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

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/

1 1

NBIC/SIB Summer School: Quantitative imaging and modelling of biological processes, 2-6 Aug 2010, Amsterdam
by Celia van Gelder 30 May '10

30 May '10

NBIC/SIB Summer School: Quantitative imaging and modelling of biological processes 2-6 August 2010, Science Park, Amsterdam The ability to directly observe how biological systems "work" at a molecular level would help in finding answers to many biological questions. Current imaging technologies enable the acquisition of massive numbers of images, yet a timely and accurate analysis of such data can only be done with appropriate computational methods. Systems biology, with its aim of integrating complex measurements in order to understand the functioning of biological systems, is expected to make heavy use of imaging data. Recognising the importance of bioimaging for systems biology, the Swiss Institute of Bioinformatics (SIB) and the Netherlands Bioinformatics Centre (NBIC) have joined forces to organise the first NBIC/SIB Summer School on 2-6 August, 2010 in Amsterdam. The Summer School focuses on "Quantitative imaging and modelling of biological processes". The topics that will be covered by leading scientists in the field include: fundamentals of biomedical image processing and image annotation, image-based modelling and simulation, imaging of specific cellular compartments, cell motility, morphogenetic processes and small animals. For more information about the programme and registration please visit http://www.nbic.nl/education/nbic-phd-school/nbicsib-summerschool/ or contact Celia van Gelder at NBIC Education (celia.van.gelder(a)nbic.nl) -- 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 __________ Information from ESET NOD32 Antivirus, version of virus signature database 5155 (20100530) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com

1 0

Last call for papers (deadline extended): Workshop and Tutorials on Natural Computing
by Ion Petre 25 May '10

25 May '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: Extended to June 11, 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/

1 0

International Conference on Pattern Recognition in Bioinformatics: submission deadline 5 June
by Elena Marchiori 22 May '10

22 May '10

Apologies if you receive multiple copies of this annoucement. ============================================================================= Deadline for PRIB 2010 has been moved to 5 June 2010! ***************** PRIB-2010 CALL FOR PAPERS ****************** 5th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB-10) 22-24 September 2010, Nijmegen, The Netherlands http://www.prib2010.org/ +++ PRIB-2010 +++ The Pattern Recognition in Bioinformatics conference aims to bring together top researchers, practitioners and students from around the world to discuss the applications of pattern recognition methods in the field of bioinformatics to tackle problems in the life sciences. Prospective authors are invited to submit papers in the research areas of interest to the conference. These include: * Bio-sequence analysis * Gene and protein expression analysis * 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 * Biological databases, integration and visualisation * Bio-imaging Pattern recognition techniques of interest include, but are not limited to: * Static, syntactic and structural pattern recognition * Data mining, Data based modelling * Neural networks, Fuzzy systems * Evolutionary computation and swarm intelligence * Hidden Markov models, Graphical models... +++ Papers Publication +++ Like the previous editions, accepted papers of PRIB-2010 will be published in the Springer series of Lecture Notes in Computer Science (LNCS) - Lecture Notes in Bioinformatics (LNBI). Enhanced versions of selected papers will be included in a special issue of Neurocomputing Journal (Elsevier).

1 0

PhD studentship in bioinformatics/text mining
by Thomas Van Parys 21 May '10

21 May '10

Mining protein interaction data and its context from the scientific literature Goran Nenadic1 and David Robertson2 1School of Computer Science, Univ. of Manchester, 2Faculty of Life Sciences, Univ. of Manchester. We invite applications for a four year BBSRC-funded CASE studentship commencing in the academic year 2010/11. The studentship is open to UK/EU applicants and will pay tuition fees in addition to a starting stipend of £15,790 pa for UK students and £13,000 pa for EU student. It will also involve a research placement with the industrial CASE partner, Pfizer Global R&D in Sandwich, Kent. The project will involve research on the context of protein interaction data from the scientific literature. The main archive of life sciences literature currently contains more then 17 million references and grows by approximately 2,000 articles every day. This biomedically relevant information is invaluable and represents a rich source of knowledge. However its current, let alone future size, is rendering it virtually impossible for individuals scientists to keep the pace with publications in their own area, let alone related ones. This has led to the generation of secondary databases that mine specific information from the published literature. For example, much emphasis has been placed on using text mining (often manually) to identify protein interactions. However, little attempt is made to capture the context of such information, how reliable it is, what is the nature of interaction etc. This project will study the way findings, experiments and knowledge about protein interactions is presented in the literature, and in particular how contextual information that details a protein interactions are encoded and presented. To do this we will implement a state of the art text mining framework to extract from full-text articles, link and contrast protein interaction contextual information with data in other (structured) resources to support informed decisions for understanding the complexity of interactions and identification of potential drug targets. To be relevant to the industrial partner (Pfizer R&D), focus will be placed on pharmaceutically relevant protein interaction data sets, for example, pathogens such as HIV, hepatitis viruses, malaria etc. The knowledge extracted will be characterised by quantitative measures that may be indicative of its quality or relevance for a specific interaction (bibliometrics such as number of citations and mentions; peaks and changes over time; association with specific entities such as experimental methods, model systems, drug associations, outcomes, etc.). Importantly, the general framework developed for placing biomedical 'facts' in context will be applicable to other text mining domains. Applicants should ideally have experience in computational biology, bioinformatics, computer science or a related subject area. Knowledge of a programming language and text and/or data mining would be a distinct advantage. For details on how apply go tohttp://www.ls.manchester.ac.uk/postgraduate/studentships . Please e-mailDavid.Robertson(a)manchester.ac.uk orG.Nenadic(a)manchester.ac.uk if you require further details

