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FRONT MATTER
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| BIOMOLECULAR NETWORKS: FROM ANALYSIS TO SYNTHESIS |
BIOMOLECULAR NETWORKS: FROM ANALYSIS TO SYNTHESIS – SESSION INTRODUCTION
GIL ALTEROVITZ, JUDITH A. BLAKE, JONATHAN M. DREYFUSS, DREW ENDY and MARCO F. RAMONI | 1 |
STOCHASTIC TRANSIENT ANALYSIS OF BIOCHEMICAL SYSTEMS AND ITS APPLICATION TO THE DESIGN OF BIOCHEMICAL LOGIC GATES
BIN CHENG and MARC RIEDEL | 4 |
DATA-DRIVEN ONTOLOGIES
JAMES C. COSTELLO, DAN SCHRIDER, JEFF GEHLHAUSEN and MEHMET DALKILIC | 15 |
IDENTIFICATION OF DISCRIMINATING BIOMARKERS FOR HUMAN DISEASE USING INTEGRATIVE NETWORK BIOLOGY
JOEL T. DUDLEY and ATUL J. BUTTE | 27 |
LEARNING THE STRUCTURE OF PROTEIN-PROTEIN INTERACTION NETWORKS
OLEKSII KUCHAIEV and NATAŠA PRŽULJ | 39 |
INFERENCE OF FUNCTIONAL NETWORKS OF CONDITION-SPECIFIC RESPONSE - A CASE STUDY OF QUIESCENCE IN YEAST
SUSHMITA ROY, TERRAN LANE, MARGARET WERNER-WASHBURNE and DIEGO MARTINEZ | 51 |
LEARNING CYCLIC SIGNALING PATHWAY STRUCTURES WHILE MINIMIZING DATA REQUIREMENTS
K. SACHS, S. ITANI, J. FITZGERALD, L. WILLE, B. SCHOEBERL, M. A. DAHLEH and G. P. NOLAN | 63 |
CONTEXT-SPECIFIC GENE REGULATIONS IN CANCER GENE EXPRESSION DATA
INA SEN, MICHAEL P. VERDICCHIO, SUNGWON JUNG, ROBERT TREVINO, MICHAEL BITTNER and SEUNGCHAN KIM | 75 |
QUERYING PARSE TREE DATABASE OF MEDLINE TEXT TO SYNTHESIZE USER-SPECIFIC BIOMOLECULAR NETWORKS
LUIS TARI, JÖRG HAKENBERG, GRACIELA GONZALEZ and CHITTA BARAL | 87 |
PAIRWISE ALIGNMENT OF INTERACTION NETWORKS BY FAST IDENTIFICATION OF MAXIMAL CONSERVED PATTERNS
WENHONG TIAN and NAGIZA F. SAMATOVA | 99 |
| COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS: GENE FAMILY EVOLUTION, ANCESTRAL GENOME RECONSTRUCTION, AND APPLICATIONS TO HUMAN GENETICS |
COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS: GENE FAMILY EVOLUTION, ANCESTRAL GENOME RECONSTRUCTION, AND APPLICATIONS TO HUMAN GENETICS – SESSION INTRODUCTION
BERNARD M. E. MORET, WEBB MILLER, PAVEL A. PEVZNER and DAVID SANKOFF | 111 |
IDENTIFYING PARENT-DAUGHTER RELATIONSHIPS AMONG DUPLICATED GENES
MIRA V. HAN and MATTHEW W. HAHN | 114 |
A PARSIMONY APPROACH TO ANALYSIS OF HUMAN SEGMENTAL DUPLICATIONS
CRYSTAL L. KAHN and BENJAMIN J. RAPHAEL | 126 |
AN EXACT SOLVER FOR THE DCJ MEDIAN PROBLEM
MENG ZHANG, WILLIAM ARNDT and JIJUN TANG | 138 |
INFERRING GENOME-WIDE MOSAIC STRUCTURE
QI ZHANG, WEI WANG, LEONARD MCMILLAN, FERNANDO PARDO-MANUEL DE VILLENA and DAVID THREADGILL | 150 |
SIMULTANEOUS HISTORY RECONSTRUCTION FOR COMPLEX GENE CLUSTERS IN MULTIPLE SPECIES
YU ZHANG, GILTAE SONG, CHIH-HAO HSU and WEBB MILLER | 162 |
| DYNAMICS OF BIOLOGICAL NETWORKS |
DYNAMICS OF BIOLOGICAL NETWORKS – SESSION INTRODUCTION
TANYA Y. BERGER-WOLF, TERESA M. PRZYTYCKA and MONA SINGH | 174 |
DENSE GRAPHLET STATISTICS OF PROTEIN INTERACTION AND RANDOM NETWORKS
R. COLAK, F. HORMOZDIARI, F. MOSER, A. SCHÖNHUTH, J. HOLMAN, M. ESTER and S. C. SAHINALP | 178 |
REVERSE ENGINEERING THE EVOLUTION OF PROTEIN INTERACTION NETWORKS
