BMC Bioinformatics, Volume 6

Volume 6, 2005

• Aditi Kanhere, Manju Bansal:
  A novel method for prokaryotic promoter prediction based on DNA stability. 1
  
• David A. Rasko, Garry S. A. Myers, Jacques Ravel:
  Visualization of comparative genomic analyses by BLAST score ratio. 2
  
• Les Dethlefsen, Thomas M. Schmidt:
  Differences in codon bias cannot explain differences in translational power among microbes. 3
  
• Jean-Christophe Gelly, Laurent Chiche, Jérôme Gracy:
  EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments. 4
  
• Marko Srdanovic, Ulf Schenk, Michael Schwieger, Fabien Campagne:
  Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. 5
  
• Dave Bridges, Marie E. Fraser, Greg B. G. Moorhead:
  Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes. 6
  
• Pantelis G. Bagos, Theodore Liakopoulos, Stavros J. Hamodrakas:
  Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. 7
  
• Dongxiao Zhu, Zhaohui S. Qin:
  Structural comparison of metabolic networks in selected single cell organisms. 8
  
• David A. Nix, Michael B. Eisen:
  GATA: a graphic alignment tool for comparative sequence analysis. 9
  
• Helene H. Thygesen, Aeilko H. Zwinderman:
  Modelling the correlation between the activities of adjacent genes in drosophila. 10
  
• Thomas MacCarthy, Andrew Pomiankowski, Robert Seymour:
  Using large-scale perturbations in gene network reconstruction. 11
  
• Ran Rubinstein, Itamar Simon:
  MILANO - custom annotation of microarray results using automatic literature searches. 12
  
• Francisco Azuaje, Haiying Wang, Alban Chesneau:
  Non-linear mapping for exploratory data analysis in functional genomics. 13
  
• Deli Wang, Jian Huang, Hehuang Xie, Liliana Manzella, Marcelo Bento Soares:
  A robust two-way semi-linear model for normalization of cDNA microarray data. 14
  
• Antje Krause, Jens Stoye, Martin Vingron:
  Large scale hierarchical clustering of protein sequences. 15
  
• William H. Majoros, Mihaela Pertea, Arthur L. Delcher, Steven Salzberg:
  Efficient decoding algorithms for generalized hidden Markov model gene finders. 16
  
• Don Simone Daly, Amanda M. White, Susan M. Varnum, Kevin K. Anderson, Richard C. Zangar:
  Evaluating concentration estimation errors in ELISA microarray experiments. 17
  
• Rifat A. Hamoudi, Amina El-Hamidi, Ming-Qing Du:
  Identification of novel prognostic markers in cervical intraepithelial neoplasia using LDMAS (LOH Data Management and Analysis Software). 18
  
• Vilmos Ágoston, Masa Cemazar, László Kaján, Sándor Pongor:
  Graph-representation of oxidative folding pathways. 19
  
• Pengyu Hong, Wing Hung Wong:
  GeneNotes - A novel information management software for biologists. 20
  
• John L. Moreland, Apostol Gramada, Oleksandr V. Buzko, Qing Zhang, Philip E. Bourne:
  The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. 21
  
• Maria Novatchkova, Andreas Bachmair, Birgit Eisenhaber, Frank Eisenhaber:
  Proteins with two SUMO-like domains in chromatin-associated complexes: The RENi (Rad60-Esc2-NIP45) family. 22
  
• Joe Whitney, David J. Esteban, Chris Upton:
  Recent Hits Acquired by BLAST (ReHAB): A tool to identify new hits in sequence similarity searches. 23
  
• Victor Kunin, Christos A. Ouzounis:
  Clustering the annotation space of proteins. 24
  
• Sylvain Foissac, Thomas Schiex:
  Integrating alternative splicing detection into gene prediction. 25
  
• Kerby Shedden, Wei Chen, Rork Kuick, Debashis Ghosh, James W. MacDonald, Kathleen R. Cho, Thomas J. Giordano, Stephen B. Gruber, Eric R. Fearon, Jeremy M. G. Taylor, Samir Hanash:
  Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data. 26
  
• Franck Picard, Stéphane Robin, Marc Lavielle, Christian Vaisse, Jean-Jacques Daudin:
  A statistical approach for array CGH data analysis. 27
  
• Yingdong Zhao, Ming-Chung Li, Richard Simon:
  An adaptive method for cDNA microarray normalization. 28
  
• Harold J. Drabkin, Christopher Hollenbeck, David P. Hill, Judith A. Blake:
  Ontological visualization of protein-protein interactions. 29
  
• Alena Shmygelska, Holger H. Hoos:
  An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem. 30
  
• Guy St. C. Slater, Ewan Birney:
  Automated generation of heuristics for biological sequence comparison. 31
  
• James A. Koziol, Anne C. Feng:
  A note on generalized Genome Scan Meta-Analysis statistics. 32
  
• Shandar Ahmad, Akinori Sarai:
  PSSM-based prediction of DNA binding sites in proteins. 33
  
• Sohrab P. Shah, Yong Huang, Tao Xu, Macaire M. S. Yuen, John Ling, B. F. Francis Ouellette:
  Atlas - a data warehouse for integrative bioinformatics. 34
  
• Markus Neuhäuser, Tanja Boes, Karl-Heinz Jöckel:
  Two-part permutation tests for DNA methylation and microarray data. 35
  
• Robert G. Beiko, Robert L. Charlebois:
  GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA. 36
  
• Timothy Lu, Christine M. Costello, Peter J. P. Croucher, Robert Häsler, Günther Deuschl, Stefan Schreiber:
  Can Zipf's law be adapted to normalize microarrays? 37
  
• Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, Xuegong Zhang:
  htSNPer1.0: software for haplotype block partition and htSNPs selection. 38
  
• Ruth Dunn, Frank Dudbridge, Christopher M. Sanderson:
  The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks. 39
  
