TUTORIALS:
(All registered conference participants are invited to attend the tutorials, for which there is no additional fee.)

   1.  Bioconductor
        Lecturer: Robert Gentleman, Harvard School of Public Health and Dana Farber Cancer Institute,  USA

Invited session A1: Proteomics

THE ANALYSIS OF PROTEOMIC SPECTRA FROM SERUM SAMPLES
Keith Baggerly, University of Texas and MD Anderson Cancer Center, Houston, TX, USA

METHODS AND MYTHS IN PROGNOSTIC PREDICTION WITH MICROARRAY AND PROTEOMIC DATA
Richard Simon, National Cancer Institute, Bethesda, MD, USA

Invited session R1: Functional Genomics

COMPARATIVE FUNCTIONAL AND SEQUENCE GENOMICS
I.S. Kohane, Children’s Hospital, Harvard Partners Center for Genetics and Genomics, Division of Health Science and Technology, Harvard and MIT.

EXTRACTING MEANING FROM FUNCTIONAL GENOMICS DATA
John Quackenbush, The Institute for Genomic Research (TIGR), Rockville, MD, USA

Session  S217-1: Comparative Genomic Hybridization

A STATISTICAL APPROACH FOR CGH MICROARRAY DATA ANALYSIS
F. Picard^1,*, S. Robin¹, M. Lavielle², C. Vaisse³, J-J Daudin¹; 1: INA P-G, Paris, France; 2: Université Paris-Sud, Paris, France; 3: University of California San Francisco, San Francisco, CA, USA

DATA FUSION OF EXPRESSION MICROARRAY AND COMPARATIVE GENOMIC HYBRIDISATION ARRAY DATA IN NORMAL KARYOTYPE AML.
S.Skoulakis*¹, S.Debernardi¹, D. Lillington¹, H. Fiegler², N.P.Carter², B.D.Young¹; 1: Cancer Research UK, Medical Oncology Dept., John Vane Science Building, Charterhouse Square, London, UK. 2: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

COMPARATIVE ANALYSIS OF SEQUENCING AND COMPARATIVE GENOMIC HYBRIDIZATION DATA
J. Dunning Hotopp*, M. Ermolaeva, S. Peterson, H. Tettelin, The Institute for Genomic Research, Rockville, MD, USA

Invited session S216-1: Motif Discovery

REGULATORY MOTIF DISCOVERY USING COMPARATIVE GENOMICS
Manolis Kellis, Massachusetts Institute of Technology, Cambridge, MA, USA

RAPID ANALYSIS OF YEAST TRANSCRIPTION FACTORS' DNA BINDING SPECIFICITIES BY PROTEIN BINDING MICROARRAY (PBM) EXPERIMENTS
Martha Bulyk, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA

Invited session  A2:  Microarray Analysis

STRATEGIES FOR QUANTIFYING GENECHIP EXPRESSION FOR LARGE STUDIES
Darlene R. Goldstein, Institut Suisse de Recherche Experimentale sur le Cancer, NCCR-Molecular Oncology, Switzerland

A GEOMETRIC APPROACH TO DETERMINE ASSOCIATION AND COHERENCE OF THE ACTIVATION TIMES OF CELL-CYCLING GENES UNDER DIFFERING EXPERIMENTAL CONDITIONS
Delong Liu, Clarice R. Weinberg and Shyamal D. Peddada*, Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, USA; National Institutes of Health; Research Triangle Park, NC, USA

VARIABILITY AND DATA TRANSFORMATION FOR GENE EXPRESSION, PROTEOMICS, AND METABOLOMICS DATA
David M. Rocke, Division of Biostatistics, Department of Applied Science, and Center for Image Processing and Integrated Computing, University of California, Davis, CA USA

Invited session  R2: Proteomics

ANALYSIS AND SYNTHESIS OF GENOMES AND PROTEOMES
George Church, Harvard Medical School  and MIT Health Sciences, Boston, MA, USA

SMALL WORLDS, UNCERTAIN PATHS, AND ORACULAR TREES: ANALYSIS OF PROTEIN INTERACTION NETWORKS
Frederick Roth, Harvard University, Boston, MA, USA

Molecular interaction networks: discovery and verification
Chen-Hsiang Yeang, MIT;  Trey Ideker, UCSD; Tommi Jaakkola*, Electrical Engineering and Computer Sciences, MIT, Cambridge, MA, USA

Invited session  S217-2: Sequence Alignment

MARKOV MODELS AND HIDDEN MARKOV MODELS IN GENOME ANALYSIS
Bernard Prum, Laboratoire Statistique et Génome, France

MORE ACCURATE PREDICTION OF REPLICATION ORIGINS IN HERPESVIRUS GENOMES
David S.H. Chew¹, Kwok Pui Choi², Ming-Ying Leung*^{3 1}. National University of Singapore, Singapore; 2.National University of Singapore, Singapore; 3. University of Texas at El Paso, USA

MODELING DETERMINISTIC AND STOCHASTIC EFFECTS IN THE NFkB REGULATORY MODULE.
M. Kimmel*, T. Lipniacki and P. Paszek, Rice University, USA; A. Brasier and B. Luxon, University of Texas Medical Branch, USA

Session  S216-2: Classification Methods

DEPTH BASED CLASSIFICATION FOR MICROARRAY DATA
S. López-Pintado1, J. Romo^*1, A. Torrente^1,2, 1: Universidad Carlos III de Madrid, Leganés, Spain, 2: European Bioinformatics Institute, Hinxton, UK

