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

Senior Bioinformatics position with AgResearch Ltd
by Mark Fiers 10 Jun '13

10 Jun '13

FYI: ------------------------------------- SENIOR BIOINFORMATICIAN Palmerston North, New Zealand AgResearch is a Crown Research Institute with the purpose of enhancing the value, productivity and profitability of New Zealand’s agricultural sector. The Bioinformatics team supports the Biological research in a range of areas working for the improvement of pastoral agricultural sector. We are seeking a highly motivated individual with excellent training in Bioinformatics to join our team. This is a permanent position. You will be responsible for providing Bioinformatics consultancy to a range of Science projects involved in the scientific discovery in plants, animals, fungi and microbes and will be responsible for analysing high throughput/high-dimensional ‘Omics data from non-model organisms. This includes the design, development, implementation and testing of bioinformatics pipelines and tools, assembly of NGS and RNA-Seq data, network and pathway analyses. You will also have some experience or interest in integrating multi-faceted Omics data to understand underlying systems and biological networks. Successful applicant will have a PhD or high level postgraduate qualification in Bioinformatics or related field with five years of related work experience. A thorough knowledge of Unix, scripting language (Perl/Python or similar) and an understanding of Biological databases along with various Bioinformatics tools is required. This is a highly collaborative role, where the incumbent will be working with Scientists on a regular basis thus requiring a good knowledge of Genetics and Molecular Biology. Strong communication skills, with the ability to effectively articulate complex, technical information to the clients is highly desirable. You will also have good organisational abilities along with excellent interpersonal and relationship building skills. The position will be based at AgResearch Grasslands campus in Palmerston North and will be part of wider Bioinformatics and Statistics team. Palmerston North, a university city, is 30 km from the coast, 2 hours from ski fields, and 2 hours from Wellington. The AgResearch Grasslands campus is situated in pleasant rural surroundings with easy access to the central city. The surrounding area offers many outdoor recreational opportunities. To find out more about this position and to apply online please visit: https://secure.agresearch.co.nz/careers/vacancies.aspx Applications not submitted online will not be accepted. Contact Philippa.Maternaghan(a)agresearch.co.nz if you have any questions about this vacancy. Applications close Sunday 07 July 2013. -------------------------------------

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SLSP 2013: call for participation
by GRLMC 09 Jun '13

09 Jun '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************************************************ 1st INTERNATIONAL CONFERENCE ON STATISTICAL LANGUAGE AND SPEECH PROCESSING SLSP 2013 Tarragona, Spain July 29-31, 2013 http://grammars.grlmc.com/SLSP2013/ ************************************************************************************************ PROGRAMME Monday, July 29: 8:00 - 8:50 Registration 8:50 - 9:00 Opening 9:00 - 9:50 Yoshua Bengio: Deep Learning of Representations: Looking Forward (I) - Invited Tutorial 9:50 - 10:20 Coffee Break 10:20 - 11:35 Horacio Saggion, Stefan Bott, and Luz Rello: Comparing Resources for Spanish Lexical Simplification Borbála Siklósi, Attila Novák, and Gábor Prószéky: Context-aware Correction of Spelling Errors in Hungarian Medical Documents Attia Nehar, Djelloul Ziadi, and Hadda Cherroun: Rational Kernels for Arabic Text Classification 11:35 - 11:45 Break 11:45 - 13:00 Horia Cucu, Andi Buzo, Laurent Besacier, and Corneliu Burileanu: Statistical Error Correction Methods for Domain-Specific ASR Systems Myung-Jae Kim, Il-Ho Yang, and Ha-Jin Yu: Histogram Equalization Using Centroids of Fuzzy C-Means of Background Speakers' Utterances for Speaker Identification Layla El Asri, Romain Laroche, and Olivier Pietquin: Reward Shaping for Statistical Optimisation of Dialogue Management 13:00 - 14:30 Lunch 14:30 - 15:20 Samuel W. K. Chan and Mickey M. C. Chong: Predicting Part-of-Speech Tags and Morpho-Syntactic Relations using Similarity-based Technique Nobal Niraula, Rajendra Banjade, Dan Ștefănescu, and Vasile Rus: Experiments with Semantic Similarity Measures based on LDA and LSA 15:20 - 15:30 Break 15:30 - 16:20 Yoshua Bengio: Deep Learning of Representations: Looking Forward (II) - Invited Tutorial Tuesday, July 30: 9:00 - 9:50 Christof Monz: Challenges and Opportunities of Multilingual Information Access - Invited Lecture 9:50 - 10:20 Coffee Break 10:20 - 11:35 Akira Hayashi, Kazunori Iwata, and Nobuo Suematsu: Finding the Most Likely Upper Level State Sequence for Hierarchical HMMs Jordan Rodu, Dean P. Foster, Weichen Wu, and Lyle H. Ungar: Using Regression for Spectral Estimation of HMMs Amit Kirschenbaum: Unsupervised Segmentation for Different Types of Morphological Processes Using Multiple Sequence Alignment 11:35 - 11:45 Break 11:45 - 13:00 Abdessalam Bouchekif, Géraldine Damnati, and Delphine Charlet: Complementarity of Lexical Cohesion and Speaker Role Information for Story Segmentation of French TV Broadcast News Markus Saers, Karteek Addanki, and Dekai Wu: Iterative Rule Segmentation under Minimum Description Length for Unsupervised Transduction Grammar Induction Ngoc Thang Vu, Heike Adel, and Tanja Schultz: An Investigation of Code-Switching Attitude Dependent Language Modeling 13:00 - 14:30 Lunch 14:30 - 15:20 Hans Moen and Erwin Marsi: Cross-Lingual Random Indexing for Information Retrieval Javad Nouri, Lidia Pivovarova, and Roman Yangarber: MDL-based Models for Transliteration Generation 15:20 - 15:30 Break 15:30 - 16:20 Sanja Štajner and Richard Evans: Can Statistical Tests Be Used for Feature Selection in Diachronic Text Classification? Luis Trindade, Hui Wang, William Blackburn, and Niall Rooney: Factored Semantic Sequence Kernel for Sentiment Polarity Classification 17:30 Visit to the City Wednesday, July 31: 9:00 - 9:50 Tanja Schultz: Multilingual Speech Processing with a special emphasis on Rapid Language Adaptation - Invited Lecture 9:50 - 10:20 Coffee Break 10:20 - 11:35 Fethi Bougares, Mickael Rouvier, Nathalie Camelin, Paul Deléglise, and Yannick Estève: An Investigation of Single-pass ASR System Combination for Spoken Language Understanding Marwa Graja, Maher Jaoua, and Lamia Hadrich Belguith: Discriminative Framework for Spoken Tunisian Dialect Understanding Bassam Jabaian, Fabrice Lefèvre, and Laurent Besacier: Generalization of Discriminative Approaches for Speech Language Understanding in a Multilingual Context 11:35 - 11:45 Break 11:45 - 13:00 Felix Stahlberg, Tim Schlippe, Stephan Vogel, and Tanja Schultz: Pronunciation Extraction from Phoneme Sequences Through Cross-Lingual Word-to-Phoneme Alignment Stanisław Kacprzak and Mariusz Ziółko: Speech/Music Discrimination via Energy Density Analysis Karteek Addanki and Dekai Wu: Unsupervised Rhyme Scheme Identification in Hip Hop Lyrics using Hidden Markov Models 13:00 Closing