• Itay Tirosh, Naama Barkai:
  Computational verification of protein-protein interactions by orthologous co-expression. 40
  
• Florent Angly, Beltran Rodriguez-Brito, David Bangor, Pat McNairnie, Mya Breitbart, Peter Salamon, Ben Felts, James Nulton, Joseph Mahaffy, Forest Rohwer:
  PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. 41
  
• Julie Aubert, Avner Bar-Hen, Jean-Jacques Daudin, Stéphane Robin:
  Correction: Determination of the differentially expressed genes in microarray experiments using local FDR. 42
  
• Koji Kadota, Ryutaro Fukumura, Joseph J. Rodrigue, Ryoko Araki, Masumi Abe:
  A normalization strategy applied to HiCEP (an AFLP-based expression profiling) analysis: Toward the strict alignment of valid fragments across electrophoretic patterns. 43
  
• Wen-Chieh Chang, Chang-Wei Li, Bor-Sen Chen:
  Quantitative inference of dynamic regulatory pathways via microarray data. 44
  
• John Colbourne, Vasanth R. Singan, Don G. Gilbert:
  wFleaBase: the Daphnia genome database. 45
  
• Noam Kaplan, Michal Linial:
  Automatic detection of false annotations via binary property clustering. 46
  
• Guangjie Feng, Nick Burton, Bill Hill, Duncan Davidson, Janet Kerwin, Mark Scott, Susan Lindsay, Richard A. Baldock:
  JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases. 47
  
• Roderic D. M. Page:
  A Taxonomic Search Engine: Federating taxonomic databases using web services. 48
  
• Olivier Bastien, Philippe Ortet, Sylvaine Roy, Eric Maréchal:
  A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities. 49
  
• Eva Freyhult, Peteris Prusis, Maris Lapinsh, Jarl E. S. Wikberg, Vincent Moulton, Mats G. Gustafsson:
  Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. 50
  
• Blaise T. F. Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman, Guido Jenster:
  CoPub Mapper: mining MEDLINE based on search term co-publication. 51
  
• Siv Midtun Hollup, Gisle Sælensminde, Nathalie Reuter:
  WEBnm@: a web application for normal mode analyses of proteins. 52
  
• Jaime E. Blair, Prachi Shah, S. Blair Hedges:
  Evolutionary sequence analysis of complete eukaryote genomes. 53
  
• Harri Lähdesmäki, Ilya Shmulevich, Valerie Dunmire, Olli Yli-Harja, Wei Zhang:
  In silico microdissection of microarray data from heterogeneous cell populations. 54
  
• Euan A. Adie, Richard R. Adams, Kathryn L. Evans, David J. Porteous, Ben S. Pickard:
  Speeding disease gene discovery by sequence based candidate prioritization. 55
  
• Andrew G. Garrow, Alison Agnew, David R. Westhead:
  TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. 56
  
• John R. Stevens, R. W. Doerge:
  Combining Affymetrix microarray results. 57
  
• Zheng Guo, Tianwen Zhang, Xia Li, Qi Wang, Jianzhen Xu, Hui Yu, Jing Zhu, Haiyun Wang, Chenguang Wang, Eric J. Topol, Qing Wang, Shaoqi Rao:
  Towards precise classification of cancers based on robust gene functional expression profiles. 58
  
• Gajendra P. S. Raghava, Joon H. Han:
  Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein. 59
  
• Lin Wang, Simin Liu, Tianhua Niu, Xin Xu:
  SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management. 60
  
• Yadhu Kumar, Ralf Westram, Sebastian Behrens, Bernhard Fuchs, Frank Oliver Glöckner, Rudolf Amann, Harald Meier, Wolfgang Ludwig:
  Graphical representation of ribosomal RNA probe accessibility data using ARB software package. 61
  
• Alexey Larionov, Andreas Krause, William Miller:
  A standard curve based method for relative real time PCR data processing. 62
  
• Elena Rivas:
  Evolutionary models for insertions and deletions in a probabilistic modeling framework. 63
  
• James J. Cai, David K. Smith, Xuhua Xia, Kwok-yung Yuen:
  MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution. 64
  
• Mayte Suárez-Fariñas, Asifa Haider, Knut M. Wittkowski:
  "Harshlighting" small blemishes on microarrays. 65
  
• Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern:
  DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. 66
  
• Li M. Fu, Casey S. Fu-Liu:
  Evaluation of gene importance in microarray data based upon probability of selection. 67
  
• Ilya Levner:
  Feature selection and nearest centroid classification for protein mass spectrometry. 68
  
• Francis Tang, Ching Lian Chua, Liang-Yoong Ho, Yun-Ping Lim, Praveen Issac, Arun Krishnan:
  Wildfire: distributed, Grid-enabled workflow construction and execution. 69
  
• C. Titus Brown, Yuan Xie, Eric H. Davidson, R. Andrew Cameron:
  Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison. 70
  
• Hartmut Scheel, Kay Hofmann:
  Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes. 71
  
• S. A. Kirov, X. Peng, E. Baker, D. Schmoyer, B. Zhang, J. Snoddy:
  GeneKeyDB: A lightweight, gene-centric, relational database to support data mining environments. 72
  
• Ian Holmes:
  Accelerated probabilistic inference of RNA structure evolution. 73
  
• Aba-Sah Dadzie, Albert Burger:
  Providing visualisation support for the analysis of anatomy ontology data. 74
  
• Brian P. Suomela, Miguel A. Andrade:
  Ranking the whole MEDLINE database according to a large training set using text indexing. 75
  
• Xiaoxing Liu, Arun Krishnan, Adrian Mondry:
  An Entropy-based gene selection method for cancer classification using microarray data. 76
  
• Ya Zhang, John-Marc Chandonia, Chris H. Q. Ding, Stephen R. Holbrook:
  Comparative mapping of sequence-based and structure-based protein domains. 77
  
