15. ISMB / 6. ECCB 2007: Vienna, Austria (Supplement of Bioinformatics)

• ISMB/ECCB 2007. 1-4
  
• ISMB/ECCB 2007 Organization. 5-9
  
• Evrim Acar, Canan Aykut-Bingol, Haluk Bingol, Rasmus Bro, Bülent Yener:
  Multiway analysis of epilepsy tensors. 10-18
  
• Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, Kevin P. Murphy:
  Efficient parameter estimation for RNA secondary structure prediction. 19-28
  
• Sitaram Asur, Duygu Ucar, Srinivasan Parthasarathy:
  An ensemble framework for clustering protein-protein interaction networks. 29-40
  
• William A. Baumgartner Jr., K. Bretonnel Cohen, Lynne M. Fox, George Acquaah-Mensah, Lawrence Hunter:
  Manual curation is not sufficient for annotation of genomic databases. 41-48
  
• Tanya Y. Berger-Wolf, Saad I. Sheikh, Bhaskar DasGupta, Mary V. Ashley, Isabel C. Caballero, Wanpracha Art Chaovalitwongse, Satya Lahari Putrevu:
  Reconstructing sibling relationships in wild populations. 49-56
  
• Kevin Bleakley, Gérard Biau, Jean-Philippe Vert:
  Supervised reconstruction of biological networks with local models. 57-65
  
• Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy:
  Automated image analysis of protein localization in budding yeast. 66-71
  
• Xiaoyu Chen, Timothy R. Hughes, Quaid Morris:
  RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. 72-79
  
• Ho-Ryun Chung, Dennis Kostka, Martin Vingron:
  A physical model for tiling array analysis. 80-86
  
• Miklós Csürös, J. Andrew Holey, Igor B. Rogozin:
  In search of lost introns. 87-96
  
• Xuefeng Cui, Tomás Vinar, Brona Brejová, Dennis Shasha, Ming Li:
  Homology search for genes. 97-103
  
• Samuel A. Danziger, Jue Zeng, Ying Wang, Rainer K. Brachmann, Richard H. Lathrop:
  Choosing where to look next in a mutation sequence space: Active Learning of informative p53 cancer rescue mutants. 104-114
  
• Gihan Dawelbait, Christof Winter, Yanju Zhang, Christian Pilarsky, Robert Grützmann, Jörg-Christian Heinrich, Michael Schroeder:
  Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data. 115-124
  
• Tijl De Bie, Léon-Charles Tranchevent, Liesbeth M. M. van Oeffelen, Yves Moreau:
  Kernel-based data fusion for gene prioritization. 125-132
  
• Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Lodewyk F. A. Wessels, Marcel J. T. Reinders:
  Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes. 133-141
  
• Charlotte M. Deane, Mingqiang Dong, Fabien P. E. Huard, Braddon K. Lance, Graham R. Wood:
  Cotranslational protein folding - fact or fiction? 142-148
  
• Janusz Dutkowski, Jerzy Tiuryn:
  Identification of functional modules from conserved ancestral protein-protein interactions. 149-158
  
• Matthew D. Dyer, T. M. Murali, Bruno W. S. Sobral:
  Computational prediction of host-pathogen protein-protein interactions. 159-166
  
• Jesús K. Estrada-Gil, Juan C. Fernández-López, Enrique Hernández-Lemus, Irma Silva-Zolezzi, Alfredo Hidalgo-Miranda, Gerardo Jiménez-Sánchez, Edgar E. Vallejo-Clemente:
  GPDTI: A Genetic Programming Decision Tree Induction method to find epistatic effects in common complex diseases. 167-174
  
• Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar:
  Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. 175-184
  
• Ivelin Georgiev, Bruce Randall Donald:
  Dead-End Elimination with Backbone Flexibility. 185-194
  
• Stefan Gräf, Fiona G. G. Nielsen, Stefan Kurtz, Martijn A. Huynen, Ewan Birney, Henk Stunnenberg, Paul Flicek:
  Optimized design and assessment of whole genome tiling arrays. 195-204
  
• Michelle L. Green, Peter D. Karp:
  Using genome-context data to identify specific types of functional associations in pathway/genome databases. 205-211
  
• Jim C. Huang, Anitha Kannan, John M. Winn:
  Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations. 212-221
  
• Yu Huang, Haifeng Li, Haiyan Hu, Xifeng Yan, Michael S. Waterman, Haiyan Huang, Xianghong Jasmine Zhou:
  Systematic discovery of functional modules and context-specific functional annotation of human genome. 222-229
  
• Wataru Iwasaki, Toshihisa Takagi:
  Reconstruction of highly heterogeneous gene-content evolution across the three domains of life. 230-239
  
• Etai Jacob, Amnon Horovitz, Ron Unger:
  Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study. 240-248
  
• Miriam R. Kantorovitz, Gene E. Robinson, Saurabh Sinha:
  A statistical method for alignment-free comparison of regulatory sequences. 249-255
  
• Jee-Hyub Kim, Alex Mitchell, Teresa K. Attwood, Melanie Hilario:
  Learning to extract relations for protein annotation. 256-263
  
• Corinna Kolárik, Martin Hofmann-Apitius, Marc Zimmermann, Juliane Fluck:
  Identification of new drug classification terms in textual resources. 264-272
  
