April 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

== ISCB Student Council Symposium: DEADLINE EXTENSION FOR ABSTRACT SUBMISSION ==
by Christiaan Klijn 28 Apr '10

28 Apr '10

Apologies to those who receive this email and to those to whom this email does not apply. If this email does not apply to you, but you do know someone who would benefit from this information, please feel free to forward it. The deadline for submitting your abstracts to the 6th ISCB Student Council Symposium has been extended to the *30th of April*, the same as for travel fellowships which is unchanged. Please submit your abstracts and travel fellowship applications before this time. The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 12 student presentations will be selected from the submitted abstracts. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel fellowships are available (see website) and awards will be given to best poster and best presentation. Furthermore, the Wellcome Trust provides 4 travel fellowships for students from developing countries that cover travel and lodging expenses. *Submission website*: http://symposium.iscbsc.org/content/submissions *Travel Fellowship information*: http://symposium.iscbsc.org/content/travel-fellowships *Room sharing information*: http://www.iscbsc.org/forum-topic/student-council/6th-student-council-sympo… *General information*: http://symposium.iscbsc.org/ Important dates: *April 30*: 6th Student Council Symposium Abstract submission and Travel Fellowships submission close *May 14*: Travel Fellowship winners and Abstract acceptance notification We look forward to receiving your abstract, Thomas Abeel Chair, 6th ISCB Student Council Symposium Magali Michaut Co-Chair, 6th ISCB Student Council Symposium Gold Sponsor of the event: EMBL-EBI

1 0

[ECCB10] Call for posters
by Sylvain Brohée 28 Apr '10

28 Apr '10

=== Apologies for multiple postings - Please distribute widely within your lab === Dear Colleague, The European Conference on Computational Biology (ECCB10) will be held on September 26-29, 2010 in Ghent, Belgium. === POSTER SUBMISSION DEADLINE: June 20, 2010 === www.eccb10.org ECCB10 is the key European computational biology event in 2010 uniting scientists working in a broad range of disciplines, including bioinformatics, computational biology, medicine, biology, and systems biology. This year we have had a record number of 216 manuscript submissions. We are thus looking forward to a fruitful scientific meeting. Ghent is centrally located in Western Europe and is reachable by car within a day of travel from most cities in The Netherlands, Germany, Switzerland, France, and the UK. It is also easily reachable by high-speed train since Belgium is a hub of the European high-speed rail networks (Thalys, Eurostar, TGV, and ICE). Ghent is one of Europe's most exciting medieval settings, a glorious eclectic city with spectacular buildings and a vivid cultural experience (National Geographic Traveler recently ranked it 3rd best historic place to visit internationally). Ghent is directly accessible by train from Brussels airport. The conference venue is highly convenient and located in a beautiful park within the city center. We invite you to submit posters in any area of computational biology and bioinformatics. Topics of interest include, but are not limited to * Sequence analysis, alignment, and next-generation sequencing * Comparative genomics, phylogeny, and evolution * Protein & nucleotide structure * Annotation and prediction of molecular function * Gene regulation and transcriptomics * Text mining, ontologies, and databases * Protein interactions, molecular networks, and systems biology * Genomic medicine * Other bioinformatics applications Posters, representing condensed descriptions of ongoing work, will be displayed during the meeting. Posters should describe original, interesting, and solid scientific content that is relevant to bioinformatics and computational biology. See guidelines at http://www.eccb10.org/index.php/guidelines/posters. At least one of the authors of the poster will have to attend the meeting. The presenting author of each poster must register for the conference by the early registration deadline of August 13, 2010 for the poster to be included in the program. We kindly request that you forward this announcement to the members of your team. We look forward to welcoming you to Ghent. The ECCB10 Organizing Committee www.eccb10.org ECCB10 KEY DATES POSTERS * Call for posters open - January 10, 2010 * Poster submission deadline - June 20, 2010 * Poster acceptance notification - July 11, 2010 PAPERS * Call for papers open - January 10, 2010 - CLOSED * Paper submission deadline - April 9, 2010 - CLOSED * Paper acceptance notification - June 4, 2010 * Submission of final version of accepted papers deadline - June 18, 2010 WORKSHOPS AND TUTORIALS * Call for tutorials and workshops open - January 10, 2010 - CLOSED * Workshop and tutorial submission deadline - March 26, 2010 - CLOSED * Workshop and tutorial acceptance notification - April 23, 2010 - CLOSED INDUSTRY AND DEMO TRACK * Call for software demos and industrial presentations open - January 10, 2010 * Industry and demo track submission deadline - June 3, 2010 * Industry and demo track acceptance notification - June 24, 2010 REGISTRATION * Registration open - May 7, 2010 * Early registration deadline - August 13, 2010 CONFERENCE * Workshop and tutorials - Sunday September 26, 2010 * Conference opening - Sunday evening, September 26, 2010 * Main conference (proceedings, posters, and industry/demo track) - September 26-29, 2010

