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Postdoctoral Fellow in Bioinformatics / Systems Medicine

A more complete PDF version of this job posting is available from the following URL:

http://epigenomics.cemm.oeaw.ac.at/files/Postdoc_Cancer_Personal_Omics.pdf

We are recruiting postdocs who want to work at the forefront of precision medicine, analyzing and integrating various types of omics data with 3D imaging and wearable device data into systems models of cancer.

Our group is based at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna. It combines advanced technologies (epigenomics, single-cell sequencing, drug screening, mass spectrometry, imaging, etc.) with a deep interest in computational modeling and relevant clinical collaborations. We collaborate closely with physicians at the Vienna General Hospital and the Medical University of Vienna to establish proof-of-concept for precision medicine in several types of cancer.

The Project

For the first time, it is now realistic to follow individual patients in full clinical and molecular detail over the course of diagnosis, first-line treatment and recovery, cure and/or relapse. Prospectively studying representative patients for several cancers, we will combine (i) Omics Profiling including Single-Cell Epigenome/Transcriptome Sequencing, (ii) Patient-specific 3D Culture Models, (iii) Multimodal Imaging, (iv) Digital Pathology and (v) Clinical Phenotyping, in order to establish systems medicine accounts of individual patients. At this level of detail, each patient becomes a powerful study in itself, providing novel insights into complex disease mechanisms and informing personalized therapy.

The Candidate

We are looking for highly motivated and academically outstanding candidates who want to pursue a scientific career in the field of computational and medical epigenomics. A strong candidate may have a background in the computational sciences (bioinformatics, statistics, physics, engineering, etc.) and some prior experience with collaborative research in high-throughput biology. In the same way, we are considering applicants with a background in medicine or in biology (e.g., functional genomics, chemical biology, human genetics, molecular medicine, etc.) who have strong quantitative skills and a keen interest in pursuing systems medicine projects.

The Lab (http://www.medical-epigenomics.org/)

The Medical Epigenomics Lab at CeMM pursues an interdisciplinary and highly collaborative research program aimed at understanding the cancer epigenome and establishing its utility for precision medicine. The lab is internationally well-connected and active in several fields:

- Epigenomics. We perform large-scale epigenome mapping in order to dissect the dynamics of cancer development and emerging drug resistance. This work is part of the European BLUEPRINT project and the International Human Epigenome Consortium.

- Technology. Exciting biomedical research is often driven by new technologies. Our lab is therefore heavily invested into technology development, including single-cell protocols, nanopore sequencing, CRISPR, and epigenome editing.

- Bioinformatics. New algorithms and advanced computational methods allow us to accurately infer epigenetic cell states from large-scale datasets, in order to reconstruct the epigenetic landscape that controls cellular differentiation and reprogramming.

- Diagnostics. Using large-scale DNA methylation mapping, bioinformatic prioritization, and functional characterization, we strive to develop clinically relevant biomarkers for informing personalized cancer therapy.

The Principal Investigator (https://scholar.google.com/citations?user=9qSsTcIAAAAJ)

Christoph Bock is a principal investigator at CeMM, guest professor at the Medical University of Vienna, scientific coordinator of Vienna’s Biomedical Sequencing Facility, and adjunct group leader at the Max Planck Institute for Informatics. Previous appointments include the Max Planck Institute for Informatics (PhD studies) and the Broad Institute of MIT and Harvard (postdoctoral research). CB is a 2009 recipient of the Otto Hahn Medal by the Max Planck Society for pioneering work in computational epigenetics, and he recently received two major career development grants – a New Frontier Group award by the Austrian Academy of Sciences (EUR 1.4 million) and an ERC Starting Grant by the European Research Council (EUR 1.3 million). CB leads Genom Austria, which is the Austrian contribution to the International Network of Personal Genome Projects, and he is a member of several European and global initiatives on epigenetics & precision medicine.

