Table of Contents

• ISMB/ECCB 20071-4 [doi]
• ISMB/ECCB 2007 Organization5-9 [doi]
• Multiway analysis of epilepsy tensorsEvrim Acar, Canan Aykut-Bingol, Haluk Bingol, Rasmus Bro, Bülent Yener. 10-18 [doi]
• Efficient parameter estimation for RNA secondary structure predictionMirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy. 19-28 [doi]
• An ensemble framework for clustering protein-protein interaction networksSitaram Asur, Duygu Ucar, Srinivasan Parthasarathy. 29-40 [doi]
• Manual curation is not sufficient for annotation of genomic databasesWilliam A. Baumgartner Jr., K. Bretonnel Cohen, Lynne M. Fox, George Acquaah-Mensah, Lawrence Hunter. 41-48 [doi]
• Reconstructing sibling relationships in wild populationsTanya Y. Berger-Wolf, Saad I. Sheikh, Bhaskar DasGupta, Mary V. Ashley, Isabel C. Caballero, Wanpracha Art Chaovalitwongse, Satya Lahari Putrevu. 49-56 [doi]
• Supervised reconstruction of biological networks with local modelsKevin Bleakley, Gérard Biau, Jean-Philippe Vert. 57-65 [doi]
• Automated image analysis of protein localization in budding yeastShann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy. 66-71 [doi]
• RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factorsXiaoyu Chen, Timothy R. Hughes, Quaid Morris. 72-79 [doi]
• A physical model for tiling array analysisHo-Ryun Chung, Dennis Kostka, Martin Vingron. 80-86 [doi]
• In search of lost intronsMiklós Csürös, J. Andrew Holey, Igor B. Rogozin. 87-96 [doi]
• Homology search for genesXuefeng Cui, Tomás Vinar, Brona Brejová, Dennis Shasha, Ming Li. 97-103 [doi]
• Choosing where to look next in a mutation sequence space: Active Learning of informative p53 cancer rescue mutantsSamuel A. Danziger, Jue Zeng, Ying Wang, Rainer K. Brachmann, Richard H. Lathrop. 104-114 [doi]
• Structural templates predict novel protein interactions and targets from pancreas tumour gene expression dataGihan Dawelbait, Christof Winter, Yanju Zhang, Christian Pilarsky, Robert Grützmann, Jörg-Christian Heinrich, Michael Schroeder. 115-124 [doi]
• Kernel-based data fusion for gene prioritizationTijl De Bie, Léon-Charles Tranchevent, Liesbeth M. M. van Oeffelen, Yves Moreau. 125-132 [doi]
• Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenesJeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Lodewyk F. A. Wessels, Marcel J. T. Reinders. 133-141 [doi]
• Cotranslational protein folding - fact or fiction?Charlotte M. Deane, Mingqiang Dong, Fabien P. E. Huard, Braddon K. Lance, Graham R. Wood. 142-148 [doi]
• Identification of functional modules from conserved ancestral protein-protein interactionsJanusz Dutkowski, Jerzy Tiuryn. 149-158 [doi]
• Computational prediction of host-pathogen protein-protein interactionsMatthew D. Dyer, T. M. Murali, Bruno W. S. Sobral. 159-166 [doi]
• GPDTI: A Genetic Programming Decision Tree Induction method to find epistatic effects in common complex diseasesJesús K. Estrada-Gil, Juan C. Fernández-López, Enrique Hernández-Lemus, Irma Silva-Zolezzi, Alfredo Hidalgo-Miranda, Gerardo Jiménez-Sánchez, Edgar E. Vallejo-Clemente. 167-174 [doi]
• Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network modelsEran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar. 175-184 [doi]
• Dead-End Elimination with Backbone FlexibilityIvelin Georgiev, Bruce Randall Donald. 185-194 [doi]
• Optimized design and assessment of whole genome tiling arraysStefan Gräf, Fiona G. G. Nielsen, Stefan Kurtz, Martijn A. Huynen, Ewan Birney, Henk Stunnenberg, Paul Flicek. 195-204 [doi]
• Using genome-context data to identify specific types of functional associations in pathway/genome databasesMichelle L. Green, Peter D. Karp. 205-211 [doi]
• Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populationsJim C. Huang, Anitha Kannan, John M. Winn. 212-221 [doi]
• Systematic discovery of functional modules and context-specific functional annotation of human genomeYu Huang 0003, Haifeng Li, Haiyan Hu, Xifeng Yan, Michael S. Waterman, Haiyan Huang, Xianghong Jasmine Zhou. 222-229 [doi]
• Reconstruction of highly heterogeneous gene-content evolution across the three domains of lifeWataru Iwasaki, Toshihisa Takagi. 230-239 [doi]
• Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice studyEtai Jacob, Amnon Horovitz, Ron Unger. 240-248 [doi]
• A statistical method for alignment-free comparison of regulatory sequencesMiriam R. Kantorovitz, Gene E. Robinson, Saurabh Sinha. 249-255 [doi]
• Learning to extract relations for protein annotationJee-Hyub Kim, Alex Mitchell, Teresa K. Attwood, Melanie Hilario. 256-263 [doi]
• Identification of new drug classification terms in textual resourcesCorinna Kolárik, Martin Hofmann-Apitius, Marc Zimmermann, Juliane Fluck. 264-272 [doi]
• A geometric approach for the alignment of liquid chromatography - mass spectrometry dataEva Lange, Clemens Gröpl, Ole Schulz-Trieglaff, Andreas Leinenbach, Christian G. Huber, Knut Reinert. 273-281 [doi]
• Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networksWei Keat Lim, Kai Wang, Céline Lefebvre, Andrea Califano. 282-288 [doi]
• Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomesGerton Lunter. 289-296 [doi]
