From karypis from cs.umn.edu Tue Oct 6 17:56:54 2009 From: karypis from cs.umn.edu (George Karypis) Date: Wed Oct 7 13:20:35 2009 Subject: [Bionews] CFP: HiCOMB 2010 - 9th IEEE International Workshop on High Performance Computational Biology Message-ID: <004801ca46d8$4ccfaf80$e66f0e80$@umn.edu> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Call For Papers HiCOMB 2010 9th IEEE International Workshop on High Performance Computational Biology http://www.hicomb.org/ held in conjunction with the International Parallel and Distributed Processing Symposium http://www.ipdps.org/ Monday, April 19, 2010 Atlanta, Georgia -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Computational Biology are related disciplines are fast emerging as an important area for academic research and industrial application. The large size of biological data sets, inherent complexity of biological problems and the ability to deal with error-prone data all result in large run-time and memory requirements. The goal of this workshop is to provide a forum for discussion of latest research in developing high-performance computing solutions to problems arising from molecular biology and related life sciences areas. We are especially interested in parallel algorithms, memory-efficient algorithms, large scale data mining techniques, and design of high-performance software. The workshop will feature contributed papers as well as invited talks from reputed researchers in the field. Topics of interest include but are not limited to: * Bioinformatic databases * Computational genomics * Computational proteomics * DNA assembly, clustering and mapping * Gene expression and microarrays * Gene identification and annotation * Parallel algorithms for biological analysis * Parallel architectures for biological applications * Molecular evolution * Molecular sequence analysis * Phylogeny reconstruction algorithms * Protein structure prediction and modeling * String data structures and algorithms * Parallel algorithms in chemical genetics and chemical informatics Submission Guidelines: ---------------------- Papers reporting original research (both theoretical and experimental) in all areas of bioinformatics and computational biology are sought. Surveys of important recent results and directions are also welcome. To submit a paper, upload a postscript or PDF copy of the paper from the workshop web page (http://www.hicomb.org/). The paper should not exceed 12 single-spaced pages (US Letter or A4 size) in 11pt font or larger. All papers will be reviewed. IEEE CS Press will publish the IPDPS symposium and workshop abstracts as a printed volume. The complete symposium and workshop proceedings will also be published by IEEE CS Press on CD-ROM and will also be available in the IEEE Digital Library. Important Dates: ---------------- November 30, 2009 Workshop Submissions Due December 25, 2009 Author Notification February 1, 2009 Camera-ready Paper Due Workshop Co-Chairs: ------------------- David A. Bader College of Computing Georgia Institute of Technology Atlanta, GA 30332 USA Phone: +1.404.894.3152 http://www.cc.gatech.edu/~bader Srinivas Aluru Dept. of Electrical & Computer Engg. Iowa State University 3227 Coover Hall Ames, IA 50011 USA Phone: +1.515.294.3539 Email: aluru@iastate.edu Program Chair: -------------- George Karypis Dept. of Computer Science & Engineering University of Minnesota Minneapolis, MN 55455 Email: karypis@cs.umn.edu http://www.cs.umn.edu/~karypis Program Committee: ------------------ Pratul K. Agarwal, Oak Ridge National Laboratory, USA Inanc Birol, Genome Sciences Centre, British Columbia, Canada Georg Fuellen, University of Rostock, Rostock, Germany Ananth Grama, Purdue University, Indiana, USA Mark Miller, San Diego Supercomputer Center, California, USA Sandeep Patel, University of Delaware, USA Andrew Rau-Chaplin, Dalhousie University, Nova Scotia, Canada Huzefa Rangwala, George Mason University, Virginia, USA Jared Simpson, Wellcome Trust Sanger Institute, Cambridge, UK Alexandros Stamatakis, Technische Universit?t Munchen, Munich, Germany John Stone, University of Illinois at Urbana-Champaign, USA Evripidis Sotiriadis, Tech. Univ. of Crete, Greece Denis Trystram, LIG, France Chau-Wen