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FRONT MATTER
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| COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS |
COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS – Session Introduction
BERNARD M.E. MORET, WEBB C. MILLER, PAVEL A. PEVZNER and DAVID SANKOFF | 1 |
ACCURATE TAXONOMIC ASSIGNMENT OF SHORT PYROSEQUENCING READS
JOSÉ C. CLEMENTE, JESPER JANSSON and GABRIEL VALIENTE | 3 |
BENCHMARKING BLAST ACCURACY OF GENUS/PHYLA CLASSIFICATION OF METAGENOMIC READS
STEVEN D. ESSINGER and GAIL L. ROSEN | 10 |
GUIDED GENOME HALVING: PROVABLY OPTIMAL SOLUTIONS PROVIDE GOOD INSIGHTS INTO THE PREDUPLICATION ANCESTRAL GENOME OF SACCHAROMYCES CEREVISIAE
HARIS GAVRANOVIĆ and ERIC TANNIER | 21 |
A PRACTICAL ALGORITHM FOR ESTIMATION OF THE MAXIMUM LIKELIHOOD ANCESTRAL RECONSTRUCTION ERROR
GLENN HICKEY and MATHIEU BLANCHETTE | 31 |
OPTIMIZATION METHODS FOR SELECTING FOUNDER INDIVIDUALS FOR CAPTIVE BREEDING OR REINTRODUCTION OF ENDANGERED SPECIES
WEBB MILLER, STEPHEN J. WRIGHT, YU ZHANG, STEPHAN C. SCHUSTER and VANESSA M. HAYES | 43 |
| COMPUTATIONAL STUDIES OF NON-CODING RNAS |
COMPUTATIONAL STUDIES OF NON-CODING RNAS – Session Introduction
ROLF BACKOFEN, HAMIDREZA CHITSAZ, IVO HOFACKER, S. CENK SAHINALP and PETER F. STADLER | 54 |
RNA STRUCTURAL SEGMENTATION
IVAN DOTÚ, WILLIAM A. LORENZ, PASCAL VAN HENTENRYCK and PETER CLOTE | 57 |
RNAZ 2.0: IMPROVED NONCODING RNA DETECTION
ANDREAS R. GRUBER, SVEN FINDEIß, STEFAN WASHIETL, IVO L. HOFACKER and PETER F. STADLER | 69 |
IDENTIFICATION AND CLASSIFICATION OF SMALL RNAS IN TRANSCRIPTOME SEQUENCE DATA
D. LANGENBERGER, C.I. BERMUDEZ-SANTANA, P.F. STADLER and S. HOFFMANN | 80 |
IMPROVEMENT OF STRUCTURE CONSERVATION INDEX WITH CENTROID ESTIMATORS
YOHEI OKADA, KENGO SATO and YASUBUMI SAKAKIBARA | 88 |
DYNAMIC PROGRAMMING ALGORITHMS FOR RNA STRUCTURE PREDICTION WITH BINDING SITES
UNYANEE POOLSAP, YUKI KATO and TATSUYA AKUTSU | 98 |
AN ALGORITHM FOR THE ENERGY BARRIER PROBLEM WITHOUT PSEUDOKNOTS AND TEMPORARY ARCS
CHRIS THACHUK, JÁN MAŇUCH, ARASH RAFIEY, LEIGH-ANNE MATHIESON, LADISLAV STACHO and ANNE CONDON | 108 |
| DYNAMICS OF BIOLOGICAL NETWORKS |
DYNAMICS OF BIOLOGICAL NETWORKS – Session Introduction
TANYA Y. BERGER-WOLF, TERESA M. PRZYTYCKA, MONA SINGH and DONNA K. SLONIM | 120 |
LOCAL OPTIMIZATION FOR GLOBAL ALIGNMENT OF PROTEIN INTERACTION NETWORKS
LEONID CHINDELEVITCH, CHUNG-SHOU LIAO and BONNIE BERGER | 123 |
IDENTIFICATION OF COORDINATELY DYSREGULATED SUBNETWORKS IN COMPLEX PHENOTYPES
SALIM A. CHOWDHURY and MEHMET KOYUTÜRK | 133 |
SUBSPACE DIFFERENTIAL COEXPRESSION ANALYSIS: PROBLEM DEFINITION AND A GENERAL APPROACH
GANG FANG, RUI KUANG, GAURAV PANDEY, MICHAEL STEINBACH, CHAD L. MYERS and VIPIN KUMAR | 145 |
ESTIMATION OF PROTEIN AND DOMAIN INTERACTIONS IN THE SWITCHING MOTILITY SYSTEM OF MYXOCOCCUS XANTHUS
F. MORCOS, M. SIKORA, M. ALBER, D. KAISER and J. A. IZAGUIRRE | 157 |