TODD A. GIBSON and DEBRA S. GOLDBERG | 190 |
IDENTIFYING DYNAMIC NETWORK MODULES WITH TEMPORAL AND SPATIAL CONSTRAINTS
RUOMING JIN, SCOTT MCCALLEN, CHUN-CHI LIU, YANG XIANG, EIVIND ALMAAS and XIANGHONG JASMINE ZHOU | 203 |
EFFICIENT AND ROBUST PREDICTION ALGORITHMS FOR PROTEIN COMPLEXES USING GOMORY-HU TREES
A. MITROFANOVA, M. FARACH-COLTON and B. MISHRA | 215 |
PARAMETER ESTIMATION OF IN SILICO BIOLOGICAL PATHWAYS WITH PARTICLE FILTERING TOWARDS A PETASCALE COMPUTING
KAZUYUKI NAKAMURA, RYO YOSHIDA, MASAO NAGASAKI, SATORU MIYANO and TOMOYUKI HIGUCHI | 227 |
FROM ODES TO LANGUAGE-BASED, EXECUTABLE MODELS OF BIOLOGICAL SYSTEMS
A. PALMISANO, I. MURA and C. PRIAMI | 239 |
UNRAVELING DYNAMIC ACTIVITIES OF AUTOCRINE PATHWAYS THAT CONTROL DRUG-RESPONSE TRANSCRIPTOME NETWORKS
YOSHINORI TAMADA, HIROMITSU ARAKI, SEIYA IMOTO, MASAO NAGASAKI, ATSUSHI DOI, YUKIKO NAKANISHI, YUKI TOMIYASU, KAORI YASUDA, BEN DUNMORE, DEBORAH SANDERS, SALLY HUMPHREYS, CRISTIN PRINT, D. STEPHEN CHARNOCK-JONES, KOUSUKE TASHIRO, SATORU KUHARA and SATORU MIYANO | 251 |
DISSECTING THE INTERFACE BETWEEN SIGNALING AND TRANSCRIPTIONAL REGULATION IN HUMAN B CELLS
KAI WANG, MARIANO J. ALVAREZ, BRYGIDA C. BISIKIRSKA, RUNE LINDING, KATIA BASSO, RICCARDO DALLA FAVERA and ANDREA CALIFANO | 264 |
| EMERGING CHALLENGES IN MULTI-SCALE MODELING IN BIOLOGY |
EMERGING CHALLENGES IN MULTISCALE MODELING IN BIOLOGY – SESSION INTRODUCTION
ROY KERCKHOFFS, JAMES BASSINGTHWAIGHTE, JEFF REINBOLT and PETER ARZBERGER | 276 |
FINITE ELEMENT ANALYSIS OF DRUG ELECTROSTATIC DIFFUSION: INHIBITION RATE STUDIES IN N1 NEURAMINIDASE
YUHUI CHENG, MICHAEL J. HOLST and J. A. MCCAMMON | 281 |
MULTI-SCALE MODELING OF THE HUMAN VERTEBRAL BODY: COMPARISON OF MICRO-CT BASED HIGH-RESOLUTION AND CONTINUUM-LEVEL MODELS
SENTHIL K. ESWARAN, AARON J. FIELDS, PREM NAGARATHNAM and TONY M. KEAVENY | 293 |
ADVANCES IN SEMANTIC REPRESENTATION FOR MULTISCALE BIOSIMULATION: A CASE STUDY IN MERGING MODELS
MAXWELL LEWIS NEAL, JOHN H. GENNARI, THEO ARTS and DANIEL L. COOK | 304 |
INTEGRATION OF ANGIOGENESIS MODULES AT MULTIPLE SCALES: FROM MOLECULAR TO TISSUE
AMINA A. QUTUB, GANG LIU, PRAKASH VEMPATI and ALEKSANDER S. POPEL | 316 |
TOWARDS COMPUTATIONAL MODELING OF EXCITATION-CONTRACTION COUPLING IN CARDIAC MYOCYTES: RECONSTRUCTION OF STRUCTURES AND PROTEINS FROM CONFOCAL IMAGING
FRANK B. SACHSE, ELEONORA SAVIO-GALIMBERTI, JOSHUA I. GOLDHABER and JOHN H. B. BRIDGE | 328 |
A MULTISCALE APPROACH TO SAMPLING NASCENT PEPTIDE CHAINS IN THE RIBOSOMAL EXIT TUNNEL
V. A. VOELZ, P. PETRONE and V. S. PANDE | 340 |
| KNOWLEDGE-DRIVEN ANALYSIS AND DATA INTEGRATION FOR HIGH-THROUGHPUT BIOLOGICAL DATA |
KNOWLEDGE-DRIVEN ANALYSIS AND DATA INTEGRATION FOR HIGH-THROUGHPUT BIOLOGICAL DATA – SESSION INTRODUCTION
M. F. OCHS, J. QUACKENBUSH, R. DAVULURI and H. RESSOM | 353 |
CHARACTERIZATION OF UNKNOWN ADULT STEM CELL SAMPLES BY LARGE SCALE DATA INTEGRATION AND ARTIFICIAL NEURAL NETWORKS
G. BIDAUT and C. J. STOECKERT, JR. | 356 |
