June 2009 - BBClist - maillist.psb.ugent.be

Bioinformatics Postdoc, Amsterdam, NL
by Lodewyk Wessels 05 Aug '09

05 Aug '09

BIOINFORMATICS POSTDOC Topic: Pathway-based tumour characterisation by alignment against cell panels along multiple molecular dimensions. Research: Astra Zeneca Oncology has constructed large cell panels to serve as in vitro models for drug response. These cell panels have been extensively characterized by mutation analysis, mRNA expression, aCGH, response to a wide variety of drugs, micro-RNA expression and phosphoprotein characterization. In parallel, the same measurements are being performed on a collection of colorectal samples. In this project two aims are pursued. First, a comparative analysis will be performed between the cell line data and the tumor data to determine the multi-dimensional molecular states spanned by the cell lines and whether these states faithfully recapitulate the space spanned by a representative and clinically relevant selection of tumor samples. Guided by this mapping and by following a pathway-based approach, integrative modeling will be applied on the cell line panel data to construct models predictive of resistance. Job description: The successful candidate will be responsible for the bioinformatics analysis of the cell line and tissue data. More specifically, these tasks include 1) constructing a comprehensive gene list of the PI3K and ERK network; 2) Molecular characterisation of the colorectal cell panel and tumour samples through integrative analysis of the various data sources within the space spanned by the identified network genes and 3) Pathway-based alignment of cell panel to tumours to determine the extent to which the cell panel recapitulates the heterogeneity in the tissue set. Location: The position is embedded within the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) at the Netherlands Cancer Institute, Amsterdam and the Oncology Informatics group, Discovery Medicine, Astra Zeneca, Alderley Park, UK lead by Dr Tim French. We plan to have regular meetings, and the postdoc will also spend time at both locations. Requirements: Candidates should fulfill the following criteria. - MSc or PhD in one of the following areas: bioinformatics, engineering, computer science, statistics, physics, biotechnology, or biology. - Knowledge of fundamental aspects of cancer biology, especially signalling pathways. - Knowledge of fundamental aspects of computer science (algorithms and data structures, programming languages). - Knowledge or experience of informatics. - Knowledge of statistics, artificial intelligence or bioinformatics is highly desirable. Conditions of Employment: The successful candidate will be employed by the Netherlands Cancer Institute. The employment conditions follow general employment rules as laid down in the 'CAO' for hospitals. The salary will be determined depending on education and experience. Contact and Applications: Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr Tim French Discovery Medicine, Cancer Bioscience, tel. +44 1625-519922 or e-mail: Tim.French(a)AstraZeneca.com. Applicants should send a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. Website: http://bioinformatics.nki.nl Closing date: 30 January 2009 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/ 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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Bioinformatics research position at DSM
by Roubos, Hans 26 Jun '09

26 Jun '09

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Tenure track: Knowledge Discovery for Predictive Personalized Medicine at K.U.Leuven, Belgium
by Kurt Driessens 24 Jun '09

