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NBIC/BioSB course Comparative Genomics: from evolution to function (2nd edition), 2-6 June 2014
by Celia.vanGelder＠radboudumc.nl 27 Apr '14

27 Apr '14

NBIC/BioSB Course Comparative Genomics: from evolution to function (2nd edition) Date: June 2 - June 6, 2014 Location: VU University, Amsterdam, the Netherlands Course coordinators: Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU), Celia van Gelder (NBIC/BioSB, education(a)biosb.nl<mailto:education@biosb.nl> ) Course website: http://biosb.nl/comparative-genomics-2014/ Registration: Registration is not yet open. You can express your interest in the course by filling out the pre-registration form at http://biosb.nl/education/enrollment/pre-registration-courses/. More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why they fail (or misdetect) as a consequence of a variety of biological /evolutionary causes. The first two days of the course provide a basis for the course with the aim to move "beyond blast" in terms of more sensitive homology searches, domain level analysis of protein evolution as well as more fine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology).This foundation is used to discuss in the three following days in more detail three topics: (1) the study of functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements. Target audience The course is intended for PhD students and master students in bioinformatics, especially those interested in evolution and/or those who want to compare various genomics data between species. Participants are expected to have some hands on experience with blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains. Programme Monday June 2: Distant homology and protein domains (lecturer Jaap Heringa) Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment, psiblast, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction Tuesday June 3: Comparative Interactomics (lecturers Jaap Heringa, Martijn Huynen/John van Dam) Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization Wednesday June 4: Small scale orthology and large scale databases (lecturers Martijn Huynen, Berend Snel) Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission Thursday June 5: Genome duplications (lecturer Berend Snel) Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart Friday June 6: Finding functional elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen) Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs sampling, RNA secondary structure prediction based on sequences and on experimental data, biased gene conversion & positive selection. BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Call for abstracts – 3rd European Student Council Symposium 2014 (ESCS2014)
by ISCBSC announcement 24 Apr '14

24 Apr '14

Dear Colleagues, Submit your abstract now for the 3rd European Symposium of the International Society for Computational Biology Student Council, to be held on September 6th 2014 in Strasbourg, France, as a satellite meeting of the European Conference on Computational Biology (ECCB)! ESCS2014 will bring together young computational biologists from several research areas and regions of the world. As the central part of our symposium, 10 students will be selected for an oral presentation from the submitted abstracts. This is your chance to present your work to an international audience of young scientists! In addition, we are proud to host several keynotes from distinguished scientists, such as Dr. Lennart Martens from the University of Ghent and Dr. Jeroen de Ridder from the Delft University of Technology. We welcome abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. As in previous editions, awards will be given to outstanding posters and presentations. All abstracts accepted for oral presentation will be published in a special issue of the BMC Bioinformatics journal. Submission information: http://escs2014.iscbsc.org/escs-submission General information: http://escs.iscbsc.org/ Important dates April 24, 2014: Abstract submission opens June 23, 2014: Abstract submission closes July 15, 2014: Abstract acceptance notifications We look forward to receiving your abstract! On behalf of the ESCS organizers, Pieter Meysman Chair, 3rd European Student Council Symposium 2014 Margherita Francescatto Co-Chair, 3rd European Student Council Symposium 2014

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[Gtpb] Fwd: Bioinformatics training course announcement SMLMC14 in Oeiras, Portugal
by Pedro Fernandes 23 Apr '14

23 Apr '14

GTPB Announcement Applications are open for another Bioinformatics Training course: SMLMC14 Structural Modeling for Large Macromolecular Complexes with Joanna Kasprzak and Grzegorz Chojnowski IMPORTANT DATES for this Course Deadline for applications: May 15st 2014 Latest notification of acceptance: May 17th 2014 Course date: June 11th - June 13th 2014 Course description One of the major challenges in structural biology is to determine the structures of macromolecular complexes and to understand their function and mechanism of action. However, structural characterisation of macromolecular assemblies is very difficult. To begin addressing this problem, we have developed PyRy3D. In a nutshell, PyRy3D employs a hybrid computational approach that incorporates spatial information from a variety of experimental methods into the modelling procedure to build low-resolution models of large macromolecular complexes. The PyRy3D model building procedure uses a Monte Carlo approach to sample the solutions-space. It uses spatial restraints to define components interacting with each other, and a simple scoring function is applied to pack them tightly into contours of the entire complex (e.g. cryoEM density maps). More details at http://gtpb.igc.gulbenkian.pt/bicourses/SMLMC14/ Thank you for your interest! 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

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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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