GRAPH-THEORETIC APPROACHES TO CONSTRUCTING FUNCTIONAL GENE CLUSTERS
K. Schlauch^1*, J. Cushman², J. Branco², J. Weller¹, 1:George Mason University, Manassas, VA, USA 2:University of Nevada at Reno, Reno, NV, USA

SUPERVISED LEARNING FROM MICROARRAY DATA
B. K. Lavine and C. E. Davidson, Department of Chemistry, Clarkson University, Potsdam, NY USA

ASSESSING STATISTICAL SIGNIFICANCE IN MICROARRAY EXPERIMENTS USING THE DISTANCE BETWEEN MICROARRAYS
D.L. Hayden*, D.A. Schoenfeld, and Inflammation and the Host Response to Injury Investigators,  Boston, MA

Invited session  H2: Lingkage/Association  Studies

MEASURING THE STRENGTH OF ASSOCIATION AT CANDIDATE GENES FOR FAMILY-BASED ASSOCIATION STUDIES
Mei-Chiung Shih, Harvard School of Public Health and Children's Hospital, USA

ON FAMILY-BASED ASSOCIATION TEST FOR SURVIVAL AND TIME-TO-ONSET DATA: A NEW TEST STATISTIC USING THE COX-PROPORTIONAL HAZARD MODEL
H. Jiang, A. Murphy, L. Bertram, D. Blacker and C. Lange*, Harvard School of Public Health, USA

QUANTITATIVE ANALYSIS OF LOSS OF HETEROZYGOSITY
R.A. Betensky*^₁, J.G. Cairncross², D.N. Louis³, O. Bogler⁴
1: Harvard School of Public Health, USA; 2: University of Calgary, Canada; 3: Massachusetts General Hospital, Boston, MA, USA

Invited session  A3: Pharmacogenomics

POTENTIAL GENOMIC AND PROTEOMIC APPLICATIONS IN THE WOMEN’S HEALTH INITIATIVE POSTMENOPAUSAL THERAPY TRIALS
Ross L. Prentice, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA

TREE-BASED DATA MINING AND PHARMACOGENETICS
R.B. Martin*¹, V. Farutin¹, K. Rinard¹, X. Zhou¹, and K. Yu².1:Millennium Pharmaceuticals, USA; 2: Washington University, USA

PERSPECTIVES ON THE USE OF CLINICAL PHARMACOGENOMICS IN DRUG DEVELOPMENT AND CLINICAL PRACTICE.
William L. Trepicchio, Millennium Pharmaceuticals, Inc., Cambridge, MA, USA

Invited session  R3: Networks/Pathways

EXPLORING GENOMIC DATA USING GO
Robert Gentleman, Harvard University, USA

INTEGRATIVE GENOMICS USING BAYESIAN NETWORKS
Marco F Ramoni*¹, Paola Sebastiani²,1:Children’s Hospital Boston and Harvard Medical School, 2: Boston University School of Public Health

INFERRING PATHWAYS FROM GENE LISTS USING A LITERATURE-DERIVED NETWORK OF BIOLOGICAL RELATIONSHIPS
D. Rajagopalan*  and P. Agarwal, Bioinformatics Sciences, GlaxoSmithKline R&D, 709 Swedeland Road, King of Prussia, PA 19406

Invited session  S217-3: Genomic-scale Approaches to Chromatin Structure

GENOME-SCALE APPROACHES TO CHROMATIN STRUCTURE: Part I and Part II
Oliver Rando and Steve Altschuler, Harvard University

Session  S216-3: Microarray Applications

GENE EXPRESSION BIOINFORMATICS IN NEUROAIDS
P. Shapshak^{1 *}, R. Duncan ², A. Minagar³, K. Goodkin⁴, E. Duran¹, A. Nath⁴, J. Turchan⁴, W. Davis⁵, R. Seth⁶, & T. Kazic⁶. 1 Psychiatry & Beh Sci, U of Miami Med School, Miami, FL USA, 2 Epidemiology, U of Miami Med School, Miami, FL USA, 3 Neurology, LSU Health Science Center, Shreveport, LA USA, 4 Neurology, Johns Hopkins Univ. Med School, Baltimore, MD USA, 5 Statistics, Baylor University, Waco, TX USA, 6 Computer Sci & Engineering, U of Missouri, Columbia, MO USA

DIFFERENTIAL GENE EXPRESSION PROFILING OF HUMAN MAST CELLS FOLLOWING IgE STIMULATION AND FceRI CROSS LINKING
M. Jayapal, R. Reghunathan٭, H. K. Tay, L. Zhi, A. J. Melendez, Department of Physiology, National University of Singapore, Singapore-117597

BIOLOGICAL AND TECHNICAL VARIATION OF GENE EXPRESSION IN NORMAL HUMAN TISSUES
C.D. Coldren^*1, M.P. Gruber¹, G.P. Cosgrove^1,2, G.S. Worthen^1,2, E. Abraham¹, M.W. Geraci¹; 1:University of Colorado Health Sciences Center, Division of Pulmonary Sciences and Critical Care Medicine, Denver, USA; 2:National Jewish Medical and Research Center, Denver, USA

CLINICAL AND GENE EXPRESSION DATA INTEGRATION REVEALS COMMON MODES OF BREAST CANCER METASTASES
Hongyue Dai, Rosetta Inpharmatics, Merck

Invited session  H3: Gene-environment Interactions

BAYESIAN HIERARCHICAL MODELING OF METABOLIC PATHWAYS
DV Conti*, V Cortessis, J Molitor, and DC Thomas, Department of Preventive Medicine, University of Southern California, Los Angeles, CA. USA.

