June 2013 - BBClist - maillist.psb.ugent.be

TPNC 2013: 3rd call for papers
by GRLMC 23 Jun '13

23 Jun '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************************* 2nd INTERNATIONAL CONFERENCE ON THE THEORY AND PRACTICE OF NATURAL COMPUTING TPNC 2013 Cáceres, Spain December 3-5, 2013 Organized by: Computer Architecture and Logic Design Group (ARCO) University of Extremadura Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/tpnc2013/ ********************************************************************* AIMS: TPNC is a conference series intending to cover the wide spectrum of computational principles, models and techniques inspired by information processing in nature. TPNC 2013 will reserve significant room for young scholars at the beginning of their career. It aims at attracting contributions to nature-inspired models of computation, synthesizing nature by means of computation, nature-inspired materials, and information processing in nature. VENUE: TPNC 2013 will take place in Cáceres, in Western Spain, 300 kms. to the southwest of Madrid and 100 kms. to the Portuguese border. The old city is a UNESCO World Heritage site. SCOPE: Topics of either theoretical, experimental, or applied interest include, but are not limited to: * Nature-inspired models of computation: - amorphous computing - cellular automata - chaos and dynamical systems based computing - evolutionary computing - membrane computing - neural computing - optical computing - swarm intelligence * Synthesizing nature by means of computation: - artificial chemistry - artificial immune systems - artificial life * Nature-inspired materials: - computing with DNA - nanocomputing - physarum computing - quantum computing and quantum information - reaction-diffusion computing * Information processing in nature: - developmental systems - fractal geometry - gene assembly in unicellular organisms - rough/fuzzy computing in nature - synthetic biology - systems biology * Applications of natural computing to: algorithms, bioinformatics, control, cryptography, design, economics, graphics, hardware, learning, logistics, optimization, pattern recognition, programming, robotics, telecommunications etc. A flexible "theory to/from practice" approach would be the perfect focus for the expected contributions. STRUCTURE: TPNC 2013 will consist of: ‐ invited talks ‐ invited tutorials ‐ peer-reviewed contributions INVITED SPEAKERS: Risto Miikkulainen (Austin), Evolving Neural Networks (tutorial) Yew-Soon Ong (Singapore), Advances in Memetic Computation Xin Yao (Birmingham), Evolutionary Algorithm Portfolios for Numerical Optimisation PROGRAMME COMMITTEE: Selim G. Akl (Kingston, CA) Thomas Bäck (Leiden, NL) Peter J. Bentley (London, UK) Hans-Georg Beyer (Dornbirn, AT) Mauro Birattari (Brussels, BE) Jinde Cao (Nanjing, CN) Vladimir Cherkassky (Minneapolis, US) Sung-Bae Cho (Seoul, KR) John A. Clark (York, UK) Carlos A. Coello Coello (Mexico DF, MX) David W. Corne (Edinburgh, UK) Peter Dayan (London, UK) Bernard De Baets (Ghent, BE) Andries P. Engelbrecht (Pretoria, ZA) Enrique Herrera-Viedma (Granada, ES) Yaochu Jin (Guildford, UK) Nikola Kasabov (Auckland, NZ) Vladik Kreinovich (El Paso, US) Kwong-Sak Leung (Hong Kong, CN) Xiaohui Liu (London, UK) Manuel Lozano (Granada, ES) Carlos Martín-Vide (Tarragona, ES, chair) Julian F. Miller (York, UK) Frank Neumann (Adelaide, AU) Leandro Nunes de Castro (São Paulo, BR) Nikhil R. Pal (Kolkata, IN) Günther Palm (Ulm, DE) José Carlos Príncipe (Gainesville, US) Helge Ritter (Bielefeld, DE) Conor Ryan (Limerick, IE) Hava Siegelmann (Amherst, US) Moshe Sipper (Beer-Sheva, IL) Thomas Stützle (Brussels, BE) Ponnuthurai N. Suganthan (Singapore, SG) Johan Suykens (Leuven, BE) Kay Chen Tan (Singapore, SG) Dacheng Tao (Sydney, AU) Jon Timmis (York, UK) Marco Tomassini (Lausanne, CH) Michael D. Vose (Knoxville, US) Michael N. Vrahatis (Patras, GR) Harald Weinfurter (Munich, DE) Rolf Würtz (Bochum, DE) Jun Zhang (Guangzhou, CN) ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Carlos Martín-Vide (Tarragona, co-chair) Bianca Truthe (Magdeburg) Miguel A. Vega-Rodríguez (Cáceres, co-chair) Florentina Lilica Voicu (Tarragona) LOCAL COMMITTEE: Víctor Berrocal-Plaza José M. Chaves-González Juan A. Gómez-Pulido David L. González-Álvarez José M. Granado-Criado Alejandro Hidalgo-Paniagua José M. Lanza-Gutiérrez Álvaro Rubio-Largo Sergio Santander-Jiménez Miguel A. Vega-Rodríguez (chair) SUBMISSIONS: Authors are invited to submit non-anonymized papers in English presenting original and unpublished research. Papers should not exceed 12 single-spaced pages (including eventual appendices) and should be formatted according to the standards of the Springer Verlag's LNCS series (see http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0) Submissions have to be uploaded to: https://www.easychair.org/conferences/?conf=tpnc2013 PUBLICATIONS: A volume of proceedings published by Springer in the LNCS series will be available by the time of the conference. A special issue of the journal Soft Computing (Springer, 2011 impact factor: 1.880) will be later published containing peer-reviewed extended versions of some of the papers contributed to the conference. Submissions to it will be by invitation. REGISTRATION: The period for registration is open from April 17 to December 3, 2013. The registration form can be found at: http://grammars.grlmc.com/tpnc2013/Registration DEADLINES: Paper submission: July 16, 2013 (23:59h, CET) Notification of paper acceptance or rejection: August 27, 2013 Final version of the paper for the LNCS proceedings: September 3, 2013 Early registration: September 10, 2013 Late registration: November 19, 2013 Starting of the conference: December 3, 2013 End of the conference: December 5, 2013 Submission to the post-conference special issue: March 5, 2014 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: TPNC 2013 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34-977-559543 Fax: +34-977-558386 ACKNOWLEDGEMENTS: Departament d’Economia i Coneixement, Generalitat de Catalunya Universidad de Extremadura Universitat Rovira i Virgili

