- BBClist - maillist.psb.ugent.be

Vacancy bioinformatician @ PSB
by Thomas Van Parys 22 Jun '11

22 Jun '11

Dear all, In order to strengthen the synergy between wet- and dry-labs within PSB, and to support the use of bioinformatics approaches by wet-lab scientists, PSB is looking for an *Experienced Bioinformatician* May we ask you to spread the vacancy attached to your colleagues in the field? -- ================================================================== Thomas Van Parys Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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PhD position on Mathematical Modeling and Machine Learning in Systems Biology, at LCSB Luxembourg
by Pierre Geurts 22 Jun '11

22 Jun '11

A fully-funded PhD position is open at the Luxembourg Centre for Systems Biomedicine, Luxembourg (http://wwwen.uni.lu/lcsb) on Mathematical Modeling and Machine Learning in Systems Biology. The research will focus on the analysis, control, and learning of (discrete) graph dynamical systems (e.g., Boolean networks) as models of real biological networks (e.g., gene regulatory networks). Particular topics include: 1) Relating stability properties of a (discrete) graph dynamical system (e.g., number of attractors) to structural properties of the underlying graph (e.g., cycle space). 2) Analysis and control of (stochastic) graph dynamical systems (e.g., via the tools of Markov decision processes, nonnegative matrices, decompositions). 3) Mathematical programming / combinatorial optimization approaches to learning such graphical models (or inferring relevant properties of those) from experimental data. The ideal candidate should have a good mathematical background (in graph theory, dynamical systems, machine learning) and speak and write fluent English. The salary is very competitive and the candidate can start immediately. Please contact Nikos Vlassis <nikos.vlassis(a)gmail.com> or <nikolaos.vlassis(a)uni.lu> for more details.

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Postdoc Positions Metabolomic Systems Biology
by R.Breitling 06 Jun '11

06 Jun '11

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head of bioinformatics solutions (job opening at BASF Plant Science)
by koen.bruynseels＠cropdesign.com 06 Jun '11

06 Jun '11

Job opening: Head of Bioinformatics solutions, BASF Plant Science Location: Ghent The main purpose of the function is to implement an overall strategy, and to plan and to coordinate resources, services and people in the global IT/Bioinformatics subfunction ?Bioinformatics Solutions?. He/she is ultimately responsible for the delivery of Bioinformatics services for all internal and external partners of the function.

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Call for papers PRIB 2011
by Thomas Abeel 02 Jun '11

02 Jun '11

International Conference on Pattern Recognition in Bioinformatics Delft, The Netherlands, November 2-4 2011 http://prib2011.org/ Call for Papers - UPDATED DEADLINE Please distributed to interested people In modern biology, high-throughput measurement devices allow scientists to gather data at unprecedented rates. To make sense of this data, computational biologists and system biologists construct quantitative models, many of which depend on pattern recognition techniques. Their application is challenging due to the large volumes of data and background information, noisy measurements and target outputs, highly diverse data types etc. The Pattern Recognition in Bioinformatics conference series aims to bring together researchers, practitioners and students from around the world to present and discuss recent developments and applications of pattern recognition methods in current bioinformatics, computational biology and systems biology. Authors are invited to submit full papers in relevant research areas, which include but are not limited to: · Bio-sequence analysis · Gene and protein expression analysis · Biomarker discovery · Protein structure and interaction prediction · Motifs and signal detection · Metabolic modelling and analysis · Systems and synthetic biology · Pathway and network analysis · Immuno- and chemo-informatics · Evolution and phylogeny · Bio-imaging · Biological databases, integration and visualisation Pattern recognition techniques of interest include: · Statistical, syntactic and structural pattern recognition · Datamining and data-based modeling · Evolutionary computation · Bayesian networks and graphical models · Neural networks and fuzzy systems Invited speakers · Yves Moreau, Bioinformatics Research Group, K.U.Leuven, Belgium. · Mark Girolami, Department of Statistical Science, University College London. · Pierre Baldi, Institute of Genomics and Bioinformatics, University of California, Irvine. · Alvis Brazma, European Bioinformatics Institute. · Berend Snel, Department of Biology, Utrecht University. Submission, Publication and Grants Papers should be submitted electronically through the conference website. Springer will publish accepted papers in its Lecture Notes in Bioinformatics series (LNBI). A limited number of Ph.D. student travel grants will be made available; please keep an eye on the website for more information. Important dates · Paper submission June 26, 2011 · Author notification July 25, 2011 · Camera-ready paper August 24, 2011 · Poster abstract submission October 2, 2011 Organisation General chairs Marcel Reinders, Delft University of Technology Dick de Ridder, Delft University of Technology Programme chairs Marco Loog, Delft University of Technology Lodewyk Wessels, Netherlands Cancer Institute Publicity chairs David Tax, Delft University of Technology Thomas Abeel, Ghent University Invited speaker chairs Jeroen de Ridder, Delft University of Technology Manuele Bicego, University of Verona Steering committee Ray Acharya, Pennsylvania State University Madhu Chetty, Monash University Tom Heskes, Radboud University Nijmegen Visakan Kadirkamanathan, University of Sheffield Elena Marchiori, Radboud University Nijmegen Jagath Rajapakse, Nanyang Technological University Guido Sanguinetti, University of Sheffield