Tseng, University of Maryland, College Park, USA Ian Watson, Lilly, Indiana, USA Tiffani Williams, Texas A&M University, Texas, USA Ying Zhao, Tsinghua University, Beijing, China Albert Zomaya, University of Sydney, Sydney, Australia From conf from topaz.gatech.edu Thu Oct 8 19:23:20 2009 From: conf from topaz.gatech.edu (Georgia Tech Conference Announcement) Date: Thu Oct 8 21:25:49 2009 Subject: [Bionews] 7th Georgia Tech - ORNL Conference on Bioinformatics Message-ID: <20091009002320.2612CE104@topaz.gatech.edu> Call for Paper Abstracts is extened --------------------------------- Dear Colleagues The 7th Georgia Tech - ORNL Conference on Bioinformatics - In silico Biology: Genome Biology and Bioinformatics will be held in Atlanta, Georgia, November 12-14, 2009 http://www2.isye.gatech.edu/binf2009/ Georgia Tech continues the tradition of organizing biennial International Conference on Bioinformatics, bringing together leading researchers in genomics, bioinformatics and genome biology to present recent advances in the field and to discuss open problems. Important Dates Deadline for poster abstract subsmission: October 11, 2009 Notification of acceptance of abstracts: October 20, 2009 Deadline for early registration: October 23, 2009 We invite papers submissions in the following areas * genomics * transcriptomics * proteomics * reconstruction and modeling of gene networks * evolutionary biology SPEAKERS Margaret O. Dayhoff lecture: David Lipman, NCBI/NIH, Bethesda, MD, USA Plenary Speakers: Vineet Bafna, University of California at San Diego, USA Gill Bejerano, Stanford University, Stanford, CA, USA Jeffrey Bennetzen, University of Georgia, Athens, GA, USA Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA Nick Grishin, University of Texas, Dallas, TX, USA Curtis Huttenhower, Harvard University, Boston, MA, USA King Jordan, Georgia Tech, Atlanta, GA, USA Igor Jouline (Zhulin), University of Tennessee - ORNL, Oak Ridge, TN, USA Eugene Koonin, NCBI/NIH, Bethesda, MD, USA Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA Boris Lenhard, University of Bergen, Norway Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA Yael Mandel-Gutfreund, Technion, Israel Insitute of Technology, Haifa, Israel Joanna Masel, University of Arizona, Tucson, AZ, USA Andrey Mironov, Moscow State University, Russia Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA Natasa Przulj, Imperial College London, UK John Reinitz, State Uiversity of New York at Stony Brook, NY, USA Pierre Rouze, Gent University, Gent, Belgium CONFERENCE CHAIRS Mark Borodovsky, Georgia Tech and Emory University Eva K. Lee, Georgia Tech and Emory University PROGRAM COMMITTEE Nicholas Bergman, Georgia Tech Dmitrij Frishman, Technische Universitaet Muenchen, Germany Andrey Gorin, Oak Ridge National Laboratory Andrzej M. Kierzek, University of Surrey, UK. Eileen Kraemer, University of Georgia Jun Liu, Harvard University Hannah Margalit, Hebrew University Andrey Rzhetsky, University of Chicago Andre Rogatko, Samuel Oschin Comprehensive Cancer Institute Gary Stormo, Washington University Lance Waller, Emory University Ying Xu, University of Georgia and Oak Ridge National Laboratory Soojin Yi, Georgia Tech Igor Zhulin, Oak Ridge National Laboratory and University of Tennessee ADMINISTRATION Harry Sharp, Georgia Tech CONFERENCE LOCATION The Georgia Tech Ferst Center for the Arts. From gws from ncifcrf.gov Thu Oct 22 10:12:33 2009 From: gws from ncifcrf.gov (Gary Smythers) Date: Thu Oct 22 11:52:55 2009 Subject: [Bionews] Announcement: GenPept 174.0 available Message-ID: <20091022151233.4B2BEA4001@bio1.ncifcrf.gov> This is to announce the availability of release 174.0 of the GenPept(R) (GenBank Gene Products) Database. GenPept is provided in a format similar to that formerly distributed by GenBank(R) under the administration of Intelligenetics Inc. This GenPept release IS _NOT_ AN OFFICIAL RELEASE FROM THE NCBI-GENBANK, but an attempt to provide a data file format compatible with existing software products. This data format is suitable as an input data file for the GCG program genbanktogcg -genpept. Compatibility with other software has not been tested. Site: ftp.ncifcrf.gov Directory: pub/genpept Files: