March 2011 - BBClist - maillist.psb.ugent.be

Bioinformatics Postdoc
by Lodewyk Wessels 02 Dec '12

02 Dec '12

POST DOCTORAL BIOINFORMATICIAN IDENTIFICATION AND VALIDATION OF NEW TARGETS FOR COLORECTAL CANCER OVERALL OBJECTIVES The aim of this project is to redefine colorectal cancer (CRC) at the molecular level, by identifying and validating new activated pathways and specific drug targets for defined CRC patient populations. The project will employ the complementary expertise and tools at Astra Zeneca, two academic laboratories (those of Lodewyk Wessels and Rene Bernards at the Netherlands Cancer Institute, Amsterdam) and a leading diagnostics company with an established presence in oncology (Agendia BV, Amsterdam). PROJECT OUTLINE AND STRATEGY We will first use computational approaches to perform a ‘pathway’ or ‘module’ level integration of molecular profiling (gene expression and next generation sequencing data) and extensive clinical annotation data from a collection of 400 CRC tumours to identify and prioritise pathways that are deregulated in each CRC sub-disease. Next, we will define for each pathway, targets that are amenable to drug discovery efforts, and that can be validated in cell culture models. To enable target validation, we will develop approaches to identify, based on molecular profiling data, CRC cell lines in the AZ collection that represent each molecular sub-disease. Once these are in place, target validation experiments will be conducted, using established RNAi methodology. Targets whose functions are shown to be essential for cell viability in the appropriate cell line models will then be recommended for new drug discovery projects. These results will be fed back to refine the target section procedure based on the tumor data. 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 (Wessels lab.) 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. REQUIREMENTS The ideal candidate is a highly motivated postdoc with a strong background in bioinformatics or computational biology. 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: Bernards lab, Astra Zeneca and Agendia. The ideal candidate has a background in the analysis of high throughput molecular data, computational diagnostics, bioinformatics, computer science, statistics or physics with strong analytical and algorithmic skills. 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? Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr George Orphanides, Director of Discovery Medicine, tel. +44 1625 232312 or e-mail George.Orphanides(a)astrazeneca.com. When applying please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. http://bioinformatics.nki.nl CLOSING DATE 1 May 2011

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Integrative Bioinformatics 2011: 2nd call for abstracts
by Jack Leunissen 16 Jul '12

16 Jul '12

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We invite you to register for the conference, and to send in an abstract for a presentation at the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the IB2011 Special Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract is January 15th; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011. The best poster will receive an award sponsored by IMBio e.v. The conference website is open for registration and abstract submission, and can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. We hope to meet you in March in Wageningen. On behalf of the organizing committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V. == Disclaimer: We have tried our best to remove duplicate e-mail addresses from our mailing list to reduce the amount of clutter in your mailbox. It may nevertheless still happen that you receive this mail via different channels. We apologize if you receive this mail more than once.

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reminder - Conference: Comparative and Regulatory Genomics in Plants , 11-12 April 2011
by Klaas Vandepoele 28 Mar '11

28 Mar '11

Friendly reminder: the registration deadline is March 31st 2011. Full programme is available at http://bioinformatics.psb.ugent.be/crg_event/conference/programme The first international Conference on *Comparative and Regulatory Genomics in Plants* will be held at VIB - Ghent University, Belgium April 11-12, 2011. This conference will give an overview of the most recent developments in plant genomics and will discuss the integration of experimental high-throughput data with computational approaches to study gene functions, genome organization and transcriptional regulation. A panel of international invited speakers includes experts in the field of plant next-gen genome sequencing, genome evolution, comparative transcriptomics, ChIP profiling and plant regulatory networks. More information including invited + contributed speakers is available here: http://bioinformatics.psb.ugent.be/crg_event/conference/about Best regards, the scientific committee, Klaas Vandepoele /apologies for double postings/ -- Prof. Dr. Klaas Vandepoele Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/cig/ --------------------------------------------------------- Conference& Workshop Comparative& Regulatory Genomics in Plants Website: http://bioinformatics.psb.ugent.be/crg_event/ ---------------------------------------------------------

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Sixth Summer School on Advanced Statistics and Data Mining (Madrid, July 4th - July 15th, 2011)
by Rubén Armañanzas 25 Mar '11

