Beyond the Identification of Transcribed Sequences:
Functional, Evolutionary and Expression Analysis
12th International Workshop
October 25-28, 2002
Washington, DC

List of Abstracts * Speakers * Organizers * Authors * Original Announcement

List of Abstracts

Global analysis of translation in yeast
Yoav Arava, Yulei Wang, John D. Storey, Patrick O. Brown and Daniel Herschlag
Stanford University
Gene identification and study of paralogy on the human X chromosome
Ian Barrett and Mark Ross
The Wellcome Trust Sanger Institute
Systematic cloning of open reading frames into expression systems
Stephanie Bechtel, Anny Duda, Kerstin Hettler, Detlev Bannasch, Alex Mehrle, Annemarie Poustka, and Stefan Wiemann
German Cancer Research Center
Drawing inferences from microarray data
Michael Bittner
NIH/NHGRI
Identification and characterization of a novel thermostable RNA ligase
Thorarinn Blondal, O. Fridjonsson, S. Hjorleifsdottir, A. Ævarsson, S. Skirnisdottir, A.G. Hermannsdottir, G.O. Hreggvidsson, Albert Vernon Smith, and J.K. Kristjansson
deCODE Genetics Inc.
C. elegans operons: A novel tool to find functionally related genes
Tom Blumenthal
University of Colorado School of Medicine
Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: The potential of predicting functional gene domains
S. Goetze, A. Gluch, C. Benham and J. Bode
GBF Braunschweig
Functional characterization of ETV6, a candidate tumor suppressor gene associated with childhood acute lymphoblastic leukemia
Gino Boily and Daniel Sinnett
Sainte-Justine Hospital
Reconstructing and analysing gene networks from microarray data
Alvis Brazma
European Bioinformatics Institute, EMBL-EBI
Identifying novel transcripts/novel genes in the human genome by using novel SAGE tags
Jianjun Chen , Miao Sun, Sanggyu Lee, Guolin Zhou, Janet D. Rowley, and San Ming Wang
University of Chicago
Computational screening for peroxisomal proteins using new methods, old methods, and human expertise
Olof Emanuelsson, Susana Cristobal, Arne Elofsson, Gunnar von Heijne
Stockholm Bioinformatics Center, Stockholm University
Pathways, molecular processes and disease association: Needs and solutions in the pharmaceutical industry
James Fickett
AstraZeneca R&D Boston
Mapping the transcriptome
Thomas Freeman
HGMP-Resource Centre
Computational proteomics: Genome-scale analysis of protein structure, function, & evolution
Mark Gerstein, P Harrison, J Qian, R Jansen, V Alexandrov, P Bertone, R Das, D Greenbaum, W Krebs, Y Liu, H Hegyi, N Echols, J Lin, C Wilson, A Drawid, Z Zhang, Y Kluger, N Lan, N Luscombe, and S Balasubramanian
Yale University
Large scale transcriptional activity observed in chromosomes 21 and 22
Thomas Gingeras
Affymetrix
Functional genomics of Runx3 and DRG neurogenesis
Yoram Groner
Dept of Molecular Genetics The Weizmann Institute of Science
The natural history of human gene families: Genome-wide duplication(s) v.s. small-scale duplications
Xun Gu
Iowa State University
Multiprotein evolutionary analyses of diverse eukaryotes
S. Blair Hedges
Pennsylvania State University
Translational control at the interface between the genome and the proteome
Matthias W. Hentze
EMBL
3' untranslated regions and selenocysteine incorporation: From modulation of translation to a novel single nucleotide polymorphism
Stéphane Villette, G. Bermano, John R. Arthur and John E. Hesketh
University of Newcastle
S-Gal™: An autoclavable, water-soluble dye for enhanced color-selection of cloned DNA inserts
Sara Borchardt and Ken Heuermann
Sigma-Aldrich Corporation
Development of a novel high throughput directional cloning platform
Ron Hernan, Leanne Snyder, Ken Heuermann, and Brian Ward