24 Jun '09

Tenure track Academic Position Knowledge Discovery for Predictive Personalized Medicine The Science, Engineering and Technology Group of K.U.Leuven invites applications for a full-time academic position in the domain of Knowledge discovery for predictive personalized medicine at the Department of Computer Science. 1. DUTIES 1.1. Research The tenure track positions are intended to foster high quality research in strategically selected domains. The successful candidate will be expected to develop a research program that delivers excellent, international level research results and to support and enhance national and international research collaboration. More specifically, this research will concentrate on ‘Knowledge discovery for predictive personalized medicine’. This research is motivated by the fast development of science and technology for medicine. The use of ‘Patient Data Management Systems’ in intensive care units, combined with extensive lab tests and genetic screening, generates massive amounts of personal data on patients. The study of data from different sources and time periods provides unprecedented possibilities to discover new knowledge. One of the outcomes could be a personalized medicine that orients the therapy according to the genetic profile of the patient. The sheer amount of data, their heterogeneity and complexity, necessitates the use of knowledge discovery and data mining techniques. Knowledge discovery is a novel branch in computational sciences, which integrates techniques from databases, machine learning, knowledge technology and artificial intelligence with statistics. It is concerned with the development of new algorithms, the formalization and introduction of background knowledge and ultimately the discovery of new knowledge that can be added to the knowledge base of a given discipline. The research program should develop in close contact with the bio banking initiative for translational medicine, and lead to a fruitful collaboration with applied research in the area of patient care. Research will be conducted within the framework of the Leuven ICT Centre (LICT) and the Department of Computer Science. The successful candidate will collaborate intensively with biomedical research groups (e.g. Intensive Care Medicine). 1.2. Teaching The successful candidate will take on teaching responsibilities allocated to the Department of Computer Science in study programs of the Faculty of Engineering, Faculty of Science or other faculties. They are expected to meet the reigning K.U.Leuven standards regarding academic program level and orientation and to adhere to the K.U.Leuven’s concept of education. Commitment to quality of education as a whole is a matter of course. 2. QUALIFICATIONS Candidates should hold a PhD or doctoral degree in Engineering or in Science, with specific expertise in the domain of computer sciences or informatics. They are expected to be excellent researchers who show independence and originality. More specifically we are looking for candidates with a strong background and experience in data mining and knowledge discovery for complex data (relational data mining, graph and network mining, heterogeneous data,…), in knowledge technology and artificial intelligence for medical applications (e.g. intensive care), in interdisciplinary collaborations and fund raising. They are dedicated to high-quality teaching and will contribute to the quality of both research and teaching at the Faculty and the Department. The candidate’s research ability should be evidenced by publications in international peer-reviewed journals. International research experience is most important. In their application, candidates should include a description of objectives they wish to realise/methods they plan to use during the five-year period of the position. At K.U.Leuven the main language of instruction is Dutch. Successful applicants who are not proficient in Dutch, will be provided language training in order to be able to also instruct in the Dutch language within three years time. Near-native proficiency in the English language is expected of all applicants. The full-time position will be offered for a period of five years starting on March 15, 2010 at the level of assistant professor (docent). A positive evaluation at the end of the five-year appointment will result in a tenured appointment as associate professor (hoofddocent). The K.U.Leuven pursues a policy of equal opportunity and diversity. More information: Pierre.Verbaeten(a)cs.kuleuven.be (chair Dept. of Computer Science), Luc.DeRaedt(a)cs.kuleuven.be (Machine Learning Research Group) Maurice.Bruynooghe(a)cs.kuleuven.be (Lab for Declarative Languages and Artificial Intelligence); Should you encounter any problems with the electronic registration, please contact Katoe Buyle e-mail: katoe.buyle(a)pers.kuleuven.be tel.: +32 (0)16 328 324. See also Website: http://www.kuleuven.be/personeel/jobsite/vacatures/engineering.html Deadline for Applications 30 September 2009 -- Kurt Driessens Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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Last CfP and deadline extension: Computational Models for Cell Processes 2009
by Ion Petre 21 Jun '09

