- BBClist - maillist.psb.ugent.be

CALL FOR ABSTRACTS: first European Student Council Symposium, Ghent, Sept 26
by Thomas Abeel 26 Jul '10

26 Jul '10

Dear Colleagues, The abstract submission deadline has been extended to accommodate late breaking research! The first European Student Council Symposium (ESCS1) will be held on September 26, 2010 in Ghent, Belgium, as a satellite meeting of the European Conference on Computational Biology (ECCB). === ABSTRACT SUBMISSION DEADLINE: July 26, 2010 === http://escs.iscbsc.org/submission/ The program is available on our website and includes: - a keynote presentation by Yves Van de Peer about Generating hypotheses for molecular biology through (top-down) systems biology - a soft skill workshop on the use of theatre skills for presenting - student presentations from abstract submissions - a poster session See http://escs.iscbsc.org/program We invite you to submit an abstract. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the fields of computational biology and bioinformatics. A few abstracts will be selected for oral presentations. Other interesting contributions will be accepted for poster presentations. Looking forward to receiving your abstract! Magali Michaut ESCS1 chair Thomas Abeel ESCS1 co-chair

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job opening computational biologist
by Tobias Verbeke 20 Jul '10

20 Jul '10

L.S. OpenAnalytics provides data analysis services and products across geographies and industrial sectors. We currently have an open position for a molecular or computational biologist with strong experience in R / BioConductor. More detailed information on the position can be found at http://www.openanalytics.eu/careers.html Kind regards, Tobias Verbeke -- Tobias Verbeke Manager OpenAnalytics BVBA Kortestraat 30A 2220 Heist-op-den-Berg Belgium E tobias.verbeke(a)openanalytics.eu M +32 499 36 33 15 http://www.openanalytics.eu

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Postdoctoral Fellow in Cancer Systems Biology
by Filip Pattyn 20 Jul '10

20 Jul '10

Postdoctoral Fellow in Cancer Systems Biology A 3-year FP7-funded postdoctoral position is available from November 1, 2010 in the Oncogenomics Laboratory at the Center for Medical Genetics, Ghent University. Job description: The candidate will perform gene expression network analysis and systems biology research aiming to gain insights into the perturbed signaling in the pediatric peripheral nervous tumor neuroblastoma. The project is part of a broader ongoing research effort at the Oncogenomics Laboratory in collaboration with various other research groups in Europe and worldwide. The candidate will be expected to develop and utilize bioinformatics algorithms to interpret and integrate various comprehensive genomic datasets including mRNA and miRNA expression data (Affymetrix, RNA-seq) of large unique pediatric tumor series and similar datasets, ChIP-seq and proteome data from in vitro model systems with emphasis on protein coding genes and miRNAs implicated in developmental pathways. Integrated gene regulatory network building will form the basis for further search for molecular targets for targeted therapies. This position offers many opportunities for collaboration in a diversity of methodologically and biologically challenging areas of cancer research and links fundamental cancer research to translational research with direct potential towards development of new therapeutic strategies. Requirements: The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners. The ideal candidate has a PhD degree or equivalent in bioinformatics, computer science, statistics, physics, or biology and has preferably a strong background in algorithm development and/or machine learning, and experience with analyzing high-throughput data. Employer information: The laboratory of Prof. F. Speleman (http://medgen.ugent.be/CMGG/) has a proven track record both in the study of the genetic basis of neuroblastoma and bioinformatic algorithm development (see selected publications below). The past years, our laboratory has received substantial funding including grants from EU and the Belgian Federal government. We have a young, dynamic and highly interactive research team. The new postdoctoral fellow will be integrated in this team and will in particular work very closely and interact with a rapidly growing group of researchers with bioinformatics skills. The work is supported by in-house developed bioinformatic tools and a high level informatics environment. We support possibilities for further training through participation in workshops, meetings etc.. Ghent is a beautiful medieval city and one of the biggest student cities in Belgium with a vivid social and cultural life (www.visitgent.be<http://www.visitgent.be/>). Salary: The salary will be in accordance with university regulations for academic personnel at postdoc level depending on the level of experience (43,022 – 47,989 €). How to apply: Applicants should submit a CV, letters of recommendation of two orevious employers, pdf files of your best papers to Prof. Frank Speleman (franki.speleman(a)ugent.be) with email subject “Postdoctoral application”. The Oncogenomics Laboratory Center for Medical Genetics Ghent (CMGG) Ghent University Hospital Medical Research Building (MRB), 2nd floor, room 120.029 De Pintelaan 185, B-9000 Ghent, Belgium +32 9 332 2451 (phone) | +32 9 332 6549 (fax)

