Bioinformatics

LETTER TO THE EDITOR:

DATABASES AND ONTOLOGIES:

Get checked abstract Andrean Goede, Mathias Dunkel, Nina Mester, Cornelius Frommel, and Robert Preissner

SuperDrug: a conformational drug database
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 1751-1753; doi:10.1093/bioinformatics/bti295 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John Arthur, and Jonas S. Almeida

AGML Central: web based gel proteomic infrastructure
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 1754-1757; doi:10.1093/bioinformatics/bti246 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, and Masaru Tomita

Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 1758-1763; doi:10.1093/bioinformatics/bti253 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jeffrey S. Morris, Kevin R. Coombes, John Koomen, Keith A. Baggerly, and Ryuji Kobayashi

Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum
Bioinformatics Advance Access published on January 26, 2005
Bioinformatics 2005 21: 1764-1775; doi:10.1093/bioinformatics/bti254 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Darrell Conklin, Betty Haldeman, and Zeren Gao

Gene finding for the helical cytokines
Bioinformatics Advance Access published on January 20, 2005
Bioinformatics 2005 21: 1776-1781; doi:10.1093/bioinformatics/bti283 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract W. H. Majoros, M. Pertea, and S. L. Salzberg

Efficient implementation of a generalized pair hidden Markov model for comparative gene finding
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 1782-1788; doi:10.1093/bioinformatics/bti297 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Maria Stepanova, Tatiana Tiazhelova, Mikle Skoblov, and Ancha Baranova

A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas
Bioinformatics Advance Access published on February 4, 2005
Bioinformatics 2005 21: 1789-1796; doi:10.1093/bioinformatics/bti307 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Dirk Husmeier, Frank Wright, and Iain Milne

Detecting interspecific recombination with a pruned probabilistic divergence measure
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1797-1806; doi:10.1093/bioinformatics/bti151 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Shaun Mahony, David Hendrix, Aaron Golden, Terry J. Smith, and Daniel S. Rokhsar

Transcription factor binding site identification using the self-organizing map
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 1807-1814; doi:10.1093/bioinformatics/bti256 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo, and Jan Gorodkin

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 1815-1824; doi:10.1093/bioinformatics/bti279 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract J. M. Cameron, T. Hurd, and B. H. Robinson

Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteins
Bioinformatics Advance Access published on January 25, 2005
Bioinformatics 2005 21: 1825-1830; doi:10.1093/bioinformatics/bti280 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Zheng Rong Yang

Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks
Bioinformatics Advance Access published on January 25, 2005
Bioinformatics 2005 21: 1831-1837; doi:10.1093/bioinformatics/bti281 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Han-Lin Li and Chang-Jui Fu

A linear programming approach for identifying a consensus sequence on DNA sequences
Bioinformatics Advance Access published on January 25, 2005
Bioinformatics 2005 21: 1838-1845; doi:10.1093/bioinformatics/bti286 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Niklaus Fankhauser and Pascal Mäser

Identification of GPI anchor attachment signals by a Kohonen self-organizing map
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 1846-1852; doi:10.1093/bioinformatics/bti299 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Robel Y. Kahsay, Guang Gao, and Li Liao

An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 1853-1858; doi:10.1093/bioinformatics/bti303 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Thomas D. Wu and Colin K. Watanabe

GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 1859-1875; doi:10.1093/bioinformatics/bti310 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Betty Lazareva-Ulitsky, Karen Diemer, and Paul D. Thomas

On the quality of tree-based protein classification
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 1876-1890; doi:10.1093/bioinformatics/bti244 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Karen Coeytaux and Anne Poupon

Prediction of unfolded segments in a protein sequence based on amino acid composition
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 1891-1900; doi:10.1093/bioinformatics/bti266 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Fred P. Davis and Andrej Sali

PIBASE: a comprehensive database of structurally defined protein interfaces
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 1901-1907; doi:10.1093/bioinformatics/bti277 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Alasdair T. R. Laurie and Richard M. Jackson