21 Jun '09

Second International Workshop on Computational Models for Cell Processes Eindhoven, the Netherlands, November 3, 2009 http://combio.abo.fi/compmod09/ In conjunction with Formal Methods 2009 -------------------------------------------------------------------- === Deadline extended: July 15, 2009 === === Proceedings will be published in the new EPTCS series === -------------------------------------------------------------------- THE MEETING ----------- Computational systems biology is an exciting new application area for applied mathematics and computer science. This workshop of the 16th International Symposium on Formal Methods fosters an excellent platform gathering researchers in formal methods and related fields that are interested in the wealth of opportunities and challenges in systems biology. SUBMISSIONS ----------- We seek papers and extended abstracts in all areas that relate to the relevance and potential of formal methods and computational modeling/simulation in systems biology. In particular, we welcome contributions that present biological processes requiring special computational and formal techniques that have not been investigated so far in the context of formal methods, as well as extensions of formal methods formalisms introduced to improve their applicability to biology. 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, concurrency theory, or logical methods - 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 Authors are invited to submit extended abstracts or full papers of up to 15 pages formatted according to EPTCS guidelines. Electronic submissions should be formatted in PDF. Simultaneous submission to other conferences or workshops with published proceedings is not allowed. A special issue of a high-level international journal, based on the workshop, is planned after the workshop. INVITED SPEAKERS ---------------- - Jasmin Fisher (Microsoft Research Cambridge) - Hidde de Jong (INRIA Grenoble - Rhone-Alpes) - Grzegorz Rozenberg (University of Leiden) IMPORTANT DATES --------------- - Deadline extended: July 15, 2009 - Notification: September 10, 2009 - Final version: October 1, 2009 - Workshop: November 2, 2009 PROGRAMME COMMITTEE ------------------- - Ralph Back, Abo Akademi, Finland - Lubos Brim, Masaryk University, Czech Republic - Muffy Calder, University of Glasgow, UK - Eugen Czeizler, Abo Akademi, Finland - Vincent Danos, University of Edinburgh, UK - Russ Harmer, University of Paris 7, France - Monika Heiner, Brandenburg University of Technology Cottbus, Germany - Jane Hillston, University of Edinburgh, UK - Ina Koch, Max Planck Institute for Molecular Genetics, Germany - Vincenzo Manca, University of Verona, Italy - Giancarlo Mauri, University of Milan-Bicocca, Italy - Satoru Miyano, University of Tokyo, Japan - Andrei Paun, Louisiana Tech University, US - Ion Petre, Abo Akademi, Finland - Jaco van de Pol, University of Twente, the Netherlands - Alberto Policriti, University of Udine, Italy - Erik de Vink, Eindhoven University of Technology, the Netherlands ORGANIZERS ---------- - Ion Petre, ipetre 'AT' abo.fi - Erik de Vink, evink 'AT' win.tue.nl - Ralph-Johan Back, backrj 'AT' abo.fi VENUE: Technische Universiteit Eindhoven, the Netherlands

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Position for postdoc and PhD student
by AHC van Kampen 19 Jun '09

19 Jun '09

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PhD position in Gent
by Stefanie De Bodt 18 Jun '09

18 Jun '09

-- PhD student Systems Biology of Yield -- Job description: For our group, we are looking for enthusiastic PhD students in bioinformatics/systems biology. You will be involved in a project which is highly complementary to ongoing research in the group, where microarray, proteomics and interaction data related to growth control is generated. You will be responsible for the application and development of computational methods to analyze and integrate these data. You will collaborate with both experimental and computational biologists to obtain a systems-level understanding of leaf growth (http://www.psb.ugent.be/groups/systems-biology-of-yield-group) . Profile: • You have a degree in Bioinformatics, Informatics or in Biotechnology/ Biochemistry/Bioengineering. • You have a good knowledge/experience in programming (Perl, R, Java and/or C++). • You have knowledge or experience with databases (mySQL). • You have an interest in web design (PHP). • You speak English fluently. • You have good communication skills. You are a team player. You are independent and like to take initiative. You are flexible. We offer a contract of 2 years, within University Gent, with the possibility of prolongation. We offer a diverse job in a young team, an open and informal work atmosphere and in modern facilities. The Department of Plant Systems Biology, VIB, University Gent (www.psb.ugent.be) is an internationally renowned and dynamic research institute that employs molecular genetics, genomics and bioinformatics to unravel developmental processes in plants and is led by Prof. Dirk Inzé. Start date: as soon as possible, the position remains vacant until a suitable candidate is found. Information: Further information can be obtained by contacting Stefanie De Bodt (stefanie.debodt(a)psb.ugent.be) Application: Send your letter of motivation, your CV and if possible references to: Hilde Diegenant Department of Plant Systems Biology Technologiepark 927 9052 Gent Tel: +32 93313806 or through email to hilde.diegenant(a)psb.ugent.be -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://www.psb.ugent.be ==================================================================

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Final CFP Machine Learning in Systems Biology (deadline extended)
by Pierre Geurts 02 Jun '09

