Archive: Genome-Related Meetings and Reports

TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology

March 10-13, 2002
Seattle, Washington, USA

Speaker Abstracts (PDF)

Plenary Session 1: The Role of Transcriptome

Chair: John Quakenbush,  The Institute for Genomic Research

Keynote Speakers:

• Systems Biology: Integrating Genomics, Proteomics, Computation and Biology
  Leroy Hood
• Bioinformatics and Genome Sciences
  Mark S. Boguski

Plenary Session 2: Transcription and Processing I

Chair: Stefan Wiemann, German Cancer Research Center

• Globin Gene Activation: A Stochastic Process
  Frank Grosveld, Mariken de Krom, Mariette van de Corput, and John Strouboulis
• Molecular Mechanisms of Pre-mRNA Splicing Regulation
  Juan Valcárcel
• Alternate Splicing and Gene Expression States: Using cDNAs to Explore the Human Genome
  Winston Hide, Vladimir N. Babenko and Janet F. Kelso
• Size-Dependent Pareto-like Distributions in Genomics and Prediction of the Number of Protein-coding Genes in Human Genome
  Vladimir A. Kuznetsov

Plenary Session 3: Transcription and Processing II

Chair: Bento Soares, University of Iowa

• Multiple Determinants of RNA Editing in Physarum Mitochondria
  Jonatha M. Gott
• Employing DNA Microarrays to Study Eukaryotic Translation
  Thomas Preiss, EMBL, Heidelberg, GERMANY
  Abstract not available for publication
• RNA Transcription Detected on Chromosomes 21 and 22 Using High Density Oligonucleotide Arrays
  Thomas R. Gingeras
• The Genetics of Gene Expression
  Eric E. Schadt

Plenary Session 4: CDNA Based Gene Discovery I

Chair: Charles Auffray, CNRS

• The NIH Mammalian Gene Collection
  Robert Strausberg, National Cancer Institute, Bethesda, MD
  Abstract not received in time for publication
• Kazusa cDNA Project 2002: From Transcript to Protein
  Osamu Ohara, Reiko Kikuno, and Takahiro Nagase
• FLJ cDNA Project in Japan
  Sumio Sugano
• The German cDNA Network – cDNAs for Functional Genomics and Proteomics
  Stefan Wiemann, Jeremy Simpson, Ruth Wellenreuther, Petra Heidrich, Regina Albert, Ingo Schupp, Vladimir Kuryshev, Detlev Bannasch, Rainer Pepperkok, Annemarie Poustka, and the German cDNA Consortium
  Slides: PDF file. Addendum added May 2, 2002

Plenary Session 5: CDNA Based Gene Discovery II

Chair: Winston Hide, South African National Bioinformatics Institute

• RIKEN Mouse Genome Encyclopedia
  Yoshihide Hayashizaki
• Gene Catalog of Mouse Stem Cells and Early Embryos
  Minuro Ko
  
• Definition of Human Transcriptomes Using ORESTES
  Andrew Simpson, Ludwig Institute, Sao Paulo, BRAZIL
  Abstract not available for publication
• The University of Iowa Mammalian Gene Discovery and Expression Program
  Bento Soares, University of Iowa, Iowa City, IA
  Abstract not available for publication

Plenary Session 6: Transcription and Processing III

Chair: Yoshihide Hayashizaki, RIKEN Genomic Sciences Center

• Microarray Technology for Transcript Profiling and Analysis of Genetic Variability
  Joakim Lundeberg
• cDNA-Microarray Profiling of Ovarian Cancer
  Claudio Schneider, LNCIB, Trieste, ITALY
  Abstract not available for publication
• Zhu Chen, Chinese Academy of Sciences, Shanghai, PEOPLE'S REPUBLIC OF CHINA
  Abstract not available for publication
• Clone Selection and Analysis Methods for Full-Insert cDNA Sequencing
  Lukas Wagner, NIH, Bethesda, MD
  Abstract not available for publication