The Institute (http://www.cemm.at/)

CeMM is an international research institute of the Austrian Academy of Sciences. Driven by medical needs, CeMM integrates basic research and medical expertise to pursue innovative approaches focused on cancer, inflammation, and immune disorders. CeMM is located at the center of one of the largest medical campuses in Europe, within walking distance of Vienna’s historical city center. A study by “The Scientist” placed CeMM among the top-5 best places to work in academia world-wide (http://the-scientist.com/2012/08/01/best-places-to-work-academia-2012). Vienna is frequently ranked the world’s best city to live. It is a United Nations city with a large English-speaking community. The official language at CeMM is English, and more than 30 different nationalities are represented at the institute.

Applicants should submit cover letter, CV, academic transcripts, and contact details of three referees to This email address is being protected from spambots. You need JavaScript enabled to view it.. Please submit your application documents as a single combined PDF, if possible, and refer to the reference code (PD CB) in the subject line. Applications will be reviewed on a rolling basis, and any application received by 15 April 2016 will be considered. Start dates are very flexible.

Postdoctoral Scholar Position in Bioinformatics/Systems Cancer Biology

We are looking for a highly motivated postdoctoral scholar at Stanford University School of Medicine. Our lab is focused on developing novel biomarkers (diagnostic, prognostic, or predictive) toward precision medicine in cancer. We have significant expertise in quantitative image analysis and machine learning applied to multi-modality imaging such as PET, CT, and/or MRI. We are interested in the integrative analysis of imaging and genomic data in cancer, with the goals of discovering fundamental genotype-phenotype connections and transforming clinical care through translational research. We work closely with cancer biologists and oncologists. Our research is generously supported by multiple research grants from the NIH as well as industry.

We are seeking a highly motivated individual with the desire and talent to tackle challenging technical problems in medicine. The project involves the development and/or application of computational algorithms and statistical/machine learning approaches that integrate diverse types of high-throughput molecular data, towards understanding patient specific cancer networks and their response to therapy. The ideal candidate would have training in bioinformatics and/or computational biology, or a related field such as biostatistics, biomedical engineering, electrical engineering, computer science, and physics. Prior knowledge and experience with cancer genomics are preferred but not required. Strong programming skills in R or MATLAB are required.

I am dedicated to mentoring and educating the future leaders in biomedical research. Some major awards recently won by postdocs in the lab include: Resident Clinical/Basic Science Research Award (2014), Basic/Translational Science Award (2015) from the American Society of Radiation Oncologists, and Science Council Research Award (2015) from the American Association of Physicists in Medicine.

Interested applicants should send CV and a brief statement of research to:

Ruijiang Li, PhD, DABR
Assistant Professor
Department of Radiation Oncology
Stanford University
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

PhD in Barcelona (students finishing their MSc in Bioinformatics or similar)

Two PhD positions are available in the Barril’s lab (University of Barcelona) in the context of a Marie Curie Initial Training Network (FragNet). Applications from MSc students finishing their Bioinformatics (or related) degree on/before summer 2016 are particularly welcome. 
 
Prof. Barril (https://goo.gl/EXdBi2) is a world expert on structure-based drug design. His research combines computational and experimental methods to discover bioactive molecules, with a particular emphasis on novel mechanisms of action.
 
The Marie Curie fellowships offer a very competitive salary, while the ITN program is designed to provide excellent training and networking opportunities. FragNet will train students on all aspects of fragment-based drug discovery (FBDD), a powerful technique to discover good quality leads. As such, this is an exceptional opportunity for students interested in drug discovery or chemical biology.
 
A brief description of the projects is provided below. More details about these and other positions in the nertwork can be found in the project’s web page: http://fragnet.eu/index.php/projects
 
Position ESR9 - Construction of a computational platform for fragment evolution. The platform will combine existing chemoinformatics and computational chemistry software to deliver a tool that can effectively navigate chemical space and guide the evolution of fragments into hits.
 
Position ESR10 - Molecular simulations applied to FBDD. Biased and unbiased molecular dynamics simulations will be used to investigate binding of fragments to their protein targets and to guide the fragment evolution process. 
 
