Bioinformatics -- Table of Contents (23 [13])

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Contents: Volume 23, Number 13, July 2007   [Index by Author]

ISMB/ECCB 2007 CONFERENCE PROCEEDINGS 21-25 JULY 2007, VIENNA

     EDITORIALS

     ORIGINAL PAPERS

ORIGINAL PAPERS

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     STRUCTURAL BIOINFORMATICS

     GENE EXPRESSION

     SYSTEMS BIOLOGY

     DATA AND TEXT MINING

     DATABASES AND ONTOLOGIES

APPLICATIONS NOTES

     GENOME ANALYSIS

     SEQUENCE ANALYSIS

     STRUCTURAL BIOINFORMATICS

     GENE EXPRESSION

     SYSTEMS BIOLOGY

     DATABASES AND ONTOLOGIES

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ISMB/ECCB 2007 CONFERENCE PROCEEDINGS 21-25 JULY 2007, VIENNA

EDITORIALS

: ISMB/ECCB 2007
Bioinformatics 2007 23: i1-i4; doi:10.1093/bioinformatics/btm285 [Extract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

: ISMB/ECCB 2007 Organization
Bioinformatics 2007 23: i5-i9; doi:10.1093/bioinformatics/btm286 [Extract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

ORIGINAL PAPERS

Get checked abstract Evrim Acar, Canan Aykut-Bingol, Haluk Bingol, Rasmus Bro, and Bülent Yener: Multiway analysis of epilepsy tensors
Bioinformatics 2007 23: i10-i18; doi:10.1093/bioinformatics/btm210 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Mirela Andronescu, Anne Condon, Holger H. Hoos, David H. Mathews, and Kevin P. Murphy: Efficient parameter estimation for RNA secondary structure prediction
Bioinformatics 2007 23: i19-i28; doi:10.1093/bioinformatics/btm223 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Sitaram Asur, Duygu Ucar, and Srinivasan Parthasarathy: An ensemble framework for clustering protein–protein interaction networks
Bioinformatics 2007 23: i29-i40; doi:10.1093/bioinformatics/btm212 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract William A. Baumgartner, Jr, K. Bretonnel Cohen, Lynne M. Fox, George Acquaah-Mensah, and Lawrence Hunter: Manual curation is not sufficient for annotation of genomic databases
Bioinformatics 2007 23: i41-i48; doi:10.1093/bioinformatics/btm229 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Tanya Y. Berger-Wolf, Saad I. Sheikh, Bhaskar DasGupta, Mary V. Ashley, Isabel C. Caballero, Wanpracha Chaovalitwongse, and S. Lahari Putrevu: Reconstructing sibling relationships in wild populations
Bioinformatics 2007 23: i49-i56; doi:10.1093/bioinformatics/btm219 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Kevin Bleakley, Gérard Biau, and Jean-Philippe Vert: Supervised reconstruction of biological networks with local models
Bioinformatics 2007 23: i57-i65; doi:10.1093/bioinformatics/btm204 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, and Robert F. Murphy: Automated image analysis of protein localization in budding yeast
Bioinformatics 2007 23: i66-i71; doi:10.1093/bioinformatics/btm206 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Xiaoyu Chen, Timothy R. Hughes, and Quaid Morris: RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors
Bioinformatics 2007 23: i72-i79; doi:10.1093/bioinformatics/btm224 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Ho-Ryun Chung, Dennis Kostka, and Martin Vingron: A physical model for tiling array analysis
Bioinformatics 2007 23: i80-i86; doi:10.1093/bioinformatics/btm167 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Miklós Csurös, J. Andrew Holey, and Igor B. Rogozin: In search of lost introns
Bioinformatics 2007 23: i87-i96; doi:10.1093/bioinformatics/btm190 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Xuefeng Cui, Tomás Vinar, Brona Brejová, Dennis Shasha, and Ming Li: Homology search for genes
Bioinformatics 2007 23: i97-i103; doi:10.1093/bioinformatics/btm225 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Samuel A. Danziger, Jue Zeng, Ying Wang, Rainer K. Brachmann, and Richard H. Lathrop: Choosing where to look next in a mutation sequence space: Active Learning of informative p53 cancer rescue mutants
Bioinformatics 2007 23: i104-i114; doi:10.1093/bioinformatics/btm166 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Gihan Dawelbait, Christof Winter, Yanju Zhang, Christian Pilarsky, Robert Grützmann, Jörg-Christian Heinrich, and Michael Schroeder: Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data
Bioinformatics 2007 23: i115-i124; doi:10.1093/bioinformatics/btm188 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Tijl De Bie, Léon-Charles Tranchevent, Liesbeth M. M. van Oeffelen, and Yves Moreau: Kernel-based data fusion for gene prioritization
Bioinformatics 2007 23: i125-i132; doi:10.1093/bioinformatics/btm187 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Lodewyk Wessels, and Marcel Reinders: Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes
Bioinformatics 2007 23: i133-i141; doi:10.1093/bioinformatics/btm202 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Charlotte M. Deane, Mingqiang Dong, Fabien P.E. Huard, Braddon K. Lance, and Graham R. Wood: Cotranslational protein folding—fact or fiction?
Bioinformatics 2007 23: i142-i148; doi:10.1093/bioinformatics/btm175 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Janusz Dutkowski and Jerzy Tiuryn: Identification of functional modules from conserved ancestral protein–protein interactions
Bioinformatics 2007 23: i149-i158; doi:10.1093/bioinformatics/btm194 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral: Computational prediction of host-pathogen protein–protein interactions
Bioinformatics 2007 23: i159-i166; doi:10.1093/bioinformatics/btm208 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Jesús K. Estrada-Gil, Juan C. Fernández-López, Enrique Hernández-Lemus, Irma Silva-Zolezzi, Alfredo Hidalgo-Miranda, Gerardo Jiménez-Sánchez, and Edgar E. Vallejo-Clemente: GPDTI: A Genetic Programming Decision Tree Induction method to find epistatic effects in common complex diseases
Bioinformatics 2007 23: i167-i174; doi:10.1093/bioinformatics/btm205 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, and Ivet Bahar: Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models
Bioinformatics 2007 23: i175-i184; doi:10.1093/bioinformatics/btm186 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data] OPEN ACCESS ARTICLE

