SymBioSys KU Leuven Center for Computational Systems Biology

PhD Position: Engineering Executable Models of Biological Networks

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Last Updated on Thursday, 07 March 2013 15:19

At the Department of Computer Science at the Vrije Universiteit (VU) in Amsterdam, one PhD position for four years is available on a research project devoted to

Engineering Executable Models of Biological Networks

Starting date of the PhD position: as soon as possible.

The project

The goal of the project is to describe gene regulatory networks by formal interaction patterns/models. Using these formal models, we aim to derive new insights in the behaviour of gene networks. These models, ultimately, describe cells' behaviour, and cell components, as independent, communicating entities. Simulating cell behaviour this way at the same time promises new insights and poses new challenges on the execution and verification environment due to the complexity, heterogeneity and variability of the modeled entities.

The work will start with the application of our formal framework using Petri nets to model gene network behaviour. Additionally, extensions of the framework and new methods and tools for analysis of the behaviour patterns will be developed.

For more detailed information on the project, see
http://www.few.vu.nl/~feenstra/projects/bioexe.pdf

Research groups

This project is a collaboration between two research groups at the VU: Bioinformatics (Anton Feenstra and Jaap Heringa), and Theoretical Computer Science (Wan Fokkink). For experimental validation of predictions, we collaborate with two experimental groups; the group Receptor Systems Biology at the VU (Martine Smit), and Bertie Göttgens at the Cambridge Institute for Medical Research.

For more information on the involved research groups, see
http://www.cs.vu.nl/en/sec/cs/
http://www.ibi.vu.nl/
http://www.cs.vu.nl/~tcs

Qualifications

Candidates should have completed their studies in computer science, bioinformatics or a closely related area. Experience with biological systems, a good theoretical background, and an open attitude to applications are considered advantages. You should enjoy working in an internationally oriented and interdisciplinary research environment. Communicative skills and the ability to work in a team are important.

Information and application

For further information about these positions please contact either:
Dr. Anton Feenstra This email address is being protected from spambots. You need JavaScript enabled to view it. tel. +31 (0)20 5987783
Prof.dr. Wan Fokkink This email address is being protected from spambots. You need JavaScript enabled to view it. tel. +31 (0)20 5987735
Prof.dr. Jaap Heringa This email address is being protected from spambots. You need JavaScript enabled to view it. tel. +31 (0)20 5987649

You are invited to send an application by email to the above email addresses no later than September 1, 2012. Your application should consist of a cover letter, a curriculum vitae (including detailed information regarding your academic degree), and the names and addresses of two references.

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Head of a bioinformatics/biostatistics platform (ICM, Paris, France)

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Last Updated on Thursday, 07 March 2013 15:19

INRIA and the IHU of Translational Neurosciences hire Scientific coordinator of a bioinformatics/biostatistics platform

Starting date: as soon as possible

Context

The ICM (Brain and Spine Institute) is located in the heart of the Pitié-Salpêtrière hospital in Paris, France. The institute is dedicated to fundamental and clinical research on the central nervous system. The institute hosts in a single building about 500 clinicians and scientists, who work altogether to make new discoveries about the human brain function, to develop new treatments for neurologic diseases and to deliver them to the patients. The institute covers a large clinical scope with a particular emphasis on Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, epilepsy, depression and paraplegia.

The ICM is a founder member of the university hospital institute (IHU-A-ICM) for translational neurosciences. In the framework of this program, the ICM and the IHU-A-ICM want to collaborate with INRIA to set up a mutual biostatistics and bioinformatics platform (WP7 project). They are looking for the scientific coordinator of the platform.

Mission

The platform coordinator will set up, develop and maintain the platform that is dedicated to bioinformatics and biostatistics. He/She will be responsible of a staff of about 7 people composed of data manager, statisticians, computer scientists, etc.. Staff will be recruited using the funds available trough the IHU grant. These funds will also cover the costs of the computing facilities.