25 Mar '11

Dear colleagues, The Technical University of Madrid (UPM) again organizes the summer school on 'Advanced Statistics and Data Mining' in Madrid between July 4th and July 15th. This year's programme comprises 17 courses divided in 2 weeks. There are new 5 courses not previously offered in the previous edition. Attendees may register in each course independently. Registration is now *OPEN*. Extended information on courses programme, price, venue, accommodation and transport is available at the school's website: http://www.dia.fi.upm.es/ASDM Best regards, -- The coordinators of the school. *List of courses and brief description* Week 1 (July 4th - July 8th, 2011) Course 1: Bayesian networks (15 h) Bayesian networks basics. Inference in Bayesian networks. Learning Bayesian networks from data. Course 2: Statistical inference (15 h) Introduction. Some basic statistical test. Multiple testing. Introduction to bootstrapping. Course 3: Probabilistic modelling for evolutionary computation (15 h) Evolutionary algorithms. Estimation of distribution algorithms. EDAs for discrete, continuous and multi objective optimization problems. Real-world applications. Course 4: Supervised pattern recognition (Classification) (15 h) Introduction. Assessing the Performance of Supervised Classification Algorithms. Classification techniques. Combining Classifiers. Comparing Supervised Classification Algorithms. Course 5: Multivariate data analysis (15 h) Introduction. Data Examination. Principal component analysis (PCA). Factor Analysis. Multidimensional Scaling (MDS). Correspondence analysis. Multivariate Analysis of Variance (MANOVA). Canonical correlation. Course 6: Neural networks (15 h) Introduction to the biological models. Nomenclature. Perceptron networks. The Hebb rule. Foundations of multivariate optimization. Numerical optimization. Rule of Widrow-Hoff. Backpropagation algorithm. Practical data modelling with neural networks. Course 7: Features Subset Selection (15 h) Introduction. Redundancy and irrelevance. Filter approaches. Wrapper methods. Embedded methods. Drawbacks and future strands. Stability and consistency. Practical session with presentation. Course 8: Regression (15 h) Introduction. Simple Linear Regression Model. Measures of model adequacy. Multiple Linear Regression. Regression Diagnostics and model violations. Polynomial regression. Variable selection. Indicator variables as regressors. Logistic regression. Non-linear Regression. Week 2 (July 11th - July 15th, 2011) Course 9: Hot topics in intelligent data analysis (15 h) Multi-label and multi-dimensional classification. Advanced Bayesian classifiers. Data streams in a semi-supervised learning context. Advanced Clustering. Spatial and circular point patterns. Course 10: Machine learning in computer vision (15 h) The scene understanding problem. Visual features for object detection and classification. Usual classification techniques in computer vision. Object detection. Object classification. Course 11: Hidden Markov Models (15 h) Introduction. Discrete Hidden Markov Models. Basic algorithms for Hidden Markov Models. Semi-continuous Hidden Markov Models. Continuous Hidden Markov Models. Unit selection and clustering. Speaker and Environment Adaptation for HMMs. Other applications of HMMs. Course 12: Time series analysis (15 h) Introduction. Probability models to time series. Regression and Fourier analysis. Forecasting and Data mining. Course 13: Data mining: A practical perspective (15 h) Introduction to Data Mining and Knowledge Discovery. Prediction in data mining. Classification. Association studies. Data mining in free-form texts: text mining. Course 14: Unsupervised pattern recognition (clustering) (15 h) Introduction. Prototype-based clustering. Density-based clustering. Graph-based clustering. Cluster evaluation. Miscellanea. Course 15: Support vector machines and kernel methods (15 h) Linear classifiers. Perceptrons. Linear SMVs. Non-linear SVMs. Kernelization. Support Vector Regression. Related models. SVM Learning algorithms. Kernel PCA. Kernel FDA. Kernel K-means. Course 16: Practical statistical questions (15 h) The basics. How do I collect the data? Experimental design. Parameter estimation. Correlation. Hypothesis testing. Sample size. Study of cases of different fields. Course 17: Statistics and machine learning with R (15h) The R environment. Data in R. Programming in R. Graphics in R. Statistical Analysis with R. Practical sessions

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Vacancy: Scientific database curator
by Henning Hermjakob 24 Mar '11