Get checked abstract Ivelin Georgiev and Bruce R. Donald: Dead-End Elimination with Backbone Flexibility
Bioinformatics 2007 23: i185-i194; doi:10.1093/bioinformatics/btm197 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Stefan Gräf, Fiona G. G. Nielsen, Stefan Kurtz, Martijn A. Huynen, Ewan Birney, Henk Stunnenberg, and Paul Flicek: Optimized design and assessment of whole genome tiling arrays
Bioinformatics 2007 23: i195-i204; doi:10.1093/bioinformatics/btm200 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Michelle L. Green and Peter D. Karp: Using genome-context data to identify specific types of functional associations in pathway/genome databases
Bioinformatics 2007 23: i205-i211; doi:10.1093/bioinformatics/btm213 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Jim C. Huang, Anitha Kannan, and John Winn: Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations
Bioinformatics 2007 23: i212-i221; doi:10.1093/bioinformatics/btm217 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Yu Huang, Haifeng Li, Haiyan Hu, Xifeng Yan, Michael S. Waterman, Haiyan Huang, and Xianghong Jasmine Zhou: Systematic discovery of functional modules and context-specific functional annotation of human genome
Bioinformatics 2007 23: i222-i229; doi:10.1093/bioinformatics/btm222 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Wataru Iwasaki and Toshihisa Takagi: Reconstruction of highly heterogeneous gene-content evolution across the three domains of life
Bioinformatics 2007 23: i230-i239; doi:10.1093/bioinformatics/btm165 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Etai Jacob, Amnon Horovitz, and Ron Unger: Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study
Bioinformatics 2007 23: i240-i248; doi:10.1093/bioinformatics/btm180 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Miriam R. Kantorovitz, Gene E. Robinson, and Saurabh Sinha: A statistical method for alignment-free comparison of regulatory sequences
Bioinformatics 2007 23: i249-i255; doi:10.1093/bioinformatics/btm211 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Jee-Hyub Kim, Alex Mitchell, Teresa K. Attwood, and Melanie Hilario: Learning to extract relations for protein annotation
Bioinformatics 2007 23: i256-i263; doi:10.1093/bioinformatics/btm168 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Corinna Kolárik, Martin Hofmann-Apitius, Marc Zimmermann, and Juliane Fluck: Identification of new drug classification terms in textual resources
Bioinformatics 2007 23: i264-i272; doi:10.1093/bioinformatics/btm196 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Eva Lange, Clemens Gröpl, Ole Schulz-Trieglaff, Andreas Leinenbach, Christian Huber, and Knut Reinert: A geometric approach for the alignment of liquid chromatography—mass spectrometry data
Bioinformatics 2007 23: i273-i281; doi:10.1093/bioinformatics/btm209 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Wei Keat Lim, Kai Wang, Celine Lefebvre, and Andrea Califano: Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks
Bioinformatics 2007 23: i282-i288; doi:10.1093/bioinformatics/btm201 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Gerton Lunter: Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes
Bioinformatics 2007 23: i289-i296; doi:10.1093/bioinformatics/btm185 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Shaun Mahony, Philip E. Auron, and Panayiotis V. Benos: Inferring protein–DNA dependencies using motif alignments and mutual information
Bioinformatics 2007 23: i297-i304; doi:10.1093/bioinformatics/btm215 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Florian Markowetz, Dennis Kostka, Olga G. Troyanskaya, and Rainer Spang: Nested effects models for high-dimensional phenotyping screens
Bioinformatics 2007 23: i305-i312; doi:10.1093/bioinformatics/btm178 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Tristan Mary-Huard, Jean-Jacques Daudin, Michela Baccini, Annibale Biggeri, and Avner Bar-Hen: Biases induced by pooling samples in microarray experiments
Bioinformatics 2007 23: i313-i318; doi:10.1093/bioinformatics/btm182 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach, and Tal Pupko: Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates
Bioinformatics 2007 23: i319-i327; doi:10.1093/bioinformatics/btm176 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Sean McIlwain, David Page, Edward L. Huttlin, and Michael R. Sussman: Using dynamic programming to create isotopic distribution maps from mass spectra
Bioinformatics 2007 23: i328-i336; doi:10.1093/bioinformatics/btm198 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Christopher J. Mungall, David B. Emmert, and The FlyBase Consortium: A Chado case study: an ontology-based modular schema for representing genome-associated biological information
Bioinformatics 2007 23: i337-i346; doi:10.1093/bioinformatics/btm189 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Yanay Ofran, Venkatesh Mysore, and Burkhard Rost: Prediction of DNA-binding residues from sequence