Plenary Session 7: Sequenced-Based Tools for Gene Discovery I

Chair: Andrew Simpson, Ludwig Institute for Cancer Research

• Comparative Genomics Tools: TIGR Gene Indices and TIGR Orthologous Gene Alignments (TOGA)
  Yuandan Lee, Jennifer Tsai, Foo Chung, Svetlana Karamycheva, Babak Parvizi, Geo Pertea, Razvan Sultana, Valentine Antonescu, Joseph White, and John Quackenbush
• UTRDB and UTRSITE: Specialized Databases of Sequences and Functional Elements of 5' And 3' Untranslated Regions of Eukaryotic mRNAs
  Pesole, Graziano, Gissi C., Grillo G., Licciulli F., Mignone F., Iacono M., Liuni S.
• I.M.A.G.E. Data Mining Tools:  Introducing the IQ
  Peg Folta
  Slides: PDF version
• Using NCBI Resources for Gene Discovery
  Kim D. Pruitt, Richa Agarwala, Hsiu-Chuan Chen, Slava Chetvernin, Deanna Church, Olga Ermolaeva, Wonhee Jang, Paul Kitts, Jonathan Kans, David Lipman, Jim Ostell, Sergey Resenchuk, Greg Schuler, Lynn Schrim, Steve Sherry, Tatiana Tatusova, Lukas Wagner, Sarah Wheelan
  Slides: PDF

Plenary Session 8: Sequenced-Based Tools for Gene Discovery II

Chair: Greg Lennon, Cell Logic, Inc.

• Tim Hubbard, The Sanger Centre, Cambridge, UK
  Abstract not available for publication
• Extraction of Biological Meaning from Array Data:  What is Required?
  Roger Bumgarner, University of Washington, Seattle, WA
  Abstract not available for publication
• Comparative and Functional Analysis of Cardiovascular-Related Genes
  Len A. Pennacchio, Michael Olivier, Jaroslav A. Hubacek, Jonathan C. Cohen, Ronald M. Krauss, and Edward M. Rubin
• The Detection of Env-Transcripts in Gossypium
  Zaki, E.A.

Plenary Session 9: Gene Expression – Transcript Abundance and Disease

Chair: John Quackenbush, The Institute for Genomic Research

• Delineation of transcriptional Pathways in Vivo:  Temporal Profiling in Muscle Regeneration
  Eric Hoffman, Children's National Medical Center, Washington, DC
  Abstract not available for publication
• Application of Arrays to the Study of Colon Cancer
  Timothy J. Yeatman, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
  Abstract not available for publication
• Using SAGE to Explore the Genome
  Saurabh Saha, Alberto Bardelli, Kenneth W. Kinzler, & Bert Vogelstein
• System Biology:  From Genome to Physiology
  Howard Jacob, Medical College of Wisconsin, Milwaukee, WI
  Abstract not available for publication

Plenary Session 10: Alternate Measures of Expression

Chair: Winston Hide, South African National Bioinformatics Institute

• Gels, Mass Spectrometry and Chips:  Large Scale Acquisition of Protein Abundance Fingerprints
  N. Leigh Anderson, Large Scale Biology Corporation, Germantown, MD
  Abstract not available for publication
• Toward a Proteome Atlas for C-elegans
  Marc Vidal, Harvard Medical School, Boston, MA
  Abstract not available for publication
• Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-Scale Data
  Frank Holstege, University Medical Center-Utrecht, AB Utrecht, THE NETHERLANDS
  Abstract not available for publication
• Mihael Polymeropoulos, Novartis Pharmaceuticals Corporation, Gaithersburg, MD
  Abstract not available for publication
• Breaking the Bottle Neck of Genomics and Proteomics
  Moncef Jendoubi
• A Novel 22,000 Feature In Situ-Synthesized 60-Mer Oligonucleotide Microarray: Expression Profiling Of E12.5 Mouse Embryo and Placenta
  Mark G. Carter, Condie E. Carmack, Yong Qian, Toshio Hamatani, Pius Brzoska, S. Stuart Hwang, and Minoru S.H. Ko

Plenary Session 11: The Future

Chair: Zhu Chen, Chinese Academy of Sciences

• Back to the Future: Integrating Expression with Genomic, Genetic, and Metabolic Data
  John Quackenbush
• Bioinformatics and Genomics to Gain Insight into the Etiology of Cancer
  Ken Buetow, National Cancer Institute, Bethesda, MD
  Abstract not available for publication
• ArrayExpress - A Public Database for Microarray Data
  Helen Parkinson
  Slides: PDF version
• A Novel Platform for High-Sensitivity Analysis of Cell-Specific Gene Expression using Microarrays
  Rajiv Raja, Jim Stanchfield, Mark Erlander and Steve Kunitake

