April 2014 - BBClist - maillist.psb.ugent.be

CALL FOR ISMB 2014 ART AND SCIENCE WORKS
by ISCBSC announcement 23 Apr '14

23 Apr '14

[image: logo] [image: 1] ******** CALL FOR ISMB 2014 ART AND SCIENCE WORKS ********** *Deadline: May 9, 2014* Submission website: https://www.iscb.org/ismb2014-submission/ismb2014-artandscienceexhibition Facebook Page: https://www.facebook.com/artNscienceISMB?ref=hl Dear ISCB Members and Colleagues, ISMB/ECCB brings together scientists from a wide range of disciplines, including biology, medicine, computerscience, mathematics and statistics. In these fields we are constantly dealing with information in visual form: from microscope images and photographs of gels to scatter plots, network graphs and phylogenetic trees, and visual aids for problem-solving are omnipresent. For the ISMB 2014 Art & Science Exhibition the organizers invite all interested conference attendees to submit such images and videos that have been generated as part of a research project. They are also soliciting images and videos resulting from creative efforts that involve scientific concepts or employ scientific tools and methods. All cover images produced by researchers for scientific journals are welcome as well. A cash award may be given for the winning image as voted by conference attendees. Attend this exciting event to surprise and inspire us, to open our eyes and minds! *Deadlines* Monday, October 14, 2013 Call for Art & Science Exhibiton Opens Friday, May 9, 2014 *Artwork Submission Deadline* Friday, May 16, 2014 Art & Science Exhibition Acceptance Notification We look forward to receiving your submission, The Art and Science Organizing Committee.

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SCS2014 - Extended abstract submission deadline - May 9th
by ISCBSC announcement 23 Apr '14

23 Apr '14

*ISCB Student Council Symposium 2014, Boston, USA.* Dear Colleagues, We are pleased to announce that the call is now open for the submission of abstracts to the 10th ISCB Student Council Symposium, to be held on the 11 of July 2014 in Boston, USA, as a satellite meeting of the International Conference on Intelligent Systems for Molecular Biology (ISMB). The Student Council Symposium is a forum for students, post docs, and young researchers in the fields of Computational Biology and Bioinformatics. Participants will have the opportunity to present their work to an international audience of young scientists, build a network within the computational biology community and develop important soft skills in an environment that fosters exchange of ideas and knowledge. We encourage you to submit an abstract to showcase your work at the Symposium’s poster session. As the central part of our symposium, 10 abstracts will be selected for an oral presentation. Awards will be given to outstanding posters and presentations. Travel fellowships will be available and candidates with accepted abstracts will be invited to apply. *Important Dates:* May 9, 2014: Abstract submission deadline May 16, 2014: Acceptance notifications May 23, 2014: Travel fellowship deadline June 4, 2014: Travel fellowship acceptance notification July 11, 2014: Student Council Symposium Submit your work at http://scs2014.iscbsc.org/scs14-call . For updates and news, keep an eye on symposium website http://scs2014.iscbsc.org/ . We look forward to receiving your abstract. On behalf of the SCS organizers, Farzana Rahman (Chair) Tomás Di Domenico (Co-Chair)

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BeMGI 2014 Meeting - Invitation and Scientific program
by marilou.ramospamplona＠ulg.ac.be 22 Apr '14

22 Apr '14

Dear BBC colleagues, We cordially invite you to the 2014 Annual Meeting of the Belgian Medical Genomics Initiative (BeMGI): “Genomic Advances in Disease Biology and Diagnostics.” The meeting will take place on 24 April, Thursday in the Université de Liège Sart Tilman campus (GIGA building, B34) from 11h15-17h15. The SCIENTIFIC PROGRAM (http://www.bemgi.be/events/bemgi-2014-annual-meeting/bemgi-2014-meeting-sci…) will highlight medical genomics research and applications and will feature a keynote lecture by Prof Cisca Wijmenga (University Medical Center Groningen), a number of scientific presentations from the BeMGI partner institutes and a poster session. This meeting is open to the public and attendance is free of charge. We will be applying for medical accreditation of the meeting. PARTICIPANTS ARE REQUESTED TO REGISTER ONLINE BY 10 APRIL 2014. ONLINE REGISTRATION URL: https://docs.google.com/spreadsheet/viewform?fromEmail=true&formkey=dF84T3N… The BeMGI network, a PAI-Belspo-funded project, works on collaborative activities (Research, Bioinformatics, Education, ELSI) to promote the clinical application of genomics research and technologies. We have as members academic and clinical researchers in the field of medical genetics and genomics who are associated with the Belgian Centers of Human Genetics. Meeting information: www.bemgi.be. Regards, The BeMGI network