A MONTE CARLO METHOD FOR LINKAGE ANALYSIS WITH SIBSHIP GENOTYPE DATA
I.S. Chang*, National Health Research Institutes, Taiwan; W.C. Wang, National Central University, Taiwan; Y.C. Chuang, Ming Chuan University, Taiwan; W.C. Chen, National Health Research Institutes, Taiwan; C.A. Hsiung, National Health Research Institutes, Taiwan, R.O.C.

DATA MINING APPROACHES TO DETECTING GENE-ENVIRONMENT INTERACTIONS
Nancy Cook, Harvard Medical School

Invited session  A4: Pharmacogenomics

SUPERVISED CLASSIFICATION OF COMPOUND BIOLOGICAL RESPONSE AND OF MECHANISMS OF ACTION USING HIGH-THROUGHPUT GENE EXPRESSION PROFILING
J. Theilhaber*; Aventis Cambridge Genomics Center, Cambridge, MA, USA, and Aventis Department of Oncology, Vitry, France.

VARIABLE SCREENING AND SELECTION OF PREDICTIVE CLINICAL MODEL WITH HIGH-DIMENSIONAL MICROARRAY DATA
Jun Shao*¹ , Kongming Wang², Shein-Chung Chow², Li Li³.1: University of Wisconsin-Madison; 2: Millennium Pharmaceuticals, Inc, USA; 3:Temple University, USA

USING SIMPLE PROPERTIES OF COMPLEX NETWORK STRUCTURE FOR THE ANALYSIS OF GENOMIC DATA.
J.R. Pradines*, D. Rose, J. Rees, A. Ruttenberg, and V. Farutin, Millennium Pharmaceuticals, Inc., Cambridge, MA, USA

TUTORIAL session R4:  Power and Sample Size for Microarray Studies

      Lecturers: Mei-Ling Ting Lee, Brigham and Women's Hospital and Harvard Medical School, USA
                      G. Alex Whitmore, McGill University, Canada.

Invited session  S217-4: Microarray Analysis

Invited session  S216-4: Genomics & Proteomics

SYSTEMATIC ANALYSIS OF THE FUNCTION OF NOVEL PROTEINS BY HIGH-THROUGHPUT CELLULAR ASSAYS
Wolfgang Huber, German Cancer Research Center, Germany

GENOMEWIDE CO-EXPRESSION DYNAMICS IN YEAST AND IN HUMAN CELL-LINES, WITH APPLICATION TO A FUNCTIONAL GENOMIC STUDY ON NCI'S ANTICANCER DRUG SCREEN
Li, K.C.* and Yuan, S, Department of Statistics, UCLA, Los Angeles, CA, USA

NONPARAMETRIC APPROACHES  TO THE CLASSIFICATION OF PROTEOMIC PROFILES
Kim-Anh Do*, Peter Mueller, University of Texas, MD Anderson Cancer Center, USA

Session  H-4: Linkage/Association  and  Proteomics

TESTING ASSOCIATION IN THE PRESENCE OF LINKAGE USING FAMILY DATA – A COMPARISON BETWEEN A VARIANCE COMPONENTS MODEL AND FBAT.
G. Jonasdottir^*1, J. Palmgren², K. Humphreys², 1:Stockholm University, Stockholm, Sweden, 2: Karolinska Institutet, Stockholm, Sweden.

BAYESIAN NETWORK MODELING OF COMPLEX TRAITS IN ASSOCIATION STUDIES
P. Sebastiani*, Department of Biostatistics, Boston University,  Boston, USA; M. Ramoni, Children’s Hospital, Harvard Medical School, Boston, USA; M. Steinberg,  Department of Medicine, Boston University, Boston, USA

LINEAR PARAMETER HAPLOTYPE MODELS WITH ADMIXTURE
T.L. Bergemann*, L. Eclipse, and D.B. Clarkson, Insightful Corporation, Seattle, WA

A COMPARATIVE ANALYSIS OF CLASSIFICATION METHODS FOR CANCER DIAGNOSTICS USING THE COMPLETE SPECTRUM OF MASS-SPECTROMETRY DATA FROM HUMAN SERUM.
Lucio Andrade-Cetto* and  Robert Henson, The MathWorks Inc., Natick, MA, USA

Invited session  A5: Fine Mapping of Complex Traits 

FINE MAPPING IN COPD: EFFECTS OF THE ENVIRONMENT
Ed Silverman, Brigham and Women's Hospital and Harvard Medical School, USA

SELECTING SUBSETS OF SNPS FOR FINE MAPPING
Ross Lazarus, Brigham and Women's Hospital; Harvard Medical School, Boston, USA

POOLING VERSUS SINGLE SNPS FOR FINE MAPPING IN ASTHMA
Benjamin Raby: Brigham and Women's Hospital and Harvard Medical School, USA

Invited session  R5: Power and False Discover Rates

MULTIPLE TESTING PROCEDURES FOR CONTROL OF THE GENERALIZED FAMILY WISE ERROR RATE AND PROPORTION OF FALSE POSITIVES
Mark J. van der Laan*, Sandrine Dudoit, and Katherina Pollard, University of California, Berkeley, USA

GENE SELECTIONS IN MICROARRAY DATA ANALYSIS
James Chen, Food and Drug Administration, USA

POWER AND SAMPLE SIZE FOR SPLIT-PLOT MICROARRAY EXPERIMENTS
Pi-Wen Tsai, Academia Sinica, Taiwan, R.O.C.