Poster Abstracts (PDF)

Number	Poster
P-01	Definition of Sources of Variability and Noise Factors in Affymetrix Expression Profiling Marina Bakay, Yi-Wen Chen, Rehannah Borup, Po Zhao, Kanneboyina Nagaraju, and Eric P Hoffman
P-02	Image Analysis and Signal Extraction for cDNA Microarray Images Bergemann, T.L., Laws, R.J., and Zhao L.P., Fred Hutchinson Cancer Research Center, Seattle WA
P-03	A Superparamagnetic Particle-Based Kit for the Purification of Fluorescent Dye-Labeled cDNA Lisa R. Booth, Dwayne T. Campogan, Karin A. Hughes, Douglas A. Spicer, Amy L. Springer, Prolinx, Inc., Bothell, WA Slides (PDF)
P-04	Development and Production of a Redundant Oligonucleotide Musclechip: Use for Verification and Prioritization of ESTs Rehannah HA Borup, Stefano Troppo, Yi-Wen Chen, Tanya M Teslovich, Gerolamo Lanfranchi, Giorgio Valle, and Eric P Hoffman
P-05	Paracel TranscriptAssembler:   Identification of Splice Variants for Gene Discovery and Gene Expression Profiling Cecilie Boysen, Stephanie S. Pao, Jun Qian, Charles P. Smith, Lingyan Zhu, and Joseph A. Borkowski
P-06	Downstream of an RNA Regulatory Protein Causing a Common Human Disease: Expression Profiling Human SMN-Deficient Muscle Cinzia Brandoli, Serenella Servidei, and Eric Hoffman
P-07	Gene Expression Profiling in Dysferlinopathies Using a Dedicated Muscle Microarray Stefano Campanaro, Marina Fanin, Beniamina Pacchioni, Silvia Trevisan, Barbara Celegato, Elena Pegoraro, Yukiko K. Hayashi, Giorgio Valle, Corrado Angelini and Gerolamo Lanfranchi
P-08	Progress to Construct the RIKEN Mouse Full-Length cDNA Encyclopedia P. Carninci, K. Shibata, M. Itoh, T. Arakawa, Y. Ishii, H. Konno, K. Sato, N. Hayatsu, T. Shiraki, T. Hirozane, K. Aizawa, H. Bono, S. Kondo, K. Waki, J. Kawai, A. Yoshiki, Y. Okazaki and Y. Hayashizaki
P-09	Characterizing Transcriptional Determinants of the Innate Immune Response to Infection Through Gene Expression and Literature Profiling Damien Chaussabel, Roshanak Semnani, Mary Ann McDowell, David L Sacks, Alan Sher, Thomas B Nutman
P-10	PGA-CPR (Chip Profiling Resource): A Web Queried Database of Affymetrix Profiles with Cross-Profile Analysis Tools Josephine Chen, Dietrich Stephan, and Eric Hoffman
P-11	Using Multivariate Regression Analysis to Detect Differential Co-Regulation of Transcriptions Between Subgroups of Medulloblastomas Chun Cheng, Andrew R. Hallahan, James M.Olson, and Lue Ping Zhao
P-12	Definition of the Transcriptional and Translational Response to a Physiological Stimulus: A Cross-Species Time Series Muscle Study in Human Volunteers and Rats Yi-Wen Chen, Eric P Hoffman, Gustavo Nader, Keith R. Baar, Karyn A. Esser, Monica J. Hubal, Paul D. Thompson, Priscilla M. Clarkson
P-13	Transcription Profiling of Cell Death in Drosophila Melanogaster S. Chittaranjan, E. Garland, D. Freeman, S. Jones, M. Marra, and S. Gorski
P-14	From Human Tissue Samples to Transcriptome Analysis : How to Obtain High Quality RNA Virginie Copois, Frédéric Bibeau, Patrick Chalbos, Sandrine Imbeaud, Carmella Cappellano, Marc Ychou, Charles Auffray, Emmanuel Conseiller, Bernard Pau, Maguy Del Rio
P-15	Pathogenic Pathways in Spinal Cord Injury Identified by Gene Expression Profiling Simone Di Giovanni, Susan Knoblach, Cinzia Brandoli, Alan Faden, Eric Hoffman