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CFP - MLSB14, the 8th Machine Learning in Systems Biology workshop
by Pierre Geurts 17 Apr '14

17 Apr '14

Call for contributions MLSB14, the eighth International Workshop on Machine Learning in Systems Biology http://www.mlsb.cc Organized in conjunction with ECCB 2014 Strasbourg, France, September 6-7, 2014. Submission deadline: June 11, 2014 WORKSHOP DESCRIPTION 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 "omics" information has become a condition 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. MLSB14, the Eighth International Workshop on Machine Learning in Systems Biology, is a workshop of the ECCB 2014 conference. It aims to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology by bringing together method developers and experimentalists. We are soliciting submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis Please see the workshop website http://www.mlsb.cc for more details. SUBMISSIONS INSTRUCTIONS We invite you to submit an extended abstract of up to 4 pages in PDF format describing new or very recently published results. Submissions will be reviewed by the scientific programme committee. They will be selected for oral or poster presentation according to their originality and relevance to the workshop topics. KEY DATES Submission deadline: June 11, 2014 Author notification: July 15, 2014 Early registration deadline ECCB14: August 2, 2014 Workshop: September 6-7, 2014 CHAIRS Florence d'Alché-Buc (University of Evry, France) Pierre Geurts (University of Liege, Belgium) ORGANIZING COMMITTEE Florence d'Alché-Buc (University of Evry, France) Markus Heinonen (University of Evry, France) Pierre Geurts (University of Liege, Belgium) Vân Anh Huynh-Thu (University of Edinburgh, UK) Nizar Touleimat (Centre National de génotypage, CEA, Evry, France) CONTACT For further information, please contact chairsmlsb2014(a)gmail.com

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SLSP 2014: 3rd call for papers
by GRLMC 14 Apr '14

14 Apr '14

**************************************************************************** ****** 2nd INTERNATIONAL CONFERENCE ON STATISTICAL LANGUAGE AND SPEECH PROCESSING SLSP 2014 Grenoble, France October 14-16, 2014 Organised by: Équipe GETALP Laboratoire dInformatique de Grenoble Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/slsp2014/ **************************************************************************** ****** AIMS: SLSP is a yearly conference series aimed at promoting and displaying excellent research on the wide spectrum of statistical methods that are currently in use in computational language or speech processing. It aims at attracting contributions from both fields. Though there exist large, well-known conferences and workshops hosting contributions to any of these areas, SLSP is a more focused meeting where synergies between subdomains and people will hopefully happen. In SLSP 2014, significant room will be reserved to young scholars at the beginning of their career and particular focus will be put on methodology. VENUE: SLSP 2014 will take place in Grenoble, at the foot of the French Alps. SCOPE: The conference invites submissions discussing the employment of statistical methods (including machine learning) within language and speech processing. The list below is indicative and not exhaustive: phonology, phonetics, prosody, morphology syntax, semantics discourse, dialogue, pragmatics statistical models for natural language processing supervised, unsupervised and semi-supervised machine learning methods applied to natural language, including speech statistical methods, including biologically-inspired methods similarity alignment language resources part-of-speech tagging parsing semantic role labelling natural language generation anaphora and coreference resolution speech recognition speaker identification/verification speech transcription speech synthesis machine translation translation technology text summarisation information retrieval text categorisation information extraction term extraction spelling correction text and web mining opinion mining and sentiment analysis spoken dialogue systems author identification, plagiarism and spam filtering STRUCTURE: SLSP 2014 will consist of: invited talks invited tutorials peer-reviewed contributions INVITED SPEAKERS: Claire Gardent (LORIA, Nancy, FR), Grammar Based Sentence Generation and Statistical Error Mining Roger K. Moore (Sheffield, UK), Spoken Language Processing: Time to Look Outside? Martti Vainio (Helsinki, FI), Phonetics and Machine Learning: Hierarchical Modelling of Prosody in Statistical Speech Synthesis PROGRAMME COMMITTEE: Sophia Ananiadou (Manchester, UK) Srinivas Bangalore (Florham Park, US) Patrick Blackburn (Roskilde, DK) Hervé Bourlard (Martigny, CH) Bill Byrne (Cambridge, UK) Nick Campbell (Dublin, IE) David Chiang (Marina del Rey, US) Kenneth W. Church (Yorktown Heights, US) Walter Daelemans (Antwerpen, BE) Thierry Dutoit (Mons, BE) Alexander Gelbukh (Mexico City, MX) James Glass (Cambridge, US) Ralph Grishman (New York, US) Sanda Harabagiu (Dallas, US) Xiaodong He (Redmond, US) Hynek Hermansky (Baltimore, US) Hitoshi Isahara (Toyohashi, JP) Lori Lamel (Orsay, FR) Gary Geunbae Lee (Pohang, KR) Haizhou Li (Singapore, SG) Daniel Marcu (Los Angeles, US) Carlos Martín-Vide (Tarragona, ES, chair) Manuel Montes-y-Gómez (Puebla, MX) Satoshi Nakamura (Nara, JP) Shrikanth S. Narayanan (Los Angeles, US) Vincent Ng (Dallas, US) Joakim Nivre (Uppsala, SE) Elmar Nöth (Erlangen, DE) Maurizio Omologo (Trento, IT) Mari Ostendorf (Seattle, US) Barbara H. Partee (Amherst, US) Gerald Penn (Toronto, CA) Massimo Poesio (Colchester, UK) James Pustejovsky (Waltham, US) Gaël Richard (Paris, FR) German Rigau (San Sebastián, ES) Paolo Rosso (Valencia, ES) Yoshinori Sagisaka (Tokyo, JP) Björn W. Schuller (London, UK) Satoshi Sekine (New York, US) Richard Sproat (New York, US) Mark Steedman (Edinburgh, UK) Jian Su (Singapore, SG) Marc Swerts (Tilburg, NL) Jun'ichi Tsujii (Beijing, CN) Gertjan van Noord (Groningen, NL) Renata Vieira (Porto Alegre, BR) Dekai Wu (Hong Kong, HK) Feiyu Xu (Berlin, DE) Roman Yangarber (Helsinki, FI) Geoffrey Zweig (Redmond, US) ORGANISING COMMITTEE: Laurent Besacier (Grenoble, co-chair) Adrian Horia Dediu (Tarragona) Benjamin Lecouteux (Grenoble) Carlos Martín-Vide (Tarragona, co-chair) Florentina Lilica Voicu (Tarragona) 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 prepared according to the standard format for Springer Verlag's LNAI/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=slsp2014 PUBLICATIONS: A volume of proceedings published by Springer in the LNAI/LNCS series will be available by the time of the conference. A special issue of a major journal 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 January 16, 2014 to October 14, 2014. The registration form can be found at: http://grammars.grlmc.com/slsp2014/Registration.php DEADLINES: Paper submission: May 7, 2014 (23:59h, CET) Notification of paper acceptance or rejection: June 18, 2014 Final version of the paper for the LNAI/LNCS proceedings: June 25, 2014 Early registration: July 2, 2014 Late registration: September 30, 2014 Submission to the post-conference journal special issue: January 16, 2015 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: SLSP 2014 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559 543 Fax: +34 977 558 386 ACKNOWLEDGEMENTS: Departament dEconomia i Coneixement, Generalitat de Catalunya Laboratoire dInformatique de Grenoble Universitat Rovira i Virgili