1 0

Last call for participation Text Mining tutorials and workshop BioTM
by Yvan Saeys 23 Apr '10

23 Apr '10

=========================== LAST CALL FOR PARTICIPATION =========================== Workshop BioTM-2010 Advances in Bio Text Mining May 10-11, 2010, Ghent, Belgium http://www.clips.ua.ac.be/BioTM2010/index.html ============================================================ REGISTRATION DEADLINE : May 1st 2010 ============================================================ The program of the workshop includes: - an extensive tutorial on Bio Text Mining by Martin Krallinger (CNIO, Spain) - invited talks by leading scientists in the field: Sampo Pyysalo (University of Tokyo, Japan) Kevin Cohen (Center for Computational Pharmacology and The MITRE Corporation, USA) Filip Ginter (University of Turku, Finland) - invited talks by experienced scientists from industry: Jean-Marc Neefs (Janssen Pharmaceuticals) Luc Dehaspe and Maté Ongenaert (Oncomethylome) ============================================================ 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, selected abstracts will be presented during a flash presentation session, as well as a poster session 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. ORGANISATION / PROGRAM COMMITTEE Sofie Van Landeghem Yvan Saeys Thomas Abeel 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/ ==================================================================

1 0

PhD position computational biology
by Thomas Van Parys 19 Apr '10

19 Apr '10

Sorry if you received this announcement multiple times. -------- Original Message -------- Subject: PhD position computational biology Date: Mon, 19 Apr 2010 08:48:43 +0200 From: Stefan Rensing <stefan.rensing(a)biologie.uni-freiburg.de> Organization: Faculty of Biology, University of Freiburg To: Stefan Rensing <stefan.rensing(a)biologie.uni-freiburg.de> Dear colleagues, I would be grateful if you could forward the attached announcement to those who might be interested. Thanks and kind regards, Stefan -- PD Dr. Stefan A. Rensing Lecturer Bioinformatics and Systems Biology FRISYS, Faculty of Biology, University of Freiburg Hauptstr. 1, D-79104 Freiburg, Fon: +49 761 203-6974 http://plantco.de/ stefan.rensing(a)biologie.uni-freiburg.de 3rd cosmoss.org Physcomitrella Genome Workshop Sep 13th-15th: https://www.cosmoss.org/physcome_project/wiki/Cosmoss_workshop "Everything is backwards now, like out there is the true world, and in here is the dream."

1 0

Fifth Summer School on Advanced Statistics and Data Mining (Madrid, June 28th - July 9th, 2010)
by Rubén Armañanzas 13 Apr '10

13 Apr '10

Dear colleagues, the Technical University of Madrid (UPM) again organizes the summer school on 'Advanced Statistics and Data Mining' in Madrid between June 28th and July 9th. This year programme comprises 14 courses divided in 2 weeks. Attendees may register in each course independently. Information on the registration process will be available soon in the web page. Please, visit the following site for more information. http://www.dia.fi.upm.es/ASDM2010 Best regards. P. Larrañaga and R. Armañanzas. *List of courses and brief description* Week 1 (June 28th - July 2nd, 2010) Course 1: Bayesian networks (15 h) Bayesian networks basics. Inference in Bayesian networks. Learning Bayesian networks from data. Course 2: 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. Nonlinear Regression. Course 3: 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 4: 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 5: Dimensionality reduction (15 h) Introduction. Matrix factorization methods. Clustering methods. Projection methods. Applications. Course 6: Supervised pattern recognition (Classification) (15 h) Introduction. Assessing the Performance of Supervised Classification Algorithms. Classification techniques. Combining Classifiers. Comparing Supervised Classification Algorithms. Course 7: Evolutionary computation (15 h) Genetic algorithms. Genetic programming. Robust and self-adapting intelligent systems. Introduction to Estimation of Distribution Algorithms. Improvements, extensions and applications of EDAs. Current research in EDAs. Week 2 (July 5th - July 9th, 2010) Course 8: Datamining: 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 9: Hidden Markov Models (15 h) Introduction. Discrete Hidden Markov Models. Basic algorithms for Hidden Markov Models. Semicontinuous Hidden Markov Models. Continuous Hidden Markov Models. Unit selection and clustering. Speaker and Environment Adaptation for HMMs. Other applications of HMMs. Course 10: Time series analysis (15 h) Introduction. Probability models to time series. Regression and Fourier analysis. Forecasting and Data mining. Course 11: Features Subset Selection (15 h) Introduction. Redundance and irrelevance. Filter approaches. Wrapper methods. Embedded methods. Course 12: Statistical inference (15 h) Introduction. Some basic statistical test. Multiple testing. Introduction to bootstrapping. Course 13: Unsupervised pattern recognition (clustering) (15 h) Introduction. Prototype-based clustering. Density-based clustering. Graph-based clustering. Cluster evaluation. Miscellanea. Course 14: Introduction to R (15 h) An introductory R session. Data in R. Importing/Exporting data. Programming in R. R Graphics. Statistical Functions in R.