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[Gtpb] GTPB Course Announcement: ABBTU13 Advanced Biostatistics for Bioinformatics Tool Users
by Pedro Fernandes 07 Jun '13

07 Jun '13

Course announcement ABBTU13 Advanced Biostatistics for Bioinformatics Tool Users with Lisete Sousa and Carina Silva-Fortes IMPORTANT DATES for this Course Deadline for applications: June 28th 2013 Course date: July 8st - July 12th 2013 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. NOTE: Some participants in this course may ish to acquire the pre-reqested skills via the introductory course IBBTU13 that is scheduled for just before. In that case separate applications are required. Course description This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques used in Bioinformatics. This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBB) course that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples. Methodology The course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. Target Audience Everybody using Bioinformatics methods is implicitly using statistical methods. Moreover, proper judgment of the results often calls for a deeper level of understanding than what is required to solve scholarly exercises. We will look into particular areas such Simulation, Bayesian Inference, Hidden Markov Chains and Multivariate methods with the attitude, eyes and brains of a statistician that wants to understand how the methods work. and systematic way. Course Pre-requisites Intermediate knowledge in Statistics is necessary. Elementary skills in computer usage are also needed. We will assume that all the participants have checked their knowledge in: - probability - conditional probability - distributions - statistical tests - hypothesis testing - inference More information, including "how to apply", detailed schedule, etc. is available at: http://gtpb.igc.gulbenkian.pt/bicourses/ABBTU13 -- Pedro Fernandes GTPB Coordinator 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] GTPB Course Announcement: IBBTU13 Introductory Biostatistics for Bioinformatics Tool Users
by Pedro Fernandes 07 Jun '13

07 Jun '13

Course announcement IBBTU13 Introductory Biostatistics for Bioinformatics Tool Users with Ana Luisa Papoila and Fernanda Diamantino IMPORTANT DATES for this Course Deadline for applications: June 21st 2013 Course date: July 1st - July 5th 2013 Candidates with the adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. NOTE: Some participants in this course may be interested in the advanced course ABBTU13 that is scheduled for right after. In that case separate applications are required. Course description This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques used in Bioinformatics. Many analytical and inferential methods, regardless of their novelty, have their niches of application all over the place in Bioinformatics. We will be looking at statistical methods, digging into their inner workings, wearing the skins of professional statisticians. Participants can expect a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods, and extensive hands-on practice, exclusively based on biological examples. Methodology The course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. Target Audience Everybody using Bioinformatics methods is implicitly using statistical methods. Most people have had one or more semester courses in Statistics in their graduate education. For many, Statistics happened in their lives a long time ago, and that makes it difficult to go back and manipulate the concepts with full confidence. Attending this course is a chance of revisiting subjects like experimental design, hypothesis testing, inference and prediction in an intensive and systematic way. More information, including "how to apply", detailed schedule, etc. is available at: http://gtpb.igc.gulbenkian.pt/bicourses/IBBTU13 -- Pedro Fernandes GTPB Coordinator 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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PhD / Postdoc position on Evolutionary Cell Biology of the Mitotic Checkpoint
by berend snel 06 Jun '13

