March 2010 - BBClist - maillist.psb.ugent.be

PhD or postdoctoral position at Vesalius Research Center (KU Leuven, Belgium)
by Joke Reumers 30 Mar '10

30 Mar '10

A PhD or postdoctoral position in bioinformatics is available immediately at the Translational Genetics Group of the Vesalius Research Center, VIB, KU Leuven Job description: The Vesalius Research Center (VRC) is part of the Flemish Institute for Biotechnology (VIB) and is located within the University of Leuven (Belgium). In the past, VRC has has focused its research activities on angiogenesis, cardiovascular research and oncology. Using various transgenic technologies (fruit fly, frog and mouse), the functional relevance of numerous gene products has functionally been addressed in VRC, and has already led to several scientific breakthroughs with promising therapeutic applications. Currently, VRC is seeking to expand its scientific activities and interested in identifying novel genetic causes of clinically relevant disorders. To this extend, state-of-the-art high throughput technologies are being used, including large-scale next-generation sequencing of DNA and RNA samples. One of the most exciting ongoing projects concerns the analysis of full genome sequencing data of tumor samples. However, to identify the numerous genetic variations present in these tumors, complicated downstream bio-informatics analyses at the genome-wide level are necessary. We are therefore working with specialized bioinformaticians for primary data analyses (sequence assembly, mapping of deletions, amplifications, tandem duplications, invertions and inter-chromosomal rearrangements, etc), the development of novel algorithms, and downstream validation experiments (prioritization of identified genetic variants through data fusion). Additionally, novel analysis methods for the identification of mutations in highly arranged tumor samples, and to account for tumor heterogeneity (multiple tumor clones) and infiltration of normal cells (endothelial cells, fibroblasts or myeloid cells) in the tumor should be developed. Therefore, we are currently seeking for an additional bioinformatician (postdoc or PhD level) to aid in the development of these novel tools or to adapt existing tools. Requirements: - you have a master’s degree in industrial engineering or a master’s degree in biological, biomedical sciences or bio-engineering, or you have obtained a PhD in the topics of genomics or bioinformatics; - you have organizational and management skills, and you can inspire and motivate the team for work; - you have good communication skills and can cooperate easily with the different team members ; - you have passion for science and the motivation to work on an innovative and ambitious project in a open, dynamic and skilled team; - you have experience with programming languages (such as Perl, Matlab or R). Prefered skills: - experience with SNP analysis and/or structural variation analyses; - knowledge of Linux and SQL databases; - basic system administration skills are considered a plus. We offer: - a fascinating work environment in which quality, professionalism and human contact are encouraged; - the possibility to be at the start of a scientifically cutting-edge and socially relevant project; - the opportunity to contribute to the optimalisation of the workflows in genetic and transgenic research in a young and dynamic team. Starting date: As soon as a suited candidate is found. Predoctoral candidates are invited to send in a short CV, postdoctoral candidates should accompany their CV with contact details for three qualified referees, a detailed list of publications and a brief research statement by email to Diether Lambrechts ( diether.lambrechts(a)vib-kuleuven.be)

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Last CfP: Special issue of Trans Comp Sys Biol on "Computational models for cell processes"
by Ion Petre 20 Mar '10

20 Mar '10

Last call for papers: Transactions on Computational Systems Biology, special issue on Computational models for cell processes. Submission deadline: March 31, 2010 http://combio.abo.fi/special_issue_10.php Guest editors: - Ralph Johan Back (Åbo Akademi University, Finland) - Ion Petre (Åbo Akademi University, Finland) - Corrado Priami (Microsoft Research - University of Trento, Centre for Computational and Systems Biology, Italy) - Erik de Vink (Eindhoven University of Technology, the Netherlands) LNBI Transactions on Computational Systems Biology calls for paper submissions for a special issue on Computational Models for Cell Processes. Original papers are sought in all areas that relate to the relevance and potential of formal methods and computational modeling and simulation in systems biology. Of special interest are contributions that present biological processes requiring special tools and techniques that have not been investigated so far in the context of formal methods, as well as extensions of already existing formalisms introduced to improve their applicability in the life sciences. Topics of interest include, but are not limited to: - Formal models for cellular pathways - Qualitative biological modeling - Quantitative formal methods - Theoretical comparison of formalisms for biological processes - Biologically-inspired extensions to formal methods and concurrency theory - Differential, discrete and/or stochastic modeling languages - Reconstruction of biological networks based on empirical data - Decomposition and modularization of large biological networks - Applications of formal methods and computational modeling - Membrane systems as a modeling platform The list of topics is suggestive rather than exhaustive. We are open to a wide range of approaches from theoretical methodological papers to case studies. Papers should be submitted to ipetre(a)abo.fi in the LNCS format (see link below). Manuscripts submitted to this special issue should have at most 25 pages, including figures, tables, and the list of references. For queries about this special issue, please feel free to contact the special issue guest editors, Ralph-Johan Back (backrj(a)abo.fi) Ion Petre (ipetre(a)abo.fi) Corrado Priami (priami(a)cosbi.eu) and Erik de Vink(evink(a)win.tue.nl). Important dates: - Paper submissions: March 31, 2010 - Acceptance notification: June 30, 2010 - Final papers: August 31, 2010 Submission guidelines: - http://www.springer.com/computer/lncs - http://www.springer.com/computer/lncs?SGWID=0-164-7-72376-0 --- Prof. Ion Petre Department of IT, Åbo Akademi University Computational Biomodelling Laboratory Turku 20520, Finland http://www.users.abo.fi/ipetre/ --- Prof. Ion Petre Department of IT, Åbo Akademi University Computational Biomodelling Laboratory Turku 20520, Finland http://www.users.abo.fi/ipetre/

