Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis

9th Annual Workshop, October 28-31, 1999

Co-sponsored by the U.S. Department of Energy


Contents

Abstracts from other meetings.

Speakers

DICKINSON: Evolutionary perspectives on functional analysis: some cautionary tales
W. J. (Joe) Dickinson
RINGWALD: Gene expression database for the laboratory mouse
M. Ringwald, Jon Beal, D. Begley, G. Davis, J. T. Eppig, K. Frazer, D. Hill, J. Kadin, J. Richardson, M. Sasner, L. Trepanier
OHARA: Analysis of uncharacterized human cDNAs which encode large proteins in brain: The Kazusa Approach
Osamu Ohara
HEISS: Functional characterisation of genes in Xq28
Nina S. Heiss, Zdenek Sedlacek, Annemarie Poustka
BERNARDI: The formation and maintenance of the isochores from the genomes of warm-blooded vertebrates is due to natural selection
Giorgio Bernardi
KOHARA: Post-genomics strategies in C. elegans toward understanding of the molecular mechanisms of development
Yuji Kohara
GARDINER: Genomic sequence analysis and novel gene characterization on human chromosome 21
Katheleen Gardiner, Dobromir Slavov, Roger Lucas, Andrew Fortna and Alla Rynditch
FREEMAN: Development of expression profiling technologies for the rat
Tom Freeman, David Vetrie, Clare East, Adam Butler, Liz Campbell and Peter Wooding
DURET: Codon usage in animals and plants: new data, new paradox
Laurent Duret and Dominique Mouchiroud
THIESEN: Genomic sequences of KOX zinc finger gene clusters are used to determine (auto) regulatory networks of gene regulation
Dirk Koczan, Christian Sina, Peter Lorenz, Tom Hearn, Saleh Ibrahim, Andreas Rump, Andre Rosenthal, Michael Jackson, M.-F. Rousseau-Merck,  I. Legrand, and Hans-Juergen Thiesen
EISEN: Phylogenomics and the benefits of an evolutionary perspective in genome analysis
Jonathan A. Eisen
PELTZ: Understanding the role of mRNA turnover in regulating gene expression and in disease states
Stuart Peltz
EMANUELSSON: Identifying localization signals in proteins
Olof Emanuelsson
KORN: Tools for functional analysis using resources of RZPD
B. Korn1, 2, J. Boer, P. Kioschis1,2, A. Vente, H. Lehrach3,4 and A. Poustka1,2
WASSERMAN: De novo discovery of transcription factor binding sites in co-regulated sets of human genes
Wyeth W. Wasserman
FONTES: Using large cloned genomic fragments as expression vectors to create or correct mutant phenotypes
E. Passage and M. Fontés
SOMOGYI: Expression profiling and genetic networks
R. Somogyi, S. Fuhrman, X. Wen, P. D'haeseleer*, S. Liang, and J.F. Loring
ZHOU: Gene expression profiling in molecular pharmacology
Y. Zhou, U. Scherf, M. Waltham, W.C. Reinhold, L.H. Smith, J.K. Lee, D.A. Scudiero, E.A. Sausville, D. Ross, M. Eisen, D. Botstein, P.O. Brown, L. Miller, E. Liu and J.N. Weinstein
HOWELL: Annotation of the human X chromosome sequence
Gareth R. Howell, Alison J. Coffey, Susan Rhodes, Robert A. Brooksbank, Shirin S. Joseph, Jackie M. Bye, Andrew King, Laurens Wilming, David R. Bentley and Mark T. Ross
SOARES: Development of non-redundant arrays of full-length cDNAs
Maria F. Bonaldo, Brian Berger, Todd Scheetz1, 2, Kyle Munn, Chad Roberts, Kang Liu, Thomas Casavant and Marcelo Bento Soares1, 3
WERNER: Promoter prediction in large genomic sequences: compromise between sensitivity and specificity
Scherf, M., Klingenhoff, A., and Werner, T.
HESKETH: Perinuclear mRNA localisation by 3'untranslated sequences
John Hesketh, Marilyne Levadoux, Gillian Dalgleish, John Beattie, Heather Wallace, and Jean-Marie Blanchard
MORSE: Substrate specificity of adenosine deaminases that act on RNA (ADARs) in C. elegans