EXPLORING BIOLOGICAL NETWORK DYNAMICS WITH ENSEMBLES OF GRAPH PARTITIONS
SAKET NAVLAKHA and CARL KINGSFORD | 166 |
GEOMETRIC EVOLUTIONARY DYNAMICS OF PROTEIN INTERACTION NETWORKS
NATAŠA PRŽULJ, OLEKSII KUCHAIEV, ALEKSANDAR STEVANOVIĆ and WAYNE HAYES | 178 |
THE STEADY STATES AND DYNAMICS OF UROKINASE-MEDIATED PLASMIN ACTIVATION
LAKSHMI VENKATRAMAN, HANRY YU, SOURAV S. BHOWMICK, FORBES DEWEY, JR. and LISA TUCKER-KELLOGG | 190 |
| MULTI-RESOLUTION MODELING OF BIOLOGICAL MACROMOLECULES |
MULTI-RESOLUTION MODELING OF BIOLOGICAL MACROMOLECULES – Session Introduction
SAMUEL FLORES, JULIE BERNAUER, XUHUI HUANG, RUHONG ZHOU and SEOKMIN SHIN | 201 |
MULTI-RESOLUTION APPROACH FOR INTERACTIVELY LOCATING FUNCTIONALLY LINKED ION BINDING SITES BY STEERING SMALL MOLECULES INTO ELECTROSTATIC POTENTIAL MAPS USING A HAPTIC DEVICE
OLIVIER DELALANDE, NICOLAS FEREY, BENOIST LAURENT, MARC GUEROULT, BRIGITTE HARTMANN and MARC BAADEN | 205 |
PREDICTING RNA STRUCTURE BY MULTIPLE TEMPLATE HOMOLOGY MODELING
SAMUEL C. FLORES, YAQI WAN, RICK RUSSELL and RUSS B. ALTMAN | 216 |
CONSTRUCTING MULTI-RESOLUTION MARKOV STATE MODELS (MSMS) TO ELUCIDATE RNA HAIRPIN FOLDING MECHANISMS
XUHUI HUANG, YUAN YAO, GREGORY R. BOWMAN, JIAN SUN, LEONIDAS J. GUIBAS, GUNNAR CARLSSON and VIJAY S. PANDE | 228 |
MULTISCALE DYNAMICS OF MACROMOLECULES USING NORMAL MODE LANGEVIN
J. A. IZAGUIRRE, C. R. SWEET and V. S. PANDE | 240 |
INSIGHTS INTO THE INTRA-RING SUBUNIT ORDER OF TRIC/CCT: A STRUCTURAL AND EVOLUTIONARY ANALYSIS
NIR KALISMAN and MICHAEL LEVITT | 252 |
"CROSS-GRAINING": EFFICIENT MULTI-SCALE SIMULATION VIA MARKOV STATE MODELS
PETER M. KASSON and VIJAY S. PANDE | 260 |
TOWARD UNDERSTANDING ALLOSTERIC SIGNALING MECHANISMS IN THE ATPASE DOMAIN OF MOLECULAR CHAPERONES
YING LIU and IVET BAHAR | 269 |
3D-BLAST: 3D PROTEIN STRUCTURE ALIGNMENT, COMPARISON, AND CLASSIFICATION USING SPHERICAL POLAR FOURIER CORRELATIONS
LAZAROS MAVRIDIS and DAVID W. RITCHIE | 281 |
STRUCTURAL PREDICTION OF PROTEIN-RNA INTERACTION BY COMPUTATIONAL DOCKING WITH PROPENSITY-BASED STATISTICAL POTENTIALS
LAURA PÉREZ-CANO, ALBERT SOLERNOU, CARLES PONS and JUAN FERNÁNDEZ-RECIO | 293 |
| PERSONAL GENOMICS |
PERSONAL GENOMICS – Session Introduction
Can Alkan, Michael Brudno, Evan E. Eichler, Maricel G. Kann and S. Cenk Sahinalp | 302 |
IMPROVING THE PREDICTION OF PHARMACOGENES USING TEXT-DERIVED DRUG-GENE RELATIONSHIPS
YAEL GARTEN, NICHOLAS P TATONETTI and RUSS B ALTMAN | 305 |
FINDING UNIQUE FILTER SETS IN PLATO: A PRECURSOR TO EFFICIENT INTERACTION ANALYSIS IN GWAS DATA
BENJAMIN J. GRADY, ERIC TORSTENSON, SCOTT M. DUDEK, JUSTIN GILES, DAVID SEXTON and MARYLYN D. RITCHIE | 315 |
ENABLING PERSONAL GENOMICS WITH AN EXPLICIT TEST OF EPISTASIS
CASEY S. GREENE, DANIEL S. HIMMELSTEIN, HEATHER H. NELSON, KARL T. KELSEY, SCOTT M. WILLIAMS, ANGELINE S. ANDREW, MARGARET R. KARAGAS and JASON H. MOORE | 327 |
LOSS OF POST-TRANSLATIONAL MODIFICATION SITES IN DISEASE