Note that, as a Marie Curie program, the mobility rule applies. Essentially, this means that the students are not be elegible to carry out their PhD in the same country where they’ve resided for the past few years.
 
Apply as soon as possible through the project web page. Direct any queries directly to Prof. Barril: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

PhD student openings in the RNA Bioinformatics Group in Jena

The Research Group RNA Bioinformatics and High Throughput Analysis in Jena is looking for talented and motivated PhD students who are interested in (at least) one of the following topics:

• High throughput sequencing analysis: We are specialized to analyze huge amounts of RNA-Seq data produced by current high-throughput sequencing methods. We are looking for a bioinformatician to process data based on state-of-the-art techniques (quality control, reference mapping, de novo assembly, quantification, visualization) as well as to develop own scripts and tools to find genes differential expressed between certain conditions. Based on RNA-Seq data of a host and its pathogen we try to find out more about the ecology and species barriers in emerging viral diseases by detecting protein- and non-coding genes differential expressed between different combinations of species, tissues and time points post infection.
• Virus bioinformatics: Since the last emerging viral epidemics/pandemics, caused by SARS, MERS and Ebola, viruses are extensively studied in wet lab, however specific bioinformatic tools are still missing. We develop new tools to find conserved RNA secondary structures and RNA-RNA interactions in viral genomes to understand the viral replication. Furthermore we want to facilitate the viral genome assembly. It is a challenging task to assemble viral sequences out of samples, including millions of host sequences. A new challenge is also the design of synthetic viruses with weak clinical symptoms along with still viable viruses. A successful design can be used to produce cheap vaccinations within decent time.
• Monitoring antibody profiles: To rapidly monitor the specific antibody profile of a patient and decide on vaccination, currently used methods of serological analysis need to be improved. We are looking for a bioinformatician to develop better tools for identification of immunodominant domains (epitopes, antigenic determinants) on bacterial, viral and other microbial proteins. In a four-party project, the results of this in silico study will be verified in the diagnostic lab by testing patient sera, and the feedback will be used to refine the epitope identification software.
• Epigenetic regulation by long non-coding RNAs: The project will focus on elucidating lncRNA-genome interactions and their impact on gene regulation in mam- malian cells. The candidate will be involved in developing tools and techniques to detect novel lncRNA/DNA structures genome-wide, to identify the associated binding proteins and to unravel the underlying regulatory mechanisms. The work will include state-of-the-art laboratory techniques (e.g. ChIP, ChRIP, high throughput sequencing, proteomics) and bioinformatical analysis of the data.
• Combined metabolome and transcriptome analysis: In this project we analyse transcriptomics and metabolomics data of cyanobacteria to analyse their fitness regarding the circadian clock. On transcriptomic level we want to identify unknown genes and differentially analyse different time points of the circadian rhythm. On metabolomic level we want to fill the gaps in the metabolic networks. In particular, we want to combine the analysis of both data types to compensate for incompleteness in one of the data sources.
 
Applicants should have: 
• a Master in bioinformatics, computational biology or a related area,
• a passion for developing and using computational tools and algorithms to analyze large biological data sets,
• good programming skills in a unix environment,
• high motivation and the ability to work both independently and in a team.
 
Candidates are encouraged to send their application including CV and a short description of research experience and interests to 
This email address is being protected from spambots. You need JavaScript enabled to view it.
 

PhD Positions available at IMPRS for Computer Science: Computational Biology and Applied Algorithms

The International Max Planck Research School for Computer Science (IMPRS-CS) is a graduate program jointly run by the Max Planck Institute for Informatics (MPI-INF), the Max Planck Institute for Software Systems (MPI-SWS), and the Computer Science Department at Saarland University. The MPI-INF and the MPI-SWS are among the more than 80 institutes run by the Max Planck Society. The MPIs are Germany's prime basic research facilities with world-class, basic research in the fields of medicine, biology, chemistry, physics, technology, and the humanities. Since 1948, MPI researchers have been awarded 18 Nobel prizes, which testifies to the quality and innovation of MPI research programs.

