects. We welcome applications from highly motivated students eager to explore exciting and innovative ideas. Your background can be from broad disciplines ranging from Biology to Computer Science. Don’t hesitate to get in touch if you want to find out more. In fact, you are encouraged to do so!

Keywords

Pathogenic Bacteria, Antibiotics, Genomics, Systems Biology, High-throughput Screening

Entry requirements

MSc. Degree in Biotechnology, Bioinformatics, Biology, Molecular Biology, Computer Science or similar

Location

Chair of Microbiology, University of Würzburg, Germany

Starting date

September 2021 (flexible)

Funding

Limited to 3 years

How to apply

Please apply via the HFA application portal.

The Hector Research Career Development Awardees will arrange interviews (via skype or if feasible in-person) with the most promising applicants. The final candidates will be invited for a personal presentation on July 8, 2021 in Bremen (Germany). The final decisions will be announced by August 2021.

Application Deadline

April 15th, 2021

Enquiries

For questions related to making your application, please contact Hector Fellow Academy Office: Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein! or www.hector-fellow-academy.de

Doctoral Position in Systems Immunology & Data Sciences

The start date is May 1st, 2021 or by agreement. The position is available until January 31, 2023 with the aim for extension towards the finalization of your doctoral degree.

The University of Konstanz is one of the eleven Excellence Universities in Germany. Since 2007 it has been successful in the German Excellence Initiative and its follow-up programme, the Excellence Strategy.

This position is an exciting opportunity for you, if you wish to develop strong data science skills and gain knowledge in molecular immunology by conducting bioinformatics research towards a better understanding of immune cell identity and function. The position is available within the newly established research group of Tenure Track Prof. Dr. Andreas Gruber, which has a focus on developing and applying data science approaches to study gene expression regulation in health and disease (further information: https://gruber-sciencelab.netlify.app).

Amongst others, you will be using computational tools to analyze bulk as well as single-cell RNA sequencing data of immune cells aiming to study the transcriptional programs that regulate isoform diversity observed across immune cell subpopulations. The results of your work will contribute to current efforts to better understand the molecular mechanisms underlying immune cell function as well as immune cell-associated diseases, such as auto-immune disorders, but also cancers. You will also have the opportunity to work on your own data science approaches / tools, as required, and contribute to research collaborations of the lab. If you have some experience in programming and/or analyzing data and you would like to conduct a doctoral thesis with a focus on data sciences and systems immunology, we are looking very much forward to your application!


Your Competencies

 - A Master or equivalent in a relevant field (e.g. Bioinformatics, Informatics, Molecular Biology, Biotechnology, Biology, Statistics, Data Sciences)

 - Ability to work independently and as part of a team (in English language)

 - Passion to analyse large high-throughput sequencing datasets

 - Some experience in programming and/or analysing data (e.g. using R or Python)


Your responsibilities

 - Analyze data from high-throughput sequencing experiments

 - Explore and select appropriate data analysis approaches

 - Implement and document sequencing data analysis workflows

 - Apply and develop your own data science tools and approaches

 - Interpret analysis results and contribute to publications, presentations and funding proposals of the lab


We Offer

 - Excellent development opportunities, extensive training and an attractive remuneration package

 - An exciting interdisciplinary working environment at the interface of data sciences and molecular cell biology

 - The opportunity to extend your data science and informatics skill set, while gaining knowledge in systems immunology and the molecular basis of health and disease


If you have any additional questions, please get directly in contact via e-mail: andreas.j.gruber [.at.] uni-konstanz [.dot.] de

Please submit your application (motivation letter, CV, degree certificates incl. grades) in one single pdf file until March 11, 2021 via the Online Application Portal of the University of Konstanz: https://stellen.uni-konstanz.de/jobposting/72c6d1f07934f09e58cee61cdb187690d678817a0

PhD Position: Modeling microbial interactions in marine ecosystems

We are offering a PhD position (E13 TV-L HU, 65%) at the Institute for Theoretical Biology (ITB) of the Humboldt-University of Berlin.

The project seeks to understand (the evolution of) metabolic interactions between phototrophic and heterotrophic microorganisms and the "self-organization" of ecosystems. The tasks for the PhD project are primarily computational and include reconstruction and constraint-based analysis of genome-scale metabolic models of microbial organisms, in particular cyanobacteria.

The project is inspired by recent works that provide novel insights into phototroph-heterotroph interactions and division of labour in marine ecosystems. In collaboration with experimental partners, our aim is to develop quantitative computational models that explain the trade-offs and metabolic prerequisites of such interactions. In particular, our hypothesis is that the concept of "cellular resource allocation" offers a unique and novel angle to understand the constraints and energetic trade-offs that govern the emergence of dependencies between photo- and heterotrophic microorganisms. The planned work directly builds upon our recent works to describe microbial/cyanobacterial resource allocation and growth:

- Sharma S and Steuer R (2019) Modeling microbial communities using biochemical resource allocation analysis. J. R. Soc. Interface 16: 20190474.
- Zavřel T et al. (2019) Quantitative insights into the cyanobacterial cell economy. eLife 2019;8:e42508
- Reimers AM et al. (2017) Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth. Proc Natl Acad Sci U S A. pii: 201617508.

In addition to the usual requirements (a passion for the topic, a university degree (typically M.Sc. in an appropriate field), very good programming skills in python or matlab, ...), the ideal candidate would have some experience with/strong interest in computational models of metabolism, constraint-based analysis of metabolism, biochemistry, comparative genomics and/or related concepts.  

The formal call and further instructions are available on the webpage of the HU (in german only, Reference: DR/012/21, the german text takes precedence):  https://www.personalabteilung.hu-berlin.de/de/stellenausschreibungen/wissenschaftliche-r-mitarbeiter-in-m-w-d-mit-65-v-h-d-regelm-arbeitszeit-e-13-tv-l-hu-drittmittelfinanzierung-befristet-bis-31-12-2023

The position will be embedded into the highly collaborative scientific environment here at the Institute for Theoretical Biology (ITB) in the center of Berlin, and offers further training opportunities, as well as the possibility to visit and work closely with our experimental partners.

Deadline for applications is March 2, 2021.

I am happy to also answer any questions or informal enquiries (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!) and would also encourage any students who are interested to send me an informal email.

Links: 

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