02 Jun '09

[apologies for multiple postings] Deadline for submission has been extended to ** FRIDAY, JUNE 12 ** ************************** Call for Papers ***************************** MLSB 09 Third International Workshop on Machine Learning in Systems Biology 5-6 September 2009, Ljubljana, Slovenia *********************************************************************** http://mlsb09.ijs.si/ MOTIVATION Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the "-omics" suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. The availability of these new, highly effective tools for biological exploration is dramatically changing the way one performs research in at least two respects. First, the amount of available experimental data is not a limiting factor any more; on the contrary, there is a plethora of it. Given the research question, the challenge has shifted towards identifying the relevant pieces of information and making sense out of it (a "data mining" issue). Second, rather than focus on components in isolation, we can now try to understand how biological systems behave as a result of the integration and interaction between the individual components that one can now monitor simultaneously (so called "systems biology"). Taking advantage of this wealth of "genomic" information has become a conditio sine qua non for whoever ambitions to remain competitive in molecular biology and in the biomedical sciences in general. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms. The Workshop is organized as "core - event" of Pattern Analysis, Statistical Modelling and Computational Learning - Network of Excellence 2 (PASCAL 2, http://www.pascal-network.org/) OBJECTIVE The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. LOCATION AND CO-LOCATION The workshop will take place 5-6 September 2009 at the Jozef Stefan Institute, Ljubljana, Slovenia. It will immediately precede ECML PKDD 2009, taking place 7-11 September 2009 in Bled, Slovenia (Bled is 30 miles from Ljubljana, transport will be organized). SUBMISSIONS INSTRUCTIONS We invite you to submit an extended abstract of maximum 8 pages, formatted according to the Springer Lecture Notes in Computer Science style. Each extended abstract must be submitted online via the Easychair submission system: http://www.easychair.org/conferences/?conf=mlsb09 The extended abstracts will be reviewed by the scientific programme committee. The papers will be selected for oral or poster presentation according to their originality and relevance to the workshop topics. Electronic versions of the extended abstracts will be accessible to the participants prior to the conference and will be made publicly available on the conference web site after the conference. The accepted papers will be published in Journal of Machine Learning Research (JMLR) Workshop and Conference Proceedings (http://jmlr.csail.mit.edu/) KEY DATES ** 12 June ** deadline for submission of extended abstracts for oral presentation 03 July: notification for oral presentations 03 August: deadline for submission of abstracts for poster presentations 10 August: notification for posters & camera ready versions due 5-6 September: workshop TOPICS A non-exhaustive list of topics suitable for this workshop is given below: Methods Machine learning algorithms Bayesian methods Data integration/fusion Feature/subspace selection Clustering Biclustering/association rules Kernel methods Probabilistic inference Structured output prediction Systems identification Graph inference, completion, smoothing Semi-supervised learning Applications Sequence annotation Gene expression and post-transcriptional regulation Inference of gene regulation networks Gene prediction and whole genome association studies Metabolic pathway modeling Signaling networks Systems biology approaches to biomarker identification Rational drug design methods Metabolic reconstruction Protein function and structure prediction Protein-protein interaction networks Synthetic biology CONFIRMED INVITED SPEAKERS Ross D. King, Aberystwyth University, UK William Stafford Noble, University of Washington, USA Diego di Bernardo, University of Naples "Federico II", Italy MLSB09 PROGRAM CHAIRS Sašo Džeroski, Jozef Stefan Institute, Ljubljana, Slovenia Pierre Geurts, Department of EE and CS & GIGA-Research, University of Liège, Belgium Juho Rousu, Department of Computer Science, University of Helsinki, Finland SCIENTIFIC PROGRAM COMMITTEE Florence d'Alché-Buc, University of Evry, France Saso Dzeroski, Jozef Stefan Institute, Slovenia Paolo Frasconi, Università degli Studi di Firenze, Italy Cesare Furlanello, Fondazione Bruno Kessler, Trento, Italy Pierre Geurts, University of Liège, Belgium Mark Girolami, University of Glasgow, UK Dirk Husmeier, Biomathematics & Statistics Scotland, UK Samuel Kaski, Helsinki University of Technology, Finland Ross D. King, Aberystwyth University, UK Neil Lawrence, University of Manchester, UK Elena Marchiori, Vrije Universiteit Amsterdam, The Netherlands Yves Moreau, Katholieke Universiteit Leuven, Belgium William Stafford Noble, University of Washington, USA Gunnar Rätsch, FML, Max Planck Society, Tübingen Juho Rousu, University of Helsinki, Finland Céline Rouveirol, University of Paris XIII, France Yvan Saeys, University of Gent, Belgium Guido Sanguinetti, University of Sheffield, UK Ljupco Todorovski, University of Ljubljana, Slovenia Koji Tsuda, Max Planck Institute, Tuebingen Jean-Philippe Vert, Ecole des Mines, France Louis Wehenkel, University of Liège, Belgium Jean-Daniel Zucker, University of Paris XIII, France Blaz Zupan, University of Ljubljana, Slovenia LOCAL ORGANIZATION Ivica Slavkov, Dragi Kocev, Tina Anžič, Jozef Stefan Institute, Ljubljana, Slovenia