• Chris D. Bajdik, Byron Kuo, Shawn Rusaw, Steven Jones, Angela Brooks-Wilson:
  CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes. 78
  
• Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva:
  MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. 79
  
• Alexander Ploner, Lance D. Miller, Per Hall, Jonas Bergh, Yudi Pawitan:
  Correlation test to assess low-level processing of high-density oligonucleotide microarray data. 80
  
• Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel, Ulf Leser:
  Columba: an integrated database of proteins, structures, and annotations. 81
  
• Igor V. Tetko, Axel Facius, Andreas Ruepp, Hans-Werner Mewes:
  Super paramagnetic clustering of protein sequences. 82
  
• Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen, Jotun Hein:
  Bayesian coestimation of phylogeny and sequence alignment. 83
  
• Markus T. Friberg, Peter von Rohr, Gaston H. Gonnet:
  Scoring functions for transcription factor binding site prediction. 84
  
• Wei Chen, Fikret Erdogan, H.-Hilger Ropers, Steffen Lenzner, Reinhard Ullmann:
  CGHPRO - A comprehensive data analysis tool for array CGH. 85
  
• Prinal Trivedi, Jode W. Edwards, Jelai Wang, Gary L. Gadbury, Vinodh Srinivasasainagendra, Stanislav O. Zakharkin, Kyoungmi Kim, Tapan Mehta, Jacob P. L. Brand, Amit Patki, Grier P. Page, David B. Allison:
  HDBStat!: A platform-independent software suite for statistical analysis of high dimensional biology data. 86
  
• Alexander García Castro, Samuel Thoraval, Leyla Jael García-Castro, Mark A. Ragan:
  Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. 87
  
• Lei Shi, Fabien Campagne:
  Building a protein name dictionary from full text: a machine learning term extraction approach. 88
  
• Jianghui Liu, Jason Tsong-Li Wang, Jun Hu, Bin Tian:
  A method for aligning RNA secondary structures and its application to RNA motif detection. 89
  
• Mark J. Gibbs, John S. Armstrong, Adrian J. Gibbs:
  Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences. 90
  
• Andreas Möglich, Daniel Weinfurtner, Till Maurer, Wolfram Gronwald, Hans Robert Kalbitzer:
  A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles. 91
  
• Le Sy Vinh, Arndt von Haeseler:
  Shortest triplet clustering: reconstructing large phylogenies using representative sets. 92
  
• Scot E. Dowd, Joaquin Zaragoza, Javier R. Rodriguez, Melvin J. Oliver, Paxton R. Payton:
  Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST). 93
  
• Nicole Donofrio, Ravi Rajagopalon, Douglas E. Brown, Stephen E. Diener, Donald Windham, Shelly Nolin, Anna Floyd, Thomas K. Mitchell, Natalia Galadima, Sara Tucker, Marc J. Orbach, Gayatri Patel, Mark L. Farman, Vishal Pampanwar, Cari Soderlund, Yong-Hwan Lee, Ralph A. Dean:
  'PACLIMS': A component LIM system for high-throughput functional genomic analysis. 94
  
• Judith E. Stenger, Hong Xu, Carol Haynes, Elizabeth R. Hauser, Margaret A. Pericak-Vance, Pascal J. Goldschmidt-Clermont, Jeffery M. Vance:
  Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. 95
  
• Jeffrey P. Mower:
  PREP-Mt: predictive RNA editor for plant mitochondrial genes. 96
  
• Leslie Grate:
  Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery. 97
  
• Michael Watson:
  ProGenExpress: Visualization of quantitative data on prokaryotic genomes. 98
  
• Markus Wistrand, Erik L. L. Sonnhammer:
  Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. 99
  
• Ashwini Patil, Haruki Nakamura:
  Filtering high-throughput protein-protein interaction data using a combination of genomic features. 100
  
• Michael Maurer, Robert Molidor, Alexander Sturn, Jürgen Hartler, Hubert Hackl, Gernot Stocker, Andreas Prokesch, Marcel Scheideler, Zlatko Trajanoski:
  MARS: Microarray analysis, retrieval, and storage system. 101
  
• Michael S. Rosenberg:
  Evolutionary distance estimation and fidelity of pair wise sequence alignment. 102
  
• Aaron M. Cohen, William R. Hersh, Christopher Dubay, Kent A. Spackman:
  Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts. 103
  
• Nikolaos G. Sgourakis, Pantelis G. Bagos, Panagiotis K. Papasaikas, Stavros J. Hamodrakas:
  A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models. 104
  
• Kshitiz Gupta, Dina Thomas, S. V. Vidya, K. V. Venkatesh, S. Ramakumar:
  Detailed protein sequence alignment based on Spectral Similarity Score (SSS). 105
  
• Hua Liu, Sergey Tarima, Aaron S. Borders, Thomas V. Getchell, Marilyn L. Getchell, Arnold J. Stromberg:
  Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments. 106
  
• Scott L. Carter, Aron C. Eklund, Brigham H. Mecham, Isaac S. Kohane, Zoltan Szallasi:
  Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. 107
  
• Erik L. L. Sonnhammer, Volker Hollich:
  Scoredist: A simple and robust protein sequence distance estimator. 108
  
• Irina I. Abnizova, Rene te Boekhorst, Klaudia Walter, Walter R. Gilks:
  Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test. 109
  
• Davide Corà, Carl Herrmann, Christoph Dieterich, Ferdinando Di Cunto, Paolo Provero, Michele Caselle:
  Ab initio identification of putative human transcription factor binding sites by comparative genomics. 110
  
• Jeff Reneker, Chi-Ren Shyu:
  Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals. 111
  
• Andreas Hahn, Jörg Rahnenführer, Priti Talwar, Thomas Lengauer:
  Confirmation of human protein interaction data by human expression data. 112
  
• Daniel Shegogue, W. Jim Zheng:
  Integration of the Gene Ontology into an object-oriented architecture. 113
  