1 0

post-doc position systems biology
by Schroen B (CARDIO) 20 May '10

20 May '10

Open position for post-doc or senior investigator. Systems biology of diastolic heart failure. We are looking for a highly motivated post-doc or senior investigator with a (bio)medical background to perform gene network analyses in the field of heart failure, in particular diabetes-induced diastolic heart failure. He/she will work at the dynamic Cardiovascular Research Institute of Maastricht (CARIM), Maastricht University, within the department of Cardiology. The present research project will focus on the integration of different omics, computational modeling of disease and search for epigenetic marks of diastolic heart failure (DHF). This project is part of an EFP7 consortium (MEDIA), which will start at the end of 2010. Aims: 1. Study sequential changes of cardiac omics in diastolic heart failure (DHF). 2. Investigate gene networks and complex interactions between omics in DHF. 3. Search for modified epigenetic marks (acetylation, methylation) in myocardial genes during DHF. Profile: Cfr aims. * Candidate should hold a PhD degree in a relevant field, with a background in both bioinformatics and biomedical sciences. * Experience in bioinformatical integration of different level omics in disease as compared to normal tissues: applicant holds experience in integrating this information to build complex gene networks. * Knowledge about the epigenetic processes and post-translational modifications that control gene expression. We are offering a competitive salary and funding for 3 years. To apply please send a CV to, or for more information contact, S.Heymans(a)cardio.unimaas.nl<mailto:S.Heymans@cardio.unimaas.nl>

1 0

12th International EMBL PhD Student Symposium - From Science Fiction to Science Fact
by Sander Timmer 19 May '10

19 May '10

The European Molecular Biology Laboratory (EMBL) is a leading institute for research in molecular life sciences and the annual International EMBL PhD student symposium in Heidelberg is an outstanding event in the scientific world. For this event, every autumn over the past 11 years, EMBL gathers young researchers from numerous scientific institutes, mostly graduate students and postdoctoral fellows. Previous symposia covered many interesting topics, including decision making in biology, neurobiology and patterns in biology. The organisers are proud to announce the 12th EMBL PhD Symposium "From Science Fiction to Science Fact: What's next?", which will take place in Heidelberg, Germany on 21-23 October 2010. Join us for a unique experience of a student-led symposium complemented by participation of the world's renowned scientists. The current boundaries in different fields of life sciences will be investigated, in light of how past frontiers have been overturned. World-renowned speakers will be invited to share their ideas on latest technological breakthroughs, achievements and future developments with the young generation of scientists. We will explore a diverse array of topics ranging from structural and cell biology to biophysics and medicine. Participants will also have the opportunity to present and discuss their own work in poster sessions and selected short talk segments. The program and registration is now available on the website: http://phdsymposium.embl.org. Keynote speakers are: Peter Hildebrandt, TU Berlin Paul Jarvis, University of Leicester Angus Lamond, University of Dundee Petra Schwille, TU Dresden Fabrizio d'Adda di Fagagna, IFOM Milano Christian Haass, TU München Rudolf Aebersold, ETH Zürich Len Pennacchio, JGI, California Gero Miesenböck, University of Oxford Miroslav Radman, Université Paris 5 Early bird fee ends June 15th. There are several registration stipends available. We highly encourage participants to share their work and present a talk or poster and to participate in the writing prize. Please forward this announcement to anyone who might be interested. -- Sander Timmer PhD Student - Ewan Birney Group EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom http://www.ebi.ac.uk/~swtimmer/