Q-SiteFinder: an energy-based method for the prediction of protein–ligand binding sites
Bioinformatics Advance Access published on February 8, 2005
Bioinformatics 2005 21: 1908-1916; doi:10.1093/bioinformatics/bti315 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Håvard Nesvold, Anja Bråthen Kristoffersen, Arne Holst-Jensen, and Knut G. Berdal

Design of a DNA chip for detection of unknown genetically modified organisms (GMOs)
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 1917-1926; doi:10.1093/bioinformatics/bti248 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dae-Won Kim, Kwang H. Lee, and Doheon Lee

Detecting clusters of different geometrical shapes in microarray gene expression data
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 1927-1934; doi:10.1093/bioinformatics/bti251 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Cristian Mircean, Ilya Shmulevich, David Cogdell, Woonyoung Choi, Yu Jia, Ioan Tabus, Stanley R. Hamilton, and Wei Zhang

Robust estimation of protein expression ratios with lysate microarray technology
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 1935-1942; doi:10.1093/bioinformatics/bti258 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract William T. Barry, Andrew B. Nobel, and Fred A. Wright

Significance analysis of functional categories in gene expression studies: a structured permutation approach
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 1943-1949; doi:10.1093/bioinformatics/bti260 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jelle J. Goeman, Jan Oosting, Anne-Marie Cleton-Jansen, Jakob K. Anninga, and Hans C. van Houwelingen

Testing association of a pathway with survival using gene expression data
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 1950-1957; doi:10.1093/bioinformatics/bti267 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xiaojun Di, Hajime Matsuzaki, Teresa A. Webster, Earl Hubbell, Guoying Liu, Shoulian Dong, Dan Bartell, Jing Huang, Richard Chiles, Geoffrey Yang, Mei-mei Shen, David Kulp, Giulia C. Kennedy, Rui Mei, Keith W. Jones, and Simon Cawley

Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 1958-1963; doi:10.1093/bioinformatics/bti275 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Staal A. Vinterbo, Eun-Young Kim, and Lucila Ohno-Machado

Small, fuzzy and interpretable gene expression based classifiers
Bioinformatics Advance Access published on January 20, 2005
Bioinformatics 2005 21: 1964-1970; doi:10.1093/bioinformatics/bti287 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Claudio Lottaz and Rainer Spang

Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data
Bioinformatics Advance Access published on January 27, 2005
Bioinformatics 2005 21: 1971-1978; doi:10.1093/bioinformatics/bti292 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Wenjiang J. Fu, Raymond J. Carroll, and Suojin Wang

Estimating misclassification error with small samples via bootstrap cross-validation
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 1979-1986; doi:10.1093/bioinformatics/bti294 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Susmita Datta and Somnath Datta

Empirical Bayes screening of many p-values with applications to microarray studies
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 1987-1994; doi:10.1093/bioinformatics/bti301 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Marie-Laure Martin-Magniette, Julie Aubert, Eric Cabannes, and Jean-Jacques Daudin

Evaluation of the gene-specific dye bias in cDNA microarray experiments
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 1995-2000; doi:10.1093/bioinformatics/bti302 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Shih-Chieh Su, C.-C. Jay Kuo, and Ting Chen

Inference of missing SNPs and information quantity measurements for haplotype blocks
Bioinformatics Advance Access published on February 4, 2005
Bioinformatics 2005 21: 2001-2007; doi:10.1093/bioinformatics/bti261 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Marcin Imielinski, Calin Belta, Ádám Halász, and Harvey Rubin

Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities
Bioinformatics Advance Access published on January 25, 2005
Bioinformatics 2005 21: 2008-2016; doi:10.1093/bioinformatics/bti245 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ross D. King, Simon M. Garrett, and George M. Coghill

On the use of qualitative reasoning to simulate and identify metabolic pathways
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 2017-2026; doi:10.1093/bioinformatics/bti255 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sampsa Hautaniemi, Sourabh Kharait, Akihiro Iwabu, Alan Wells, and Douglas A. Lauffenburger