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3rd RSG Belgium seminar - update
by Jurgen CLAESEN 07 Apr '14

07 Apr '14

Dear all, We are very pleased to invite submissions for talks at the third RSG Belgium seminar. For more information about RSG Belgium, please have a look at the following link: http://www.iscbsc.org/rsg/rsg-belgium The goal of this seminar day is to allow PhD students from different research groups around Belgium to present their work and interact with each other. It will take place in *Antwerp* on Wednesday, the 28th of May 2014 from 14h to 17h. We will be accepting the first four submitted talks for this session. So don't wait too long to submit. The featured talks will have 20 minutes to present followed by about 10 minutes of questions. To submit a talk proposal, simply email rsg-belgium(a)iscbsc.org with the title of the talk and the name of the presenter. The submission deadline is Monday, the 12th of May. Please diffuse this call to anyone who might also be interested in joining. Hope to see you there! Regards, RSG Belgium committee

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3rd RSG Belgium symposium
by Jurgen CLAESEN 07 Apr '14

07 Apr '14

Dear all, We are very pleased to invite submissions for talks at the third RSG Belgium seminar. For more information about RSG Belgium, please have a look at the following link: http://www.iscbsc.org/rsg/rsg-belgium The goal of this seminar day is to allow PhD students from different research groups around Belgium to present their work and interact with each other. It will take place in Brussels on Wednesday, the 28th of May 2014 from 14h to 17h. We will be accepting the first four submitted talks for this session. So don't wait too long to submit. The featured talks will have 20 minutes to present followed by about 10 minutes of questions. To submit a talk proposal, simply email rsg-belgium(a)iscbsc.org with the title of the talk and the name of the presenter. The submission deadline is Monday, the 12th of May. Please diffuse this call to anyone who might also be interested in joining. Hope to see you there! Regards, RSG Belgium committee

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Bioinformatician vacancy at Leiden University Medical Center
by Leon Mei 04 Apr '14