BIOFILTER: A KNOWLEDGE-INTEGRATION SYSTEM FOR THE MULTI-LOCUS ANALYSIS OF GENOME-WIDE ASSOCIATION STUDIES
WILLIAM S. BUSH, SCOTT M. DUDEK and MARYLYN D. RITCHIE | 368 |
INTERPRETING GENETICS OF GENE EXPRESSION: INTEGRATIVE ARCHITECTURE IN BIOCONDUCTOR
V. J. CAREY and R. GENTLEMAN | 380 |
HIGH THROUGHPUT INTERACTION DATA REVEALS DEGREE CONSERVATION OF HUB PROTEINS
A. FOX, D. TAYLOR and D. K. SLONIM | 391 |
UNISON: AN INTEGRATED PLATFORM FOR COMPUTATIONAL BIOLOGY DISCOVERY
REECE K. HART and KIRAN MUKHYALA | 403 |
TREEQA: QUANTITATIVE GENOME WIDE ASSOCIATION MAPPING USING LOCAL PERFECT PHYLOGENY TREES
FENG PAN, LEONARD MCMILLAN, FERNANDO PARDO-MANUEL DE VILLENA, DAVID THREADGILL and WEI WANG | 415 |
IMPROVING THE EFFICIENCY OF BIOMARKER IDENTIFICATION USING BIOLOGICAL KNOWLEDGE
JOHN H. PHAN, QIQIN YIN-GOEN, ANDREW N. YOUNG and MAY D. WANG | 427 |
TOWARDS A CYTOKlNE-CELL INTERACTION KNOWLEDGEBASE OF THE ADAPTIVE IMMUNE SYSTEM
SHAI S. SHEN-ORR, OFIR GOLDBERGER, YAEL GARTEN, YAEL ROSENBERG-HASSON, PATRICIA A. LOVELACE, DAVID L. HIRSCHBERG, RUSS B. ALTMAN, MARK M. DAVIS and ATUL J. BUTTE | 439 |
A BAYESIAN INTEGRATION MODEL OF HIGH-THROUGHPUT PROTEOMICS AND METABOLOMICS DATA FOR IMPROVED EARLY DETECTION OF MICROBIAL INFECTIONS
BOBBIE-JO M. WEBB-ROBERTSON, LEE ANN MCCUE, NATHANIAL BEAGLEY, JASON E. MCDERMOTT, DAVID S. WUNSCHEL, SUSAN M. VARNUM, JIAN ZHI HU, NANCY G. ISERN, GARRY W. BUCHKO, KATHLEEN MCATEER, JOEL G. POUNDS, SHAWN J. SKERRETT, DENNY LIGGITT and CHARLES W. FREVERT | 451 |
| MOLECULAR BIOINFORMATICS FOR DISEASE |
MOLECULAR BIOINFORMATICS FOR DISEASE – SESSION INTRODUCTION
YVES A. LUSSIER, YOUNGHEE LEE, PREDRAG RADIVOJAC, YANAY OFRAN, ATUL BUTTE and MARICEL KANN | 464 |
MOLECULAR INTERACTION NETWORK BASED DISCOVERY OF MASTER REGULATOR GENES
ANDREA CALIFANO | 467 |
SUPERVISED CLASSIFICATION OF ARRAY CGH DATA WITH HMM-BASED FEATURE SELECTION
ANNELEEN DAEMEN, OLIVIER GEVAERT, KARIN LEUNEN, ERIC LEGIUS, IGNACE VERGOTE and BART DE MOOR | 468 |
INFERRING DISEASE-RELATED PATHWAYS USING A PROBABILISTIC EPISTASIS MODEL
P. N. KANABAR, C. J. VASKE, C. H. YEANG, F. H. YILDIZ and J. M. STUART | 480 |
COMBINING MUTUAL INFORMATION WITH STRUCTURAL ANALYSIS TO SCREEN FOR FUNCTIONALLY IMPORTANT RESIDUES IN INFLUENZA HEMAGGLUTININ
PETER M. KASSON and VIJAY S. PANDE | 492 |
MASTER REGULATORS USED AS BREAST CANCER METASTASIS CLASSIFIER
WEI KEAT LIM, EUGENIA LYASHENKO and ANDREA CALIFANO | 504 |
PREDICTION OF INTERACTIONS BETWEEN HIV-1 AND HUMAN PROTEINS BY INFORMATION INTEGRATION
OZNUR TASTAN, YANJUN QI, JAIME G. CARBONELL and JUDITH KLEIN-SEETHARAMAN | 516 |
FASTCHI: AN EFFICIENT ALGORITHM FOR ANALYZING GENE-GENE INTERACTIONS
XIANG ZHANG, FEI ZOU and WEI WANG | 528 |
OPEN SCIENCE: TOOLS, APPROACHES, AND IMPLICATIONS
CAMERON NEYLON and SHIRLEY WU | 540 |
POST-TRANSCRIPTIONAL GENE REGULATION: RNA-PROTEIN INTERACTIONS, RNA PROCESSING, MRNA STABILITY AND LOCALIZATION
BENJAMIN BLENCOWE, STEVEN BRENNER, TIMOTHY HUGHES and QUAID MORRIS | 545 |
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