Invited session  S217-5: Sequence Alignment

DISCOVERING CIS REGULATORY MODULES VIA GIBBS SAMPLING
Jun Liu, Harvard University, USA

A NEW APPROACH TOWARD COMPLEX TRAITS
Shaw-Hwa Lo, Department of Statistics, Columbia University, New York, NY, USA            

PALINDROMES IN SARS AND OTHER CORONAVIRUSES
D. Chew, National University of Singapore, Singapore; K.P. Choi*, National University of Singapore, Singapore; H. Heidner, University of Texas at San Antoinio, USA.; M.Y. Leung, University of Texas at El Paso, USA

Session  S216-5: Microarray Analysis 

LOCAL POOLED ERROR TESTS FOR SMALL SAMPLE MICROARRAY DATA
Jae K. Lee, Division of Biostatistics and Epidemiology, University of Virginia School of Medicine, Charlottesville, VA-22908

A GLOBAL TEST FOR GROUPS OF GENES: TESTING ASSOCIATION OF A PATHWAY WITH A CLINICAL OUTCOME USING A SINGLE TEST
Jelle Goeman*, Leiden University Medical Center, The Netherlands; Floor de Kort, Leiden University Medical Center, The Netherlands; Sara van de Geer, Mathematical Institute, Leiden University, The Netherlands; Hans van Houwelingen, Leiden University Medical Center, The Netherlands

ANALYSIS OF MICROARRAY TIME-COURSE DATA
T. Logvinenko, Division of Biostatistics, Massachusetts General Hospital, Boston, MA, USA, and the Inflammation and the Host Response to Trauma collaborative project

IMPROVING ESTIMATION OF THE CONDITIONAL FALSE DISCOVERY RATE
S. Pounds* and C. Cheng,  Department of Biostatistics, St. Jude Children’s Research Hospital, 332 N. Lauderdale St. Memphis, TN  38105, USA

Invited session  A6: Linkage/Association Studies

COVARIATE ADJUSTMENT IN THE TRANSMISSION DISEQUILIBRIUM TEST
Alice Whittemore, Stanford University, USA

THE ANALYSIS OF FAMILY-BASED ASSOCIATION TESTS, INCLUDING HAPLOTYPES
N.M. Laird, Harvard School of Public Health, USA

GENETIC ASSOCIATION STUDIES USING HAPLOTYPES
Glen A. Satten^1*, Michael P. Epstein², Andrew Allen³, 1:National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta GA; 2:Department of Human Genetics, Emory University, Atlanta GA; 3:Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham NC

Invited session  R6: Microarray Analysis

TIGHT CLUSTERING: A RESAMPLING-BASED APPROACH FOR IDENTIFYING STABLE AND TIGHT PATTERNS IN DATA
George Tseng, University of Pittsburgh, USA

Session  S217-6: Microarray Analysis

METHODS FOR IDENTIFYING MARKER GENES MOST CONTRIBUTING TO TUMOR PROGRESSION BY OVERCOMING THE PROBLEM OF p >> n
Hae-Hiang Song* and Hee-Jin Cho, Department of Biostatistics, Medical College, The Catholic University of Korea, Seoul 137-701, Korea

BAYESIAN NORMALIZATION AND IDENTIFICATION FOR DIFFERENTIAL GENE EXPRESSION DATA
Dabao Zhang^*1, Martin T. Wells², Christine D. Smart³ and William E. Fry³, 1. Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 2. Department of Biological Statistics and Computational Biology, Cornell University, 3. Department of Plant Pathology, Cornell University

MODEL-BASED ESTIMATION OF TRANSCRIPT CONCENTRATIONS FROM SPOTTED MICROARRAY DATA
A. Frigessi, Department of Statistics, Institute of Basic Medical Sciences, University of Oslo, Norway; M. A. van de Wiel, Department of Mathematics and Computer Science, Technische Universiteit Eindhoven, The Netherlands; M. Holden, Norwegian Computing Center, Oslo, Norway; I. K. Glad*, Department of Mathematics, University of Oslo, Norway; H. Lyng, Department of Biophysics, The Norwegian Radium Hospital, Oslo, Norway

FAST, SIMPLE ANOVA METHODS FOR THE ANALYSIS OF MICROARRAY TIME AND CONCENTRATION SERIES USING S-PLUS AND S+ARRAYANALYZER.
M. O’Connell¹*, S. Kaluzny², E Chao², V. Chan³, N. Del Raso³, C. Tusk², G. Marchisio²; 1:Insightful Corp, Durham, USA, 2:Insightful Corp, Seattle, USA, 3:Air Force Research Laboratory, Dayton, USA

Session  S216-6: Microarray Analysis

STATISTICAL METHODS FOR  ANALYZING CHROMATIN IMMUNOPRECIPITATION-HIGH DENSITY OLIGONUCLEOTIDE ARRAY DATA
S. Keles*, Division of Biostatistics, UC Berkeley, Berkeley, CA 94270;  M.J. van der Laan, UC Berkeley, Berkeley; S.L. Teng, UC Berkeley;   S. Dudoit, UC Berkeley, Berkeley, CA 94270

MINING TRANSCRIPTIONAL REGULATORY MODULES: ANALYSIS, INTERPRETATION AND IMPLICATION OF GENOME-WIDE LOCATION DATA USING A MIXED MODEL
Xiang Yu^{*1, 2}, Tzu-Ming Chu², Greg Gibson^{1, 3}, Russell D Wolfinger^{2, 6}1.  North Carolina State University, Raleigh, NC; 2. SAS Institute Inc., Cary, NC; 3. University of North Carolina at Chapel Hill, Chapel Hill, NC; 4. North Carolina State University, Raleigh, NC USA.