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[Gtpb] New deadlines for Bioistatistics training courses
by Pedro Fernandes 20 Jun '13

20 Jun '13

FORMAL notification We still have a handful of vacancies for the two Biostatistics training courses. To give you a better chance of considering applying, we have postponed the application deadlines as follows: IBBTU13 http://gtpb.igc.gulbenkian.pt/bicourses/IBBTU13/ *Introductory Biostatistics for Bioinformatics Tool Users* IMPORTANT DATES for this Course Deadline for applications: June 21st 2013 Course date: July 1st - July 5th 2013 ABBTU13 http://gtpb.igc.gulbenkian.pt/bicourses/ABBTU13/ *Advanced Biostatistics for Bioinformatics Tool Users* IMPORTANT DATES for this Course Deadline for applications: July 2nd 2013 Course date: July 8st - July 12th 2013 Please take in full consideration the course descriptions available on the website Thank you Pedro Fernandes GTPB Coordinator -- -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] AWGSMD13 FORMAL last reminder
by Pedro Fernandes 20 Jun '13

20 Jun '13

REMINDER Applications for the course AWGSMD13 - Analysing Whole-Genome Shotgun Metagenomic Data 27 and 28 of June http://gtpb.igc.gulbenkian.pt/bicourses/AWGSMD13/ *will close tomorrow, JUNE 21st at 23h59m!* We still have a small number of vacancies. Pedro -- -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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RECOMB-CG 2013 - extension of submission deadline to June 24
by Macha Nikolski 19 Jun '13

