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Committees p. vii
Referees p. ix
Preface p. xi
EXPLORING THE OCEAN'S MICROBES: SEQUENCING THE SEVEN SEAS p. 1
Marvin E. Frazier, Douglas B. Rusch, Aaron L. Halpern, Karla B. Heidelberg, Granger Sutton, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff Hoffman, Charles H. Howard, Cyrus Foote, Brooke A. Dill, Karin Remington, Karen Beeson, Bao Tran, Hamilton Smith, Holly Baden-Tillson, Clare Stewart, Joyce Thorpe, Jason Freemen, Cindy Pfannkoch, Joseph E. Venter, John Heidelberg, Terry Utterback, Yu-Hui Rogers, Shaojie Zhang, Vineet Bafna, Luisa Falcon, Valeria Souza, German Bonilla, Luis E. Eguiarte, David M. Karl, Ken Nealson, Shubha Sathyendranath, Trevor Platt, Eldredge Bermingham, Victor Gallardo, Giselle Tamayo, Robert Friedman, Robert Strausberg, J. Craig Venter
DON'T KNOW MUCH ABOUT PHILOSOPHY: THE CONFUSION OVER BIO-ONTOLOGIES p. 3
Mark A. Musen
BIOMEDICAL INFORMATICS RESEARCH NETWORK (BIRN): BUILDING A NATIONAL COLLABORATORY FOR BIOMEDICAL AND BRAIN RESEARCH p. 5
Mark H. Ellisman
PROTEIN NETWORK COMPARATIVE GENOMICS p. 7
Trey Ideker
SYSTEMS BIOLOGY IN TWO DIMENSIONS: UNDERSTANDING AND ENGINEERING MEMBRANES AS DYNAMICAL SYSTEMS p. 9
Erik Jakobsson
BIOINFORMATICS AT MICROSOFT RESEARCH p. 11
Simon Mercer
MOVIE CRUNCHING IN BIOLOGICAL DYNAMIC IMAGING p. 13
Jean-Christophe Olivo-Marin
ENGINEERING NUCLEIC ACID-BASED MOLECULAR SENSORS FOR PROBING AND PROGRAMMING CELLULAR SYSTEMS p. 15
Christina D. Smolke
REACTOME: A KNOWLEDGEBASE OF BIOLOGICAL PATHWAYS p. 17
Lincoln Stein, Peter D'Eustachio, Gopal Gopinathrao, Marc Gillespie, Lisa Matthews, Guanming Wu, Imre Vastrik, Esther Schmidt, Bernard de Bono, Bijay Jassal, David Croft, Ewan Birney, Suzanna Lewis
EFFECTIVE OPTIMIZATION ALGORITHMS FOR FRAGMENT-ASSEMBLY BASED PROTEIN STRUCTURE PREDICTION p. 19
Kevin W. DeRonne, George Karypis
TRANSMEMBRANE HELIX AND TOPOLOGY PREDICTION USING HIERARCHICAL SVM CLASSIFIERS AND AN ALTERNATING GEOMETRIC SCORING FUNCTION p. 31
Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu
PROTEIN FOLD RECOGNITION USING THE GRADIENT BOOST ALGORITHM p. 43
Feng Jiao, Jinbo Xu, Libo Yu, Dale Schuurmans
A GRAPH-BASED AUTOMATED NMR BACKBONE RESONANCE SEQUENTIAL ASSIGNMENT p. 55
Xiang Wan, Guohui Lin
A DATA-DRIVEN, SYSTEMATIC SEARCH ALGORITHM FOR STRUCTURE DETERMINATION OF DENATURED OR DISORDERED PROTEINS p. 67
Lincong Wang, Bruce Randall Donald
MULTIPLE STRUCTURE ALIGNMENT BY OPTIMAL RMSD IMPLIES THAT THE AVERAGE STRUCTURE IS A CONSENSUS p. 79
Xueyi Wang, Jack Snoeyink
IDENTIFICATION OF α-HELICES FROM LOW RESOLUTION PROTEIN DENSITY MAPS p. 89
A. Dal Palù, J. He, E. Pontelli, Y. Lu
EFFICIENT ANNOTATION OF NON-CODING RNA STRUCTURES INCLUDING PSEUDOKNOTS VIA AUTOMATED FILTERS p. 99
Chunmei Liu, Yinglei Song, Ping Hu, Russell L. Malmberg, Liming Cai
THERMODYNAMIC MATCHERS: STRENGTHENING THE SIGNIFICANCE OF RNA FOLDING ENERGIES p. 111
T. Höchsmann, M. Höchsmann, R. Giegerich
PEM: A GENERAL STATISTICAL APPROACH FOR IDENTIFYING DIFFERENTIALLY EXPRESSED GENES IN TIME-COURSE CDNA MICROARRAY EXPERIMENT WITHOUT REPLICATE p. 123
Xu Han, Wing-Kin Sung, Lin Feng
EFFICIENT GENERALIZED MATRIX APPROXIMATIONS FOR BIOMARKER DISCOVERY AND VISUALIZATION IN GENE EXPRESSION DATA p. 133
Wenyuan Li, Yanxiong Peng, Hung-Chung Huang, Ying Liu
EFFICIENT COMPUTATION OF MINIMUM RECOMBINATION WITH GENOTYPES (NOT HAPLOTYPES) p. 145
Yufeng Wu, Dan Gusfield
SORTING GENOMES BY TRANSLOCATIONS AND DELETIONS p. 157
Xingqin Qi, Guojun Li, Shuguang Li, Ying Xu