1 0

CSCDA2010: deadline extended
by Pierre Geurts 13 Apr '10

13 Apr '10

- Deadline for abstract submission has been extended until 19 APRIL 2010 - Registrations are now open --- APOLOGIES FOR CROSS-POSTING--- Dear Friends and Colleagues, On behalf of the entire organizing committee, we are 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 exist of two parts: 1) tutorial sessions in the afternoon of day 1 (25 August 2010) 2) keynote speaker sessions, with discussion afternoons, on days 2-3 (26-27 August 2010) ABSTRACT SUBMISSION DEADLINE IS 19 APRIL 2010. More information about abstracts submission is available on the conference websitehttp://www.aimontefiore.org/cscda2010/index.php?option=com_content&v… 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! 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 On behalf of the organizing committee Céline Dizier AIM Rue Saint-Gilles 31 4000 Liège Tel : +32 (0) 4 222 29 46 Fax : +32 (0) 4 222 23 88 site : http://www.aimontefiore.org

1 0

== ISCB Student Council Symposium: CALL FOR ABSTRACTS ==
by Christiaan Klijn 08 Apr '10

08 Apr '10

Submit your abstract today to participate in the 6th Symposium of the International Society for Computational Biology Student Council on July 9th 2010 in Boston! The Student Council Symposium aims at bringing together young computational biologists from all areas of research and parts of the world. As the central part of our symposium 12 student presentations will be selected from the submitted abstracts. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. Travel Fellowships are available (see website) and awards will be given to best poster and best presentation. Furthermore, Wellcome Trust Institute provides 4 travel felloships for students from developing countries. Details about the application process can be found here <http://symposium.iscbsc.org/content/wellcome-trust-fund-scs-6-travel-fellow…>. *Submission website*: http://symposium.iscbsc.org/content/submissions *Travel Fellowship information*: http://symposium.iscbsc.org/content/travel-fellowships *Wellcome Trust Travel Fellowship*: http://symposium.iscbsc.org/content/wellcome-trust-fund-scs-6-travel-fellow… *Room sharing information*: http://www.iscbsc.org/forum-topic/student-council/6th-student-council-sympo… *General information*: http://symposium.iscbsc.org/ Important dates: *February 22*: Abstract and Travel Fellowship submission opens *April 23*: 6th Student Council Symposium Abstract submission closes *April 30*: 6th Student Council Symposium Travel Fellowships submission closes *May 14*: Travel Fellowship winners and Abstract acceptance notification We look forward to receiving your abstract, Thomas Abeel Chair, 6th ISCB Student Council Symposium Magali Michaut Co-Chair, 6th ISCB Student Council Symposium

1 0

PhD Course: Optimisation Techniques in Bioinformatics and Systems Biology
by Celia van Gelder 07 Apr '10

07 Apr '10

*PhD Course: Optimisation Techniques in Bioinformatics and Systems Biology* On May 17-21, 2010 the NBIC PhD School organises the PhD Course ‘Optimisation Techniques in Bioinformatics and Systems Biology’ in Amsterdam. Course Lecturers: Jaap Kaandorp (coordinator), Jaap Heringa, Antoine van Kampen Course Description Optimization, in general, is concerned with finding one or more optimal solutions given a problem. Many optimization problems are very difficult to solve. In many different problems from bioinformatics and systems biology (e.g. multi parameter estimation, reverse engineering of gene networks, multi-alignment problem, 3D structure prediction etc.) various optimisation methods are applied. In this course you will get acquainted with the underlying mathematics of optimization and with a selection of local and global optimization methods. In addition, several examples of optimization problems in life sciences will be presented and discussed. The course is aimed at at PhD students with a background in bioinformatics, systems biology, computer science or a related field. A working knowledge of basic statistics, linear algebra and differential equations is assumed, but will be reviewed during the first day of the course. After this course a student should have an overview and basic understanding of optimisation methods frequently applied in bioinformatics and systems biology. More information about the course, including information about the course programme, can be found on http://www.nbic.nl/education/nbic-phd-school/course-schedule/optimisation-t… . Please note: the course is free for PhD students working in a BioRange (including matching) or BioAssist project. Others can participate as well when paying a course fee (see http://www.nbic.nl/education/nbic-phd-school/enrolment/) This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organize high level education and training for PhD-students in bioinformatics. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website (www.nbic.nl <http://www.nbic.nl> -> Education -> NBIC PhD School). Best regards, Celia van Gelder -- 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 5005 (20100406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com

1 0

Announcement ISNB2010: program available
by AHC van Kampen 05 Apr '10

05 Apr '10

1 0