The platform aims to gather and analyze all kinds of data acquired within the IHU. The final goal will be to integrate multi-modal databases and to use them to model multi-scale physiological and pathological processes. At first, the platform will focus on genetic, genomic and transcriptomic (DNA-Array and RNAseq) data, and then on epigenetic, proteomic and metabolomic data, aiming to identify and/or use biomarkers of neurologic diseases. These databases will be integrated with the available clinical data. Moreover, these data will be used in conjunction with neuroimaging data such as MRI, PET images and MEG/EEG signals. This later aspect will be done in close collaboration with the neuroimaging platform (CENIR), the research team Cogimage and the platform for image and signal analysis (CATI). The candidate does not need to have a particular expertise in neuro-imaging, since he/she could rely on the current expertise within the IHU on this topic. More precisely, the scientific coordinator will supervise the:

• development and maintenance of the databases,
• integration and utilization of these databases for statistical studies,
• data modeling and validation of the models,
• dissemination of results and methods.

In terms of research, the platform will be developing its own methodological research in biostatistics/bioinformatics in relation to the acquired data (in priority the “omics” and
clinical data). In biostatistics, one could develop original methods for multivariate data analysis, regression or model selection within massive amount of data, for instance. The platform could rely at first on the research team Cogimage and CATI, before developing its own research activity with the support of INRIA.

Profile

The position requires a strong expertise in the field of biostatistics and/or bioinformatics.The candidate should hold a PhD in these fields and have a postdoctoral experience of at least 5 years.The candidate should have strong relational and managerial skills with a great interest for multi-disciplinary work, and in particular for interactions with neuroscientists and clinicians. The salary will be determined according to the candidate’s experience at the best international standards.

Please send resume and cover letter (mail or electronic format) to:

Cecile Proust : This email address is being protected from spambots. You need JavaScript enabled to view it.
Institut du Cerveau et de la Moelle epiniere (ICM)
Groupe Hospitalier de la Pitie Salpetrier
47 boulevard de l’hopital
75013 Paris
France

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Position Available: Bioinformatics & Integrative Genomics Specialist, VIB & KU Leuven

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Last Updated on Thursday, 07 March 2013 15:19

The VIB Center for the Biology of Disease at the University of Leuven is a vibrant and international research centre where key issues relevant to major human health challenges are tackled. Within this Center, we are seeking a highly motivated and experienced Bioinformatics & Integrative Genomics Specialist. You will collaborate with the 14 research groups within the Center and provide essential input on computational biology aspects of their research projects. In this job you will be confronted with exciting research questions in cancer and neurodegeneration; and with a broad spectrum of computational challenges and omics data sets. You will be embedded in the Laboratory of Computational Biology at the University of Leuven (Stein Aerts Lab: http://med.kuleuven.be/bioinformatics), and you will be part of an active bioinformatics community in Leuven, allowing daily interactions with colleague bioinformaticians.

Your main activity will be to provide support for large-scale data analysis, and to setup and manage a Bioinformatics consulting core within the Center through which:

• you will collaborate with wet-lab scientists on a variety of research problems. You will deal with the data analysis part of the research project. The focus of the service will be mainly on genome bioinformatics: microarrays, RNA-Seq, ChIP-Seq, exome/genome re-sequencing, gene regulation, network biology, pathway analysis, gene prioritization, data integration, text-mining, etc.
• you will gradually manage a team of 1-3 Bioinformatics experts
• you will interact with the core facility of the VIB-BITS (http://www.bits.vib.be/), with the Genomics Core facility at the University Hospital (allowing close interaction with the next-generation sequencing instruments Illumina HiSEQ2000, Illumina MiSEQ, Roche 454, PacBio), and with other consulting units and research groups, for example for advanced biostatistics or proteomics data analysis.
• you will make hardware (e.g., local linux servers, high performance computing, cloud), software (e.g., a local Galaxy instance), and analysis pipelines (e.g., scripts, workflows) available to scientists; train and guide scientists to analyze their own datasets; and organize training courses and seminars.
• you will take your own initiatives to continuously optimize the bioinformatics flux through the Center, through the VIB and through the Group of Biomedical Sciences, for example to organize a weekly "data clinic" where small user problems can be solved.