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Stanford Center for Cancer Systems Biology Postdoc Position Available
by Olivier Gevaert 01 Jun '11

01 Jun '11

Job Location: School of Medicine Job Category: Research Date Posted: June 1, 2011 Postdoctoral Fellow in Computational Biology We are seeking a postdoctoral fellow in computational biology to study the self-renewal properties of cancer in our NIH funded Center for Cancer Systems Biology (ccsb.stanford.edu) The successful candidate will work in a multidisciplinary environment to develop and apply new computational algorithms that integrate diverse high-throughput molecular cancer datasets, including microarray gene expression, sequencing and proteomics data. The candidate will be expected to reconstruct transcriptional and signaling networks of cancer and identify likely drivers of disease progression. S/he will work closely with experimental molecular biologists to translate computationally-derived results into experimentally testable hypotheses and analyze the resulting data from the experiments. Candidates must have a strong quantitative background, with a PhD in computational biology, or related work in engineering, computer science, statistics, or mathematics. Strong knowledge in machine learning and programming (C/C++. MATLAB, or R) are required. Knowledge in graph theory, survival analysis, and sparse regression are desirable. Excellent verbal and written communication skills are essential. Interested candidates should e-mail a cover letter describing research experience, accomplishments and research interests, CV and 3 references to Professor Sylvia Plevritis, sylvia.plevritis(a)stanford.edu, with the subject line: Postdoctoral Fellowship in Computational Biology -- Anita Samantaray, MPH anitas1(a)stanford.edu Program Manager Center for Cancer Systems Biology Stanford University School of Medicine Phone: 650.725.6070 http://ccsb.stanford.edu

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INTERNSHIPS at DSM - Bioinformatics / Protein Engineering / Biostatistics
by Roubos, Hans 26 May '11

26 May '11

INTERNSHIPS: BIO-INFORMATICS / PROTEIN ENGINEERING / BIO-STATISTICS On a regular basis we have opportunities for internships in the Delft-based bioinformaticsgroup for M.Sc. students in Bioinformatics, Metabolic engineering, Protein engineering,Genomics, Synthetic Biology or Biostatistics. We apply these technologies to microbial andfungal strain engineering, bio-process and bio-product development in the areas of food,feed, pharma, biofuels and bio-based products. If you are interested in a 5-8 month periodat DSM, please send your CV and a motivation letter to: marco.groot-de(a)dsm.com<mailto:marco.groot-de@dsm.com> DSM - Life Sciences & Materials Sciences Company DSM creates innovative products and services in Life Sciences and Materials Sciences thatcontribute to the quality of life. DSM's products and services are used globally in a widerange of markets and applications, supporting a healthier, more sustainable and moreenjoyable way of life. End markets include human and animal nutrition and health, personalcare, pharmaceuticals, automotive, coatings and paint, electrics and electronics, lifeprotection and housing. DSM has annual sales of almost EUR 8.8 billion and employs some 23,000 people worldwide.Please visit our website at www.dsm.com<http://www.dsm.com/> Hans Roubos Senior Scientist Bioinformatics DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 [cid:692192906@26052011-0E3C] ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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Ph.D. studentship in bioinformatics
by Dirk VALKENBORG 19 May '11

19 May '11

Dear Colleagues, May I draw your attention to the following joint vacancy at UHasselt and VITO: Development of novel algorithms for the analysis of post-translational modifications in mass spectrometry data For more information and to apply, please visit: http://www2.uhasselt.be/actueel/vacatures/vac32147e.asp Kind regards, Dirk Valkenborg

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INSERM training workshops: genome-scale approaches to genetic and epigenetic regulation
by Jacques van Helden 16 May '11