Modeling of signal–response cascades using decision tree analysis
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 2027-2035; doi:10.1093/bioinformatics/bti278 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Weijiang Li and Hiroyuki Kurata

A grid layout algorithm for automatic drawing of biochemical networks
Bioinformatics Advance Access published on January 27, 2005
Bioinformatics 2005 21: 2036-2042; doi:10.1093/bioinformatics/bti290 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kinya Okada, Shigehiko Kanaya, and Kiyoshi Asai

Accurate extraction of functional associations between proteins based on common interaction partners and common domains
Bioinformatics Advance Access published on February 4, 2005
Bioinformatics 2005 21: 2043-2048; doi:10.1093/bioinformatics/bti305 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract R. Jelier, G. Jenster, L. C. J. Dorssers, C. C. van der Eijk, E. M. van Mulligen, B. Mons, and J. A. Kors

Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 2049-2058; doi:10.1093/bioinformatics/bti268 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Oliver Hofmann and Dietmar Schomburg

Concept-based annotation of enzyme classes
Bioinformatics Advance Access published on January 20, 2005
Bioinformatics 2005 21: 2059-2066; doi:10.1093/bioinformatics/bti284 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Gordon K. Smyth, Joëlle Michaud, and Hamish S. Scott

Use of within-array replicate spots for assessing differential expression in microarray experiments
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 2067-2075; doi:10.1093/bioinformatics/bti270 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kevin R. Brown and Igor Jurisica

Online Predicted Human Interaction Database
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 2076-2082; doi:10.1093/bioinformatics/bti273 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Jian Song, Yan Xu, Scott White, Kevin W. P. Miller, and Murray Wolinsky

SNPsFinder—a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes
Bioinformatics Advance Access published on February 3, 2005
Bioinformatics 2005 21: 2083-2084; doi:10.1093/bioinformatics/bti176 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Per Gärdén, Rikard Alm, and Jari Häkkinen

PROTEIOS: an open source proteomics initiative
Bioinformatics Advance Access published on February 3, 2005
Bioinformatics 2005 21: 2085-2087; doi:10.1093/bioinformatics/bti291 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jason W.H. Wong, Gerard Cagney, and Hugh M. Cartwright

SpecAlign—processing and alignment of mass spectra datasets
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 2088-2090; doi:10.1093/bioinformatics/bti300 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kuljeet S. Sandhu and Kshitish K. Acharya

ExPrimer: to design primers from exon—exon junctions
Bioinformatics Advance Access published on February 4, 2005
Bioinformatics 2005 21: 2091-2092; doi:10.1093/bioinformatics/bti304 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Morris Michael, Christoph Dieterich, and Martin Vingron

SITEBLAST–rapid and sensitive local alignment of genomic sequences employing motif anchors
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 2093-2094; doi:10.1093/bioinformatics/bti224 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract F. Chalmel, A. Lardenois, J.D. Thompson, J. Muller, J.-A. Sahel, T. Léveillard, and O. Poch

GOAnno: GO annotation based on multiple alignment
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 2095-2096; doi:10.1093/bioinformatics/bti252 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Weixi Li, Cathryn J. Rehmeyer, Chuck Staben, and Mark L. Farman

TruMatch—a BLAST post-processor that identifies bona fide sequence matches to genome assemblies
Bioinformatics Advance Access published on January 25, 2005
Bioinformatics 2005 21: 2097-2098; doi:10.1093/bioinformatics/bti257 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract F. Azuaje

Integrative data analysis for functional prediction: a multi-objective optimization approach
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 2099-2100; doi:10.1093/bioinformatics/bti272 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Adi Doron-Faigenboim, Adi Stern, Itay Mayrose, Eran Bacharach, and Tal Pupko

Selecton: a server for detecting evolutionary forces at a single amino-acid site
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 2101-2103; doi:10.1093/bioinformatics/bti259 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Federico Abascal, Rafael Zardoya, and David Posada