• Jianhua Ruan, Weixiong Zhang:
  CAGER: classification analysis of gene expression regulation using multiple information sources. 114
  
• Matthew A. Hibbs, Nathaniel C. Dirksen, Kai Li, Olga G. Troyanskaya:
  Visualization methods for statistical analysis of microarray clusters. 115
  
• David La, Dennis R. Livesay:
  Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. 116
  
• Miika Ahdesmäki, Harri Lähdesmäki, Ronald K. Pearson, Heikki Huttunen, Olli Yli-Harja:
  Robust detection of periodic time series measured from biological systems. 117
  
• André Lambert, Matthieu Legendre, Jean-Fred Fontaine, Daniel Gautheret:
  Computing expectation values for RNA motifs using discrete convolutions. 118
  
• Nan Lin, Hongyu Zhao:
  Are scale-free networks robust to measurement errors? 119
  
• Xing Qiu, Andrew I. Brooks, Lev Klebanov, Andrei Yakovlev:
  The effects of normalization on the correlation structure of microarray data. 120
  
• Stefania Bortoluzzi, Alessandro Coppe, Andrea Bisognin, Cinzia Pizzi, Gian Antonio Danieli:
  A multistep bioinformatic approach detects putative regulatory elements in gene promoters. 121
  
• Elke Michalsky, Mathias Dunkel, Andrean Goede, Robert Preissner:
  SuperLigands - a database of ligand structures derived from the Protein Data Bank. 122
  
• Bernhard Haubold, Nora Pierstorff, Friedrich Möller, Thomas Wiehe:
  Genome comparison without alignment using shortest unique substrings. 123
  
• Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven Van Vooren, Joris Vermeesch, Yves Moreau, Bart De Moor, Stefan Vermeulen, Frank Speleman, Jo Vandesompele:
  arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. 124
  
• Shugo Hamahashi, Shuichi Onami, Hiroaki Kitano:
  Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking. 125
  
• Mythily Ganapathi, Pragya Srivastava, Sushanta Kumar Das Sutar, Kaushal Kumar, Dipayan Dasgupta, Gajinder Pal Singh, Vani Brahmachari, Samir K. Brahmachari:
  Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes. 126
  
• Roald Rossnes, Ingvar Eidhammer, David A. Liberles:
  Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data. 127
  
• Pingzhao Hu, Celia M. T. Greenwood, Joseph Beyene:
  Integrative analysis of multiple gene expression profiles with quality-adjusted effect size models. 128
  
• Ola Larsson, Claes Wahlestedt, James A. Timmons:
  Considerations when using the significance analysis of microarrays (SAM) algorithm. 129
  
• Matthew J. Wakefield, Peter Maxwell, Gavin A. Huttley:
  Vestige: Maximum likelihood phylogenetic footprinting. 130
  
• Eduardo Eyras, Alexandre Reymond, Robert Castelo, Jacqueline M. Bye, Francisco Camara, Paul Flicek, Elizabeth J. Huckle, Genis Parra, David D. Shteynberg, Carine Wyss, Jane Rogers, Stylianos E. Antonarakis, Ewan Birney, Roderic Guigó, Michael R. Brent:
  Gene finding in the chicken genome. 131
  
• Björn Peters, Alessandro Sette:
  Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. 132
  
• Mark L. Crowe:
  SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms. 133
  
• Adrian Schneider, Gina Cannarozzi, Gaston H. Gonnet:
  Empirical codon substitution matrix. 134
  
• Roland Schwarz, Patrick Musch, Axel von Kamp, Bernd Engels, R. Heiner Schirmer, Stefan Schuster, Thomas Dandekar:
  YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. 135
  
• Taijiao Jiang, Amy E. Keating:
  AVID: An integrative framework for discovering functional relationships among proteins. 136
  
• Xiang Gao, Kent Vander Velden, Daniel F. Voytas, Xun Gu:
  SplitTester: software to identify domains responsible for functional divergence in protein family. 137
  
• Davin Butt, Andrew J. Roger, Christian Blouin:
  libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny. 138
  
• Lutz Hamel, Olga Zhaxybayeva, J. Peter Gogarten:
  PentaPlot: A software tool for the illustration of genome mosaicism. 139
  
• Matthew J. Cockerill:
  BMC Bioinformatics comes of age. 140
  
• Peter Murray-Rust, John B. O. Mitchell, Henry S. Rzepa:
  Chemistry in Bioinformatics. 141
  
• Barend Mons:
  Which gene did you mean? 142
  
• James W. Cooper, Aaron Kershenbaum:
  Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information. 143
  
• Seon-Young Kim, David J. Volsky:
  PAGE: Parametric Analysis of Gene Set Enrichment. 144
  
• Perseus I. Missirlis, Carri-Lyn R. Mead, Stefanie L. Butland, B. F. Francis Ouellette, Rebecca S. Devon, Blair R. Leavitt, Robert A. Holt:
  Satellog: A database for the identification and prioritization of satellite repeats in disease association studies. 145
  
• Chad L. Myers, Xing Chen, Olga G. Troyanskaya:
  Visualization-based discovery and analysis of genomic aberrations in microarray data. 146
  
• Stephen E. Diener, Thomas D. Houfek, Sam E. Kalat, D. E. Windham, Mark Burke, Charles Opperman, Ralph A. Dean:
  Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system. 147
  
• Thanyaluk Jirapech-Umpai, J. Stuart Aitken:
  Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes. 148
  
• Bob J. A. Schijvenaars, Barend Mons, Marc Weeber, Martijn J. Schuemie, Erik M. van Mulligen, Hester M. Wain, Jan A. Kors:
  Thesaurus-based disambiguation of gene symbols. 149
  
• Christelle Hennequet-Antier, Hélène Chiapello, Karine Piot, Séverine Degrelle, Isabelle Hue, Jean-Paul Renard, François Rodolphe, Stéphane Robin:
  AnovArray: a set of SAS macros for the analysis of variance of gene expression data. 150
  