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Marie Curie PhD position Systems Biology on Flowering Network, Wageningen, The Netherlands
by Ham, Roeland van 02 Jun '09

02 Jun '09

PhD Systems Biology on Flowering Network Wageningen Universiteit & Research Centre, Plant Research International, Bioinformatics Wageningen (The Netherlands), 38 hours per week Reference number: 09.Biosc.08. Background: Wageningen University and Research Centre (WUR) is an internationally renowned knowledge institute in the fields of life sciences and sustainability. It makes an essential contribution to the quality of life through pioneering research and education. One of its research focal points is Systems Biology, and the Bioinformatics group has a strategic position within several of these systems biology approaches, with extensive collaborations both with experimental biology and mathematical groups within Wageningen UR. Recently, we obtained funding for an EU-funded Marie Curie PhD project, which applies systems biology to plant reproductive development. This project is highly complementary to ongoing projects in our group, which include bioinformatics analyses of protein-protein interactions of key players in this biological process, analysis of protein-DNA interactions, and application of modelling techniques to related systems such as floral organ development and the flowering transition. Job description: A position for a PhD is available in the Bioinformatics group at Plant Research International (WUR) to work on the Marie Curie project "SYSFLO" (Training in Systems Biology Applied to Flowering). This project involves collaboration with various European partners (9 PhDs in total, both experimental and computational), linking the capture of large-scale datasets to advanced computational analysis and modelling. The aim of the project is to apply systems biology to reproductive development in Arabidopsis. Laboratory-based groups will generate datasets covering e.g. spatial and temporal gene expression, network relations and chromatin accessibility. Together with other computational groups, the PhD will apply statistics, data mining and modelling in order to generate a network model. This will specifically involve 1) prediction and analysis of network interactions; and 2) computational modelling of network dynamics. Both tasks will be tightly linked to experimental data collection and will suggest validation experiments for the laboratory teams. Profile: We are looking for a communicative team player with: * A background (MsC) in computational biology, bioinformatics or related area (either biologically oriented with knowledge of mathematics or mathematics oriented with interest in biology) * Some knowledge of programming (e.g. Perl, Python or R) * The drive and skills to collaborate with both experimental and computational biologists to obtain a systems-level understanding of plant reproductive development * Good written and spoken command of English According to Marie Curie ITN rules, this position is open to all nationalities except Dutch nationals (for detailed eligibility criteria for recruitment see: ftp://ftp.cordis.europa.eu/pub/fp7/docs/fp7-mga-annex3intramulti_en.pdf <ftp://ftp.cordis.europa.eu/pub/fp7/docs/fp7-mga-annex3intramulti_en.pdf> ). Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a range of genomics and systems biology related topics; a state-of-the art computational infrastructure; close collaboration with laboratory biologists who have expert knowledge of the biological system, and with computational and mathematical experts, embedded in an international project. The position is available for 4 years, full time; this period should be finished with a PhD examination. After 12 months, the performance of the candidate will be evaluated to decide whether there is sufficient progress to expect a successful completion of the PhD thesis within the remaining period. Preferred starting date: 1 October 2009. Estimated maximum salary per month: EUR 2000 in the first year rising to EUR 2558 in the fourth year Information: dr. Aalt-Jan van Dijk, +31-317-480994, aaltjan.vandijk(a)wur.nl <mailto:aaltjan.vandijk@wur.nl> or dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl <mailto:roeland.vanham@wur.nl> . Application: Send your letter with CV and the names of two references before July 1st, 2009 to Mrs. Lydia Bikker, Plant Research International, Department Personnel & Organisation, P.O. Box 16, 6700 AA Wageningen, The Netherlands. E-mail: vacaturemeldingen.psg(a)wur.nl <mailto:lydia.bikker@wur.nl> . When applying for this job always mention the vacancy number 09.Biosc.08.

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