P-16	Preparation of cDNA Hybridization Targets by Phi29 DNA Polymerase Rohini Dhulipala, Mubasher Dar, R. Scott Duthie and John Nelson
P-17	Production and Use of DNA Microarrays for Studies of Aging Mark W. Eshoo and Krysta Felkey
P-18	Intelligent Bioinformatics Systems for Functional Genome Analysis Daniel Gerlich, Martin Granzow, Julian Mattes, Wolfgang Tvarusko, and Roland Eils, Dr. Wolfgang Tvaruskoi
P-19	The aRNA Amplification Procedure in mRNA-Poor Samples Array Applications Esther Graudens, Xavier Barlet, Virginie el Marhomy, Charles Auffray & Sandrine Imbeaud
P-20	New Cancer Genome Anatomy Project (CGAP) Internet Resource for the Research Community Lynette H. Grouse, Carl F. Schaefer, Susan F. Greenhut, Kenneth H. Buetow and Robert L. Strausberg
P-21	Comparative Analysis of TBX1 Genes and Their Promoters from Different Species Ilya Ioshikhes, Jun Liao and Bernice Morrow
P-22	Comparative Bioinformatics Analysis of Rat and Human ALB-AFP Gene Locus Ilya Ioshikhes and Joseph Locker
P-23	Expression of Cytokines and Growth Factors in Aging and hTERT-transfected Human Fibroblasts Yukari Kanzaki, Toshinori Ide
P-24	Full-length cDNA Library Construction Using Lambda Recombination (GatewayTM Technology) Larissa G. Karnaoukhova, Mark R. Smith, Chris E. Gruber, and Martin Gleeson
P-25	LNA (Locked Nucleic Acid) Microarrays - A New Platform for Gene Expression Profiling Sakari Kauppinen, Peter Stein Nielsen, Helle Ohlsson, Dan Jeffares, Tobias Mourierand Peter Arctander,
P-26	Clinical Utility of Quantitative Real-Time PCR for Monitoring Leukemia Patients Using RNA Stabilizer In Blood Samples Ryuji Kawaguchi, Hideyuki Kudoh, Yasuhumi Matsuda, Thoru Murayama and Ralf Wyrich
P-27	In Silico Detection and Characterisation of Cancer-Specific Transcript Isoforms Janet Kelso
P-28	Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-Scale Data Patrick P.C.W. Kemmeren, Nynke L. van Berkum, Jaak Vilo, Theo Bijma, Rogier Donders, Alvis Brazma & Frank C.P. Holstege
P-29	Application of Statistical Modeling to Microarray Gene Expression Data in Human Lung Cancer Najma Khalid, Lue Ping Zhao
P-30	The Immediate Early Gene Response of Human Keratinocytes to Gamma-Rays Analyzed by DNA Micro-Arrays Jérôme Lamartine, Gilles Waksman, Xavier Gidrol, Michèle Martin
P-31	Specific Subtraction of Abundant mRNAs in Skeletal Muscle Paolo Laveder, Cristiano De Pittà, Stefano Toppo, Giorgio Valle and Gerolamo Lanfranchi
P-32	Systematic Screening of Tissue Specific Cis-regulatory Elements in Ciona intestinalis Embryo Byung-in Lee, David Keys, Mei Wang, Orsalem J. Kahsai, Sylvia Ahn, Qing Zhang, David K. Engle, Irma   Rapier, Jason Olivas, Chris J. Detter, Sharon Doyle, Naoe Harafuji, Anna Di Gregorio, Trevor Hawkins, Dan S. Rokhsar, Michael Levine, Paul M. Richardson
P-33	Molecular Genetic Profiling of Gleason Grade 4/5 Prostate Cancers Versus Benign Prostatic Hyperplasia Mamatha Mahadevappa, Zhaomei Zhang, Mitchell C. Caldwell, Zuxiong Chen, Zhenbin Fan, John E. McNeal, Rosalie Nolley, Thomas A. Stamey, Janet A. Warrington