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Postdoc UMCG
by Patrick Deelen 20 Jul '10

20 Jul '10

The Department of Genetics at the University Medical Center Groningen, the Netherlands, has a vacancy for a Postdoctoral Fellow in the field of functional genomics. The Wijmenga laboratory focuses on the genetics of immune-related diseases such as celiac disease and inflammatory bowel diseases (IBD). We have implicated some 40 genetic loci in celiac disease and shown that many of these are not unique for celiac disease but are in fact shared with other diseases, in particular with IBD, rheumatoid arthritis and type 1 diabetes. We want to investigate – systematically and on a genome-wide level – the biological processes in which the known disease-associated genes are involved. Our aim is to understand how these different genes together cause the disease phenotype. The work will be carried out in a highly dynamic team containing PhD students and postdocs with genetic, molecular biology, statistical genetic, epidemiology and bioinformatic backgrounds. We also collaborate widely with other groups, at a national as well as international level. The department is an energetic, dynamic, and international environment, with state-of-the-art technology. We are interested in recruiting self-motivated individuals with the drive to be competitive at the international level. Candidates will be strongly encouraged to develop new avenues like iPS technology or to set up cellular screens using shRNA. Candidates with good analytical skills and a strong background in genetics, molecular biology, or immunology are encouraged to apply. You should preferably have experience in high-throughput methods (SNP or gene expression microarrays, next generation sequencing) and an interest in working on large datasets with bioinformatics tools (such as PLINK, R/BioConductor). The successful candidate will be appointed at a level in accordance with his/her experience. For more advanced candidates, we can offer a tenure-track position at the assistant/associate professor level. Contact details Cisca Wijmenga, PhD Professor of Human Genetics University Medical Center Groningen Room E2.030 PO Box 30001 9700 RB Groningen The Netherlands phone: +31 50 361 7245 (Personal assistant) E-mail: c.wijmenga(a)medgen.umcg.nl www.geneticsgroningen.nl

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temporary position bioinformatics
by Van Vlijmen, Herman [TIBBE] 09 Jul '10

09 Jul '10

We have a temporary position in our bioinformatics group in Beerse. This position is open until the end of 2010. In this function you will be part of the bioinformatics team and be involved in: * Development of better analysis methodology of the results of next generation sequencing experiments in the fields of HIV, Hepatitis C, and Oncology. These experiments are done in support of the discovery and development of new drugs, and in the development of biomarkers for these drugs. We have a specific project that involves the optimization of an alignment algorithm. Qualifications * Master's or Ph.D. degree in Bioinformatics or a related field * Expertise in scientific programming and/or scripting, and algorithm development. * Outstanding communication and team work skills. Contact info: Herman van Vlijmen Director Integrative Chem-BioInformatics Tibotec-Virco BVBA Turnhoutseweg 30 2340 Beerse, Belgium hvvlijme at its.jnj.com

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Postdoc Bioinformatics: Gene Regulatory Networks in Development and Cancer
by Stein Aerts 09 Jul '10