TURNING REPEATS TO ADVANTAGE: SCAFFOLDING GENOMIC CONTIGS USING LTR RETROTRANSPOSONS p. 167
A. Kalyanaraman, S. Aluru, P. S. Schnable
WHOLE GENOME COMPOSITION DISTANCE FOR HIV-1 GENOTYPING p. 179
Xiaomeng Wu, Randy Goebel, Xiu-Feng Wan, Guohui Lin
EFFICIENT RECURSIVE LINKING ALGORITHM FOR COMPUTING THE LIKELIHOOD OF AN ORDER OF A LARGE NUMBER OF GENETIC MARKERS p. 191
S. Tewari, S. M. Bhandarkar, J. Arnold
OPTIMAL IMPERFECT PHYLOGENY RECONSTRUCTION AND HAPLOTYPING (IPPH) p. 199
Srinath Sridhar, Guy E. Blelloch, R. Ravi, Russell Schwartz
TOWARD AN ALGEBRAIC UNDERSTANDING OF HAPLOTYPE INFERENCE BY PURE PARSIMONY p. 211
Daniel G. Brown, Ian M. Harrower
GLOBAL CORRELATION ANALYSIS BETWEEN REDUNDANT PROBE SETS USING A LARGE COLLECTION OF ARABIDOPSIS ATH1 EXPRESSION PROFILING DATA p. 223
Xiangqin Cui, Ann Loraine
DISTANCE-BASED IDENTIFICATION OF STRUCTURE MOTIFS IN PROTEINS USING CONSTRAINED FREQUENT SUBGRAPH MINING p. 227
Jun Huan, Deepak Bandyopadhyay, Jan Prins, Jack Snoeyink, Alexander Tropsha, Wei Wang
AN IMPROVED GIBBS SAMPLING METHOD FOR MOTIF DISCOVERY VIA SEQUENCE WEIGHTING p. 239
Xin Chen, Tao Jiang
DETECTION OF CLEAVAGE SITES FOR HIV-1 PROTEASE IN NATIVE PROTEINS p. 249
Liwen You
A METHODOLOGY FOR MOTIF DISCOVERY EMPLOYING ITERATED CLUSTER RE-ASSIGNMENT p. 257
Osman Abul, Finn Drabløs, Geir Kjetil Sandve
IDENTIFYING BIOLOGICAL PATHWAYS VIA PHASE DECOMPOSITION AND PROFILE EXTRACTION p. 269
Yi Zhang, Zhidong Deng
EXPECTATION-MAXIMIZATION ALGORITHMS FOR FUZZY ASSIGNMENT OF GENES TO CELLULAR PATHWAYS p. 281
Liviu Popescu, Golan Yona
CLASSIFICATION OF DROSOPHILA EMBRYONIC DEVELOPMENTAL STAGE RANGE BASED ON GENE EXPRESSION PATTERN IMAGES p. 293
Jieping Ye, Jianhui Chen, Qi Li, Sudhir Kumar
EVOLUTION VERSUS “INTELLIGENT DESIGN”: COMPARING THE TOPOLOGY OF PROTEIN-PROTEIN INTERACTION NETWORKS TO THE INTERNET p. 299
Q. Yang, G. Siganos, M. Faloutsos, S. Lonardi
CAVITY-AWARE MOTIFS REDUCE FALSE POSITIVES IN PROTEIN FUNCTION PREDICTION p. 311
Brian Y. Chen, Drew H. Bryant, Viacheslav Y. Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
PROTEIN SUBCELLULAR LOCALIZATION PREDICTION BASED ON COMPARTMENT-SPECIFIC BIOLOGICAL FEATURES p. 325
Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu
PREDICTING THE BINDING AFFINITY OF MHC CLASS II PEPTIDES p. 331
Fatih Altiparmak, Altuna Akalin, Hakan Ferhatosmanoglu
CODON-BASED DETECTION OF POSITIVE SELECTION CAN BE BIASED BY HETEROGENEOUS DISTRIBUTION OF POLAR AMINO ACIDS ALONG PROTEIN SEQUENCES p. 335
Xuhua Xia, Sudhir Kumar
BAYESIAN DATA INTEGRATION: A FUNCTIONAL PERSPECTIVE p. 341
Curtis Huttenhower, Olga G. Troyanskaya
AN ITERATIVE ALGORITHM TO QUANTIFY THE FACTORS INFLUENCING PEPTIDE FRAGMENTATION FOR MS/MS SPECTRUM p. 353
Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Zhuo Zhang, Runsheng Chen, Dongbo Bu
COMPLEXITY AND SCORING FUNCTION OF MS/MS PEPTIDE DE NOVO SEQUENCING p. 361
Changjiang Xu, Bin Ma
EXPECTATION-MAXIMIZATION METHOD FOR RECONSTRUCTING TUMOR PHYLOGENIES FROM SINGLE-CELL DATA p. 371
G. Pennington, C. A. Smith, S. Shackney, R. Schwartz
SIMULATING IN VITRO EPITHELIAL MORPHOGENESIS IN MULTIPLE ENVIRONMENTS p. 381
M. R. Grant, S. H. J. Kim, C. A. Hunt
A COMBINED DATA MINING APPROACH FOR INFREQUENT EVENTS: ANALYZING HIV MUTATION CHANGES BASED ON TREATMENT HISTORY p. 385
Ray S. Lin, Soo-Yon Rhee, Robert W. Shafer, Amar K. Das
A SYSTEMS BIOLOGY CASE STUDY OF OVARIAN CANCER DRUG RESISTANCE p. 389
Jake Y. Chen, Changyu Shen, Zhong Yan, Dawn P. G. Brown, Mu Wang
Author Index p. 399