Daniel P. Morse, Leath A. Tonkin, P. Joe Aruscavage, and Brenda L. Bass
BODE: Scaffold/matrix attached regions (S/MAR Elements): Detection and activities in vivo
Jürgen Bode, Alexandra Baer, Angela Knopp, Dirk Schübeler, Jost Seibler, Craig Benham Armin Baiker , and Hans-Joachim Lipps
GOJOBORI: A gene expression profile obtained by determining over 1000 cDNA clones from a single Planarian eye cell
Takashi Gojobori, Kazuho Ikeo, Silvana Gaudieri, Akira Tazaki, Masumi Nakazawa, Masafumi Shimoda, Yuzuru Tanaka, and Kiyokazu Agata
SVERDLOV: Towards the understanding of the possible impact of human endogenous retroviruses on evolutionary changes in genome transcription
Eugene D. Sverdlov
PESOLE: Structural and evolutionary analysis of eukaryotic mRNA untranslated regions
Pesole G.1,4, Liuni S.2,4, Larizza A., Makalowski W.5 and Saccone C.3,4
SIMONNEAU: Analysis of new transcribed sequences possibly involved in same functional pathways of neuronal development and identified by differential display
Michel Simonneau, Christophe Mas, Francine Bourgeois, and Fabien Guimiot
WINGENDER: TRANSFAC: an integrated system for gene expression regulation
E. Wingender, X. Chen, H. Karas, A. Kel, I. Liebich, V. Matys, T. Meinhardt, M. Pruess, I. Reuter, and F. Schacherer
LIN: Identification and characterization of tissue-specific genes using transgenic zebrafish
Shuo Lin
EBERWINE: Molecular biology of single cells: Insights into human disease
Jim Eberwine
WIEMANN: Sequencing and analysis of full length cDNAs in the course of the German Genome Project
Stefan Wiemann, Wilhelm Ansorge, Helmut Blöcker, Helmut Blum, Andreas Düsterhöft, Karl Köhrer, Werner Mewes, Brigitte Obermaier, Rolf Wambutt, and Annemarie Poustka
VON MELCHNER: Disruption of a gene induced in early mouse development results in severe emphysema and Adenocarcinoma
Irmgard S. Thorey, Anja Sterner-Kock, Jürgen Otte, and Harald von Melchner
BRAZMA: Mining the yeast genome expression and sequence data
Alvis Brazma
WEISSMAN: Transcript profiling of hematopoietic cell development and activation
Yamaga, S., Yeramilli, S.5, Lian, Z., Prashar, Y.5, Lee, H., Berliner, N., Liu, Y-C., Goguen, J., Newburger, P., and Weissman, S.
BARBAZUK: Construction of a whole genome transcribed sequence map for the zebrafish Danio Rerio
W. Brad Barbazuk, Ian Korf, Frank Li, John McPherson and Steve Johnson
HICKS: Development of an embryonic stem cell library of defined mutations
Geoffrey G. Hicks
WORLEY: Search services to improve the identification of expressed sequences and their functions
J. Bouck, M. McLeod, T. McNeill, G. Weinstock1,3, R. A. Gibbs, and K. C. Worley
FICKETT: Finding gene boundaries on large contigs
James Fickett
JENNINGS: Dissecting transcriptional circuitry and mechanisms in yeast
Ezra Jennings
WELSH: The RAP-array approach to cDNA array hybridization
John Welsh
MURAL: Extracting meaningful information from draft sequence
R. J. Mural, F. W. Larimer, M. B. Shah and E. C. Uberbacher
PAN: Approaches towards global profiling of cDNA mutations
Pan, X. and Weissman, S.
NELSON: Functional dissection of the RANTES promoter: Insights into mechanisms of tissue specific regulation of transcription
Peter J. Nelson, Sabine Böhlk, Sabine Fessele and Thomas Werner
BORSANI: A tale of two diseases
Giuseppe Borsani
ARONOW: Stepwise chromatin restructuring and unexpected rules for interaction of distributed cis-elements that form a locus control region in vivo
Catherine Ley-Ebert, Carolyn Florio, John Maier, Chris Cost and Bruce Aronow
OVERTON: (ABSTRACT NOT AVAILABLE)
All speaker abstracts