• Liisa B. Koski, Michael W. Gray, B. Franz Lang, Gertraud Burger:
  AutoFACT: An Automatic Functional Annotation and Classification Tool. 151
  
• Deepak Sarda, Gek Huey Chua, Kuo-Bin Li, Arun Krishnan:
  pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties. 152
  
• Janina Reeder, Peter Steffen, Robert Giegerich:
  Effective ambiguity checking in biosequence analysis. 153
  
• David J. Reiss, Iliana Avila-Campillo, Vesteinn Thorsson, Benno Schwikowski, Timothy Galitski:
  Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection. 154
  
• Kapil G. Gadkar, Rudiyanto Gunawan, Francis J. Doyle III:
  Iterative approach to model identification of biological networks. 155
  
• Olaf R. P. Bininda-Emonds:
  transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. 156
  
• Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
  Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation. 157
  
• Per Stenberg, Fredrik Pettersson, Anja O. Saura, Anders Berglund, Jan Larsson:
  Sequence signature analysis of chromosome identity in three Drosophila species. 158
  
• Wouter Boomsma, Thomas Hamelryck:
  Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. 159
  
• Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler:
  Multiple sequence alignments of partially coding nucleic acid sequences. 160
  
• Felix Kokocinski, Nicolas Delhomme, Gunnar Wrobel, Lars Hummerich, Grischa Toedt, Peter Lichter:
  FACT - a framework for the functional interpretation of high-throughput experiments. 161
  
• Petri Pehkonen, Garry Wong, Petri Törönen:
  Theme discovery from gene lists for identification and viewing of multiple functional groups. 162
  
• Thomas Breslin, Morten Krogh, Carsten Peterson, Carl Troein:
  Signal transduction pathway profiling of individual tumor samples. 163
  
• Jan Hummel, Nima Keshvari, Wolfram Weckwerth, Joachim Selbig:
  Species-specific analysis of protein sequence motifs using mutual information. 164
  
• Jun Lu, John K. Tomfohr, Thomas B. Kepler:
  Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach. 165
  
• Mark Reimers, John N. Weinstein:
  Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases. 166
  
• Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer, Søren Brunak:
  Prediction of twin-arginine signal peptides. 167
  
• Barry Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine, Hong Cao, David W. Kane, Mark Reimers, Robert M. Stephens, David Bryant, Stanley K. Burt, Eldad Elnekave, Danielle M. Hari, Thomas A. Wynn, Charlotte Cunningham-Rundles, Donn M. Stewart, David Nelson, John N. Weinstein:
  High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). 168
  
• Raimund Tenhaken, Tobias Doerks, Peer Bork:
  DCD - a novel plant specific domain in proteins involved in development and programmed cell death. 169
  
• Jan C. Biro, Gergely Fördös:
  SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. 170
  
• Hélène Chiapello, I. Bourgait, F. Sourivong, G. Heuclin, Annie Gendrault-Jacquemard, Marie-Agnès Petit, Meriem El Karoui:
  Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. 171
  
• Jan Kosinski, Marcin Feder, Janusz M. Bujnicki:
  The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. 172
  
• Nema Dean, Adrian E. Raftery:
  Normal uniform mixture differential gene expression detection for cDNA microarrays. 173
  
• Jiren Wang, Wing-Kin Sung, Arun Krishnan, Kuo-Bin Li:
  Protein subcellular localization prediction for Gram-negative bacteria using amino acid subalphabets and a combination of multiple support vector machines. 174
  
• Eric C. Rouchka, Abdelnaby Khalyfa, Nigel G. F. Cooper:
  MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. 175
  
• Jiajian Liu, Gary D. Stormo:
  Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. 176
  
• J. Peter Svensson, Renée X. de Menezes, Ingela Turesson, Micheline Giphart-Gassler, Harry Vrieling:
  Dissecting systems-wide data using mixture models: application to identify affected cellular processes. 177
  
• R. Henrik Nilsson, Erik Kristiansson, Martin Ryberg, Karl-Henrik Larsson:
  Approaching the taxonomic affiliation of unidentified sequences in public databases - an example from the mycorrhizal fungi. 178
  
• Mikko Katajamaa, Matej Oresic:
  Processing methods for differential analysis of LC/MS profile data. 179
  
• Peter Murray-Rust, John B. O. Mitchell, Henry S. Rzepa:
  Communication and re-use of chemical information in bioscience. 180
  
• Rainer Breitling, Patrick Armengaud, Anna Amtmann:
  Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds. 181
  
• Fran Supek, Kristian Vlahovicek:
  Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. 182
  
• Carolina Perez-Iratxeta, Miguel A. Andrade:
  Inconsistencies over time in 5% of NetAffx probe-to-gene annotations. 183
  
• Sung Ho Yoon, Cheol-Goo Hur, Ho-Young Kang, Yeoun Hee Kim, Tae Kwang Oh, Jihyun F. Kim:
  A computational approach for identifying pathogenicity islands in prokaryotic genomes. 184
  
• Mindaugas Margelevicius, Ceslovas Venclovas:
  PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability. 185
  
• Xin Gao, Peter X. K. Song:
  Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments. 186
  
• Nitin Jain, HyungJun Cho, Michael O'Connell, Jae K. Lee:
  Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data. 187
  
• Falk Schubert, Bernhard Tausch, Stefan Joos, Roland Eils:
  CGH-Profiler: Data mining based on genomic aberration profiles. 188
  
• Jason S. M. Lee, Gurpreet Katari, Ravi Sachidanandam:
  GObar: A Gene Ontology based analysis and visualization tool for gene sets. 189
  
• Youfang Cao, Lianjie Wang, Kexue Xu, Chunhai Kou, Yulei Zhang, Guifang Wei, Junjian He, Yunfang Wang, Liping Zhao:
  Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates. 190
  
• Wei Wu, Eric P. Xing, Connie Myers, I. Saira Mian, Mina J. Bissell:
  Evaluation of normalization methods for cDNA microarray data by k-NN classification. 191
  