SHUYAN LI, LILIA M. IAKOUCHEVA, SEAN D. MOONEY and PREDRAG RADIVOJAC | 337 |
DETECTING GENOME-WIDE HAPLOTYPE POLYMORPHISM BY COMBINED USE OF MENDELIAN CONSTRAINTS AND LOCAL POPULATION STRUCTURE
XIN LI, YIXUAN CHEN and JING LI | 348 |
SEQUENCE FEATURE VARIANT TYPE (SFVT) ANALYSIS OF THE HLA GENETIC ASSOCIATION IN JUVENILE IDIOPATHIC ARTHRITIS
GLENYS THOMSON, NISHANTH MARTHANDAN, JILL A. HOLLENBACH, STEVEN J. MACK, HENRY A. ERLICH, RICHARD M. SINGLE, MATTHEW J. WALLER, STEVEN G. E. MARSH, PAULA A. GUIDRY, DAVID R. KARP, RICHARD H. SCHEUERMANN, SUSAN D. THOMPSON, DAVID N. GLASS and WOLFGANG HELMBERG | 359 |
ÇOKGEN: A SOFTWARE FOR THE IDENTIFICATION OF RARE COPY NUMBER VARIATION FROM SNP MICROARRAYS
GÖKHAN YAVAŞ, MEHMET KOYUTÜRK, MERAL ÖZSOYOĞLU, MEETHA P. GOULD and THOMAS LAFRAMBOISE | 371 |
| REVERSE ENGINEERING AND SYNTHESIS OF BIOMOLECULAR SYSTEMS |
REVERSE ENGINEERING AND SYNTHESIS OF BIOMOLECULAR SYSTEMS – Session Introduction
GIL ALTEROVITZ, SILVIO CAVALCANTI, TARO M. MUSO, MARCO F. RAMONI and MAY WANG | 383 |
CO-DESIGN IN SYNTHETIC BIOLOGY: A SYSTEM-LEVEL ANALYSIS OF THE DEVELOPMENT OF AN ENVIRONMENTAL SENSING DEVICE
DAVID A. BALL, MATTHEW W. LUX, RUSSELL R. GRAEF, MATTHEW W. PETERSON, JANE D. VALENTI, JOHN DILEO and JEAN PECCOUD | 385 |
CRITICAL ANALYSIS OF TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL REGULATORY NETWORKS IN MULTIPLE MYELOMA
MARTA BIASIOLO, MATTIA FORCATO, LINO POSSAMAI, FRANCESCO FERRARI, LUCA AGNELLI, MARTA LIONETTI, KATIA TODOERTI, ANTONINO NERI, MASSIMO MARCHIORI, STEFANIA BORTOLUZZI and SILVIO BICCIATO | 397 |
A COMPUTATIONAL MODEL OF GENE EXPRESSION IN AN INDUCIBLE SYNTHETIC CIRCUIT
FRANCESCA CERONI, SIMONE FURINI and SILVIO CAVALCANTI | 409 |
RETROVIRUS HTLV-1 GENE CIRCUIT: A POTENTIAL OSCILLATOR FOR EUKARYOTES
ALBERTO CORRADIN, BARBARA DI CAMILLO, FRANCESCA RENDE, VINCENZO CIMINALE, GIANNA MARIA TOFFOLO and CLAUDIO COBELLI | 421 |
EMULSION BASED SELECTION OF T7 PROMOTERS OF VARYING ACTIVITY
ERIC A. DAVIDSON, THOMAS VAN BLARCOM, MATTHEW LEVY and ANDREW D. ELLINGTON | 433 |
CLUSTERING CONTEXT-SPECIFIC GENE REGULATORY NETWORKS
ARCHANA RAMESH, ROBERT TREVINO, DANIEL D. VON HOFF and SEUNGCHAN KIM | 444 |
WRITING AND COMPILING CODE INTO BIOCHEMISTRY
ADAM SHEA, BRIAN FETT, MARC D. RIEDEL and KESHAB PARHI | 456 |
SYNTHESIS OF PHARMACOKINETIC PATHWAYS THROUGH KNOWLEDGE ACQUISITION AND AUTOMATED REASONING
LUIS TARI, SAADAT ANWAR, SHANSHAN LIANG, JÖRG HAKENBERG and CHITTA BARAL | 465 |
| WORKSHOPS |
IN SILICO BIOLOGY
CHRISANTHA T. FERNANDO, RICHARD A. GOLDSTEIN, PHIL HUSBANDS and DOV J. STEKEL | 477 |
GENOMIC STANDARDS CONSORTIUM WORKSHOP: METAGENOMICS, METADATA AND METAANALYSIS (M3)
PETER STERK, LYNETTE HIRSCHMAN, DAWN FIELD and JOHN WOOLEY | 481 |
EXTRACTION OF GENOTYPE-PHENOTYPE-DRUG RELATIONSHIPS FROM TEXT: FROM ENTITY RECOGNITION TO BIOINFORMATICS APPLICATION
ADRIEN COULET, NIGAM SHAH, LAWRENCE HUNTER, CHITTA BARRAL and RUSS B. ALTMAN | 485 |
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