09 Jul '10

Postdoc Bioinformatics: Gene Regulatory Networks in Development and Cancer Applications are invited for a postdoctoral position in the Laboratory of Computational Biology at the Center for Human Genetics, University of Leuven, Belgium. Your research will focus on developing algorithms for the integrated analysis of cis-regulatory and next-generation sequence data, both RNA- Seq and DNA-Seq, with the goal of identifying coding and non-coding variations underlying oncogenesis and developmental diversity. Particular focus will be on integrating genomic variation with transcriptional modules and gene regulatory networks and on the identification of genomic regulatory variations. Context: You have the opportunity to apply your methods both on patient samples and on mammalian and Drosophila model systems. You will work in collaboration with the MPL lab (Molecular Pathogenesis of Leukemia) for next-generation sequencing experiments and functional validations in leukemia cell lines. You will have contacts with the Genomics Core Facility, hosting an Illumina HiSEQ2000 and a Roche 454 sequencer. You will be part of the Leuven SymBioSys Center of Excellence for Computational Systems Biology, where you will be surrounded by several other postdocs and students in a stimulating environment consisting of four bioinformatics research groups and four genomics labs. Qualification: We are seeking a motivated and enthusiastic computational biologist, preferably with a proven track record in gene regulatory bioinformatics (e.g., prediction of enhancers, promoters, transcription factor binding sites, gene regulatory networks). Experience with transcriptomics and with the analysis of next- generation sequence data is a plus. PhD in bioinformatics; PhD in engineering or computer science provided substantial insight in genetics; PhD in biological sciences provided substantial programming experience. Skills: genome informatics, statistics, programming. Links: The Laboratory of Computational Biology: http://med.kuleuven.be/bioinformatics/ Center for Human Genetics: http://med.kuleuven.be/cme/ and http://organigram.kuleuven.be/ext/5/50000622e.htm University of Leuven: http://www.kuleuven.be/english/ Highly motivated candidates can apply by sending a motivation letter, names and contact information for three references, publication list, and CV to stein.aerts(a)med.kuleuven.be.

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Workshop "Modeling Angiogenesis: Joining Cells, Maths and Computers", Lorentz Center, Leiden, Netherlands
by Roeland Merks 07 Jul '10