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A Post-Doctoral and a Ph.D. position in Göttingen, Germany
by Rekins Janky 17 Mar '10

17 Mar '10

A Post-Doctoral and a Ph.D. position in Computational Biology and Evolutionary Biology are available immediately in the Fasshauer lab at the Max-Planck-Institute for Biophysical Chemistry in Göttingen, Germany. The group is focusing on the protein machinery involved in the fusion of transport vesicles (see http://www.mpibpc.mpg.de/groups/fasshauer/fassh_main.htm) Recently, the biochemical approaches were successfully supplemented by computational methods. We want to establish a detailed evolutionary and functional description of the entire protein interaction network involved. To tackle the involved computational problems, we are aiming to develop new tools in the fields of parallel computing and relational databases. We are seeking outstanding candidates with a firm background in computational biology, mathematics, or computer science. Applicants should have in-depth knowledge of standard bioinformatics methods as well as software and significant experience with programming (preferable in Java) and relational databases (SQL). An interest in bringing together computational biology and biology is desirable. Good knowledge in sequence analysis, phylogenetics, and protein structure & function is a plus. The postdoc candidate may hold a Ph.D. degree in life sciences, bioinformatics, computer science, or mathematics. The Ph.D. candidate may hold a Master or equivalent in the same disciplines. Candidates should send their publication list and CV including contact details of at least two references per email to Dr. Dirk Fasshauer (dfassha(a)gwdg.de) The project is funded by the German Science Foundation (DFG). The Max Planck Society is an equal opportunity employer and particularly encourages applications from women. The Max Planck Society is committed to employing more handicapped individuals and especially encourages them to apply.

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1st Call for papers: Workshop and Tutorials on Natural Computing
by Ion Petre 15 Mar '10

15 Mar '10

Apologies for cross-postings. Please distribute. ====================================================================== WTNC 2010 4th International Workshop and Tutorials on Natural Computing Enschede, the Netherlands, October 2, 2010 http://combio.abo.fi/wtnc/ In conjunction with the 5th International Conference on Graph Transformations -------------------------------------------------------------------- === Deadline for submissions: May 31, 2010 === === Proceedings will be published in the EPTCS series === -------------------------------------------------------------------- Natural Computing is a research area concerned with computing taking place in nature and with human-designed computing inspired by nature. It is a fast growing, genuinely interdisciplinary field involving, among others computer science, biology, and mathematics. The aim of the International Workshop and Tutorials on Natural Computing WTNC 2010 is to provide a high-level scientific forum for the researchers in various areas of Natural Computing as well as to provide a cooperation forum for the Natural Computing and on Graph Transformations research communities. This is the 4th event in this series of meetings, with previous editions held in Barcelona, Spain (with ICGT 2002), Rome, Italy (with ICGT 2004), and Leicester, UK (with ICGT 2008). SUBMISSIONS ----------- Papers and extended abstracts are sought in all areas that relate to Natural Computing. Topics of interest include, but are not limited to: - Membrane systems and natural processes - Petri nets in systems biology - Computational nature of biochemical reactions - Abstract state machines in systems biology - Visual languages in systems biology - Modeling with finite and hybrid automata - Unconventional solutions to graph theoretical problems - Hierarchies of models and their refinement - Modeling with evolutionary computation - Molecular computing - Quantum computing - Neural computing Authors are invited to submit extended abstracts or full papers of up to 15 pages formatted according to the EPTCS guidelines. Submissions can be uploaded at http://www.easychair.org/conferences/?conf=wtnc2010. Simultaneous submission to other conferences or workshops with published proceedings is not allowed. The papers will be peer-reviewed and the workshop proceedings, published in the EPTCS series, will be available at the meeting. INVITED SPEAKERS ---------------- - Reiko Heckel (University of Leicester, UK) - Erik de Vink (Eindhoven University of Technology, the Netherlands) - Sander Bohte (CWI, the Netherlands) IMPORTANT DATES --------------- - Submission: May 31, 2010 - Notification: June 30, 2010 - Final version: August 20, 2010 - Workshop: October 2, 2010 PROGRAMME COMMITTEE ------------------- - Elena Czeizler (Åbo Akademi University, Finland) - Mika Hirvensalo (University of Turku, Finland) - Lila Kari (University of Western Ontario, Canada) - Giancarlo Mauri (University of Milano-Bicocca, Italy) - Gheorghe Paun (Institute of Mathematics, Academy of Romania; University of Seville, Spain) - Ion Petre (Åbo Akademi University, Finland, PC chair) - Grzegorz Rozenberg (University of Leiden, the Netherlands, PC co-chair) ORGANIZERS ---------- - Ion Petre, ipetre 'at' abo.fi - Grzegorz Rozenberg, rozenber 'at' liacs.nl - Bogdan Iancu, bogdan.iancu 'at' abo.fi - Andrzej Mizera, andrzej.mizera 'at' abo.fi Venue: University of Twente, Enschede, the Netherlands --- Prof. Ion Petre Department of IT, Åbo Akademi University Computational Biomodelling Laboratory Turku 20520, Finland http://www.users.abo.fi/ipetre/