1 0

Extended deadline META'2010
by Talbi El-Ghazali 17 May '10

17 May '10

[We apologize for cross-postings] ***** SUBMISSION DEADLINE EXTENDED TO June, 5th 2010 ***** ********************************************************************** META'2010 International Conference on Metaheuristics and Nature Inspired Computing 28-30 Oct 2010 Djerba Island, Tunisia http://www.lifl.fr/META10 ********************************************************************** The 2nd International Conference on Metaheuristics and Nature Inspired Computing, META’10, will held in Djerba Island, Tunisia from 28 to 30 Oct 2010. The Conference will be an exchange space thanks to the sessions of the research works presentations and also will integrate tutorials and a vocational training of metaheuristics and nature inspired computing. The scope of the META’2010 conference includes, but is not limited to: * Local search, tabu search, simulated annealing, VNS, ILS, … * Evolutionary algorithms, swarm optimization, scatter search, … * Emergent nature inspired algorithms: quantum computing, artificial immune systems, bee colony, DNA computing, … * Parallel algorithms and hybrid methods with metaheuristics, machine learning, game theory, mathematical programming, constraint programming, co-evolutionary, … * Application to: logistics and transportation, telecommunications, scheduling, data mining, engineering design, bioinformatics, … * Theory of metaheuristics, landscape analysis, convergence, problem difficulty, very large neighbourhoods, … * Application to multi-objective optimization * Application in dynamic optimization, problems with uncertainty, … Submission papers: _________________ - Submission of papers should be in shape of an abstract of two pages sent before the June, 5th 2010 via the website. - Selected papers will be published in international journals (ISI journals): COR, ITOR, JMMA, ... - Predefined styles are available on the website http://www.lifl.fr/META10 that we invite you to visit regularly and which evolves when the organization progresses. - Invited sessions and tutorials: Deadline 15th May 2010. contact talbi(a)lifl.fr E-G. Talbi ( Conference Chair) K. Mellouli (Co-chair) PC Members (to be completed) - B. Aghezzaf (MO) - M. Aider (DZ) - A. M. Alimi (TN) - E. Alba (ES) - R. Battiti (IT) - M. Batouche (SA) - F. Ben Abdelaziz (TN) - J. Blazewicz (PL) - C. Blum (ES) - P. Bouvry (LX) - E. Burke (UK) - A. Caminada (FR) - H. Chabchoub (TN) - T. Crainic (CA) - K. F. Doerner (AT) - M. Dorigo (BE) - H-B. Duan (CN) - P. Festa (IT) - S. Fidanova (BU) - J. Figueira (PO) - M. Gendreau (CA) - M. Gourgand (FR) - M. Gravel (CA) - S. Hanafi (FR) - J-K. Hao (FR) - M. Haouari (TN) - P. Isasi (ES) - M. Krajecki (FR) - M. Laguna (US) - A. Lokketangen (NW) - T. Loukil (TN) - S. Martins (BR) - R. Middendorf (D) - N. Monmarché (FR) - I. H. Osman (LE) - M. Pirlot (BE) - G. Raidl (AT) - M. Resende (US) - C. Ribeiro (BR) - M. Schoenauer (FR) - M. Sevaux (FR) - P. Siarry (FR) - K. Sorensen (BE) - T. Stutzle (BE) - J. Teghem (BE) - M. Toulouse (CA) - K-C. Tan (SG) - X-S. Yang (GB) - A. Zomaya (AU) Organizing Committee (to be completed): * Laetitia Jourdan (chair) * Clarisse Dhaenens (INRIA) * Arnaud Liefooghe (INRIA) * Marie-Eléonore Marmion (INRIA) * H. Masri (ISG, Tunisia) * A. Klabi (ISG, Tunisia)

1 0

Postdoc position in Systems Biology
by Thomas Van Parys 17 May '10

17 May '10

Postdoc position in Systems Biology The Division of Bioinformatics and Systems Biology at the VIB Department of Plant Systems Biology, Ghent University invites applications for an Expert Scientist position in the field of Computational Systems Biology. We seek highly-motivated individuals with an interest in developing novel algorithms and software tools for the integration of high-throughput genomic data and the inference and modelling of regulatory networks. The ideal candidate should hold a doctoral degree in a relevant field (physics, computer science, applied mathematics, engineering or life sciences), with several years of postdoctoral experience, and have a proven record of its application for the life sciences. Major duties include: - Responsible for the functioning of a small group of researchers (PhD students and postdocs). - Develop new and innovative (breakthrough) projects in line with the strategic plan of the Department and VIB. - Provide scientists in the Department and VIB with transfer of in-depth knowledge. - Transfer science into publications in high impact journals. - Detect potential technology transfer possibilities. The position will initially be available for 2 years (starting September 1st, 2010), with the possibility of a 3 year extension depending on positive evaluation. For further information please consult our homepage (http://bioinformatics.psb.ugent.be/) or contact the Scientific Director Prof. Dr. Yves Van de Peer (yves.vandepeer(a)psb.vib-ugent.be <mailto:yves.vandepeer@psb.vib-ugent.be>). Applications including a motivation letter, CV, list of publications, names and contact information of three references and a research proposal (2-3 pages) should be sent to Prof. Dr. Yves Van de Peer before July 1st 2010.

1 0

Temporary Position: Scientist Bioinformatics at Tibotec
by Van Vlijmen, Herman [TIBBE] 10 May '10

10 May '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: * Analysis 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. * Visualization of complex data with specialized tools * Executing database queries for data mining Qualifications * Master's degree in Bioinformatics or a related field with at least one year of relevant experience in academia or industry, or Ph.D. 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

1 0