07 Jul '10

Modeling Angiogenesis: Joining Cells, Maths and Computers Lorentz Center, Leiden, the Netherlands, 4th-8th October Registration at: http://www.lorentzcenter.nl/lc/web/2010/407/info.php3?wsid=407 Scientific organizers: R.M.H. Merks (NISB / CWI, Netherlands) E. Giraudo (IRCC Torino, Italy) P. Koolwijk (VU University Medical Center, Netherlands) B. Ribba (INRIA Grenoble, France) The outgrowth of new blood vessels from pre-existing vessels, called angiogenesis, is a crucial step in myriad physiological and pathological mechanisms. Unfortunately, the complicated causes and effects of angiogenesis make it very difficult to control. Computational models and simulations help unravel both the basic mechanisms of angiogenesis and can help identify the steps in the mechanisms most amenable to intervention. A wide range of mathematical and computational models range from is currently available. Single cell-based models predict how vascular-like patterns follow from the behaviors and interactions of individual endothelial cells. Many discrete models describe the branching conditions of blood vessels, and predict the morphology of vascular trees near tumors. Continuum models often focus at the tissue level, and describe densities of blood vessels rather than individual vascular structures. Despite the biological insights these mathematical models have produced, modeling rarely finds application in experimental angiogenesis research yet. Why is that? One reason is a different focus: experimental and pharmaceutical research necessarily focus on the molecular level, whereas most angiogenesis models take single interacting endothelial cells or vessel branches as the smallest units of their models. Another reason is the lack of predictive, quantitative models and the required quantitative experimental data to feed such models. We will need models that bridge organizational scales, by showing how molecular intervention modifies the behavior of endothelial cells and, consequently, changes the dynamics of angiogenesis. Our workshop will host both experimental researchers and computational models working in vascular biology, endothelial cell biology, angiogenesis, and pharmaceutics. We will a) identify the requirements for computational models to make a true impact in basic angiogenesis research, tissue engineering and drug innovation, b) inventarize pre-existing and missing components of such a model, and c) discuss how we can couple such components. Monday, 4th October, State of the art of angiogenesis research 09.00 – 10:00 Registration and coffee 10:00 – 10:15 Welcome by Lorentz Center and the organizers 10:15 – 11:15 Lecture: Thomas Sato; Discussant: James Glazier 11:15 – 12:15 Discussion: Arjan Griffioen and Roeland Merks Available in vitro and in silico models 12:15 – 13:30 Lunch and informal discussions 13:30 – 14:30 Lecture: Aleksander Popel; ; Discussant: Thomas Sato 14:30 – 15:30 Poster flash presentations 15:30 – 16:00 Coffee break 16:00 – 17:00 Lecture: András Czirók; ; Discussant: Aleksander Popel 17:00 – 19:00 Wine and Cheese party with poster session Tuesday, 5th October, Characterizing and modeling endothelial cell behavior 09:30 – 10:30 Lecture: Andrea Gamba; Discussant: Cynthia Reinhart-King 10:30 – 11:00 Coffee break 11:00 – 12:00 Lecture: Cynthia Reinhart-King; Discussant: Andrea Gamba 12:00 – 13:30 Lunch and informal discussions 13:30 – 16:00 Tutorial: András Czirók Extracting and analyzing quantitative information for time-lapse microscopy, aimed at modelers 16:00 Departure by conference bus to the boat 16:30 – 20:30 Boat trip on Kaag Lakes and Conference Diner Wednesday, 6th October, Integrating cell behavior to explain angiogenesis 09:30 – 10:30 Lecture: James Glazier; Discussant: Peter Friedl 10:30 – 11:00 Coffee Break 11:00 – 12:00 Lecture: Peter Friedl; Discussant: András Czirók 12:00 – 13:30 Lunch and informal discussions 13:30 – 14:30 Lecture: Federico Bussolino; Discussant: Mats Karlsson 14:30 – 16:00 Tutorial: Systems Biology Toolbox 2 / SBPOP by Henning Schmidt, Novartis Pharma, Basel 16:00 – 16:30 Coffee Break 16:30 – 17:30 Keynote lecture: Peter Carmeliet Thursday, 7th October: Applications to drug development 09:30 – 10:30 Lecture: Zvia Agur; Discussant: Pascal Girard 10:30 – 11:00 Coffee Break 11:00 – 12:00 Discussion: Benjamin Ribba, INRIA, France; Discussant: Iñaki Troconiz Preclinical tumor growth models and requirements for angiogenesis models in drug development 12:00 – 13:30 Lunch and informal discussions 13:30 – 16:00 Tutorial: Maciej Swat Cell-based angiogenesis modeling with CompuCell3D, aimed at experimental biologists 16:00 – 16:30 Coffee break 16:30 – 17:30 Lecture: Paolo Magni; Discussant: Enrico Giraudo Friday, 8th October: Applications to tissue engineering 09:30 – 10:30 Lecture: Victor van Hinsbergh; Discussant: Roeland Merks 10:30 – 11:00 Coffee Break 11:00 – 12:00 Lecture: Hans Van Oosterwyck; Discussant: Pieter Koolwijk 12:00 – 13:30 Lunch and informal discussions 13:30 – 14:30 Lecture: Marco Harmsen; ; Discussant: Hans van Oosterwyck 14:30 – 15:00 Coffee break 15:00 – 16:00 Discussion: Hans Van Oosterwyck; ; Discussant: Victor van Hinsbergh Requirements for a computational angiogenesis model in tissue engineering 16:00 – 17:00 Wrap up: Pieter Koolwijk and Roeland Merks, Summary of findings ----- Roeland M. H. Merks Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI) Science Park 123, 1098 XG Amsterdam, The Netherlands Mailing address: P.O. Box 94079, 1090 GB Amsterdam CWI Office Room M246 Roeland.Merks(a)sysbio.nl / Roeland.Merks(a)cwi.nl http://www.cwi.nl/~merks Phone +31 20 592 4117 Fax +31 20 592 4199

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Comp Biol Postdoc , Amsterdam, The Netherlands
by Lodewyk Wessels 04 Jul '10