19 Jun '13

Due to numerous requests we have decided to extend the deadline for the submission of FULL paper versions by three days to 23:59, timezone of your choice on Monday, June 24, 2013. Best regards, Macha Nikolski and Yves Van de Peer. -------- Eleventh Annual RECOMB Satellite Workshop on Comparative Genomics October 17-19, 2013, Lyon, France Website: http://rcg2013.sciencesconf.org/ Contributions to the workshop are welcomed on any theoretical and/or empirical approach to genome-wide comparison. This includes genome evolution, algorithms for genome rearrangement, comparative tools for assembly, gene identification or annotation, comparison of functional networks, genomic variation in humans and model organisms, cancer genomics, duplication patterns of genes, segments and whole genomes, and comparative epigenetics. We encourage paper submissions that offer new biological findings or otherwise highlight their relevance to biology. Refereed papers will be published as open-access manuscripts in the journal BMC Bioinformatics. -------- KEY DATES Paper submission deadline June 24, 2013 (midnight, timezone of your choice) Acceptance notification July 19, 2013 Workshop October 17-19, 2013 - Lyon, France -------- CONFIRMED KEYNOTE SPEAKERS - Tal Dagan, Heinrich Heine Universität, Dusseldorf - France Denoeud, Genoscope CEA, France - Laurent Duret, Laboratoire de Biométrie et Biologie Évolutive, Lyon - Nicolas Galtier, Institut des Sciences d'Evolution de Montpellier - Ludovic Orlando, Centre for GeoGenetics, Natural History Museum of Denmark -------- THEME AND SCOPE The continuing advance of DNA sequencing technology has produced an avalanche of genome sequence and genome structural information across the evolutionary spectrum. Transforming that information into biological knowledge requires creative and innovative new computational and statistical methods for comparative genomics. The RECOMB Satellite Workshop on Comparative Genomics aims to provide the premier forum for new computational developments applied to all aspects of comparative genomics. We solicit contributions on topics including comparison of genome structure and organization, genome function, and evolution. We particularly encourage contributions that use new computational methods to acquire new insight into biological processes. Advances in computational theory are welcome, though all submissions should include genome-scale analyses informed by comparative data. All peer-reviewed and accepted RECOMB-CG manuscripts will be published in a supplement to BMC Bioinformatics as open-access, author-subsidized, articles. Specific topics of interest include but are not limited to: . Gene and genome duplication . Gene family evolution . Genome structural variation . Algorithms for comparative genomics . Genome rearrangements . Ancestral genome reconstruction . Multiple genome alignment . Genome sequence comparison . Modeling genome evolution . Comparative genomics for genome annotation . Gene tree reconciliation . Species and gene tree inference . Comparative metagenomics . Comparative genomics linked to proteomics, metabolomics, and other ~omic data . Comparative genomics and gene expression and regulation . Applications of comparative genomic methods . Paleogenomics -------- CALL FOR PAPERS Papers should be submitted via the EasyChair system: Submissions must be received in electronic form by 11:59pm (Samoa time), June 21th, 2013. https://www.easychair.org/conferences/?conf=recombcg2013 Papers submitted for review should represent original, previously unpublished work. At the time the paper is submitted to the conference, and for the entire review period, the paper should not be under review by any other conference or scientific journal. At least one author per each successful submission is required to register and present the paper at the workshop. The paper will be included in the conference proceedings, which will be published in BMC Bioinformatics as open-access author-subsidized articles. Authors are encouraged to use the BMC document templates when preparing manuscripts. Templates are available in Microsoft and LaTeX formats. Otherwise, submissions should be typeset as double-spaced A4 pages with at least 1-inch margins all around in a minimum of 10 point font. Submissions should be limited to 16 pages, everything included (title, authors, addresses, abstract, references, figures, tables). Exceptions to this limit may be granted by consultation with the Program Committee Chairs. Submissions must include the corresponding author’s email address. When preparing your submission please follow the instructions for authors of BMC supplements: http://www.uff.br/recombcg/docs/Instructions-for-authors-BMC-Appendix-B.pdf. Submitted manuscripts must be rendered to PDF format prior to upload into EasyChair at the review stage. Address any questions to the program committee chairs: Macha Nikolski macha (at) labri (dot) fr and Yves Van de Peer yves (dot) vandepeer (at) psb (dot) vib (dash) ugent (dot) be -------- PROGRAM COMMITTEE Chairs: Macha Nikolski (LaBRI & CBiB, Université Bordeaux, France) Yves Van de Peer (VIB / Ghent University, Belgium) PROGRAM COMMITTEE (preliminary) • Anne Bergeron (Canada) • Mathieu Blanchette (Canada) • Guillaume Blin (France) • Guillaume Bourque (Canada) • Marilia Braga (Brazil) • Titus Brown (USA) • Frederic Brunet (France) • Cedric Chauve (Canada) • Niklas Eriksen (Sweden) • Martin Frith (Japan) • Lukasz Huminiecki (Sweden) • Gerton Lunter (England) • Vsevolod Makeev (Russia) • Veli Mäkinen (Finland) • Guilherme Oliveira (Brazil) • Aida Ouangraoua (France) • Benedict Paten (USA) • Teresa Przytycka (USA) • Sven Rahmann (Germany) • Eric Rivals (France) • Hugues Roest Crollius (France) • Marie-France Sagot (France) • Cathal Seoighe (Ireland) • Hayssam Soueidan (Netherlands) • João Setubal (Brazil) • Katherine St John (USA) • Jens Stoye (Germany) • Krister Swenson (Canada) • Eric Tannier (France) • Glenn Tesler (USA) • Raluca Uricaru (France) • Miguel Vazquez (Spain) • Chris Workman (Denmark) • Louxin Zhang (Singapore) STEERING COMMITTEE Jens Lagergren (KTH Royal Institute of Technology and SciLifeLab Stockholm, Sweden) Aoife McLysaght (University of Dublin, Ireland) David Sankoff (University of Ottawa, Canada)