Posters

DE BEKKE: Experimental approach towards identification of small non-messenger RNAs in the genome of Caenorhabditis elegans
Anja op de Bekke, Alexander Huttenhofer, Martin Kiefmann, John O'Brien,  Hans Lehrach and Jurgen Brosius
HEUERMANN: Stable expression of epitope-tagged proteins in mammalian cells
Kenneth E. Heuermann and Bill L. Brizzard
KAMP: Structure and function of the spermatogenesis genes located in AZFa, a region of the human Y chromosome deleted in men with complete germ cell aplasia
Kamp, Christine, Kirsch, S, Hirschmann, P, Ditton, HJ, Brede, G, Tyler-Smith, C, Rappold, GA, and Vogt, PH
BULL: Analysis of gene expression data generated by oligonucleotide fingerprinting
Christof Bull, John O'Brien, Uwe Radelof, Ralf Herwig, Steffen Hennig, Axel Nagel and Hans Lehrach
SLAVOV: Analysis of novel genes from human chromosome 21: determination and characterization of complete protein sequences and examples of overlapping genes
Dobromir Slavov, Roger Lucas, Andrew Fortna and Katheleen Gardiner
SPENGLER: ASDB: Novel database of alternatively spliced genes
I. Dubchak,  M. S. Gelfand, I. Dralyuk, M. Zorn, S. Spengler
KIKUNO: Functional and molecular evolutional analysis of predicted gene products of human long cDNAs
Reiko Kikuno, Takahiro Nagase, Ken-Ichi Ishikawa, Mikita Suyama, Mina Waki, Makoto Hirosawa, Nobuo Nomura, and Osamu Ohara
BORISSEVITCH: Large scale cloning, sequencing and expression profiling of genes expressed in transcription factor CREM dependant manner during mouse spermatogenesis
Igor Borissevitch, Tim Beissbardth, Andreas Hoerlein and Guenter Schuetz
MONTPETIT: Genomic comparative analysis of the Fugu rubripes homologue of ETV6, a gene frequently rearranged in human leukemias
Alexandre Montpetit and Daniel Sinnett
CLIFTON: Comparison of completed genomes to sample sequences of related genomes
Sandra W. Clifton, Michael McClelland, Webb Miller, William R. Pearson, Aaron J. Mackey, and Richard K. Wilson
SCHMIDT-KITTLER: Genomic characterisation of early disseminated tumor cells isolated from bone marrow of breast cancer patients
Oleg Schmidt-Kittler, Julian Schardt, Günter Schlimok, Gert Riethmüller and Christoph Klein
ROTTIERS: Oxidative metabolism and gene expression: Gene discovery array analysis
Pieter Rottiers, Vera Goossens and Johan Grooten
RUUSKANEN: Divergent 2-adrenoceptor subtypes in the zebrafish (Danio rerio)
Jori Ruuskanen, Minna Varis, Erik Salaneck, Tiina Salminen, Tommi Nyronen, Mark S. Johnson, Dan Larhammar and Mika Scheinin
TEMPLE: GATEWAY cloning: A high-throughput gene transfer technology for rapid functional analysis and protein expression
James Hartley, Gary Temple, Michael Brasch, et al.
KAPANADZE: Sequence homology between human and mouse genomic regions to identify the tumor suppressor gene involved in B cell chronic lymphocytic leukemia
Bagrat Kapanadze, Nataliy Makeeva, Olle Sangfelt, Martin Corcoran, Anna Baranova, Eugene Zabarovsky, Nick Yankovsky, Dan Grander and Stefan Einhorn
CLARK: Comparative mapping in the Japanese pufferfish (Fugu rubripes)
Clark, M. S; Edwards, Y.J.K; Shaw, L; Snell, P.; Smith, S; and Elgar, G.
FROLOVA: Transcriptional regulation of the collagen a1(IX) gene during eye development
Elena I. Frolova and David C. Beebe
KREFT: Identification of a novel cellular protein that binds to the HBV RNA pregenome
S. Kreft and M. Nassal
All poster abstracts

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