Educating and training junior scientists is of primary importance for the future of science, research, and innovation. The Max Planck Society, in cooperation with German Universities has launched the International Max Planck Research Schools (IMPRS) initiative. Admitted students receive a first rate, research-oriented education in their chosen area of concentration. They enjoy close supervision by a world-renowned scientist in a competitive, yet collaborative, environment rich in interaction with other students, post-docs, and scientists. The program is fully funded.

Applicants for the PhD program must hold a Master's degree or a Bachelor's degree from a research-oriented institution. Successful candidates will typically have ranked at or near the top of their classes, have already engaged in research and published their results, and be highly proficient in written and spoken English. Applicants are required to deliver a 15-minute research presentation on their Master's project, followed by a question and answer period, in front of the admission committee and other audience members. All admitted students receive financial aid in the form of a support contract (according to TvöD Bund, German Collective Agreement for the Public Sector, Category: Federal).

Applicants to the IMPRS-CS PhD program should fill in the following online form: http://www.imprs-cs.de/overview/phd/application.html, and submit their complete documents until 15th February 2016. The respective application talks are currently scheduled for May 2016.

More information on the application process and our institutes, especially Department 3: Computational Biology and Applied Algorithms, can be found online: www.imprs-cs.de, and http://www.mpi-inf.mpg.de/departments/computational-biology-applied-algorithmics/.

Contact:
http://www.imprs-cs.de/index.html
Andrea Ruffing, IMPRS-CS Coordinator
This email address is being protected from spambots. You need JavaScript enabled to view it.
+49 681-9325-1800

Post-doc position in the Gagneur lab, Computational Genomics, TUM

We seek a talented and motivated post-doc to join our computational genomics group at the TUM, Munich. Our research is articulated along two axes: advancing our understanding of gene regulation through quantitative modeling and developing methods to study the mechanisms by which genetic variants condition phenotypes (systems genetics). Current projects on gene regulation include quantitative modeling of large ChIP datasets, RNA metabolism kinetics, and study of translational control by integration of RNA-seq with ribosome profiling and quantitative proteomics. Our systems genetics research is now moving to human genetic applications with new collaboration partners (Prof. Klein, auto-immune genetic diseases, and Dr Prokisch, mitochondrial disorders).

Candidates with a PhD in computational biology and bioinformatics, or in physics, statistics, and applied mathematics with practical experience with high-dimensional data are encouraged to apply. Applicants must have a proven publication record.

Applications including a cover letter, CV, and references must be sent to Julien Gagneur (This email address is being protected from spambots. You need JavaScript enabled to view it.) until February 28th 2016.

We just moved to the TUM, webpage still at: http://www.gagneur.genzentrum.lmu.de

Three open positions at HU-Berlin; biomedical text mining and data integration

The research group for „Knowledge Management in Bioinformatics“ at the  Institute for Computer Science, Humboldt-Universität zu Berlin, has three open positions for researcher in the area of biomedical text mining and biomedical data integration for cancer research. The positions are available from 1st March 2016 for three years each.

For further detail, please see

https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/jobs/idsem.html

POSTDOC POSITION IN GENOMICS AND BIOINFORMATICS

We are looking for an enthusiastic and ambitious postdoctoral fellow to study patients recruited for bariatric surgery via an integrated analysis of data generated by omics (genome, methylome, transcriptome and metabolome). The postdoctoral fellow will participate in all the omic aspects of the study, from data generation and storage to data analysis and writing papers for submission to a peer-reviewed scientific journal, with a particular involvement in integrated bioinformatics analyses.