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SSTiC 2013: next registration deadline 26 June
by GRLMC 15 Jun '13

15 Jun '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ********************************************************************* 2013 INTERNATIONAL SUMMER SCHOOL ON TRENDS IN COMPUTING SSTiC 2013 Tarragona, Spain July 22-26, 2013 Organized by Rovira i Virgili University http://grammars.grlmc.com/SSTiC2013/ ********************************************************************* +++ next registration deadline: June 26 +++ ********************************************************************* AIM: SSTiC 2013 will be an open forum for the convergence of top class well recognized computer scientists and people at the beginning of their research career (typically PhD students) as well as consolidated researchers. SSTiC 2013 will cover the whole spectrum of computer science by means of 56 six-hour courses dealing with hot topics at the frontiers of the field. By actively participating, lecturers and attendees will share the idea of scientific excellence as the main motto of their research work. ADDRESSED TO: Graduate students from around the world. There are no pre-requisites in terms of the academic degree the attendee must hold. However, since there will be several levels among the courses, in the description of some of them reference may be made to specific knowledge background. SSTiC 2013 is appropriate also for people more advanced in their career who want to keep themselves updated on developments in the field. Finally, senior researchers will find it fruitful to listen and discuss with people who are main references of the diverse branches of computing nowadays. REGIME: 7 parallel sessions will be held during the whole event. Participants will be able to freely choose the courses they will be willing to attend as well as to move from one to another. VENUE: Palau Firal i de Congressos de Tarragona Arquitecte Rovira, 2 43001 Tarragona http://www.palaucongrestgna.com COURSES AND PROFESSORS: Shun-ichi Amari (Riken) [introductory] Information Geometry and Its Applications James Anderson (Chapel Hill) [intermediate] Scheduling and Synchronization in Real-Time Multicore Systems Pierre Baldi (Irvine) [intermediate] Big Data Informatics Challenges and Opportunities in the Life Sciences Yoshua Bengio (Montréal) [introductory/intermediate] Deep Learning of Representations Stephen Brewster (Glasgow) [advanced] Multimodal Human-Computer Interaction Bruno Buchberger (Linz) [introductory] Groebner Bases: An Algorithmic Method for Multivariate Polynomial Systems. Foundations and Applications Rajkumar Buyya (Melbourne) [intermediate] Cloud Computing Jan Camenisch (IBM Zurich) [intermediate] Cryptography for Privacy Larry S. Davis (College Park) [intermediate] Video Analysis of Human Activities Paul De Bra (Eindhoven) [intermediate] Adaptive Systems Paul Dourish (Irvine) [introductory] Ubiquitous Computing in a Social Context Max J. Egenhofer (Maine) [introductory/intermediate] Qualitative Spatial Relations: Formalizations and Inferences Richard M. Fujimoto (Georgia Tech) [introductory] Parallel and Distributed Simulation David Garlan (Carnegie Mellon) [advanced] Software Architecture: Past, Present and Future Mario Gerla (Los Angeles) [intermediate] Vehicle Cloud Computing Georgios B. Giannakis (Minnesota) [advanced] Sparsity and Low Rank for Robust Data Analytics and Networking Ralph Grishman (New York) [intermediate] Information Extraction from Natural Language Francisco Herrera (Granada) [intermediate] Imbalanced Classification: Current Approaches and Open Problems Paul Hudak (Yale) [introductory] Euterpea: From Signals to Symphonies Using Haskell Niraj K. Jha (Princeton) [intermediate] FinFET Circuit Design George Karypis (Minnesota) [introductory] Introduction to Parallel Computing: Architectures, Algorithms, and Programming Aggelos K. Katsaggelos (Northwestern) [intermediate/advanced] Sparsity-based Advances in Image Processing Arie E. Kaufman (Stony Brook) [advanced] Advances in Visualization Hugo Krawczyk (IBM Research) [intermediate] An Introduction to the Design and Analysis of Authenticated Key Exchange Protocols Pierre L'Ecuyer (Montréal) [intermediate] Quasi-Monte Carlo