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Text mining vacancy Concept Web (PhD student; Netherlands)
by Marco Roos 13 Mar '10

13 Mar '10

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International Computational Drug Discovery Course 2010
by Celia van Gelder 11 Mar '10

11 Mar '10

*International Computational Drug Discovery Course 2010 * June 21 - July 2, 2010 Nijmegen, the Netherlands >From June 21 - July 2 2010, the Computational Drug Discovery (CDD) Group from the Centre of Molecular and Biomolecular Informatics (CMBI) will present the eight annual Computational Drug Discovery Course. This course was developed by the CDD group together with the pharmaceutical company MSD (http://www.merck.com) and is supported by NBIC. The two week course discusses recent advances in drug discovery informatics, with a focus on the application of e-science to real life problems. The course is targeted at MSc students, PhD students, and postdocs, who are interested in the field of computational target and drug discovery. For more information see the course website (http://www.cmbi.ru.nl/ICDD2010) -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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Advances in Bio Text Mining - Second call for abstracts
by Yvan Saeys 10 Mar '10

10 Mar '10

------- Apologies for multiple postings ------- ========================= Second Call for Abstracts ========================= Workshop BioTM-2010: Advances in Bio Text Mining May 10-11, 2010, Ghent, Belgium http://www.clips.ua.ac.be/BioTM2010/index.html ============================================================ Abstracts are invited for the two-day workshop to be held in Ghent on the 10th and 11th of May 2010. Participants are encouraged to submit an extended abstract to the workshop. Authors of selected abstracts will present their work in a five minute bullet talk and their posters will be presented in a poster session. Submitted abstracts will be reviewed by the organising committee. The best abstracts will be published in an abstract supplement of BMC Bioinformatics (http://www.biomedcentral.com/bmcbioinformatics/) Submission deadline: April 1, 2010. ============================================================ The program of the workshop includes: - an extensive tutorial on Bio Text Mining by Martin Krallinger - invited talks by leading scientists in the field: Sampo Pyysalo, Kevin Cohen and Filip Ginter - invited talks by experienced scientists from industry: Jean-Marc Neefs, Luc Dehaspe and Maté Ongenaert ============================================================ Text mining has become indispensible in many biological and biomedical sciences. Having to keep up with an increasing number of publications, text mining techniques enable retrieval and analysis of large amounts of documents in a fully automated fashion. They allow for extraction of facts described in the literature that have not yet been recorded in databases, thus providing a necessary tool to obtain a complete overview of all available knowledge. Recently, the application of text mining and natural language processing techniques to the biological and medical sciences has recieved increasing interest. In addition to many new workshops and conferences arising in this domain, recently also a number of community-wide tasks were conducted to benchmark text mining techniques on specific challenges (e.g. BioCreative, BioNLP Shared Task, ...). By discussing the latest developments and potentially new applications in text mining amongst scientists in both academia and industry, this workshop aims to provide a broad view on text mining tools in biology and biomedicine. We are reaching out to a broad public, including researchers with an interest in text mining but with little or no experience in this domain. To this end, the workshop will start with an extensive tutorial on text mining in the bio-sciences, providing sufficient background knowledge for novices. Next, a number of keynote talks will be given by leading scientists, presenting the latest advances in the field. Furthermore, participants are highly encouraged to submit an abstract describing their own work. They will be given the opportunity to present this work in 5min flash presentations, as well as to present a poster during the coffee and lunch breaks. Finally, we plan on having a round-table discussion about the broader applicability of text-mining tools in the biological sciences, trying to bridge the gap between theoretical algorithms and experimental work. ============================================================ SUBMISSIONS: SCOPE Submissions should present work related to any aspect of biomedical text mining and bioinformatics. Additionally, we strongly encourage submissions that describe shortcomings of current existing techniques, tools, or resources, in order to detect problematic issues and work towards their improvement. SUBMISSIONS: INSTRUCTIONS An abstract of maximum 400 words with at most 1 table or figure should be submitted to the following e-mail address in pdf format: biotm2010 at gmail dot com Detailed formatting instructions can be found at http://www.clips.ua.ac.be/BioTM2010/call.html Submission is blind. ============================================================ IMPORTANT DATES 1 April 2010 Submission deadline 15 April 2010 Notification of acceptance 30 April 2010 Camera-ready abstracts due 10-11 May 2010 Workshop in Ghent ============================================================ ORGANISATION / PROGRAM COMMITTEE Yvan Saeys Thomas Abeel Sofie Van Landeghem Bioinformatics and Evolutionary Genomics group VIB Department of Plant Systems Biology Ghent University, Belgium Walter Daelemans Roser Morante Vincent Van Asch CLiPS - Text Mining Group Faculty of Arts University of Antwerp, Belgium -- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys@ugent.be http://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ==================================================================