24 Mar '11

Location: EBI - Hinxton, UK Staff Category: Staff Member Contract Duration: 3 years Grading: 5 or 6, depending on experience and qualifications Closing Date: 10 April 2011 Reference number: EBI_00070 Job Description We are seeking a Scientific Database Curator, to join the Proteomics Services team at the European Bioinformatics Institute (EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK. The Database Curator will contribute to the maintenance and extension of the IntAct molecular interaction database. The main task is the analysis of published literature on protein interactions and their integration into the IntAct database. The successful candidate will also interact with external data producers and international partner databases to ensure highest quality standards for IntAct data. The European Bioinformatics Institute (EBI) provides cutting-edge research, service and training in the field of bioinformatics and is home to world class bioinformatics resources such as Ensembl, UniProt, and InterPro. For further information please visit http://www.ebi.ac.uk/intact/ Qualifications and Experience The ideal candidate will hold a PhD or MSc in molecular biology, biochemistry, or a related subject. An interest in bioinformatics is required, prior experience in database curation, analysis of protein interactions, molecular pathways or cellular complexes is a plus. The post holder should be able to work independently and interact well within a team environment. Good communication and interpersonal skills as well as a working knowledge of English language are essential. Application Instructions Please apply online through www.embl.org/jobs -- Best regards, Henning ----------------------------------------------------------------------- Henning Hermjakob Team Leader Proteomics Services Email: hhe(a)ebi.ac.uk European Bioinformatics Institute Tel: + 44 1223 49 4671 Wellcome Trust Genome Campus Fax: + 44 1223 49 4468 Hinxton, Cambridge CB10 1SD Http://www.ebi.ac.uk/proteomics United Kingdom

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Announcement Wabi 2011
by Thomas Van Parys 24 Mar '11

24 Mar '11

Dear Colleague, We are pleased to announce the call for papers for WABI'11, the 11th Workshop for Algorithms in Bioinformatics. WABI will be part of ALGO 2011, and will be hosted by the Max-Planck-Institut für Informatik, Saarbrucken, Germany. The conference will run from Sept 5 to 7, 2011, and the submission deadline is May 10, 2011. We welcome papers on algorithmic work in bioinformatics, computational biology and systems biology. Please see our provisional website for details: http://pbil.univ-lyon1.fr/members/sagot/htdocs/wabi2011/wabi2011.html We would be grateful if you could help us distribute this around, in particular send it to lists you know. Thank you! Teresa Przytycka and Marie-France Sagot

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NSBM Spring Meeting
by Nicolaes G (BIOCH) 24 Mar '11

24 Mar '11

Dear scientist, The NSBM cordially invites you to visit its spring meeting, which is being held in conjunction with the NBIC conference 2011. During several parallel sessions, the floor will be given to PhD students and postdocs who study protein structure and/or structural bioinformatics or related topics (see a list below). Speakers and attendees will have the opportunity to join the NBIC activities and visit key note lectures by *Bas van Steensel*of the Netherlands Cancer Institute and by *Phil Bourne*, Associate Director of the RCSB Protein Data Bank, past President of the International Society for Computational Biology and co-founder and Editor-in-Chief of the open access journal PLoS Computational Biology, who will be invited to the NSBM lectures. ** * * *Abstract Format* Abstracts should be limited to a maximum of 10 lines, with 12-pt font and single-spaced text, giving a short description of the research done. Please include a title in bold. The name(s) and affiliation(s) of the author(s) should follow the title. The opportunity will be given to present a poster, though this is not mandatory. If you wish to present a poster, please indicate so. *Abstract Submission* All abstracts, also for those who already registered for the NBIC meeting, should be submitted electronically in MSWord via e-mail attachment to: g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> <mailto:g.nicolaes@maastrichtuniversity.nl> The deadline for receipt of all abstracts is April 12^th 2011. Selected candidates will be notified no later than April 13^th 2011. Presentations will be 20 min, including a 5 min discussion, with the best abstract being allocated a 30 min time slot. Starting PhD students are particularly encouraged to present their research. For questions regarding the abstract or meeting please contact Gerry Nicolaes, +31-(0)43 3881688, g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> <mailto:g.nicolaes@maastrichtuniversity.nl> *Registration* Registration can be performed through the NBIC site at: http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2011/ The 1-day conference fee amounts €60,- for NBIC members and € 75,- for non-NBIC members and includes participation to the conference and poster sessions on April 20^th , abstract book, lunch, coffee/tea during breaks, internet access. Should a lack of funding be a hurdle for visiting the NSBM Spring Meeting, please contact prof. Gert Vriend at g.vriend(a)cmbi.ru.nl<mailto:g.vriend@cmbi.ru.nl> so that an arrangement can be made.** ** *Topics for presentations may include, but are not limited to:* • Computational Biology and Bioinformatics • Computer-aided drug design • Drug design and drug discovery • Grid computing • Homology modelling • Molecular and supramolecular dynamics • Molecular modeling and simulation • Mutational analysis • Protein crystallography • Protein NMR • Protein structure analysis • Protein structure prediction • Protein-protein interactions • Protein-small molecules interaction • Protein software design • Proteomics • Structural bioinformatics • Structure-function analysis • Text mining & information extraction • Virtual screening *Links* /http://www.nbic.nl/about-nbic/events/all-events/detail/article/nbic-conference-2011/ / / Gerry Nicolaes Gert Vriend NSBM ------------------------------------------------------------------------------------ G.A.F. Nicolaes, PhD Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 6200 MD Maastricht the Netherlands visiting address: Universiteitssingel 50 6229 ER Maastricht the Netherlands tel.: +31-43-3881688 fax: +31-43-3884159 -------------------------------------------------------------------------------------- The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UM cannot be held responsible for incomplete reception or delay of this transferred message.