Bioinformatics 2007 23: i347-i353; doi:10.1093/bioinformatics/btm174 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Jung Hun Ohn, Jihun Kim, and Ju Han Kim: Genomic characterization of perturbation sensitivity
Bioinformatics 2007 23: i354-i358; doi:10.1093/bioinformatics/btm172 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, and Roded Sharan: SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
Bioinformatics 2007 23: i359-i366; doi:10.1093/bioinformatics/btm170 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Yue Pan, Tim Durfee, Joseph Bockhorst, and Mark Craven: Connecting quantitative regulatory-network models to the genome
Bioinformatics 2007 23: i367-i376; doi:10.1093/bioinformatics/btm228 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Jayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, and Ananth Grama: Functional annotation of regulatory pathways
Bioinformatics 2007 23: i377-i386; doi:10.1093/bioinformatics/btm203 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract 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 H. Havgaard, Søren Brunak, Merete Fredholm, and Christian Bendixen: SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation
Bioinformatics 2007 23: i387-i391; doi:10.1093/bioinformatics/btm192 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Janina Reeder, Jens Reeder, and Robert Giegerich: Locomotif: from graphical motif description to RNA motif search
Bioinformatics 2007 23: i392-i400; doi:10.1093/bioinformatics/btm179 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Adam Roberts, Leonard McMillan, Wei Wang, Joel Parker, Ivan Rusyn, and David Threadgill: Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows
Bioinformatics 2007 23: i401-i407; doi:10.1093/bioinformatics/btm220 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Romain Rossi, Mathieu Isorce, Sandy Morin, Julien Flocard, Karthik Arumugam, Serge Crouzy, Michel Vivaudou, and Stephane Redon: Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design
Bioinformatics 2007 23: i408-i417; doi:10.1093/bioinformatics/btm191 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Yvan Saeys, Thomas Abeel, Sven Degroeve, and Yves Van de Peer: Translation initiation site prediction on a genomic scale: beauty in simplicity
Bioinformatics 2007 23: i418-i423; doi:10.1093/bioinformatics/btm177 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Olivia Sanchez-Graillet and Massimo Poesio: Negation of protein–protein interactions: analysis and extraction
Bioinformatics 2007 23: i424-i432; doi:10.1093/bioinformatics/btm184 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract David Sankoff, Chunfang Zheng, and Qian Zhu: Polyploids, genome halving and phylogeny
Bioinformatics 2007 23: i433-i439; doi:10.1093/bioinformatics/btm169 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Liat Segal, Michal Lapidot, Zach Solan, Eytan Ruppin, Yitzhak Pilpel, and David Horn: Nucleotide variation of regulatory motifs may lead to distinct expression patterns
Bioinformatics 2007 23: i440-i449; doi:10.1093/bioinformatics/btm183 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Sohrab P. Shah, Wan L. Lam, Raymond T. Ng, and Kevin P. Murphy: Modeling recurrent DNA copy number alterations in array CGH data
Bioinformatics 2007 23: i450-i458; doi:10.1093/bioinformatics/btm221 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Yanxin Shi, Michael Klustein, Itamar Simon, Tom Mitchell, and Ziv Bar-Joseph: Continuous hidden process model for time series expression experiments
Bioinformatics 2007 23: i459-i467; doi:10.1093/bioinformatics/btm218 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Motoki Shiga, Ichigaku Takigawa, and Hiroshi Mamitsuka: Annotating gene function by combining expression data with a modular gene network
Bioinformatics 2007 23: i468-i478; doi:10.1093/bioinformatics/btm173 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Kyung-Ah Sohn and Eric P. Xing: Spectrum: joint bayesian inference of population structure and recombination events
Bioinformatics 2007 23: i479-i489; doi:10.1093/bioinformatics/btm171 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Le Song, Justin Bedo, Karsten M. Borgwardt, Arthur Gretton, and Alex Smola: Gene selection via the BAHSIC family of algorithms
Bioinformatics 2007 23: i490-i498; doi:10.1093/bioinformatics/btm216 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Xiaoyun Sun and Pengyu Hong: Computational modeling of Caenorhabditis elegans vulval induction
Bioinformatics 2007 23: i499-i507; doi:10.1093/bioinformatics/btm214 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Suman Sundaresh, Arlo Randall, Berkay Unal, Jeannine M. Petersen, John T. Belisle, M. Gill Hartley, Melanie Duffield, Richard W. Titball, D. Huw Davies, Philip L. Felgner, and Pierre Baldi: From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis
Bioinformatics 2007 23: i508-i518; doi:10.1093/bioinformatics/btm207 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] OPEN ACCESS ARTICLE

