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TRANSCRIPTOME 2002: From Functional Genomics to Systems
Biology |
Photos from Meeting * Poster 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
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
Poster PDF file
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
Poster PDF file
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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