• Antoine Veldhoven, Don de Lange, Marcel Smid, Victor de Jager, Jan A. Kors, Guido Jenster:
  Storing, linking, and mining microarray databases using SRS. 192
  
• William H. Majoros, Steven Salzberg:
  An empirical analysis of training protocols for probabilistic gene finders. 193
  
• Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich:
  Functional annotation by identification of local surface similarities: a novel tool for structural genomics. 194
  
• Kevin Dawson, Raymond L. Rodriguez, Wasyl Malyj:
  Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm. 195
  
• Daniel P. Depledge, Andrew R. Dalby:
  COPASAAR - A database for proteomic analysis of single amino acid repeats. 196
  
• Paulo C. Carvalho, Rafael V. Glória, Antonio Basílio de Miranda, Wim M. Degrave:
  Squid - a simple bioinformatics grid. 197
  
• Philippe Gouret, Vérane Vitiello, Nathalie Balandraud, André Gilles, Pierre Pontarotti, Etienne G. J. Danchin:
  FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform. 198
  
• Per Broberg:
  A comparative review of estimates of the proportion unchanged genes and the false discovery rate. 199
  
• Chunlin Wang, Elliot J. Lefkowitz:
  Genomic multiple sequence alignments: refinement using a genetic algorithm. 200
  
• Hongfang Liu, Zhang-Zhi Hu, Cathy H. Wu:
  DynGO: a tool for visualizing and mining of Gene Ontology and its associations. 201
  
• Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin:
  PALSSE: A program to delineate linear secondary structural elements from protein structures. 202
  
• Witold E. Wolski, Maciej Lalowski, Peter Jungblut, Knut Reinert:
  Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. 203
  
• Deendayal Dinakarpandian, Venetia Raheja, Saumil Mehta, Erin G. Schuetz, Peter K. Rogan:
  Tandem machine learning for the identification of genes regulated by transcription factors. 204
  
• Xiaohong Huang, Wei Pan, Suzanne Grindle, Xinqiang Han, Yingjie Chen, Soon J. Park, Leslie W. Miller, Jennifer Hall:
  A comparative study of discriminating human heart failure etiology using gene expression profiles. 205
  
• Etienne Larsabal, Antoine Danchin:
  Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns". 206
  
• Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M. Bolser, Donghoon Oh, Deok-Soo Kim, Jong Bhak:
  A protein domain interaction interface database: InterPare. 207
  
• Roderic D. M. Page, Gabriel Valiente:
  An edit script for taxonomic classifications. 208
  
• Nicola Zamboni, Eliane Fischer, Uwe Sauer:
  FiatFlux - a software for metabolic flux analysis from ¹³C-glucose experiments. 209
  
• Birgit Pils, Richard R. Copley, Jörg Schultz:
  Variation in structural location and amino acid conservation of functional sites in protein domain families. 210
  
• Claudio Lottaz, Rainer Spang:
  stam - a Bioconductor compliant R package for structured analysis of microarray data. 211
  
• Katja Wegner, Ursula Kummer:
  A new dynamical layout algorithm for complex biochemical reaction networks. 212
  
• Boris Thibert, Dale E. Bredesen, Gabriel del Rio:
  Improved prediction of critical residues for protein function based on network and phylogenetic analyses. 213
  
• Stanislav O. Zakharkin, Kyoungmi Kim, Tapan Mehta, Lang Chen, Stephen Barnes, Katherine E. Scheirer, Rudolph S. Parrish, David B. Allison, Grier P. Page:
  Sources of variation in Affymetrix microarray experiments. 214
  
• Mansour Taghavi Azar Sharabiani, Markku Siermala, Tommi O. Lehtinen, Mauno Vihinen:
  Dynamic covariation between gene expression and proteome characteristics. 215
  
• Peter Sperisen, Marco Pagni:
  JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture. 216
  
• Liviu Popescu, Golan Yona:
  Automation of gene assignments to metabolic pathways using high-throughput expression data. 217
  
• Archana Sharma-Oates, Philip Quirke, David R. Westhead:
  TmaDB: a repository for tissue microarray data. 218
  
• Junwen Wang, Sridhar Hannenhalli:
  Generalizations of Markov model to characterize biological sequences. 219
  
• Jianmin Wang, Xiaoqiu Huang:
  A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage. 220
  
• Daron M. Standley, Hiroyuki Toh, Haruki Nakamura:
  GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures. 221
  
• Ravindra Pushker, Giuseppe D'Auria, Jose Carlos Alba-Casado, Francisco Rodríguez-Valera:
  Micro-Mar: a database for dynamic representation of marine microbial biodiversity. 222
  
• Andrean Goede, Ines S. Jaeger, Robert Preissner:
  SUPERFICIAL - Surface mapping of proteins via structure-based peptide library design. 223
  
• Peter Steffen, Robert Giegerich:
  Versatile and declarative dynamic programming using pair algebras. 224
  
• John K. Tomfohr, Jun Lu, Thomas B. Kepler:
  Pathway level analysis of gene expression using singular value decomposition. 225
  
• Martin A. Lema, Julian Echave:
  Assessing local structural perturbations in proteins. 226
  
• Cecily J. Wolfe, Isaac S. Kohane, Atul J. Butte:
  Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. 227
  
• Hédi Soula, Céline Robardet, François Perrin, Sébastien Gripon, Guillaume Beslon, Olivier Gandrillon:
  Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software. 228
  
• Johan Stenberg, Mats Nilsson, Ulf Landegren:
  ProbeMaker: an extensible framework for design of sets of oligonucleotide probes. 229
  
• Jan H. Vogel, Anja von Heydebreck, Antje Purmann, Silke Sperling:
  Chromosomal clustering of a human transcriptome reveals regulatory background. 230
  
• István Miklós, Irmtraud M. Meyer:
  A linear memory algorithm for Baum-Welch training. 231
  