06 Jun '13

*PhD / Postdoc position on Evolutionary Cell Biology of the Mitotic Checkpoint.* We are looking for a motivated PhD student or postdoc with experience in evolutionary bioinformatics, and with affinity for understanding the role of protein networks in biological processes. The project seeks to derive functional insights into chromosome segregation from the study of protein co-evolution at the residue, motif, domain and protein level within the mitotic checkpoint signaling pathway. Novel and improved co-evolution studies are now possible thanks to an avalanche of new complete genomes. The project will encompass development of new tools and continuous refinement of a pipeline to describe and detect co-evolution between proteins. Importantly this bioinformatic pipeline will be used for generating detailed predictions on function and evolution of mitotic checkpoint proteins. As such, the candidate is expected to develop extensive expertise on chromosome segregation in general, and the mitotic checkpoint in particular, to push the limits on these predictions. *Department information* The lab of Geert Kops is part of the department of Medical Oncology and the department of Molecular Cancer Research at the UMC Utrecht. These departments are renowned for their fundamental and translational cancer research. The lab is located in the Stratenum building, that additionally houses various state-of-the-art facilities, including microscopy, proteomics, cell-screening, biochemistry and next-generation sequencing. The Kops lab consist of 6 PhD student, 3 postdocs and 4 technicians. The lab of Berend Snel is part of the Institute for Biodynamics and Biocomplexity of the Faculty of Science. This institute aims to achieve a systems-level understanding of complex dynamic processes and their evolution through close interaction between experimentation and computational biology. The Snel group currently consists of 4 PhD students and 1 postdoc working on the evolution and function of different biological systems. *How to apply* Please send your CV, along with a cover letter outlining your specific qualifications for the preferred positions including contact information for at least two references to Dr. Berend Snel, B.Snel(a)uu.nl.

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GCC2013 Registration Closes June 14
by Dave Clements 04 Jun '13

04 Jun '13

Hello all, This is the final registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> reminder for the 2013 Galaxy Community Conference (GCC2013<http://wiki.galaxyproject.org/Events/GCC2013>), being held in Oslo, 30 June through July 2. Registration <http://wiki.galaxyproject.org/Events/GCC2013/Register> closes June 14*, ten days from today. Register now<http://wiki.galaxyproject.org/Events/GCC2013/Register> and guarantee your spot in the Training Day sessions<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> you want to take.* *Registration is still a bargain with the full 3-day registration starting at ~ €165 for post-docs and students (or just €55 per day). The program <http://wiki.galaxyproject.org/Events/GCC2013/Program> features 15 Training Day sessions<http://wiki.galaxyproject.org/Events/GCC2013/Program#Day_0:_Training_Day.2C…> in 5 tracks on 12 different topics, 25 Talks<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Talk_Abstracts> on topics ranging from Reproducibility<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA…> to Exploiting Galaxy<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA…> , 23 Posters<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Poster_Abstracts> (and counting), 2 Lightning Talk sessions, and a end-of-conference event at an historic venue high above Oslo. GCC2013 is a great opportunity to share best practices and network with other researchers who are also facing the challenges of data-intensive biology. Ser frem til å se deg i Oslo! GCC2013 Organizing Committee PS: Please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> . * Not June 7, as had been stated earlier in several places. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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SSTiC 2013: next registration deadline 26 June
by GRLMC 02 Jun '13

02 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 59 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 Jeffrey S. Chase (Duke) [intermediate] Trust Logic as an Enabler for Secure Federated Systems 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 Massoud Pedram (Southern California) [intermediate] Energy Efficient Architectures and Information Processing Systems Charles E. Perkins (FutureWei) [intermediate/advanced] Beyond 4G Prabhakar Raghavan (Google) [introductory/intermediate] Web Search and Advertising Sudhakar M. Reddy (Iowa) [introductory] Design for Test and Test of Digital VLSI Circuits 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: They are the same (a flat rate) for all people by the corresponding deadline. They give the right to attend all courses. 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 Six registration deadlines: February 26, March 26, April 26, May 26, June 26, July 26, 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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RECOMB-CG 2013 - Second Call for Papers
by Macha Nikolski 01 Jun '13

01 Jun '13

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 21, 2013 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, Evry - Laurent Duret, Laboratoire de Biométrie et Biologie Évolutive, Lyon - Nicolas Galtier, Institut des Sciences d'Evolution, 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) • 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) • Aida Ouangraoua (France) • Benedict Paten (USA) • Sven Rahmann (Germany) • Eric Rivals (France) • Hugues Roest Crollius (France) • Marie-France Sagot (France) • Cathal Seoighe (Ireland) • 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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