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Announcement CSCDA2010
by Pierre Geurts 09 Mar '10

09 Mar '10

--- APOLOGIES FOR CROSS-POSTING--- Dear Friends and Colleagues, On behalf of the entire organizing committee, my co-chairs and myself, I'm glad to announce the first edition of Capita Selecta in Complex Disease Analysis (CSCDA2010), focusing on epistasis and integration of -omics data sets in the post-genomic era. This mini-conference will consist of two parts: 1) tutorial sessions in the afternoon of day 1 and 2) keynote speaker sessions, with discussion afternoons, on days 2-3. Our targeted audience has a background in life sciences, biomedical sciences, statistics, bioinformatics, statistical genetics or medicine. Date: 25-27 August 2010 Place: Leuven, Belgium URL: http://www.aimontefiore.org/cscda2010/ We already have an extremely impressive list of confirmed speakers for this edition! The online abstract submission facilities are active. We hope to see you in August. Please do feel free to forward this e-mail correspondence to others who you might think would be interested in the event. With best regards Kristel Van Steen ---------- Prof Dr Dr KRISTEL VAN STEEN Dept of electrical engineering and computer science (Montefiore Institute) / Bioinformatics - Statistical Genetics Tel: +32 4 366 2692 Addresse: Université de Liège Montefiore Institute BAT. B28 (Office: I140) Grande Traverse, 10 4000 Liège 1 Belgium

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Bioinformatician at the Radboud University Nijmegen Medical Center, The Netherlands
by J.Hehir＠antrg.umcn.nl 02 Mar '10

02 Mar '10

Bioinformatician position at Radboud University Nijmegen Medical Center, The Netherlands Employer description The Genomic Disorders group <http://www.genomicdisorders.nl/home> within the Department of Human Genetics in the Radboud University Nijmegen Medical Center, Netherlands works on solving human diseases through novel techniques such as genomic microarrays and next-generation sequencing. Job Description Development of data analysis methods for whole genome sequencing technologies as well as supporting data management and automation within the department of human genetics Within the department of human genetics of the RUNMC we are currently working with a new technology for the analysis of the complete human DNA. For the analysis of these huge amounts of sequencing and microarray data as well as the data management and automation we are currently looking for assistance within the current group of enthusiastic bioinformaticians. Job Requirements * Java programming skills * SQL and database administration * Preferably knowledge of the Linux OS as well as basic knowledge of genetics Job Benefits You will be working in an enthusiastic team of bioinformaticians with the newest technology for DNA sequencing. * 36 hour contract * flexible working hours Information and Application Send your application and C.V. Joris Veltman Radboud University Nijmegen Medical Center Geert Grooteplein 10 6525 GA Nijmegen The Netherlands http://www.genomicdisorders.nl/positions Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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