From victor at softberry.com Fri Jan 10 20:47:05 2003 From: victor at softberry.com (Victor Solovyev) Date: Sun Jun 12 19:43:32 2005 Subject: RAT draft genome annotations fgenesh++ Message-ID: <20030131204612.702307D165@mercury.hgmp.mrc.ac.uk> ==== RAT draft genome annotations fgenesh++ We're pleased to announce the release of fgenesh++ gene annotation on the Nov. 2002 rat assembly produced by the Baylor College of Medicine Rat Genome Sequencing Center and the Rat Genome Sequencing Consortium. You can see/get gene annoation at UCSC Genome Browser on Rat Nov. 2002 Freeze http://genome.ucsc.edu/cgi-bin/hgGateway?org=Rat or alternatively in GenomeExplorer: http://www.softberry.com/berry.phtml?topic=ratexp Fgenesh++ annotated: 43008 genes includes 28955 genes supported by NR proteins, among them 3763 genes correponding RAT refseq mRNA ID and Name of similar protein added after ## in name line of fasta files *.pro Refseq corresponding proteins additionally marked NM_.. Fgenesh++ predictions are based on complex fully automatic script that mapped known Refseq RNA, predict genes and refine predicted genes that have protein support from other organisms. Reference: Solovyev V.V. (2001) Statistical approaches in Eukaryotic gene prediction. In Handbook of Statistical genetics (eds. Balding D. et al.), John Wiley & Sons, Ltd., p. 83-127.) - ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From tempacctks at lycos.com Sat Jan 11 19:23:00 2003 From: tempacctks at lycos.com (Roby Joehanes) Date: Sun Jun 12 19:43:32 2005 Subject: 2nd CFP: Workshop on Learning Graphical Message-ID: <20030131204751.09AAD7D295@mercury.hgmp.mrc.ac.uk> Second CFP: IJCAI-2003 Workshop -- Learning Graphical Models for Computational Genomics Saturday, 9 August 2003 Acapulco, Mexico http://www.kddresearch.org/KDD/Workshops/IJCAI-2003-Bioinformatics/ Recent advances in experimental tools for computational genomics have led to sharp growth in data resources for bioinformatics problems such as modeling of gene expression and gene-protein interaction. This provides an interesting application domain for intelligent systems that learn graphical models from data for causal modeling, time series simulation and prediction, and classification and regression problems in computational life sciences. In response, we propose a workshop to bring together researchers in intelligent systems who are interested in: * probabilistic reasoning and learning with the primary focus of: - learning the structure of graphical models from data, - new graphical models such as types of dynamic Bayesian networks, stochastic and other approximation algorithms for inference, - structure learning; * constraint-based knowledge representation; * parameter estimation on graphical models and dynamical systems. ---Topics Active research topics that are relevant to learning graphical models for computational genomics include: * functional genomics, which includes: - modeling of gene regulatory dynamics, - data mining from DNA hybridization microarrays, - other gene modeling tools such as northern blots; * building simulation models for metabolomics on: - biochemical pathways, - environmental stress-response, - cellular process regulation; * proteomics, such as: - secondary and tertiary fold prediction - gene-protein interaction; * other contemporary bioinformatics problems, such as: - intelligent systems for pharmacology, - plant science and crop simulation, - decision support systems for human and veterinary medicine, - phylogenetic modeling. ---Format The one day workshop will include one or more invited talks and specialized tutorials on state-of-the-art research problems and methodologies, presentations by selected participants, and a panel and open discussion on key topics. ---Attendance This workshop is intended for researchers and practitioners in the area of bioinformatics and uncertain reasoning using graphical models for computational genomics. Researchers with an interest in machine learning, medical informatics, microbiology, biophysics, and knowledge discovery in databases (KDD) will also find this workshop of interest. ---Paper Submissions Participants are encouraged to submit papers (up to 8 pages in length) on recent and continuing research, formatted according to IJCAI guidelines. Experimental results are also encouraged, especially on fielded applications, even if they are only preliminary. Papers should be submitted electronically in Postscipt, PDF, MS Word format via e-mail. To encourage participation but focus discussions on key topics, we also invite 2-page research synopses and position papers from attendants who do not submit full papers. Each submission shall be accompanied by a short statement, up to 500 words or one page in length from each participants. This should describe your interest in and perspectives on this workshop topic. DUAL SUBMISSION POLICY: Submission of short (2-page OR 6-8 page) synopses of articles currently in preparation, under review, or accepted for publication as journals or book chapters is permitted. Submission of full-length papers currently under review for other conferences and workshops is also permitted. However, these papers shall be published in the working notes for this workshop if and only if they are compliant with the dual-submission guidelines of the other conference or workshop. Please consult the workshop web page for formatting instructions. All submissions should be sent to: ijcai2003-bioinformatics(AT)kddresearch.org. (Please replace "(AT)" with the appropriate symbol.) ---Important Dates Mar 01, 2003 Submission deadline Mar 21, 2003 Acceptance notification May 16, 2003 Camera-ready version of papers ---Organizing Chairs William H. Hsu (primary contact) Department of Computing and Information Sciences Kansas State University 234 Nichols Hall Manhattan, KS 66506-2302 t: (785) 532-6350 ext. 29 f: (785) 539-7180 e: bhsu-AT-cis.ksu.edu w: http://www.cis.ksu.edu/~bhsu Roby Joehanes (primary contact) Department of Computing and Information Sciences Kansas State University 234 Nichols Hall Manhattan, KS 66506-2302 t: (785) 532-6350 ext. 55 f: (785) 537-9927 e: robbyjo-AT-cis.ksu.edu w: http://www.cis.ksu.edu/~robbyjo C. David Page, Jr. Department of Biostatistics and Medical Informatics (Medical School) and Department of Computer Sciences University of Wisconsin-Madison Medical Science Center, Room 6743 1300 University Avenue Madison, WI 53706 t: (608) 265-6168 f: (608) 263-0415 e: page-AT-biostat.wisc.edu w: http://www.cs.wisc.edu/~dpage ---Program Committee - Mark Craven, University of Wisconsin-Madison - Dan Geiger, Technion, Israel - David Gilbert, University of Glasgow - Haipeng Guo, Kansas State University - Lei Liu, University of Illinois at Urbana-Champaign - Irene Ong, University of Wisconsin-Madison - Jude Shavlik, University of Wisconsin-Madison - Stephen M Welch, Kansas State University ---Additional information Please consult the following web page: http://www.kddresearch.org/KDD/Workshops/IJCAI-2003-Bioinformatics/ for more information. -- ===== Moderated bionet.genome.gene-structure __________________________________________________ Do You Yahoo!? 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