• Ron Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosef Shiloh, Ran Elkon:
  EXPANDER - an integrative program suite for microarray data analysis. 232
  
• Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert:
  GeneRank: Using search engine technology for the analysis of microarray experiments. 233
  
• Brian D. M. Tom, Walter R. Gilks, Elizabeth T. Brooke-Powell, James W. Ajioka:
  Quality determination and the repair of poor quality spots in array experiments. 234
  
• Andrew R. Jones, Norman W. Paton:
  An analysis of extensible modelling for functional genomics data. 235
  
• Andy Pang, Andrew D. Smith, Paulo A. S. Nuin, Elisabeth R. M. Tillier:
  SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution. 236
  
• Szymon M. Kielbasa, Didier Gonze, Hanspeter Herzel:
  Measuring similarities between transcription factor binding sites. 237
  
• Bart Pieterse, Elisabeth J. Quirijns, Frank H. J. Schuren, Mariët J. van der Werf:
  Mathematical design of prokaryotic clone-based microarrays. 238
  
• Florent Baty, Michel P. Bihl, Guy Perrière, Aedín C. Culhane, Martin H. Brutsche:
  Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data. 239
  
• Thomas J. Magliery, Lynne Regan:
  Sequence variation in ligand binding sites in proteins. 240
  
• Eva Freyhult, Paul P. Gardner, Vincent Moulton:
  A comparison of RNA folding measures. 241
  
• Qicheng Ma, Gung-Wei Chirn, Richard Cai, Joseph D. Szustakowski, N. R. Nirmala:
  Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks. 242
  
• Yu Zheng, Brian P. Anton, Richard J. Roberts, Simon Kasif:
  Phylogenetic detection of conserved gene clusters in microbial genomes. 243
  
• Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole:
  ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. 244
  
• Michael C. Wendl, W. Bradley Barbazuk:
  Extension of Lander-Waterman theory for sequencing filtered DNA libraries. 245
  
• Stéphanie Monnier, David G. Cox, Tim Albion, Federico Canzian:
  T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory. 246
  
• François Enault, Karsten Suhre, Jean-Michel Claverie:
  Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis. 247
  
• Zheng Yuan:
  Better prediction of protein contact number using a support vector regression analysis of amino acid sequence. 248
  
• Khar Heng Choo, Tin Wee Tan, Shoba Ranganathan:
  SPdb - a signal peptide database. 249
  
• Max Bylesjö, Daniel Eriksson, Andreas Sjödin, Michael Sjöström, Stefan Jansson, Henrik Antti, Johan Trygg:
  MASQOT: a method for cDNA microarray spot quality control. 250
  
• Oleg N. Reva, Burkhard Tümmler:
  Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. 251
  
• Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Peter J. M. Mechlenborg, Jesper N. Madsen, Leif Schauser:
  CoaSim: A flexible environment for simulating genetic data under coalescent models. 252
  
• Tomas Ohlson, Arne Elofsson:
  ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. 253
  
• Oliver Mirus, Enrico Schleiff:
  Prediction of beta-barrel membrane proteins by searching for restricted domains. 254
  
• François Ferron, Cécile Bussetta, Hélène Dutartre, Bruno Canard:
  The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases. 255
  
• Eric W. Klee, Lynda B. M. Ellis:
  Evaluating eukaryotic secreted protein prediction. 256
  
• Hongxia Pang, Jiaowei Tang, Su-Shing Chen, Shiheng Tao:
  Statistical distributions of optimal global alignment scores of random protein sequences. 257
  
• Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li, Bor-Sen Chen:
  Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification. 258
  
• Markey C. McNutt, Ron Tongbai, Wenwu Cui, Irene Collins, Wendy J. Freebern, Idalia Montano, Cynthia M. Haggerty, G. V. R. Chandramouli, Kevin Gardner:
  Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function. 259
  
• Joshua J. Forman, Paul A. Clemons, Stuart L. Schreiber, Stephen J. Haggarty:
  SpectralNET - an application for spectral graph analysis and visualization. 260
  
• Alexander G. Churbanov, Mark Pauley, Daniel Quest, Hesham H. Ali:
  A method of precise mRNA/DNA homology-based gene structure prediction. 261
  
• Bob Y. Chan, Dennis F. Kibler:
  Using hexamers to predict cis-regulatory motifs in Drosophila. 262
  
• Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao:
  Selecting additional tag SNPs for tolerating missing data in genotyping. 263
  
• David Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, A. Joseph Wood, Karim Nashar, Douglas B. Kell, Andy Brass:
  maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination. 264
  
• Patrick Warnat, Roland Eils, Benedikt Brors:
  Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. 265
  
• A. D. Neverov, Irena I. Artamonova, Ramil N. Nurtdinov, Dmitrij Frishman, Mikhail S. Gelfand, Andrey A. Mironov:
  Alternative splicing and protein function. 266
  
• Alain Sewer, Nicodème Paul, Pablo Landgraf, Alexei Aravin, Sébastien Pfeffer, Michael J. Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan:
  Identification of clustered microRNAs using an ab initio prediction method. 267
  
• Mahendra Navarange, Laurence Game, Derek Fowler, Vihar Wadekar, Helen Banks, Nicola Cooley, Fatimah Rahman, Justin Hinshelwood, Peter Broderick, Helen C. Causton:
  MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data. 268
  
• Homin K. Lee, William Braynen, Kiran Keshav, Paul Pavlidis:
  ErmineJ: Tool for functional analysis of gene expression data sets. 269
  
• Ping Ye, Brian D. Peyser, Forrest A. Spencer, Joel S. Bader:
  Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast. 270
  
• Robin E. C. Lee, Lynn A. Megeney:
  The yeast kinome displays scale free topology with functional hub clusters. 271
  
• Craig E. Jones, Ute Baumann, Alfred L. Brown:
  Automated methods of predicting the function of biological sequences using GO and BLAST. 272
  