SEVEN MAJOR CHALLENGES THAT REMAIN IN THE ANALYSIS OF GENOMIC AND PROTEOMIC DATA STREAMS
James Lyons-Weiler, University of Pittsburgh, Pittsburgh, PA 15230

YOU CAN LEARN A LOT BY LOOKIN': INSIGHTS INTO AFFYMETRIX DATA
T. Therneau*, A. Oberg, K. Ballman, Mayo Clinic, Rochester, Minnesota

Invited session  A7: Genomic Methods

SINGLE CHANNEL NORMALIZATION FOR TWO-CHANNEL MICROARRAY EXPRESSION DATA
Terry Speed, The Walter & Eliza Hall Institute of Medical Research, Australia

CHALLENGES IN MULTI-STUDY GENOMIC DATA ANALYSIS
Giovanni Parmigiani, Johns Hopkins University, USA

NEW TOOLS FOR ANALYZING MICROARRAY DATA
Wing Wong, Harvard University, USA

Invited session  R7: Gene-environment Interactions

NOVEL CONDITIONAL-LIKELIHOODS FOR EXPLOITING GENE-ENVIRONMENT INDEPENDENCE IN FAMILY-BASED CASE-CONTROL STUDIES
N Chatterjee*, National Cancer Institute, USA; K Zeynep, Information Management System, USA; RJ Carroll, Texas A&M University, College Station, USA

HAPLOTYES IN STUDIES OF GENE ´ ENVIRONMENT INTERACTION
P. Kraft^1,2* D. Cox¹, R. Paynter¹, D. Hunter^1,3,4, I. De Vivo^1,4; Departments of ¹Epidemiology, ²Biostatistics and ³Nutrition, Harvard School of Public Health, Boston, USA; ⁴Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, USA. 

POWER AND SAMPLE SIZE FOR CASE-CONTROL STUDIES OF GENE-ENVIRONMENT INTERACTIONS: A NEW METHOD WITH COMPARISON TO THE OLD
Donna Spiegelman*, Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA, USA; Roger Logan, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA

Invited session  S217-7: Microarray Analysis 

GRAPHICAL ASSOCIATION NETWORKS FOR EXPLORATION, VISUALIZATION AND SUMMARISATION OF GENE EXPRESSION DATA
Adrian Dobra and Mike West*, Duke University, Durham, NC 27708. USA

ANALYSIS OF MICROARRAY GENE EXPRESSION DATA WITH LINKED SURVIVAL PHENOTYPES
Mark Segal, University of California, San Francisco, CA, USA

THE RELATIONSHIPS AMONG SCAN INTENSITY, EXPRESSION LEVEL, AND THE POWER TO DETECT DIFFERENTIAL EXPRESSION USING CDNA MICROARRAYS
D. Nettleton, D. S. Skibbe, L. A. Borsuk, and P. S. Schnable, Iowa State University, Ames, Iowa, USA

Session  S216-7: Bioinformatics Methods

A GRAPH THEORETIC APPROACH TO INTEGROMICS - INTEGRATING DISPARATE SOURCES OF GENOMIC DATA
T. LaFramboise*, R. Balasubramanian, D. Scholtens, R. Gentleman; Department of Biostatistics, Harvard School of Public Health, Boston, MA US

S+GENE: A NEW STATISTICAL GENETICS LIBRARY FOR S
D.B. Clarkson, L. Eclipse*, and T.L. Bergemann, Insightful Corporation, Seattle, WA.USA

STATISTICAL METHOD FOR CONSTRUCTING TRANSCRIPTIONAL REGULATORY NETWORKS USING GENE EXPRESSION AND SEQUENCE DATA
Biao Xing* and Mark J. van der Laan, Division of Biostatistics, School pf Public Health, University of California, 140 Warren Hall # 7360, Berkeley, CA USA

DATA ROTATION FOR EFFICIENT COMPARATIVE GENOMICS
A. Ziegler* and D. Repsilber, Institut fuer Medizinische Biometrie und Statistik, University at Lübeck, Germany

Invited session  A8: Microarray Applications

GENE EXPRESSION DATA ANALYSIS IN CLINICAL CANCER RESEARCH
Philippe Broet, University Paris XI, France

GENOMIC APPROACHES TO MOLECULAR ONCOLOGY
S. Ramaswamy, Dana-Farber Cancer Institute and Harvard Medical School, Whitehead / MIT Center for Genome Research, USA

RP SCORES: A COMPUTATIONAL TOOL FOR IDENTIFYING REGULATORY SEQUENCES.
J. Taylor ^1,2, J. Kasturi ^1,2, D. King ^1,4, L. Elnitski ^1,4, H. Petrykowska ^1,4, W. Miller ^1,2,3, R. Hardison ^1,4 and F. Chiaromonte^*1,5,6; 1: Center for Comparative Genomics and Bioinformatics; 2: Departments of: Computer Science;3: Biology, 4: Biochemistry and Molecular Biology, 5: Statistics, and 6: Health Evaluation Sciences. The Pennsylvania State University, University Park, PA.

SEARCHING FOR DIFFERENTIALLY EXPRESSED COMBINATIONS OF GENES
Andrei Yakovlev*, Alexander Gordon, Lev Klebanov, Yuanhui Xiao; University of Rochester, Rochester, NY USA

TUTORIAL session R8: Bioconductor

Lecturer: Robert Gentleman, Harvard School of Public Health and Dana Farber Cancer Institute,  USA

Contributed session  S217-8: Bioinformatic Methods

MACHINE LEARNING TECHNIQUES FOR PROTEOMIC CLASSIFICATION AND MARKER SELECTION USING SAMPLE FRACTIONATION WITH SELDI-TOF MS
Gil Alterovitz^1*, Manuel Aivado², Towia Libermann², Marco Ramoni^3,4, Isaac S. Kohane^3,4, 1: MIT, 2: Beth Israel Deaconess Medical Center, Harvard Institutes of Medicine, 3: Harvard Partners Center for Genetics and Genomics, Harvard Medical School, 4: Children's Hospital Informatics Program, Harvard Medical School.