• Inferring protein-DNA dependencies using motif alignments and mutual informationShaun Mahony, Philip E. Auron, Panayiotis V. Benos. 297-304 [doi]
• Nested effects models for high-dimensional phenotyping screensFlorian Markowetz, Dennis Kostka, Olga G. Troyanskaya, Rainer Spang. 305-312 [doi]
• Biases induced by pooling samples in microarray experimentsTristan Mary-Huard, Jean-Jacques Daudin, Michela Baccini, Annibale Biggeri, Avner Bar-Hen. 313-318 [doi]
• Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous ratesItay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko. 319-327 [doi]
• Using dynamic programming to create isotopic distribution maps from mass spectraSean McIlwain, David Page, Edward L. Huttlin, Michael R. Sussman. 328-336 [doi]
• A Chado case study: an ontology-based modular schema for representing genome-associated biological informationChris Mungall, David B. Emmert. 337-346 [doi]
• Prediction of DNA-binding residues from sequenceYanay Ofran, Venkatesh Mysore, Burkhard Rost. 347-353 [doi]
• Genomic characterization of perturbation sensitivityJung Hun Ohn, Jihun Kim, Ju Han Kim. 354-358 [doi]
• SPINE: a framework for signaling-regulatory pathway inference from cause-effect experimentsOved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan. 359-366 [doi]
• Connecting quantitative regulatory-network models to the genomeYue Pan, Tim Durfee, Joseph Bockhorst, Mark Craven. 367-376 [doi]
• Functional annotation of regulatory pathwaysJayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, Ananth Grama. 377-386 [doi]
• SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotationFrank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob Hull Havgaard, Søren Brunak, Merete Fredholm, Christian Bendixen. 387-391 [doi]
• Locomotif: from graphical motif description to RNA motif searchJanina Reeder, Jens Reeder, Robert Giegerich. 392-400 [doi]
• Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windowsAdam Roberts, Leonard McMillan, Wei Wang 0010, Joel Parker, Ivan Rusyn, David Threadgill. 401-407 [doi]
• Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and designRomain Rossi, Mathieu Isorce, Sandy Morin, Julien Flocard, Karthik Arumugam, Serge Crouzy, Michel Vivaudou, Stephane Redon. 408-417 [doi]
• Translation initiation site prediction on a genomic scale: beauty in simplicityYvan Saeys, Thomas Abeel, Sven Degroeve, Yves Van de Peer. 418-423 [doi]
• Negation of protein-protein interactions: analysis and extractionOlivia Sanchez-Graillet, Massimo Poesio. 424-432 [doi]
• Polyploids, genome halving and phylogenyDavid Sankoff, Chunfang Zheng, Qian Zhu. 433-439 [doi]
• Nucleotide variation of regulatory motifs may lead to distinct expression patternsLiat Segal, Michal Lapidot, Zach Solan, Eytan Ruppin, Yitzhak Pilpel, David Horn. 440-449 [doi]
• Modeling recurrent DNA copy number alterations in array CGH dataSohrab P. Shah, Wan L. Lam, Raymond T. Ng, Kevin P. Murphy. 450-458 [doi]
• Continuous hidden process model for time series expression experimentsYanxin Shi, Michael Klustein, Itamar Simon, Tom Mitchell, Ziv Bar-Joseph. 459-467 [doi]
• Annotating gene function by combining expression data with a modular gene networkMotoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka. 468-478 [doi]
• ::::Spectrum::::: joint bayesian inference of population structure and recombination eventsKyung-Ah Sohn, Eric P. Xing. 479-489 [doi]
• Gene selection via the BAHSIC family of algorithmsLe Song, Justin Bedo, Karsten M. Borgwardt, Arthur Gretton, Alexander J. Smola. 490-498 [doi]
• Computational modeling of ::::Caenorhabditis elegans:::: vulval inductionXiaoyun Sun, Pengyu Hong. 499-507 [doi]
• From protein microarrays to diagnostic antigen discovery: a study of the pathogen ::::Francisella tularensis::::Suman Sundaresh, Arlo Z. Randall, Berkay Unal, Jeannine M. Petersen, John T. Belisle, M. Gill Hartley, Melanie Duffield, Richard W. Titball, D. Huw Davies, Philip L. Felgner, Pierre Baldi. 508-518 [doi]
• Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profilesMarko Sysi-Aho, Aki Vehtari, Vidya R. Velagapudi, Jukka Westerbacka, Laxman Yetukuri, Robert Bergholm, Marja-Riitta Taskinen, Hannele Yki-Järvinen, Matej Oresic. 519-528 [doi]
• Information theory applied to the sparse gene ontology annotation network to predict novel gene functionYing Tao, Lee T. Sam, Jianrong Li, Carol Friedman, Yves A. Lussier. 529-538 [doi]
• Kinetics analysis methods for approximate folding landscapesLydia Tapia, Xinyu Tang, Shawna L. Thomas, Nancy M. Amato. 539-548 [doi]
• Automatic genome-wide reconstruction of phylogenetic gene treesIlan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev. 549-558 [doi]
• Multiple alignment by aligning alignmentsTravis J. Wheeler, John D. Kececioglu. 559-568 [doi]
• Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamicsSong Wu, Jie Yang, Rongling Wu. 569-576 [doi]
• A graph-based approach to systematically reconstruct human transcriptional regulatory modulesXifeng Yan, Michael R. Mehan, Yu Huang 0003, Michael S. Waterman, Philip S. Yu, Xianghong Jasmine Zhou. 577-586 [doi]