The postdoctoral fellow will join the INSERM unit ‘Nutrition, Genetics, and Environmental Risk Exposure’ headed by Pr. Jean-Louis Guéant and located at the Faculty of Medicine of Nancy on the University of Lorraine campus (http://welcome.univ-lorraine.fr/).  Nancy provides a pleasant setting along with a very rich cultural life, being an hour and a half away from Paris by TGV (high-speed train) and just a step from Germany, Belgium, Luxemburg and Switzerland. The postdoctoral fellow will work under the direct supervision of Dr. David Meyre, an international expert in genetic epidemiology of obesity and its complications. Dr. Meyre is an Associate Professor at McMaster University (http://fhs.mcmaster.ca/ceb/faculty_member_meyre.htm, http://www.davidmeyrelab.com/), a Visiting Professor at the University of Lorraine and the recent recipient of the AGIR research funding program of University of Lorraine and University Regional Hospital Centre of Nancy (http://fhu-cartage.com/index.php/news/agir).

We are looking for candidates with a PhD in Genetics, Epidemiology, Molecular or Systems Biology, (Bio) Statistics, Bioinformatics, or Computational Sciences and a strong record of academic achievement. Demonstrating previous doctoral and preferably postdoctoral experience working with large population based datasets which include genomics data is recommended. Excellent programming skills (R, SAS) would be an asset. The applicant must have excellent oral and written English skills. The ideal candidate will be able to work independently to develop and drive his own research ideas, taking advantage of the resources available to the group, as well as working in a team based-environment.  Excellent facilities are available and there is a strong commitment to career development.

The appointment will be for 1-3 years, depending on the candidate’s goals, qualifications, fit and productivity. Salary is commensurate with qualifications. Applicants should send their curriculum vitae, along with a letter expressing why they are interested in this position, copies of all their transcripts, as well the names and contact information for three references by email to:

 

Dr. David Meyre

Department of Clinical Epidemiology and Biostatistics

MDCL Room 3205

McMaster University

1280, Main Street West,

Hamilton, Ontario, L8S 4K1

and

Inserm UMRS 954 N-GERE

(Nutrition-Genetics-Environmental Risks)

Institute of Medical Research (Pôle BMS) - University of Lorraine

BP 184, 54511 Vandoeuvre les Nancy

Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

 

Phd candidate in bioinformatics of single cell epigenomics

The Computational Biology Group of Interdisciplinary Center for Clinical Research (IZKF) Aachen, RWTH Aachen University Hospital, Aachen, invites applicants for a PhD candidate in bioinformatics methods for statistical methods for the analysis of single cell epigenomics data.

The project is based on the development of computational methods for analysis and integration of single cell ATAC-Seq, ChIP-Seq and RNA-Seq. This project will be performed in collaboration with stem cell specialists from the RWTH Aachen University Medical Faculty and includes the analysis of in-house generated data.

Applicants should hold a M.Sc. in Bioinformatics, Computer Science or related areas. Experience in the analysis of biological sequences, regulatory genomics and/or machine learning is desirable. The candidate should have solid programming skills (C, Python and R) and acquaintance with Linux. Experience with high performance computing is a plus. The working language of the group is English.

The expected starting date is May 2016. Interested candidates should send a brief statement of research interests, CV and the names of three references to This email address is being protected from spambots. You need JavaScript enabled to view it..

The Computational Biology Group is supported by the Interdisciplinary Center for Clinical Research Aachen (IZKF) and hosted by the Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University Hospital and the Helmholtz Institute for Biomedical Engineering, RWTH Aachen.

PhD program in Bioinformatics in Berlin

The International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC) at the Max Planck Institute for Molecular Genetics (MPIMG) in Berlin invites applications to their graduate program in bioinformatics.

We offer cutting edge computer science, secure funding and travel programs, a student community and vivid exchange, and comprehensive scientific and transferable skills training! The graduate school with a reputable faculty and a world-wide Alumni network focuses on molecular dynamics and modeling, biological networks, genomics and proteomics, and stochastic processes. Candidates should have a prominent background in computer science with a strong interest in biology. Join our team in this exciting and disruptive field of research in the vibrant capital of Germany!

Apply now on www.molgen.mpg.de/IMPRS/application before February 22, 2016!
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