04 Apr '14

Dear colleagues, We have one bioinformatician vacancy (BSc/MSc level) at the department of Clinical genetics in Leiden University Medical Center. Please feel free to apply or forward the link to those who might be interested in this position. Thanks! https://www.lumc.nl/home/0005/werken-bij-het-lumc/23583/80611011354221/1403… Best regards, Leon

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Fwd: Call for abstracts: Regulatory Genomics Special Interest Group (RegGenSIG)
by Stein Aerts 02 Apr '14

02 Apr '14

FYI: http://light.ece.ohio.edu/~reggen/2014/ Best regards, Stein Regulatory Genomics Special Interest Group (RegGenSIG) Special Interest Group (SIG) at ISMB 2014 July 12, 2014, Boston, Massachusetts SIG Hours: 8:30 a.m - 6:00 p.m. Regulatory genomics involves the study of the genomic 'control system,' which determines how, when and where to activate the 'blueprint' encoded in the genome. Regulatory genomics is the topic of much research activity worldwide. Since computational methods are important in the study of gene regulation, the RegGenSIG meeting focuses on bioinformatics for regulatory genomics. An important goal of the meeting is to foster a collaborative community wherein scientists convene to solve difficult research problems in all areas of computational regulatory genomics. RegGenSIG will include presentations and posters that cover the broad spectrum of topics important to regulatory genomics research. The goal is to bring together experts in experimental methods and computational methods to consider sequence-based reconstruction of regulatory networks and prediction of gene expression. Topics to be addressed in the SIG include the following: inference of gene regulatory networks; utilization of information pertaining to epigenetics, chromatin structure, and histone modifications; determination of the roles of regulatory RNAs; prediction of transcriptional regulation from RNA-seq data and ChIP-seq data; pattern discovery in sequences; and sequence based modeling of gene expression. CALL FOR EXTENDED ABSTRACTS To make an oral presentation at RegGenSIG, extended abstracts should be submitted by April 27, 2014 to sinhas(a)illinois.edu, including "RegGen Abstract Oral" in the subject line. An abstract should be a maximum of 3 pages excluding bibliography. Authors will be notified by May 8, 2014. CALL FOR POSTERS For poster presentations, authors should submit a 250 word abstract no later than May 18, 2014 to sinhas(a)illinois.edu, including "RegGen Abstract Poster" in the subject line. Authors will be notified no later than May 25, 2014. KEY DATES April 20, 2014 Due date for extended abstracts (2-3 pages) for oral presentations May 1, 2014 Author notification for oral presentations May 18, 2014 Due date for short abstracts (250 words) for poster presentations May 25, 2014 Author notification for poster presentations June 6, 2014 Early registration cut-off date July 12, 2014 RegGenSIG meeting Program Chairs: Jason Ernst, UCLA, USA, jason.ernst(a)ucla.edu Saurabh Sinha, University of Illinois, USA, sinhas(a)illinois.edu Stein Aerts, University of Leuven, Belgium, stein.aerts(a)med.kuleuven.be Morgane Thomas-Chollier, Ecole Normale Superieure, France, mthomas(a)biologie.ens.fr General Chairs: Finn Drabløs, Norwegian University of Science and Technology, Norway, finn.drablos(a)ntnu.no Lonnie R. Welch, Ohio University, USA, welch(a)ohio.edu SIG Advisory Committee: Tim Bailey, University of Queensland, Australia Harmen Bussemaker, Columbia University Andrea Califano, Columbia University Julio Collado-Vides, National Autonomous University of Mexico Laura Elnitski, National Human Genome Research Institute, USA Ana Teresa Freitas, Technical University of Lisbon, Portugal Roderic Guigo, Centre for Genomic Regulation, Spain Alexander Hartemink, Duke University Manolis Kellis, MIT, USA (pending) Kathleen Marchal, Professor University of Ghent and K. U. Leuven, Belgium William Noble, University of Washington (tentative) Isidore Rigoutsos, Thomas Jefferson University, USA Sophie Schbath, Institut National de la RecherchÃ© Agronomique, France Gustavo Stolovitzky, IBM Gary Stormo, Washington University, USA Kai Tan, University of Iowa, USA Andrei Thomas-Tikhonenko, University of Pennsylvania Esko Ukkonen, University of Helsinki, Finland Martin Vingron, Max Planck Institute for Molecular Genetics, Germany Weixiong Zhang, Washington University, USA Igor Zwir, University of Granada

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BBC 2013 abstract submission through EasyChair
by BBC2013 01 Apr '14

01 Apr '14

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, The 8th edition of the BeNeLux Bioinformatics Conference 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 through the EasyChair system: https://www.easychair.org/conferences/?conf=bbc2013 . 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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