Methods in Simulation: Theory and Practice Laks Lakshmanan (British Columbia) [intermediate/advanced] Information and Influence Spread in Social Networks Wenke Lee (Georgia Tech) [introductory] DNS-based Monitoring of Malware Activities Maurizio Lenzerini (Roma La Sapienza) [intermediate] Ontology-based Data Integration Ming C. Lin (Chapel Hill) [introductory/intermediate] Physically-based Modeling and Simulation Jane W.S. Liu (Academia Sinica) [intermediate] Critical Information and Communication Technologies for Disaster Preparedness and Response Satoru Miyano (Tokyo) [intermediate] How to Hack Cancer Systems with Computational Methods Aloysius K. Mok (Austin) [intermediate] From Real-time Systems to Cyber-physical Systems Hermann Ney (Aachen) [intermediate/advanced] Probabilistic Modelling for Natural Language Processing - with Applications to Speech Recognition, Handwriting Recognition and Machine Translation Cathleen A. Norris (North Texas) & Elliot Soloway (Ann Arbor) [introductory] Primary & Secondary Educational Computing in the Age of Mobilism Jeff Offutt (George Mason) [intermediate] Cutting Edge Research in Engineering of Web Applications David Padua (Urbana) [intermediate] Parallel Programming with Abstractions Bijan Parsia (Manchester) [introductory] The Semantic Web: Conceptual and Technical Foundations Charles E. Perkins (FutureWei) [intermediate/advanced] Beyond 4G Prabhakar Raghavan (Google) [introductory/intermediate] Web Search and Advertising Phillip Rogaway (Davis) [introductory/intermediate] Provably Secure Symmetric Encryption Gustavo Rossi (La Plata) [intermediate] Topics in Model Driven Web Engineering Kaushik Roy (Purdue) [introductory/intermediate] Low-energy Computing Robert Sargent (Syracuse) [introductory] Validating Models Douglas C. Schmidt (Vanderbilt) [intermediate] Patterns and Frameworks for Concurrent and Networked Software Bart Selman (Cornell) [intermediate] Fast Large-scale Probabilistic and Logical Inference Methods Mubarak Shah (Central Florida) [intermediate/advanced] Visual Crowd Surveillance Ron Shamir (Tel Aviv) [introductory] Revealing Structure in Disease Regulation and Networks Dawn Xiaodong Song (Berkeley) [introductory] Selected Topics in Computer Security Mike Thelwall (Wolverhampton) [introductory] Sentiment Strength Detection for the Social Web Julita Vassileva (Saskatchewan) [introductory/intermediate] Engaging Users in Social Computing Systems Philip Wadler (Edinburgh) [introductory] Topics in Lambda Calculus and Life Yao Wang (Polytechnic New York) [introductory/advanced] Video Compression: Fundamentals and Recent Development Gio Wiederhold (Stanford) [introductory] Software Economics: How Do the Results of the Intellectual Efforts Enter the Global Market Place Limsoon Wong (National Singapore) [introductory/intermediate] The Use of Context in Gene Expression and Proteomic Profile Analysis Michael Wooldridge (Oxford) [introductory] Autonomous Agents and Multi-Agent Systems Ronald R. Yager (Iona) [introductory/intermediate] Fuzzy Sets and Soft Computing Philip S. Yu (Illinois Chicago) [advanced] Mining Big Data REGISTRATION: It has to be done at http://grammars.grlmc.com/SSTiC2013/Registration.php Since the capacity of the venue is limited, registration requests will be processed on a first come first served basis. The registration period will be closed when the capacity of the venue will be complete. FEES: Fees may be for the whole week (full-time participant) or per blocks of days (part-time participant). They are a flat rate allowing one to attend all courses within the time window set: 5, 4, 3 or 2 days. Fees vary depending on the deadline. ACCOMMODATION: Information about accommodation is available on the website of the School. CERTIFICATE: Participants will be delivered a certificate of attendance. IMPORTANT DATES: Announcement of the programme: January 26, 2013 Registration deadlines: next: June 26, 2013 last: July 25, 2013 QUESTIONS AND FURTHER INFORMATION: Lilica Voicu: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: SSTiC 2013 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34-977-559543 Fax: +34-977-558386 ACKNOWLEDGEMENTS: Departament dEconomia i Coneixement, Generalitat de Catalunya Universitat Rovira i Virgili