Qualifications:

• Master's degree in Life sciences or computational field
• PhD degree is strongly preferred
• At least five years bioinformatics experience
• Proven track record of high-impact publications in the field of computational biology, analysis of high-throughput data sets, data integration
• Solid experience with Linux, programming (e.g. Java), and database management (sql and no-sql).
• Solid experience with bioinformatics programming and statistics for bioinformatics, including scripting (e.g., Python), R (incl. Bioconductor), Galaxy, UCSC Genome Browser, Ensembl API, etc.
• Thorough understanding of molecular and developmental biology, and of disease biology (preferably cancer and/or neurological disorders).
• Experience with the analysis of next-generation sequence data is a plus: whole exome re-sequencing, whole-genome re-sequencing, SNP/indel calling, CNV, Structural variation; RNA-Seq, ChIP-Seq
• Experience with pathway analysis and cis-regulatory sequence analysis is a plus.
• Knowledge of machine learning and data mining is a plus.

Links:

• The Center for the Biology of Disease
• The Laboratory of Computational Biology
• Center for Human Genetics
• University of Leuven

Highly motivated candidates can apply by sending a motivation letter, names and contact information for three references, publication list, and CV to This email address is being protected from spambots. You need JavaScript enabled to view it. .

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Postdoc Position in systems biology with applications in prostate cancer

Details

Last Updated on Thursday, 07 March 2013 15:19

Karolinska Institutet, Inst. för medicinsk epidemiologi och biostatistik

About the Department and the biostatistics group

The Department of Medical Epidemiology and Biostatistics presently employ approximately 250 staff with 15 full professors and over 40 graduate students. The department is one of the largest departments of epidemiology in Europe. Unique data resources – such as the Swedish Twin Registry, several large prospective studies, ongoing nation-wide case-control studies, access to clinical data, biological material and high-throughput genotype, expression, proteins/metabolites and sequence data – are effectively explored at the department. Further information can be found at: www.ki.se/meb

The prostate cancer research group currently comprises 4 senior and 2 junior researcher as well as 8 PhD students. Several large case-control and cohort prostate cancer populations are available with collected biological samples (blood, urine, tumor) and complete information about clinical characteristics and disease progression. The research is performed in an interdisciplinary setting with strong collaboration with clinical departments and other national and international research groups. The position will be part of WP4 of the e-Science for Cancer Prevention and Control project (http://e-science.se/community/eCPC), a flagship project at the Swedish e-Science Research Centre (SeRC, http://www.e-science.se); a strategic research area funded by Vetenskapsrådet. The position also holds a tight connection to the studies in the Cancer Risk Prediction Center (CRisP, www.crispcenter.org).

Area of responsibilities/description of the work

Applications are invited for a two-years postdoctoral research position to characterize prostate cancer progression, aggressiveness and prognosis by integrating genetic and transcriptomics deep sequencing data with clinical information using a large population based prostate cancer cohort. The applicant is expected to work with high-level data analysis and modeling in the field of medical systems biology using high quality in-house produced data. The results from computational analyses will be validated with independent experiments.

Qualifications

The applicant should have a PhD degree in computer science, applied mathematics, bioinformatics, systems biology, or related discipline. Ideally, applicant has strong methodological expertise (e.g., graph theory, probability theory, machine learning), good programming and communication skills, and is interested in developing and applying novel computational methods in cancer research.

Application process

An employment application must contain the following documents in English or Swedish:

1. A complete curriculum vitae, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
2. A complete list of publications
3. A brief statement of research interest

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