16 May '11

The Institut National de la Santé et de la Recherche Médicale (INSERM) organizes two coupled training workshops on genome-scale approaches to genetic and epigenetic regulation. Participants can register to either workshop independently, or to both workshops. Target audience: researchers, physicians, post-docs, technicians, engineers and students in the domains of life science or bioinformatics. All conferences will be given in English. Registration deadline: June 1st, 2011. Detailed programs and registration forms: http://www.rh.inserm.fr/INSERM/IntraRh/RHPublication.nsf/mDisplayMotsClefsW… Email: ateliers(a)inserm.fr Training workshop 211: High-throughput approaches in epigenomics Organizers: Emmanuel Barillot (Institut Curie/INSERM/Mines ParisTech, Paris), Christophe Lavelle (CNRS, Muséum National d'Histoire Naturelle, Paris). Phase I (theory): October 10-12, 2011, Bordeaux (France). Phase II (practical): 2011, Paris, Montpellier, Nice/Marseille (France), and Darmstadt (Germany). Aims. Through its polymorphism, as evidenced by the heterogeneity of its physicochemical properties, chromatin is the support of an information — so-called "epigenetic" — which is superimposed to the genetic information — carried by DNA — to determine cell fate. While genetic sequencing, more and more efficient, provides data at a dizzying pace, the "epigenetic sequencing" is in turn becoming a priority in an attempt to gather all information necessary for the deciphering of cellular function. The challenge of this new quest is obvious when we know that, contrary to genetic information, epigenetic information varies from one cell to another (within the same organism) and in regard with the cell cycle, making the epigenome particularly difficult to establish. However, the first high-resolution epigenetical maps begin to emerge, including information as diverse (and complementary) as the position of nucleosomes, the presence of histone variants and their modifications, the distribution of transcription factors and remodeling factors, and location of DNA methylation. While these profiles accumulate, the need is urgent to develop analytical tools that allow efficient analysis of these data, in hopes of eventually cracking the epigenetic code. The objective of this workshop is to present the most recent techniques (mainly ChIP-seq) in this area, focusing on possible problems commonly encountered in their implementation. Beyond the "wet" technical aspects, a presentation of the most common bioinformatics tools for analysis (peak finding, differential analysis, integrative analysis of profiles, databases, ...) will also be provided. Training workshop 212: Bioinformatics approaches to decipher genome regulation from high-throughput data Organizers: Jacques van Helden (ULB, Belgium), Philipp Bucher (SIB/ISREC, Switzerland). Phase I (theory): October 12-14, 2011, Bordeaux (France). Phase II (practical): December 12-16, 2011, Marseille (France). Aims. Genome regulation plays a crucial role in embryonic development, adaptation of cells, tissues and organisms to their environment, and evolution. This regulation occurs at multiple levels: transcription, RNA maturation (splicing, degradation), micro-RNA, nucleosome occupancy, chromosome conformation. New high-throughput methods offer unprecedented ways to characterize regulatory elements at a genome scale: expression microarrays, ChIP-on-chip, ChIP-seq, RNA-seq, protein binding arrays, etc. Sequencing platforms become available in many institutes, but researchers generally feel some perplexity when they are first confronted to the terabases of novel data. New software tools re being developed to answer those new needs, but their utilization requires to understand the underlying principles, master the parameters, and interpret the significance of the result. The goal of this workshop is to provide researchers with a theoretical and practical training enabling them to apprehend the whole flow of data analysis, from data acquisition to biological interpretation of the results. Jacques van Helden Jacques.van.Helden(a)ulb.ac.be http://www.bigre.ulb.ac.be/Users/jvanheld/ Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) Université Libre de Bruxelles, CP263 Boulevard du Triomphe, Accès 2, Campus Plaine. B-1050 Bruxelles, Belgium

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Support Letter for BEDTools!!
by Stéphane Plaisance 11 May '11

11 May '11

Dear all, If you use BEDTools in your daily work, please consider supporting Aaron by following his instructions below. I am a great fan of BEDTools and find that Aaron greatly deserves this for all the time he saved me with BEDTools in the last years. Stephane Begin forwarded message: > From: bedtools-discuss+noreply(a)googlegroups.com > Date: 10 May 2011 23:53:00 GMT+02:00 > To: Digest Recipients <bedtools-discuss+digest(a)googlegroups.com> > Subject: [bedtools-discuss] Digest for bedtools-discuss(a)googlegroups.com - 2 Messages in 2 Topics > Reply-To: bedtools-discuss(a)googlegroups.com > > Today's Topic Summary > Group: http://groups.google.com/group/bedtools-discuss/topics > > BEDTools Needs Your Support! [1 Update] > Topic: BEDTools Needs Your Support! > Aaron Quinlan <aaronquinlan(a)gmail.com> May 09 10:26PM -0400 ^ > > Dear BEDTools User, > > Thus far, BEDTools has had no formal funding and has been supported by myself and a handful of talented and dedicated contributors. A primary goal of my new laboratory is to continue to improve, support and maintain these tools. More ambitiously, I intend to develop a suite of scalable and efficient algorithms for genome arithmetic (e.g., intersect, count, complement, subtract, merge) in order to accommodate the size and complexity of current and future genomic datasets. These new algorithms will be capable of interrogating multiple datasets at once (i.e., moving beyond pairwise comparisons), use less memory, exploit parallel computing architectures, and will have improved support for many more file formats. In turn, "BEDTools 2" will provide entirely new classes of tools for large-scale genomic analyses. > > In order to fulfill these goals, I am seeking NIH funding and I would like to ask for your help. If you find BEDTools to be at all useful in your research, I would like to ask you to write a brief letter of support. Your letter will be included as a supplement to the grant application and it will greatly improve the strength of the grant. > > If you would be willing to document your support of BEDTools, I ask that you: > > - Send an email directly to me (aaronquinlan(a)gmail.com) Please include your name and affiliation. > - Write a few sentences documenting: > . your support for the project > . how you use the tools > . what, if anything, you like about them. > . how they have benefited, improved, or expedited your research. > > Thanks so much in advance for your assistance - a couple of minutes writing an email of support will certainly help me immensely. > > If you know of other users that are not on the BEDTools list but might be interested in helping out, please pass this on. > > Sincerely, > Aaron > > Aaron Quinlan, Ph.D. > Assistant Professor > Department of Public Health Sciences > Center for Public Health Genomics > University of Virginia

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