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PhD and Postdoc positions KU Leuven Belgium
by Vera van Noort 13 Jun '13

13 Jun '13

van Noort Group is looking for PhD and Postdoctoral fellows We currently access an unprecedented knowledge on the basic components making up living systems. An ever growing number of new technologies are being developed with the capacity to systematically measure the behaviour of multiple cellular components, such as biochemical activities, biophysical properties, subcellular localization and interaction. These technologies produce large amounts of raw data that can be transformed into information by software and tools developed both in academia and industry. However, this biological information does not equal biological knowledge. As biology becomes large-scale, new methods have to be developed to integrate, visualize and query the large amounts of information available. This is usually beyond the expertise of experimental labs. The goal of this young computational systems biology group is to generate biological sense from the growing amount of biological data becoming available and turn biological information into biological knowledge. http://www.biw.kuleuven.be/m2s/cmpg/research/CSB Position 1: Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis. It is estimated that a third of the world’s population has been infected by this pathogen, with approximately one new infection per second resulting in around 9 million new cases of active disease and 1.6 million deaths annually. The goal of the European project Systems Biology of MTb (SysteMTb) is to understand this organism better at the molecular level in conditions that are relevant for infection. Within this project large amounts of RNA-seq, CHIP-seq, metabolomics and proteomics data are being generated. The task of the postdoctoral fellow working to be appointed is to analyse and integrate these data to form hypotheses that can be tested in the laboratories of our collaborators. For more information about the project visit http://systemtb.eu or contact prof. Vera van Noort (vera.vannoort(a)gmail.com) In your application please include a CV with research experience and interests as well as a minimum of two letters of recommendation. Starting date: from 1st of October 2013 Position 2: A specific focus of the newly founded computational biology group will be Post Translational Modifications (PTMs). Inside the cell, proteins are the main entities responsible for carrying out molecular functions. These proteins can be modified by the addition of small moieties such as phosphate or acetyl groups. The modifications are called post-translational modifications (PTMs). These moieties change the properties of proteins and can thereby cause changes in what substrates they can bind to or what reactions they catalyse. In response to changes inside or outside an organism, a cell can quickly adapt by means of these PTMs in signalling networks. The PhD student will work on the analysis and integration of data to better understand the functions and mechanisms of PTMs. Requirements include being able to write scripts in perl/python, working with databases and basic molecular biology knowledge. Additional expertise such as working with LINUX, queuing systems and phylogenetic inference methods is certainly an advantage. For more information contact prof. Vera van Noort ( vera.vannoort(a)gmail.com) In your application please include a CV describing coursework, grades and previous research experience as well as a minimum of two letters of recommendation. Starting date: from 1st of October 2013 Position 3: We seek a PhD student who will work as a computational biologist in the interdisciplinary project NATAR. Understanding the relationship between an organism’s genotype and phenotype remains one of biology’s fundamental challenges. In the project two model organisms, budding yeast and *E. coli,*will be exploited to better understand two complex genetic traits: ethanol and high temperature tolerance*. *For both organisms both natural variation and the outcomes of experimental evolution will be correlated with phenotypes. The first challenge in the project will be to identify which of the many