Sigma-Aldrich Corporation
Diversity in gene expression: Assessment of exon skipping and expression states
Winston Hide, Tzu-Ming Chern, Janet Kelso and Vladimir Babenko
University Western Cape
Insertional mutagenesis in zebrafish identifies a diversity of genes required for vertebrate development
Nancy Hopkins
Massachusetts Institute of Technology
From large scale mouse mutagenesis to gene function
Martin Hrabé de Angelis
GSF Research Center for Environment and Health
Inferring gene transcription networks: The Davidson model
Sorin Istrail
Celera Genomics/Applied Biosystems
Direct contribution of a transposable element to the protein diversity: A novel type bovine Bcnt protein that includes the endonuclease domain of RTE-1
Shintaro Iwashita, Tomohito Itoh, Kenshiro Oshima, Katsuyuki Hashimoto and Wojciech Makalowski
Mitsubishi Kagaku Institute of Life Sciences (MITILS)
Cross-species comparison of known and predicted GDF-9 and GDF-9B protein sequences
Luke Jeffery, David Mottershead & Olli Ritvos
University of Helsinki
Defining functional networks of RNA-protein interactions in the nervous system
Kirk Jensen
The Rockefeller University
Protein microarray technology
Thomas Joos
Natural and Medical Sciences Institute at the University of Tübingen
RNA-binding proteins as reporters of operational mRNA networks in tumors and complex tissues
Jack Keene, Luiz O. Penalva, Michael Burdick, Hedi Sutterluety and Patrick J. Lager
Duke University Medical Center
Systematic functional analysis of mouse genes in the region syntenic to human Xq28
Anja A. Kolb, Hanna Bausbacher, Annemarie Poustka
German cancer research center (DKFZ)
Resources for functional research: Repository and application
Bernhard Korn
RZPD
RNAs isolated from ejaculate spermatozoa provide a noninvasive means to investigate testicular gene expression
G. Charles Ostermeier, Robert J. Goodrich, Kary Thompson, John Rocket, Michael P. Diamond, Karen Collins, NICHD Reproductive Medicine Network, David J. Dix, David Miller and Stephen A. Krawetz
Wayne State University
BEST: A computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster Development
Sudhir Kumar
Center for Evolutionary & Functional Genomics
Crucial elements in array data evaluation
Michael Liebler and Till Sörensen
raytest GmbH
Modeling and predictions of estrogen response element sequences in the human genome reveal potential roles for Alu repeats in motif propagation and transcriptional regulation
Chin-Yo Lin
Genome Institute of Singapore
The next step in transcriptomics: Data mining after global array analysis and design of a sub-array specific for cardiac fibrosis of renal failure in the rat model
Christian Maercker, Heidrun Ridinger, Effi Rees, Matthias Schick, Christiane Rutenberg, Eberhard Ritz, Gerhard Mall, Bernhard Korn, and Kerstin Amann
Resource Center for Genome Research (RZPD)
Nonsense-mediated mRNA decay in mammalian cells: Evidence for a "pioneer" round of mRNA translation
Lynne Maquat
University of Rochester Medical Center
Biological roles for A to I conversion in untranslated regions of mRNAs?
Daniel P. Morse, P. Joseph Aruscavage, Leath A. Tonkin, Lisa Saccomanno, Thomas Brodigan, Michael Krause, and Brenda L. Bass
United States Naval Academy
Kazusa cDNA project 2002: Of mice and men
Osamu Ohara
Kazusa DNA Research Institute
Genome-wide analysis of the sequence region surrounding the transcription start site of human mRNAs
Michele Iacono, Carmela Gissi, Giorgio Grillo*, Flavio Mignone, Sabino Liuni and Graziano Pesole
Università di Milano
Global analysis of mRNA decay in T cells
Arvind Raghavan and Paul R. Bohjanen
University of Minnesota