P-34	A Novel Approach to Eliminate Vector Background and Increase Sequencing Efficiency of cDNAs Uday Matrubutham, Jody Mirchandani, Jian Liu, Martin A. Gleeson, K. MacDonald, J. Asano, Y. Butterfield, N. Girn, S. Lee, T. Olson, P. Pandoh, U. Skalska, D. Smailus, L. Spence, Jeff Stott, G. Yang, J. Schein and M. Marra
P-35	Identification of Putative Genes Involved in Cell Transformation Andrei M. Mikheev, Svetlana A. Mikheeva, Vivian Li, Jeffrey Delrow and Helmut Zarbl
P-36	Quality Control of Microarray Samples Using Lab-on-a-Chip Technology Odilo Müller, Monika Dittmann, Samar Lightfoot, Kathi Williams, and Robert Dubrow
P-37	Prepare a Set of Human cDNA Clones Encoding Large Proteins in an Expression-Ready Form Takahiro Nagase, Noriko Okazaki, Daisuke Nakajima, Hisashi Yamakawa, Reiko Kikuno, and Osamu Ohara
P-38	Encoding Biological Prior Information Into Gene Expression Analysis Michael F. Ochs, Frank J. Manion, Ghislain Bidaut, Thomas Moloshok, Jeffrey D. Grant
P-39	Whole Genome Functional Analysis and Metabolic Pathway of Zymomonas mobilis Sang-Ho Park, Ki-Nam Heo, Hyun-Seok Parkv, Jeong-Sun Seo
P-40	Gene Expression Profiling on Radiation Responses Woong-Yang Park, Chang-Il Hwang, Chang-Nim Im, Min-Ji Kang, Jang-Hee Woo, Ju-Hoon Kim, Kyoung-A Kim, Hyoung-Jin Yoo, Yun-Sil Lee, Su-jae Lee, Jeong-Sun Seo
P-41	Expression Profiling and TPE Analysis Generates Candidate Tumor Markers for Papillary Thyroid Carcinoma Erwin Pauws, Truus JM Veenboer, Antoine HC van Kampen, Jan JM de Vijlder, Carrie Ris-Stalpers
P-42	From Transcriptome to Proteome: Genome Scale Collection and Expression of Low Abundant Human Full-Length Transcripts Yijun Ruan, Chia-Lin Wei, Stephan Dillard-Telm, Erika Peterson, Gina Truesdell, Helen Chan, Gary Wolfe, and Dave Mannion
P-43	The Use of Representative Gene Fragments (Rgss) for Less Populated, Highly Replicated Microarrays Helena B. Samaia, André C. Zaiats, Otávia O. Caballero, Ricardo R Brentani, Sandro J. de Souza and Andrew J.G. Simpson
P-44	Differential Gene Expression in Leishmania Major Friedlin A. Saxena, S.Yan, L. Worthey, A. Leland, PJ Myler, K. Stuart
P-45	Identification of Genes in Biosynthesis of Fatty Acids and Cholesterol Pathways Using Microarrays Nila A. Shah, Young-Ah Moon, Suchismita Mohapatra, Jay D. Horton, and Janet A. Warrington
P-46	Bioinformatics for High-Throughput Mu Transposon Sequencing Ursula Skalska, Yaron Butterfield, Ran Guin, Martin Krzywinski, Kim MacDonald, Duane Smailus, Jeff Stott, George Yang, Scott Zuyderduyn, Jacqueline Schein, Steven Jones and Marco Marra
P-47	A Robust DNA Based Amplification Technique for Tissue-Limiting Experiments on cDNA Microarrays L. Smith, P. Underhill, C. Pritchard, Z. Tymowska-Lalanne, S. Abdul-Husein, H. Hilton, L. Winchester, D. Williams, T. Freeman, and A. Greenfield
P-48	Affinity-Based Immobilization Tools for Functional Genomics Amy L. Springer, Anna S. Gall, Karin A. Hughes, Robert J. Kaiser, Guisheng Li, Deborah D. Lucas, Kevin P. Lund, Doug A. Spicer, Jean P. Wiley Slides (PDF)
P-49	Full-Length cDNA and SAGE Sequencing at the British Columbia Cancer Agency Genome Sequence Centre Jeff M. Stott, J. Asano, Y. Butterfield, R. Guin, M. Krzywinski, K. MacDonald, S. Lee, T. Olson, P. Pandoh, U. Skalska, D. Smailus, L. Spence, K. Teague, G. Yang, S. Zuyderduyn, J. Schein, S. Jones and M. Marra