Get checked abstract Marko Sysi-Aho, Aki Vehtari, Vidya R. Velagapudi, Jukka Westerbacka, Laxman Yetukuri, Robert Bergholm, Marja-Riitta Taskinen, Hannele Yki-Järvinen, and Matej Oresic: Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles
Bioinformatics 2007 23: i519-i528; doi:10.1093/bioinformatics/btm181 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Ying Tao, Lee Sam, Jianrong Li, Carol Friedman, and Yves A. Lussier: Information theory applied to the sparse gene ontology annotation network to predict novel gene function
Bioinformatics 2007 23: i529-i538; doi:10.1093/bioinformatics/btm195 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Lydia Tapia, Xinyu Tang, Shawna Thomas, and Nancy M. Amato: Kinetics analysis methods for approximate folding landscapes
Bioinformatics 2007 23: i539-i548; doi:10.1093/bioinformatics/btm199 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Ilan Wapinski, Avi Pfeffer, Nir Friedman, and Aviv Regev: Automatic genome-wide reconstruction of phylogenetic gene trees
Bioinformatics 2007 23: i549-i558; doi:10.1093/bioinformatics/btm193 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Travis J. Wheeler and John D. Kececioglu: Multiple alignment by aligning alignments
Bioinformatics 2007 23: i559-i568; doi:10.1093/bioinformatics/btm226 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Song Wu, Jie Yang, and Rongling Wu: Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics
Bioinformatics 2007 23: i569-i576; doi:10.1093/bioinformatics/btm164 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