HYPOTHESIS DRIVEN PATTERN IDENTIFICATION IN MICROARRAY DATA ANALYSIS
Xuejun Peng^*1, Eric Blalock², Ralph O’Brien¹, Arnold Stromberg³; 1: Department of Biostatistics & Epidemiology, Cleveland Clinic Foundation; 2: Department of Pharmacology, and 3Department of Statistics, University of Kentucky

STOCHASTIC MODELS FOR DISCOVERY OF NOVEL TRANSCRIPTION REGULATORY MODULES
Mayetri Gupta*, University of North Carolina at Chapel Hill, Chapel Hill, U.S.A. Jun S. Liu, Harvard University, Cambridge, MA, USA

PIECEWISE CONSTANT ESTIMATION IN PREDICTION OF SURVIVAL OUTCOMES:  APPLICATIONS IN GENOMICS
Annette Molinaro*, University of California, Berkeley, Berkeley, USA; Mark J. van der Laan, University of California, Berkeley; Sandrine Dudoit,  University of California, Berkeley, CA USA

AN  EMPIRICAL BAYES TRANSFORMATION OF THE CORRELATION COEFFICIENT
Anthony Almudevar, Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York, USA

AN INTEGRATED APPROACH TO IDENTIFY VIBRIO CHOLERAE OPERONS
C. Meyer, Dana Farber Cancer Institute, Boston, USA; X. Liu,  Dana Farber Cancer Institute, Boston, USA

Session  S216-8: Nonparametric Methods

IDENTIFY DEFFERENCIALLY EXPRESSED GENES BY RANKING DISTRIBUTIONS
Y.Zhou*, C.Cras-Menuer, M.Ohsugi, E. Bernal-Mizrachi, G.Stormo, M.A.Permutt, Department of Internal Medicine, Department of Genetics, School of Medicine, Washington University, 660 S. Euclid Ave. Campus Box 8127, St. Louis, MO 63113

NESTED, NON-PARAMETRIC, CORRELATIVE ANALYSIS OF MICROARRAYS FOR HETEROGENEOUS PHENOTYPE CHARACTERIZATION
A. Blackford*, M. Zahurak, A. Mamelak, J. Kowalski, D. Sauder, Johns Hopkins University School of Medicine, USA

A COMPLETELY NONPARAMETRIC APPROACH TO THE ANALYSIS OF LONGITUDINAL DATA ARISING FROM ARRAY BASED TECHNOLOGIES
Cavan Reilly, Division of Biostatistics, University of Minnesota, Minneapolis, MN USA

NONPARAMETRIC STATISTICAL METHOD FOR DETECTING DIFFERENTIALLY EXPRESSED GENE EXPRESSION
Sunil Mathur, Department of Mathematics, Hume 325, University of Mississippi, MS 38677-1848, USA

TRANSLATING MICROARRAY DATA INTO DIAGNOSTIC INFORMATION IN COLORECTAL CANCER
B-S. Kim*¹, I. Kim², S. Lee³, S. Y. Rha^2,4, H.C. Chung^2,4 ; 1. Dept. of Applied Statistics, Yonsei Univ., Seoul, Korea, 2. Cancer Metastasis Research Center, College of Medicine, Yonsei Univ., Korea. 3. Dept. of Mathematics, Sejong Univ., Korea. 4. Brain Korea 21 Project for Medical Science, College of Medicine, Yonsei Univ.,  Korea.

PROBE RANK APPROACHES FOR GENE SELECTION IN OLIGONUCLEOTIDE ARRAYS.
DT. Chen*. University of Alabama at Birmingham, AL, USA; J. Chen. FDA, AK, USA; SJ. Soong. University of Alabama at Birmingham, AL, USA.

Duration of Poster Presentation : From 10:30am on Monday, May 10th to 3:30pm on Tuesday, May 11th.

Invited Posters Presentations

Poster A:
Statistical Methods for Discovering Differentially Expressed Genes in Replicated Microarray Experiments.
Lynn Kuo*, Fang Yu, and Yifang Zhao, University of Connecticut.

Poster B:
A Proposed Metric for Assessing the Measurement Quality of Individual Microarrays.
Kyoungmi Kim¹*, Grier P. Page¹, T. Mark Beasley¹, Stephen Barnes², David B. Allison¹
1 Department of Biostatistics, Section on Statistical Genetics; 2 Department of Pharmacology & Toxicology, University of Alabama at Birmingham

Contributed Posters Presentations (Size of Each Poster: 4' x 4')

Poster #1
PLACENTAL GENE EXPRESSION PROFILING IN NORMAL PREGNANCY VERSUS PREECLAMPSIA
José O. Alemán^2,3*, Sharon Maynard¹,  Gene W. Yeo³, Towia A. Libermann¹, Marco Ramoni^2,3, Isaac Kohane^2,3, Franklin H. Epstein¹, Vikas P. Sukhatme¹, S. Ananth Karumanchi¹. 1: Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA; 2: Endocrinology and Informatics Program, Childrens  Hospital, Boston, MA, USA; 3: Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA..

Poster #2
MINING FOR BIOMARKERS OF CHEMICAL EXPOSURE: SUPERVISED METHODS FOR LINKING CONCENTRATION-RESPONSE AND CDNA MICROARRAY DATA
Jennifer G. Catalano*¹, Averell L. Gnatt¹, Yuriko Mori², Jing Yin², Stephen Meltzer², Darrel E. Menking³ and James J. Valdes.³ 1: Department of Pharmacology and Experimental Therapeutics, 2: Department of Medicine, School of Medicine, University of Maryland, Baltimore.  3: Research and Technology Directorate, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD.