variants in these genomes have functional effects. Then we will try to facilitate unravelling complex interactions between alleles, for example through functional gene networks that are based on a combination of published data. An important part of the generated data that underlies this project consists of high-throughput sequencing of DNA and mRNA of populations and isolates. For answering specific questions data integration with other data sources will be needed as well as the application of specific machine learning techniques. Basic molecular biology knowledge and basic programming skills are a prerequisite for this position. Experience with high throughput sequencing analysis methods, machine learning, protein interaction databases, perl/python scripting or BioconductoR are preferred. For more information contact prof. Rob Jelier (r.jelier(a)gmail.com) or prof. Vera van Noort (vera.vannoort(a)gmail.com) In your application please include a CV describing coursework, grades and previous research experience as well as a minimum of two letters of recommendation. Starting date: from 1st of October 2013 -- Vera van Noort, PhD EMBL - Structural and Computational Biology Meyerhofstrasse 1 69117 Heidelberg Germany from October 2013: Centre of Molecular and Plant Genetics Department of Microbial and Molecular Systems (M2S) KU Leuven Kasteelpark Arenberg 20 3001 Leuven Belgium

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Fwd: SYMPOSIUM : New genomics toward personalized medicine LILLE - October 2013 10th
by Olivier Sand 13 Jun '13

13 Jun '13

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Course Small molecules, gene products and their interaction, 1-5 July 2013, Maastricht, the Netherlands
by Celia van Gelder 12 Jun '13

12 Jun '13

Small molecules, gene products and their interaction EBI Roadshow, Pathway-Network course and DiXa Training Course General information Date:July 1- 5, 2013 Location:Maastricht, the Netherlands Website:http://www.nbic.nl/education/course-overview/pages3/1/coursedetails/small-molecules-gene-products-and-their-interaction/ Organisers:Chris Evelo (Maastricht University), Egon Willighagen (Maastricht University), Tom Hancocks (EMBL-EBI), Vera Matser (EMBL-EBI & DiXa), Celia van Gelder (NBIC) Registration:http://www.nbic.nl/education/nbic-phd-school/enrolment/ Contact:Celia van Gelder (NBIC), education(a)nbic.nl <mailto:education@nbic.nl> Course description This five day course introduces various databases and data analysis tools to get grips on the big data in the life sciences. The course consists of two parts: Part 1 (day 1-3) introduces the advanced uses of the gene and genomes databases, small molecule resources, the protein sequence databases, and interaction and pathway databases at EBI (a.o. UniPROT, ENSEMBL, CHEMBL, IntAct and Reactome). This first part is an EBIRoadshow hosted by UM & NBIC. The second part (day 4-5) focuses on real data analysis using pathway and network approaches with links to the databases covered in first part. Tools that will be used include WikiPathways, PathVisio and Cytoscape. Covered aspects include pathway creation, data preparation for analysis, pathway analysis. network analysis and network extension using target information. This second part is provided by the department of Bioinformatics-BiGCaT at Maastricht University in collaboration with the DiXa FP7 project (www.dixa-fp7.eu) on systems biology approaches in toxicogenomics. The DiXa project will provide examples about (re)use and (re)analysis of large genomics datasets. *Teachers* Denise Carvalho-Silva, Louisa Bellis, Sandra Orchard, Chris Evelo, Martina Kutmon, Christoper Hardt, Stathis Kanterakis, Anwesha Dutta, Egon Willighagen. *Target audience *This course is intended for researchers in Life Sciences, Bioinformatics and Systems Biology, Pharmacology, Toxicology. *Course Programme* See http://www.nbic.nl/uploads/media/Programme_Maastricht.pdf -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail:C.vanGelder@cmbi.ru.nl websites:www.cmbi.ru.nl,www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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BeNeLux Bioinformatics Conference 2013 - Call for abstracts
by BBC2013 12 Jun '13