• Alexander K. Hudek, Daniel G. Brown:
  Ancestral sequence alignment under optimal conditions. 273
  
• Mehrnoush Khojasteh, Wan L. Lam, Rabab Kreidieh Ward, Calum MacAulay:
  A stepwise framework for the normalization of array CGH data. 274
  
• Emmitt R. Jolly, Chen-Shan Chin, Ira Herskowitz, Hao Li:
  Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis. 275
  
• Yunlong Liu, Matthew P. Vincenti, Hiroki Yokota:
  Principal component analysis for predicting transcription-factor binding motifs from array-derived data. 276
  
• Jianwen Fang, Ryan J. Haasl, Yinghua Dong, Gerald H. Lushington:
  Discover protein sequence signatures from protein-protein interaction data. 277
  
• Michael S. Rosenberg:
  Multiple sequence alignment accuracy and evolutionary distance estimation. 278
  
• Raja Mazumder, Darren A. Natale, Sudhir Murthy, Rathi Thiagarajan, Cathy H. Wu:
  Computational identification of strain-, species- and genus-specific proteins. 279
  
• Alexander E. Pozhitkov, Kathryn Stemshorn, Diethard Tautz:
  An algorithm for the determination and quantification of components of nucleic acid mixtures based on single sequencing reactions. 281
  
• Chin-Jen Ku, Golan Yona:
  The distance-profile representation and its application to detection of distantly related protein families. 282
  
• Christopher P. Toseland, Helen M. McSparron, Darren R. Flower:
  DSD - An integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities. 283
  
• Kimberly M. Mayer, Sean R. McCorkle, John Shanklin:
  Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality. 284
  
• Witold E. Wolski, Maciej Lalowski, Peter Martus, Ralf Herwig, Patrick Giavalisco, Johan Gobom, Albert Sickmann, Hans Lehrach, Knut Reinert:
  Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. 285
  
• Jie Chen:
  Identification of significant periodic genes in microarray gene expression data. 286
  
• Gary L. Argraves, Saurin Jani, Jeremy L. Barth, W. Scott Argraves:
  ArrayQuest: a web resource for the analysis of DNA microarray data. 287
  
• Yan Qi, Ping Ye, Joel S. Bader:
  Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality. 288
  
• Vito Di Gesù, Raffaele Giancarlo, Giosuè Lo Bosco, Alessandra Raimondi, Davide Scaturro:
  GenClust: A genetic algorithm for clustering gene expression data. 289
  
• Florian Grosse-Coosmann, Andreas M. Boehm, Albert Sickmann:
  Efficient analysis and extraction of MS/MS result data from Mascot^TM result files. 290
  
• Zhengdeng Lei, Yang Dai:
  An SVM-based system for predicting protein subnuclear localizations. 291
  
• Nameeta Shah, Michael V. Teplitsky, Simon Minovitsky, Len A. Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna Dubchak:
  SNP-VISTA: An interactive SNP visualization tool. 292
  
• Eugene Novikov, Emmanuel Barillot:
  An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments. 293
  
• Mayte Suárez-Fariñas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco:
  Harshlight: a "corrective make-up" program for microarray chips. 294
  
• Takashi Yoneya:
  PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords. 295
  
• K. V. Brinda, Saraswathi Vishveshwara:
  Oligomeric protein structure networks: insights into protein-protein interactions. 296
  
• Lalitha Viswanath, Elizabeth A. Housworth:
  InterferenceAnalyzer: Tools for the analysis and simulation of multi-locus genetic data. 297
  
• Timo Lassmann, Erik L. L. Sonnhammer:
  Kalign - an accurate and fast multiple sequence alignment algorithm. 298
  
• Katsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama, Masaru Tomita:
  A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. 299
  
• Ji-Ping Z. Wang, Bruce G. Lindsay, Liying Cui, P. Kerr Wall, Josh Marion, Jiaxuan Zhang, Claude W. dePamphilis:
  Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. 300
  
• Federico Fogolari, Silvio C. E. Tosatto, Giorgio Colombo:
  A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators. 301
  
• Emmanuel D. Levy, Christos A. Ouzounis, Walter R. Gilks, Benjamin Audit:
  Probabilistic annotation of protein sequences based on functional classifications. 302
  
• Amit R. Indap, Gabor T. Marth, Craig A. Struble, Peter J. Tonellato, Michael Olivier:
  Analysis of concordance of different haplotype block partitioning algorithms. 303
  
• Robert Kim, Francesca Demichelis, Jeffery Tang, Alberto Riva, Ronglai Shen, Doug F. Gibbs, Vasudeva Mahavishno, Arul M. Chinnaiyan, Mark A. Rubin:
  Internet-based profiler system as integrative framework to support translational research. 304
  
• Dimas Yusuf, Jonathan S. Lim, Wyeth W. Wasserman:
  The Gene Set Builder: collation, curation, and distribution of sets of genes. 305
  
• Xiaoqin Xia, Michael McClelland, Yipeng Wang:
  WebArray: an online platform for microarray data analysis. 306
  
• Sebastian Noth, Arndt Benecke:
  Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700^TM/Panther^TM probe-to-gene annotations. 307
  
• Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen:
  Evolutionary programming as a platform for in silico metabolic engineering. 308
  
• Wei Wu, Nilesh Dave, George C. Tseng, Thomas Richards, Eric P. Xing, Naftali Kaminski:
  Comparison of normalization methods for CodeLink Bioarray data. 309
  
• Chenghai Xue, Fei Li, Tao He, Guo-Ping Liu, Yanda Li, Xuegong Zhang:
  Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. 310
  
• Nils E. Magnusson, Alessandra K. Cardozo, Mogens Kruhøffer, Decio L. Eizirik, Torben F. Ørntoft, Jens L. Jensen:
  Construction and validation of the APOCHIP, a spotted oligo-microarray for the study of beta-cell apoptosis. 311