Poster #3
FINE MAPPING OF CHROMOSOMAL REGIONS IMPLICATED IN ADHD
JW Kim¹, J Fagerness¹, L Arbeitman¹, A Doyle², C Petty², J Biederman², SV Faraone^1,2 and P Sklar¹
1 Department of Psychiatry, Harvard Medical School, and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Charlestown, MA, USA; 2 Department of Psychiatry, Harvard Medical School, and Pediatric Psychopharmacology Department, Massachusetts General Hospital, Boston, MA, USA

Poster #4
IMPROVED STATISTICAL TESTS FOR DIFFERENTIAL GENE EXPRESSION BY SHRINKING VARIANCE COMPONENTS ESTIMATES
Xiangqin Cui*, J. T. Gene Hwang,  Jing Qiu, Natalie J. Blades, Shirng-Wern Tsaih and Gary A. Churchill .The Jackson Laboratory, Bar Harbor, Maine,  USA

Poster #5
HIDDEN MARKOV MODELS AND THEIR APPLICATIONS IN BIOINFORMATICS
Sujay Datta, Dept. of Mathematics, Statistics and Computer Science, Northern Michigan University, Marquette, MI 49855, USA

Poster #6
SHOULD WE USE INTENSITY OR INTENSITY RATIO IN THE DIFFERENTIAL EXPRESSION ANALYSIS OF MICROARRAY DATA?
Shibing Deng*, Department of Biostatistics, University of North Carolina Chapel Hill, NC.
Tzu-Ming Chu, SAS Institute Inc. Cary, NC; Russ Wolfinger, SAS Institute Inc. Cary, NC; Young Truong, Department of Biostatistics, University of North Carolina Chapel Hill, NC

Poster #7
NOVEL NORMALIZATION METHOD FOR ARRAY COMPARATIVE GENOMIC HYBRIDIZATION (CGH) DATA
B. Feng¹, C. Li², Y. Zhang¹, A. Protopopov¹, C. Leo¹, L. Chin¹ and C. Brennan¹*
1-Department of Medical Oncology, 2-Department of Biostatistical Science
Dana Farber Cancer Institute, Boston, Massachusetts, 02115, USA

Poster #8
A STATISTICAL PROCEDURE FOR DETECTING HIGHLY CORRELATED GENES WITH A PRE-SPECIFIED CANDIDATE GENE USING AFFYMETRIX MICROARRAYS
A. Ding¹, J. Manson², J. Lin2, T. Niu^2,3,*; 1:Department of Mathematics, Northeastern University, Boston, MA, USA; 2:Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 900 Commonwealth Ave. East, Boston, MA, USA; 3:College of Computer Science, Northeastern University, Cullinane Hall, 360 Huntington Avenue, Boston MA, USA

Poster #9
SEX GENES AS INTERNAL CONTROLS FOR THE ANALYSIS OF MICROARRAY DATA
H. Galfalvy*, Department of Neuroscience, New York State Psychiatric Institute, New York, USA; P. Pavlidis, Genome Center, Department of Biomedical Informatics, Columbia University, New York, USA; E. Sibille, Department of Neuroscience, NYSPI, and Department of Psychiatry, Columbia University, New York, USA

Poster #10
ADJUSTING ROC ANALYSIS OF FUNCTIONAL GENOMIC DATA FOR CONFOUNDING EFFECTS
C. Ittrich*, Central Unit Biostatistics, German Cancer Research Center, Heidelberg, Germany; A. Benner, Central Unit Biostatistics, German Cancer Research Center, Heidelberg, Germany

Poster #11
THE IMMUNE RESPONSE IN PATIENTS WITH SARS: DIFFERENTIAL GENE EXPRESSION PROFILING
M. Jayapal^1*, R. Regunathan¹, B. P. Leung², L.Y. Hsu³, D. Tai⁴, H. H. Chng², and A. J. Melendez ¹;1Department of Physiology, National University of Singapore, Singapore, 2Department of Rheumatology, Allergy and Immunology, 3Department of Infectious Disease, 4Department of General Medicine and, Tan Tock Seng Hospital, Singapore.

Poster #12
QUANTIFYING SOURCES OF VARIABILITY USING VARIANCE COMPONENT ANALYSIS IN AN EXPERIMENT INVOLVING MICROARRAY DATA
Edit Kurali*, GlaxoSmithKline Pharmaceuticals, Philadelphia, USA; Amit Bhattacharyya, GlaxoSmithKline Pharmaceuticals, Philadelphia, USA

Poster #13
CLUSTERING GENE EXPRESSION DATA BASED ON P-VALUES
R. Jörnsten, J. Li* and R. Liu, Department of Statistics, Rutgers University, Piscataway, NJ, USA

Poster #14
THE USE OF THE INVERSE GAUSSIAN DISTRIBUTION TO DESCRIBE MICROARRAY DATA
A. Labbe* and M.Thompson; Institution: University of Waterloo, Waterloo, Ontario, Canada.

Poster #15
A NOVEL COMPUTATIONAL APPROACH TO IDENTIFICATION OF PROTEIN NETWORK ELEMENTS COUPLING GENE EXPRESSION MACHINES IN EUKARYOTIC CELLS
K. Maciag^{1, 2}, S. Altschuler¹, L. Wu¹, T. Maniatis²; 1Center for Genomics Research, Harvard University, Cambridge, MA
2Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA

Poster #16
PREDICTION OF CANCER OUTCOME WITH MICROARRAYS: AN EMPIRICAL CHALLENGE OF THE TRAINING-VALIDATION STRATEGY
S. Michiels*, S. Koscielny, Unit of Biostatistics and Epidemiology, Institut Gustave-Roussy, Villejuif, France.