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BioMagnet General Meeting 2011 - Bridging the gap between bioinformatics and modelling
by Jacques van Helden 10 Mar '11

10 Mar '11

Dear colleagues, Please find hereby the announcement of the Annual General Meeting of the Inter-University Attraction Pole BioMagnet (IAP 6/25 funded by the Belgian Scientific Policy). Full program and registration at http://homes.esat.kuleuven.be/~sistawww/biomagnet/. Best regards 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 BioMagnet general meeting 2011 Bridging the gap between bioinformatics and modeling Monday March 21 from 10h to 18h Université Libre de Bruxelles Auditorium Solvay, Building NO, Campus Plaine, Boulevard du Triomphe Access 2, 1050 Brussels http://www.ulb.ac.be/campus/plaine/plan-NO.html Practical info Registration: before March 11 on the Web site (http://homes.esat.kuleuven.be/~sistawww/biomagnet/) Poster registration: a short abstract (1/2 page) should be sent to Myriam Loubriat (mloubria(a)ulb.ac.be) before March 11. Note that the space for posters will be limited. Registration fee: 20€/ for external participants (i.e. non-members of the BioMagnet consortium). The fee covers the sandwich lunch + 2 coffee breaks + welfare drink. Preliminary program 9:30 Welcome of the participants 10:00-12:30 Morning session 10:00-10:10 Introductory talk (Jacques van Helden) 10:10-10:50 Albert Goldbeter and Claude Gérard (Université Libre de Bruxelles) Dynamics of the network of cyclin-dependent kinases driving the mammalian cell cycle 10:50-11:10 Coffee break 11:10-11:50 Yvan Saeys (Universiteit Gent) Large scale text mining challenges for systems biology. 11:50-12:30 Yves Moreau (Katholieke Universiteit Leuven) Genomic variation for genetic diagnosis. 12:30-14:00 Sandwich lunch + posters (+ coordination meeting for the BioMagnet PIs + BELSPO representative) 14:00-17:30 Afternoon session 14:00-14:50 Keynote speaker: David Rand (Director, Centre for Systems Biology, Warwick University, UK) Stress in plants and humans: from time-series (and genomes) to networks 14:50-15:30 Pierre Geurts (Université de Liège) From genomes to networks by using tree-based supervised learning methods - GENIE3 within the DREAM4 and DREAM5 challenges 15:30-16:00 Coffee break 16:00-16:40 Florence d'Alché-Buc (Université d'Evry-Val d'Essonne, Evry, France) A new Bayesian estimation method of parameters in ordinary differential equations for biological networks 16:40-17:20 Denis Thieffry (Université de la Méditerrannée, Marseille, France and Ecole Normale Supérieure, Paris, France) Logical modelling of haematopoietic cell fate specification and reprogramming 17:20-17:30 Bart De Moor (Katholieke Universiteit Leuven) The BioMagnet project: achievements and perspectives.End of the workshop 17:30-18:00 Farewell drink

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PostDoc position
by Kuramae, Eiko 09 Mar '11

09 Mar '11

Dear All, The Netherlands Institute of Ecology (NIOO) is a top research institute of the Royal Netherlands Academy of Arts and Sciences (KNAW). Mission of the NIOO (http://www.nioo.knaw.nl) is to carry out excellent fundamental and strategic research in ecology. Within the Netherlands Institute of Ecology (NIOO-KNAW) the department of Microbial Ecology offers a POSTDOC position. The appointment is for 2 years, with a 1 year evaluation period. For more information please see http://www.nbic.nl/about-nbic/jobspositions/detail/jobdetails/exploiting-ec… Best regards, Eiko E. Kuramae Netherlands Institute of Ecology (NIOO-KNAW) Droevendaalsesteeg 10 6708 PB Wageningen The Netherlands

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Announcement PRIB 2011
by Thomas Abeel 03 Mar '11

03 Mar '11

International Conference on Pattern Recognition in Bioinformatics Delft, The Netherlands, November 2-4 2011 http://prib2011.org/ Call for Papers 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 Submission, Publication and Grants Papers should be submitted electronically through the conference website. We will work with Springer to 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 19, 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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