The Mouse Gene Expression Database (GXD) and the Gene Expression Notebook (GEN)
C.M. Smith, D.A. Begley, I.J. McCright, T.F. Hayamizu, D.P. Hill, S.R. Pretel, P. Mani, J.S. Beal, D.J. Dahmen, J.A. Blake, J.T. Eppig, J.A. Kadin, J.E. Richardson, and M. Ringwald
The Jackson Laboratory
Big genes: What? Where? Why?
Lee Rowen, Brian Birditt, Ryan Nesbitt, Amardeep Kaur, Gustavo Glusman, and Lee Hood
Institute for Systems Biology
Full domain transcript of alpha-globin genes is a component of the nuclear matrix
A.V. Rynditch, V.P. Smalko, S.V. Razin, E. Loudinkova, K. Scherrer
National Academy of Sciences of the Ukraine
Molecular evolutionary analyses of HoxA gene cluster of human and apes
Naruya Saitou
National Institute of Genetics
Point mutations occur at a faster rate in exons than in noncoding DNA in primate genomes
Subashchandran Sankarasubramanian and Sudhir Kumar
Arizona State University
Two pancreas clone sets and PancChips, new resources for diabetes
Marie Scearce and Klaus Kaestner
University of Pennsylvania
Applying genome-wide SNP analysis for complex disease gene discovery
Michael Shi
Sequenom, Inc.
Large-scale subcellular localisation and functional analysis of novel proteins
Jeremy C. Simpson, Urban I. Liebel, Vytaute Starkuviene, Holger Erfle, Annemarie Poustka, Stefan Wiemann and Rainer Pepperkok
EMBL
Statistical validation of pattern prevalence in regulatory gene loci
Gautam Singh and Stephen A. Krawetz
Oakland University
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
Christine E. Horak, Nicholas M. Luscombe, Jiang Qian, Stacy Piccirrillo, Mark Gerstein and Michael Snyder
Yale University
Regulated alternative splicing: A new dimension of the human genome
Stefan Stamm
Institute of Biochemistry
Genome-wide identification of differences in the retroelement integrations between humans and chimpanzees
E. Sverdlov, A. Buzdin, I. Mamedov, S. Ustugova, E. Gogvadze, Yu.
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
Array analysis of mRNP complexes reveals clustered mRNA subsets that may represent posttranscriptional operons
Scott Tenenbaum and Jack D. Keene
Duke University Medical Center
Functional analysis of the mammalian genome by large scale gene trap mutagenesis
Harald von Melchner
Laboratory for Molecular Hematology, University of Frankfurt am Main
Fine-tuning the clock — the relationship between variability in Per3 and circadian phenotype in mammals
Malcolm von Schantz, Donna Robilliard, Oliver Wood, Marcel Smits, Adrian Williams, Debra J Skene, Jo Arendt, and Simon N Archer
University of Surrey
Status of application of tiling genomic fragment arrays to molecular biology of mammalian cells
C. Horak, X-H Pan, J. Rimm, R. Goetsch, P. Bertone, P. Miller, N. Luscombe, P. Harrison, M. Gerstein, S.M. Weissman, and M. Snyder
Yale University School of Medicine
The German cDNA network: cDNAs for functional genomics and proteomics
Ruth Wellenreuther, Stephanie Bechtel, Petra Moosmayer, Regina Albert, Ingo Schupp, Vladimir Kuryshev, Detlev Bannasch, Dorit Arlt, Ulrike Korf, Rainer Pepperkok, Jeremy Simpson, Annemarie Poustka, Stefan Wiemann, and the German cDNA Consortium
German Cancer Research Center
Intracellular trafficking of a few inflammation-inducible ADAR1 isoforms
Jing-HuaYang, Qingchuan Zhao, Yongzhan Nie, Yingjun Su, Koroush Kibir and Reuven Rabinovici
Yale University School of Medicine
Experimental verification of predicted splice variants of human genes
Dorothea Zink, Stefan Haas, Oliver Heil, Mathias Schick, Melanie Roth, Eivind Coward, Bernhard Korn, and Martin Vingron
RZPD - Ressourcenzentrum für Genomforschung

List of Abstracts * Speakers * Organizers * Authors * Original Announcement

Genetic Meetings