Poster #17
METHODS FOR CLASS PREDICTION USING DIMENSION REDUCTION TECHNIQUES ON DNA MICROARRAY DATA
R Pfeiffer*, National Cancer Institute, NIH, HHS, Bethesda, MD 20892-7244, USA; E Bura, Department of Statistics, The George Washington University, Washington, DC, USA

Poster #18
BASAL GENE EXPRESSION IN AFFYMETRIX GENECHIPS
Hui-Rong Qian*, Kerry Bemis; Global Statistical Sciences, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN, USA

Poster #19
CLASSIFICATION OF THE ACUTE LEUKEMIA MICROARRAY DATA USING A SEPARATION INDEX
Weiliang Qiu, Department of Statistics, University of British Columbia, Vancouver, B.C., Canada 

Poster #20
DIFFERENTIAL GENE EXPRESSION PROFILING OF HUMAN MAST CELLS FOLLOWING IgE STIMULATION AND FceRI CROSS LINKING
M. Jayapal, R. Reghunathan٭, H. K. Tay, L. Zhi, A. J. Melendez
Department of Physiology, National University of Singapore, Singapore

Poster #21
STRATEGIES FOR DETECTING INTERACTIONS OF GENETIC POLYMORPHISMS AND ENVIRONMENTAL FACTORS
S. Selinski¹*, H. Schwender¹, M. Zucknick¹, S. Rabstein², K. Ickstadt¹, H. M. Bolt³ 1: Department of Statistics, University of Dortmund, 44221 Dortmund, Germany; 2: BGFA, Bürkle-de-la-Camp-Platz 1, 44789 Bochum; Germany; 3: Institute for Occupational Physiology at the University of Dortmund, Ardeystr. 67, 44139 Dortmund, Germany

Poster #22
A STATISTICAL METHOD FOR MAPPING QUANTITATIVE TRAIT LOCI IN BUDDING YEAST
Ayellet Falcovitz Segre, Jun-Yi Leu and Andrew Murray
Harvard University, Cambridge, MA, USA

Poster #23
THE UNABRIDGED C. ELEGANS REGULATORY MOTIF DICTIONARY, FIRST EDITION
S. Shen-Orr¹*, M. Lapidot², S. Kaplan², Y. Garten², R. Shalgi², I. Pechersky², Y. Mendel², L. R. Baugh¹, A. A. Hill³, C. P. Hunter¹, Y. Pilpel²
1. Department of Molecular & Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA. 02138, USA; 2. Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel; 3. Department of Genomics, Wyeth Research, Cambridge, MA, USA

Poster #24
ANALYSIS OF THE PANCREATIC ADENOCARCINOMA GENOME USING ARRAY-CGH ON HIGH-RESOLUTION CDNA MICROARRAYS
Raktim Sinha¹*, Cameron Brennan¹, Andrew J. Aguirre¹, Bin Feng¹, Chris Leo¹, and L. Chin¹; 1. Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA

Poster #25
FRAMESHIFTING MECHANISM FOR ORFS X1 AND X2 IN THE SARS CORONAVIRUS
Prathapan Thiruvilangam*, University of Texas at El Paso, El Paso, USA.; Ming-Ying Leung, University of Texas at El Paso, El Paso, TX, USA

Poster #26
MATHEMATICAL MODELING OF THE ALLOSTERIC TRANSITION BETWEEN THE T AND THE R STATE FOR SELECTED ENZYMES.
Ellen Tolonen^1*, Sanjeev Kulshreshta¹, Leticia Velazquez², Boguslaw Stec¹*; Department of Chemistry1, Department of Mathematics2, University of Texas at El Paso, El Paso, TX, USA.

Poster #27
GENETIC DIVERSITY OF VAGINAL LACTOBACILLUS SP. DETERMINED BY PULSED-FIELD GEL ELECTROPHORESIS IN WOMEN 20 AND 30 WEEKS PREGNANT
J. E. Warner*, R. A. Ross, M. L. Delaney, A. M. DuBois, and A. B. Onderdonk, Channing Laboratory, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.

Poster #28
IDENTIFYING DIFFERENTIAL EXPRESSION FROM PROBE-LEVEL DATA IN OLIGONUCLEOTIDE ARRAYS USING A UNIFYING MODEL
Zhijin Wu*, Johns Hopkins University, Baltimore, U.S.A.; Rafael Irizarry,  Johns Hopkins University, Baltimore, MD, USA.

Poster #29
A NEW TEST STATISTIC FOR TESTING TWO-SAMPLE HYPOTHESIS IN MICROARRAY DATA ANALYSIS
Lev Klebanov, Yuanhui Xiao*, Alexander Gordon, Hurtmut Land, and Andrei Yakovlev, Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA

Poster #30
ELUCIDATING SYSTEM ROBUSTNESS FROM MERGING GENETIC AND PHYSICAL INTERACTION NETWORKS IN YEAST
P. Ye* and J.S. Bader; Department of Biomedical Engineering, The Johns Hopkins University, 201Clark Hall, 3400 North Charles Street, Baltimore, MD, USA.

Poster #31
HIDDEN MARKOV MODEL INFERENCE OF DNA COPY NUMBER CHANGE ON ARRAY-CGH DATA
Y. Zhang¹*, C. Li², B. Feng¹, L. Chin¹, C. Brennan¹; 1 -Department of Medical Oncology, 2- Department of Biostatistical Science, Dana Farber Cancer Institute, Boston, MA, USA