TRANSCRIPTOME 2002: From Functional Genomics to Systems Biology
March 10-13, 2002
Seattle, Washington, USA

Photos from Meeting * Poster Abstracts

Speaker Abstracts

Plenary Session 1: The Role of Transcriptome

Chair: John Quakenbush,  The Institute for Genomic Research

Keynote Speakers:

Plenary Session 2: Transcription and Processing I

Chair: Stefan Wiemann, German Cancer Research Center

Plenary Session 3: Transcription and Processing II

Chair: Bento Soares, University of Iowa

Plenary Session 4: CDNA Based Gene Discovery I

Chair: Charles Auffray, CNRS

Plenary Session 5: CDNA Based Gene Discovery II

Chair: Winston Hide, South African National Bioinformatics Institute

Plenary Session 6: Transcription and Processing III

Chair: Yoshihide Hayashizaki, RIKEN Genomic Sciences Center

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

Chair: Andrew Simpson, Ludwig Institute for Cancer Research

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

Chair: Greg Lennon, Cell Logic, Inc.

Plenary Session 9: Gene Expression – Transcript Abundance and Disease

Chair: John Quackenbush, The Institute for Genomic Research

Plenary Session 10: Alternate Measures of Expression

Chair: Winston Hide, South African National Bioinformatics Institute

Plenary Session 11: The Future

Chair: Zhu Chen, Chinese Academy of Sciences

Poster Abstracts

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

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

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
Poster PDF file

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

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

Downstream of an RNA Regulatory Protein Causing a Common Human Disease: Expression Profiling Human SMN-Deficient Muscle
Cinzia Brandoli, Serenella Servidei, and Eric Hoffman

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

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

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

PGA-CPR (Chip Profiling Resource): A Web Queried Database of Affymetrix Profiles with Cross-Profile Analysis Tools
Josephine Chen, Dietrich Stephan, and Eric Hoffman

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

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

Transcription Profiling of Cell Death in Drosophila Melanogaster
S. Chittaranjan, E. Garland, D. Freeman, S. Jones, M. Marra, and S. Gorski

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

Pathogenic Pathways in Spinal Cord Injury Identified by Gene Expression Profiling
Simone Di Giovanni, Susan Knoblach, Cinzia Brandoli, Alan Faden, Eric Hoffman

Preparation of cDNA Hybridization Targets by Phi29 DNA Polymerase
Rohini Dhulipala, Mubasher Dar, R. Scott Duthie and John Nelson

Production and Use of DNA Microarrays for Studies of Aging
Mark W. Eshoo and Krysta Felkey

Intelligent Bioinformatics Systems for Functional Genome Analysis
Daniel Gerlich, Martin Granzow, Julian Mattes, Wolfgang Tvarusko, and Roland Eils, Dr. Wolfgang Tvaruskoi

The aRNA Amplification Procedure in mRNA-Poor Samples Array Applications
Esther Graudens, Xavier Barlet, Virginie el Marhomy, Charles Auffray & Sandrine Imbeaud

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

Comparative Analysis of TBX1 Genes and Their Promoters from Different Species
Ilya Ioshikhes, Jun Liao and Bernice Morrow

Comparative Bioinformatics Analysis of Rat and Human ALB-AFP Gene Locus
Ilya Ioshikhes and Joseph Locker

Expression of Cytokines and Growth Factors in Aging and hTERT-transfected Human Fibroblasts
Yukari Kanzaki, Toshinori Ide

Full-length cDNA Library Construction Using Lambda Recombination (GatewayTM Technology)
Larissa G. Karnaoukhova, Mark R. Smith, Chris E. Gruber, and Martin Gleeson

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,

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

In Silico Detection and Characterisation of Cancer-Specific Transcript Isoforms
Janet Kelso

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

Application of Statistical Modeling to Microarray Gene Expression Data in Human Lung Cancer
Najma Khalid, Lue Ping Zhao

The Immediate Early Gene Response of Human Keratinocytes to Gamma-Rays Analyzed by DNA Micro-Arrays
Jérôme Lamartine, Gilles Waksman, Xavier Gidrol, Michèle Martin

Specific Subtraction of Abundant mRNAs in Skeletal Muscle
Paolo Laveder, Cristiano De Pittà, Stefano Toppo, Giorgio Valle and Gerolamo Lanfranchi

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

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

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

Identification of Putative Genes Involved in Cell Transformation
Andrei M. Mikheev, Svetlana A. Mikheeva, Vivian Li, Jeffrey Delrow and Helmut Zarbl

Quality Control of Microarray Samples Using Lab-on-a-Chip Technology
Odilo Müller, Monika Dittmann, Samar Lightfoot, Kathi Williams, and Robert Dubrow

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

Encoding Biological Prior Information Into Gene Expression Analysis
Michael F. Ochs, Frank J. Manion, Ghislain Bidaut, Thomas Moloshok, Jeffrey D. Grant

Whole Genome Functional Analysis and Metabolic Pathway of Zymomonas mobilis
Sang-Ho Park, Ki-Nam Heo, Hyun-Seok Parkv, Jeong-Sun Seo

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

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

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

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

Differential Gene Expression in Leishmania Major Friedlin
A. Saxena, S.Yan, L. Worthey, A. Leland, PJ Myler, K. Stuart

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

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

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

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
Poster PDF file

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

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

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

Assessment of Candidate Genes for Fetal Alcohol Syndrome
Mshengu E. Tshabalala, Michele Ramsay and Denis Viljoen

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

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

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

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

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

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

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

Genetic Hardware and Genetic Software after Human Genome Project
Shuwei Yang

High Throughput Detection of Single Nucleotide Polymorphisms (SNPs) by OCP Microarrays
Zailin Yu, Allan Peng, Amy Cernetich and Qianjin Hu

Characterization of the Upstream Regions of 836 Orthologous Human/Mouse Genes
Mihaela Zavolan, Terry Gaasterland, and Nikolaus Rajewsky

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

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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