gprel.txt.gz, gpdat.seq.gz, gpdat.fasta.gz Directory: pub/genpept/divisions Files: 1 file for each GenBank file Directory: pub/genpept/updates (daily, cumulative) Files: gpseq_updates.dat.gz Rel. Date: 20-Oct-2009 If you have questions or comments concerning this data, or you experience any difficulty in downloading the data via ftp, please contact: Gary Smythers smytherg@mail.nih.gov 301-846-5778 ================================================================ GenPept (R) and GenBank (R) are registered trademarks of the U.S. Department of Health and Human Services for the GenBank Gene Products and the GenBank Genetic Sequence Data Banks. From mcdevitt from ibb.gatech.edu Thu Oct 22 11:31:23 2009 From: mcdevitt from ibb.gatech.edu (Megan McDevitt) Date: Thu Oct 22 13:50:12 2009 Subject: [Bionews] International Conference - Genome Biology and Bioinformatics Message-ID: Dear Colleagues, The 7th Georgia Tech - ORNL Conference - "Genome Biology and Bioinformatics" to be held on November 12-14, 2009 is now less than a month away: http://www2.isye.gatech.edu/binf2009/ The program of the conference features talks of many leading experts in the field http://www2.isye.gatech.edu/binf2009/speakers_2009.php Thanks to financial support from a larger group of sponsors we are happy to announce that the registration fee is reduced to: $20 student/postdoc $50 - academic $100 - industry Deadline for poster abstract submission is extended to November 1 We hope to see you soon in the Georgia Tech Ferst Center for the Arts _____________________________________ Invited Speakers Margaret O. Dayhoff Lecture David Lipman, NCBI/NIH, Bethesda, MD, USA Margaret Dayhoff and Molecular Evolution in the 21st Century Vineet Bafna, University of California at San Diego, USA Proteogenomics Gill Bejerano, Stanford University, Stanford, CA, USA Genomics and the Evolution of Human-Specific Traits Jeffrey Bennetzen, University of Georgia, Athens, GA, USA The Hyperevolution of Artifacts and Realities in the Structure and Function of Higher Plant Genomes Mark Borodovsky, Georgia Tech and Emory University, Atlanta, GA, USA Gene Finding in the Era of Next Generation Sequencing Nick Grishin, Howard Hughes Medical Institute, University of Texas, Dallas, TX, USA Evolutionary Classification of Protein Structures Curtis Huttenhower, Harvard University, Boston, MA, USA Large Scale Genomic Data Mining King Jordan, Georgia Tech, Atlanta, GA, USA MIR Elements Provide Chromatin Boundaries to the Human Genome Igor Jouline, University of Tennessee - Oak Ridge National Laboratory, Oak Ridge, TN, USA Molecular Evolution of a Complex Signal Transduction System in Prokaryotes Eugene Koonin, NCBI/NIH, Bethesda, MD, USA Systems Biology and the Prospects of a Post-Modern Evolutionary Synthesis Nikos Kyrpides, DOE Joint Genome Institute, Walnut Creek, CA, USA The Future of Microbial Genomics Boris Lenhard, University of Bergen, Norway Long-, Short- and Mid-Range Gene Regulation: Lessons from Genome-Wide Patterns of Sequence Conservation and Transcription Factor Binding Jian Ma, University of Illinois at Urbana Champaign, Urbana, IL, USA Unraveling the Ancestral Mammalian Genome Yields Insights into the Human Genome Yael Mandel-Gutfreund, Technion, Israel Institute of Technology, Haifa, Israel Deciphering the Role of Alternative Splicing in Modulating the Human Gene Regulatory Network Joanna Masel, University of Arizona, Tucson, AZ, USA The Origin of New Coding Sequences Andrey Mironov, Moscow State University, Russia Conserved Intronic RNA Secondary Structures Karen Nelson, J. Craig Venter Institute, Rockville, MD, USA Studies of The Human Microbiome Andrei Osterman, Burnham Institute for Medical Research, La Jolla, CA USA Integrated Genomic Reconstruction of Metabolic and Regulatory Networks in Bacteria Natasa Przulj, Imperial College London, UK >From Network Topology to Biological Function and Disease John Reinitz, State University of New York at Stony Brook, NY, USA When Two Plus Two Doesn't Equal Four: Modeling Non-Modular Enhancer Behavior in the Eve Promoter Pierre Rouze, Gent University, Gent, Belgium >From Protists to Plants, Fungi and Animals: Eukaryote Genomes Are Not Born Equal This email was sent to bionews@net.bio.net=