• Eva Lange, Clemens Gröpl, Ole Schulz-Trieglaff, Andreas Leinenbach, Christian G. Huber, Knut Reinert:
  A geometric approach for the alignment of liquid chromatography - mass spectrometry data. 273-281
  
• Wei Keat Lim, Kai Wang, Céline Lefebvre, Andrea Califano:
  Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. 282-288
  
• Gerton Lunter:
  Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes. 289-296
  
• Shaun Mahony, Philip E. Auron, Panayiotis V. Benos:
  Inferring protein-DNA dependencies using motif alignments and mutual information. 297-304
  
• Florian Markowetz, Dennis Kostka, Olga G. Troyanskaya, Rainer Spang:
  Nested effects models for high-dimensional phenotyping screens. 305-312
  
• Tristan Mary-Huard, Jean-Jacques Daudin, Michela Baccini, Annibale Biggeri, Avner Bar-Hen:
  Biases induced by pooling samples in microarray experiments. 313-318
  
• Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, Tal Pupko:
  Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. 319-327
  
• Sean McIlwain, David Page, Edward L. Huttlin, Michael R. Sussman:
  Using dynamic programming to create isotopic distribution maps from mass spectra. 328-336
  
• Chris Mungall, David B. Emmert:
  A Chado case study: an ontology-based modular schema for representing genome-associated biological information. 337-346
  
• Yanay Ofran, Venkatesh Mysore, Burkhard Rost:
  Prediction of DNA-binding residues from sequence. 347-353
  
• Jung Hun Ohn, Jihun Kim, Ju Han Kim:
  Genomic characterization of perturbation sensitivity. 354-358
  
• Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan:
  SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. 359-366
  
• Yue Pan, Tim Durfee, Joseph Bockhorst, Mark Craven:
  Connecting quantitative regulatory-network models to the genome. 367-376
  
• Jayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, Ananth Grama:
  Functional annotation of regulatory pathways. 377-386
  
• Frank 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:
  SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. 387-391
  
• Janina Reeder, Jens Reeder, Robert Giegerich:
  Locomotif: from graphical motif description to RNA motif search. 392-400
  
• Adam Roberts, Leonard McMillan, Wei Wang, Joel Parker, Ivan Rusyn, David Threadgill:
  Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. 401-407
  
• Romain Rossi, Mathieu Isorce, Sandy Morin, Julien Flocard, Karthik Arumugam, Serge Crouzy, Michel Vivaudou, Stephane Redon:
  Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design. 408-417
  
• Yvan Saeys, Thomas Abeel, Sven Degroeve, Yves Van de Peer:
  Translation initiation site prediction on a genomic scale: beauty in simplicity. 418-423
  
• Olivia Sanchez-Graillet, Massimo Poesio:
  Negation of protein-protein interactions: analysis and extraction. 424-432
  
• David Sankoff, Chunfang Zheng, Qian Zhu:
  Polyploids, genome halving and phylogeny. 433-439
  
• Liat Segal, Michal Lapidot, Zach Solan, Eytan Ruppin, Yitzhak Pilpel, David Horn:
  Nucleotide variation of regulatory motifs may lead to distinct expression patterns. 440-449
  
• Sohrab P. Shah, Wan L. Lam, Raymond T. Ng, Kevin P. Murphy:
  Modeling recurrent DNA copy number alterations in array CGH data. 450-458
  
• Yanxin Shi, Michael Klustein, Itamar Simon, Tom Mitchell, Ziv Bar-Joseph:
  Continuous hidden process model for time series expression experiments. 459-467
  
• Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka:
  Annotating gene function by combining expression data with a modular gene network. 468-478
  
• Kyung-Ah Sohn, Eric P. Xing:
  Spectrum: joint bayesian inference of population structure and recombination events. 479-489
  
• Le Song, Justin Bedo, Karsten M. Borgwardt, Arthur Gretton, Alexander J. Smola:
  Gene selection via the BAHSIC family of algorithms. 490-498
  
• Xiaoyun Sun, Pengyu Hong:
  Computational modeling of Caenorhabditis elegans vulval induction. 499-507
  
• 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:
  From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. 508-518
  
• Marko Sysi-Aho, Aki Vehtari, Vidya R. Velagapudi, Jukka Westerbacka, Laxman Yetukuri, Robert Bergholm, Marja-Riitta Taskinen, Hannele Yki-Järvinen, Matej Oresic:
  Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles. 519-528
  
• Ying Tao, Lee T. Sam, Jianrong Li, Carol Friedman, Yves A. Lussier:
  Information theory applied to the sparse gene ontology annotation network to predict novel gene function. 529-538
  
• Lydia Tapia, Xinyu Tang, Shawna L. Thomas, Nancy M. Amato:
  Kinetics analysis methods for approximate folding landscapes. 539-548
  
• Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev:
  Automatic genome-wide reconstruction of phylogenetic gene trees. 549-558
  
• Travis J. Wheeler, John D. Kececioglu:
  Multiple alignment by aligning alignments. 559-568
  
• Song Wu, Jie Yang, Rongling Wu:
  Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics. 569-576
  
• Xifeng Yan, Michael R. Mehan, Yu Huang, Michael S. Waterman, Philip S. Yu, Xianghong Jasmine Zhou:
  A graph-based approach to systematically reconstruct human transcriptional regulatory modules. 577-586
  

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