04 Jul '10

POSTDOCTORAL COMPUTATIONAL BIOLOGIST (NKI-AVL and the VU University, Amsterdam, The Netherlands) COMPUTATIONAL MODELING OF SIGNALING AND REGULATORY PATHWAYS IN Th17 DIFFERENTIATION Lymphocytes are central in the regulation of immune response. T-lymphocytes differentiate into functionally distinct subsets. Proper regulation of the balance between various subsets is crucial for an optimal immune system and for host defense against pathogens and cancer. Recently, a new T-cell subset, Th17, which plays a central role in host defense, was discovered. In this project, our aim is to identify the underlying regulatory mechanisms and molecular networks that govern the formation of Th17 cells. We will achieve this by generating comprehensive datasets and performing state-of-the art computational modeling based on these data. The data sets will include time series RNA and miRNA expression data, siRNA perturbation experiments based on kinome and phosphatome libraries, (phospho)protein expression and Chip-Seq data. To construct the computational models, we will build both data-driven machine learning models and knowledge-driven (logical and Petri-net) models of the regulatory networks. Our aim is to fuse the results of these two approaches to obtain a single, hybrid model. Computational predictions of key control mechanisms will be tested experimentally and the resulting data will be employed to refine the models. The successful candidate will be primarily responsible for constructing models of the regulatory Th17 developmental networks, developing new computational methodologies where required and liaising with the computational and biological partners in this project. EMPLOYER INFORMATION The Netherlands Cancer Institute is a dedicated cancer center conducting research in all major areas of cancer, with a strong emphasis on translational research. The Bioinformatics and Statistics group provides leadership on the collection and analysis of data for the research programs of the institute, by developing novel compuational approaches and performing state of the art analyses of a wide array of data types, including laboratory and animal experiments, clinical trials, and epidemiologic studies. The Centre for Integrative Bioinformatics (IBIVU) is a broad-based research centre at the VU University that is carried by the Faculty of Sciences (FEW) and the Faculty of Earth and Life Sciences (FALW) with strong endorsement from the University Board. Its main missions are carrying out a strong and internationally competitive research program in Integrative Bioinformatics with an additional focus on Systems Biology, and providing an excellent educational program at bachelor and master level; the latter including two-year international master's programmes in Bioinformatics and in Systems Biology. REQUIREMENTS The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners. The ideal candidate has a background in bioinformatics, computer science, statistics, physics, or biology, strong algorithmic and/or machine learning skills, and experience with the analysis of high-throughput data. EMPLOYMENT CONDITIONS The temporary employment will be for a period of three years. The gross monthly salary for a Postdoc will range from ? 3140,- to ? 3.495,- and depends on previous experience. We can help you find housing. The NKI-AVL has been listed in the top 25 of 'Best Employers' in 2009 offering a specialized cancer research institute and hospital with good working conditions and an excellent atmosphere. INTERESTED? To apply, and for further information please contact Lodewyk Wessels, tel.: +31-20-5127987, e-mail: l.wessels(a)nki.nl or Jaap Heringa, tel.: heringa(a)few.vu.nl +31 20 59 87649 (direct) or +31 20 59 87483 (secr.) CLOSING DATE 1 July 2010 L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/

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Job - Delft University of Technology - PhD or Postdoc in Multi-scale Analysis of Genomics Data
by Jeroen de Ridder 24 Jun '10

24 Jun '10

Vacancy for a PhD or Postdoc in Multi-scale Analysis of Genomics Data at the Delft University of Technology Location - Delft University of Technology, Delft, The Netherlands Job Link - http://www.academictransfer.com/employer/TUD/vacancy/5151/lang/en/ Job description - This project aims to exploit scale-space theory for the analysis of high-throughput genomics data to delineate the complex interplay among biological elements of molecular processes that takes place in living systems. The notion of scale plays an important role in how we observe our environment. For instance, considering a tree from a distance of a light-year or a nanometre is meaningless, but would make sense at a distance of a few metres. Clearly, objects only exist as meaningful entities across a certain range of scales. In the field of machine vision, it has been argued that the only appropriate approach to this problem is to analyse data at all scales simultaneously. This has led to the scale-space theory, which provides a framework for multi-scale representation of images or other signals. We will explore scale-space representations of various sources of genomics data and investigate how we can employ these representations to benefit follow-up analyses, e.g. classification or interaction inference. The challenge will be to develop innovative methodologies that can exploit available genomics data at multiple scales simultaneously rather than at a single scale, and to explore possible applications of these methods using datasets generated at the Kluyver Centre for Genomics of Industrial Fermentation, the Netherlands Cancer Institute (NKI) and publicly available datasets.

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[Fwd: post doc position]
by laurence lins 21 Jun '10

21 Jun '10

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