12 Jun '13

BBC2013 – BeNeLux Bioinformatics Conference 2013 Date: December 9 & 10, 2013 Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium Website: http://bbc2013.ibsquare.be Abstract submission deadline: October 1, 2013 Early registration deadline: November 1, 2013 Dear Colleagues, We are happy to announce the 8th edition of the BeNeLux Bioinformatics Conference, which will take place in Brussels on the 9th and 10th of December 2013. The theme of this year's conference is: "Bioinformatics at all scales of life". Since 2005, the BeNeLux Bioinformatics Conference gives bioinformaticians, from the BeNeLux and beyond, the opportunity to discuss their results and build new collaborations, in a relaxed and friendly atmosphere. This year's edition will be enhanced by the presence of three distinguished keynote speakers: Alfonso Valencia (Spanish National Cancer Research Center, http://bit.ly/14SAITQ) Anna Tramontano (University of Rome "La Sapienza", http://www.biocomputing.it) and Jim Haseloff (Plant Synthetic Biology, University of Cambridge, http://www.haseloff-lab.org) Call for abstracts We invite you to submit an abstract for an oral presentation (20 available slots: 6 long, 14 short) and/or a poster presentation. Contributions from all fields of bioinformatics are welcome and encouraged. We have provided a template to use for submission. Details on the submission procedure can be found at http://bbc2013.ibsquare.be/content/call-abstracts . We hope to see you all in Brussels! -- The BBC 2013 organising committee BeNeLux Bioinformatics Conference 2013 December 9-10, 2013 (Brussels)

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Postdoc position: Bioinformatics of gene regulation
by Stein Aerts 12 Jun '13

12 Jun '13

Postdoc position: Bioinformatics of gene regulation The Stein Aerts lab<http://med.kuleuven.be/lcb/> at the University of Leuven has a postdoc position for a highly motivated scientist to study cis-regulatory control and cis-regulatory variation. You will use and develop computational biology approaches to map gene regulatory networks and to decipher enhancer logic underlying cellular differentiation. To this end, you will combine multiple layers of regulatory information, including spatiotemporal gene expression patterns (RNA-seq, Tag-seq), genome-wide TF localization data (ChIP-seq, damID-seq), and open chromatin profiling data (FAIRE-seq). Although this is mainly a computational position, depending on your interest you can also perform wet-lab experiments, fly genetics, and next-generation sequencing yourself, together with colleagues in the lab. Finally, you can apply your systems biology approaches to study gene regulation in cancer, using a Drosophila cancer model in the eye, studying how mutations in transcription factors, but also mutations in the non-coding genome can contribute to oncogenesis. Qualifications: * PhD degree in Life sciences or related field * Strong publication record * Experience with Drosophila is a plus, but is not required. * Funding is available, but the candidate will apply for a postdoctoral fellowship<http://www.kuleuven.be/research/postdoc/> at the national level (e.g., IWT, FWO, VLK), or at the international level (e.g., EMBO, HFSP) during or after the first year. Links: * The Laboratory of Computational Biology<http://med.kuleuven.be/bioinformatics/> * Center for Human Genetics<http://med.kuleuven.be/cme/> * University of Leuven<http://www.kuleuven.be/english/> Interested? Send your CV to stein.aerts(a)med.kuleuven.be<mailto:stein.aerts@med.kuleuven.be>.

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