Get checked abstract Xifeng Yan, Michael R. Mehan, Yu Huang, Michael S. Waterman, Philip S. Yu, and Xianghong Jasmine Zhou: A graph-based approach to systematically reconstruct human transcriptional regulatory modules
Bioinformatics 2007 23: i577-i586; doi:10.1093/bioinformatics/btm227 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Daniel C. Richter, Stephan C. Schuster, and Daniel H. Huson: OSLay: optimal syntenic layout of unfinished assemblies
Bioinformatics Advance Access published on April 26, 2007
Bioinformatics 2007 23: 1573-1579; doi:10.1093/bioinformatics/btm153 [Abstract] [Full Text] [Print PDF] [Request Permissions]

SEQUENCE ANALYSIS

Get checked abstract Bruno A. Gaëta, Harald R. Malming, Katherine J.L. Jackson, Michael E. Bain, Patrick Wilson, and Andrew M. Collins: iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences
Bioinformatics Advance Access published on April 26, 2007
Bioinformatics 2007 23: 1580-1587; doi:10.1093/bioinformatics/btm147 [Abstract] [Full Text] [Print PDF] [Request Permissions]

STRUCTURAL BIOINFORMATICS

Get checked abstract Hisanori Kiryu, Yasuo Tabei, Taishin Kin, and Kiyoshi Asai: Murlet: a practical multiple alignment tool for structural RNA sequences
Bioinformatics Advance Access published on April 25, 2007
Bioinformatics 2007 23: 1588-1598; doi:10.1093/bioinformatics/btm146 [Abstract] [FREE Full Text] [Print PDF] OPEN ACCESS ARTICLE

GENE EXPRESSION

Get checked abstract Irit Fishel, Alon Kaufman, and Eytan Ruppin: Meta-analysis of gene expression data: a predictor-based approach
Bioinformatics Advance Access published on April 26, 2007
Bioinformatics 2007 23: 1599-1606; doi:10.1093/bioinformatics/btm149 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Vasyl Pihur, Susmita Datta, and Somnath Datta: Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach
Bioinformatics Advance Access published on May 5, 2007
Bioinformatics 2007 23: 1607-1615; doi:10.1093/bioinformatics/btm158 [Abstract] [Full Text] [Print PDF] [Request Permissions]

SYSTEMS BIOLOGY

Get checked abstract R. Guimerà, M. Sales-Pardo, and L.A.N. Amaral: A network-based method for target selection in metabolic networks
Bioinformatics Advance Access published on April 26, 2007
Bioinformatics 2007 23: 1616-1622; doi:10.1093/bioinformatics/btm150 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract A. Fujita, J.R. Sato, H.M. Garay-Malpartida, P.A. Morettin, M.C. Sogayar, and C.E. Ferreira: Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method
Bioinformatics Advance Access published on April 26, 2007
Bioinformatics 2007 23: 1623-1630; doi:10.1093/bioinformatics/btm151 [Abstract] [Full Text] [Print PDF] [Request Permissions]

Get checked abstract Zhenping Li, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, and Luonan Chen: Alignment of molecular networks by integer quadratic programming
Bioinformatics Advance Access published on April 27, 2007
Bioinformatics 2007 23: 1631-1639; doi:10.1093/bioinformatics/btm156 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Get checked abstract Nicola Soranzo, Ginestra Bianconi, and Claudio Altafini: Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data
Bioinformatics Advance Access published on May 7, 2007
Bioinformatics 2007 23: 1640-1647; doi:10.1093/bioinformatics/btm163 [Abstract] [Full Text] [Print PDF] [Request Permissions]

DATA AND TEXT MINING

Get checked abstract Vladimir Makarenkov, Pablo Zentilli, Dmytro Kevorkov, Andrei Gagarin, Nathalie Malo, and Robert Nadon: An efficient method for the detection and elimination of systematic error in high-throughput screening
Bioinformatics Advance Access published on April 26, 2007
Bioinformatics 2007 23: 1648-1657; doi:10.1093/bioinformatics/btm145 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]

Get checked abstract Vetle I. Torvik and Neil R. Smalheiser: A quantitative model for linking two disparate sets of articles in MEDLINE
Bioinformatics Advance Access published on April 26, 2007
Bioinformatics 2007 23: 1658-1665; doi:10.1093/bioinformatics/btm161 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data] OPEN ACCESS ARTICLE

Get checked abstract K. Jaqaman, J. F. Dorn, E. Marco, P. K. Sorger, and G. Danuser: Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics
Bioinformatics Advance Access published on May 5, 2007
Bioinformatics 2007 23: 1666-1673; doi:10.1093/bioinformatics/btm230 [Abstract] [Full Text] [Print PDF] [Request Permissions]

DATABASES AND ONTOLOGIES

Get checked abstract Thomas Bittner and Louis J. Goldberg: The qualitative and time-dependent character of spatial relations in biomedical ontologies
Bioinformatics Advance Access published on April 26, 2007
Bioinformatics 2007 23: 1674-1682; doi:10.1093/bioinformatics/btm155 [Abstract] [Full Text] [Print PDF] [Request Permissions]

APPLICATIONS NOTES