P-50	Large-Scale Identification of the Promoter Regions of Human Genes Using Full-length Enriched and 5'-end Enriched cDNA Libraries Constructed by the Oligo-Capping Method Yutaka Suzuki, Riu Yamashita, Sawako Suzuki, Aya Miura, Munetomo Hida, Junko Mizushima-Sugano, Hata Hiroko, Takao Isogai, Kenta Nakai, Sumio Sugano
P-51	Precision Gene Expression Analysis and Bioinformatics Can Track the Effect of Orally Administered, Anti-inflammatory Therapeutic Agents in Human Subjects Victor V. Tryon, J. Emmick, N. Nicholls, J. Zuzack, D. Trollinger, J. C. Cheronis, M. P. Bevilacqua
P-52	Assessment of Candidate Genes for Fetal Alcohol Syndrome Mshengu E. Tshabalala, Michele Ramsay and Denis Viljoen
P-53	Microarray Hybridization by Shear-Driven Flows, a New Approach to Enhance Both Sensitivity and Efficiency of Microarray Analysis Paul Van Hummelen, Kris Pappaert, Johan Vanderhoeven, Danny Clicq, Gino V Baron and Gert Desmet
P-54	Gene Expression Studies of In Vitro HIV-1 Infection:HIV-1 Activates Transcription of the Sterol Biosynthesis Pathway Angelique B. van 't Wout, Ginger K. Lehrman, Svetlana A. Mikheeva, Gemma O'Keeffe, Gary K. Geiss, Roger E. Bumgarner and James I. Mullins
P-55	SAGEdb: A Computational Platform for Investigations Using Serial Analysis of Gene Expression Richard Varhol, Scott Zuyderduyn, Mehrdad Oveisi-Fordoei, Erin Garland, Martin Krzywinski, Marco Marra and Steven Jones
P-56	ORESTES and the International Database of Cancer Gene Expression André L. Vettore, Anamaria A. Camargo, Sandro J. de Souza, Gregory J. Riggins, Robert L. Strausberg, Andrew J. G. Simpson
P-57	Generating and Sequencing Full-length cDNAs of Novel Human Genes Within the German cDNA Consortium Ruth E. Wellenreuther, Stefan Wiemann, Daniela Heiss, Nina Claudino, Annemarie Poustka
P-58	The Hypoxic Macrophage Transcriptome Profile: A Strategy to Increase the Discovery of Biologically Relevant and Novel Targets for Angiogenesis and Inflammation Jonathan R. White, Robert A. Harris, Marie H. Craigon, Georgina L. Beard, Sheena R. Lee, Stuart M. Naylor, Chris R. Mundy
P-59	A Regression-based Method to Identify Differentially Expressed Genes in Microarray Time Course Studies and its Application in an Inducible Huntington's Disease Transgenic Model Xie L. Xu, James M. Olson, Lue Ping Zhao
P-60	Genetic Hardware and Genetic Software after Human Genome Project Shuwei Yang
P-61	High Throughput Detection of Single Nucleotide Polymorphisms (SNPs) by OCP Microarrays Zailin Yu, Allan Peng, Amy Cernetich and Qianjin Hu
P-62	Characterization of the Upstream Regions of 836 Orthologous Human/Mouse Genes Mihaela Zavolan, Terry Gaasterland, and Nikolaus Rajewsky
P-63	Downstream of MyoD: An in vivo 27-time Point Temporal Series, Defining Novel Gene Transcriptional Pathways in Muscle Po Zhao, Simona Iezzi, Ethan Carver, Devin Dressman, Thomas Gridley, Vittorio Sartorelli, and Eric P Hoffman
P-64	Defining Disease Pathogenesis by Comparative Cross-Species Profiling in Human and Mouse Knock-Outs: the Downstream Consequences of Dystrophin Deficiency Eric P. Hoffman, Livia Pasquali, Po Zhao, Ksenija Gorni, Frank W. Booth, Brian Tseng, Yi-Wen Chen

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