ProtTest: selection of best-fit models of protein evolution
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 2104-2105; doi:10.1093/bioinformatics/bti263 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig, and Thomas Lengauer

Mtreemix: a software package for learning and using mixture models of mutagenetic trees
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 2106-2107; doi:10.1093/bioinformatics/bti274 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Joachim Friedrich, Thomas Dandekar, Matthias Wolf, and Tobias Müller

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances
Bioinformatics Advance Access published on January 27, 2005
Bioinformatics 2005 21: 2108-2109; doi:10.1093/bioinformatics/bti289 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Andreas Möglich, Daniel Weinfurtner, Wolfram Gronwald, Till Maurer, and Hans Robert Kalbitzer

PERMOL: restraint-based protein homology modeling using DYANA or CNS
Bioinformatics Advance Access published on January 25, 2005
Bioinformatics 2005 21: 2110-2111; doi:10.1093/bioinformatics/bti276 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Joern Toedling, Sebastian Schmeier, Matthias Heinig, Benjamin Georgi, and Stefan Roepcke

MACAT—microarray chromosome analysis tool
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 2112-2113; doi:10.1093/bioinformatics/bti183 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract L. J Heyer, D. Z. Moskowitz, J. A. Abele, P. Karnik, D. Choi, A. M. Campbell, E. E. Oldham, and B. K. Akin

MAGIC Tool: integrated microarray data analysis
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 2114-2115; doi:10.1093/bioinformatics/bti247 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sek Won Kong, Kyu-Baek Hwang, Richard D. Kim, Byoung-Tak Zhang, Steven A. Greenberg, Isaac S. Kohane, and Peter J. Park

CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays
Bioinformatics Advance Access published on January 31, 2005
Bioinformatics 2005 21: 2116-2117; doi:10.1093/bioinformatics/bti288 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yuan Ji, Chunlei Wu, Ping Liu, Jing Wang, and Kevin R. Coombes

Applications of beta-mixture models in bioinformatics
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2118-2122; doi:10.1093/bioinformatics/bti318 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Franz Rüschendorf and Peter Nürnberg

ALOHOMORA: a tool for linkage analysis using 10K SNP array data
Bioinformatics Advance Access published on January 12, 2005
Bioinformatics 2005 21: 2123-2125; doi:10.1093/bioinformatics/bti264 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hongyu Yang, Hongyu Wang, and Alan R. Gingle

IntegratedMap: a Web interface for integrating genetic map data
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 2126-2127; doi:10.1093/bioinformatics/bti271 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kejun Liu and Spencer V. Muse

PowerMarker: an integrated analysis environment for genetic marker analysis
Bioinformatics Advance Access published on February 10, 2005
Bioinformatics 2005 21: 2128-2129; doi:10.1093/bioinformatics/bti282 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract David Posada, Taylor J. Maxwell, and Alan R. Templeton

TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees
Bioinformatics Advance Access published on January 28, 2005
Bioinformatics 2005 21: 2130-2132; doi:10.1093/bioinformatics/bti293 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Chih-Yu (Carol) Chang and Joshua LaBaer

DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequences
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 2133-2135; doi:10.1093/bioinformatics/bti298 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Abhijit Chatterjee, Kapil Mayawala, Jeremy S. Edwards, and Dionisios G. Vlachos

Time accelerated Monte Carlo simulations of biological networks using the binomial -leap method
Bioinformatics Advance Access published on February 4, 2005
Bioinformatics 2005 21: 2136-2137; doi:10.1093/bioinformatics/bti308 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Anna Divoli and Teresa K. Attwood

BioIE: extracting informative sentences from the biomedical literature
Bioinformatics Advance Access published on February 2, 2005
Bioinformatics 2005 21: 2138-2139; doi:10.1093/bioinformatics/bti296 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Pedro A. Reche, Hong Zhang, John-Paul Glutting, and Ellis L. Reinherz

EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology
Bioinformatics Advance Access published on January 18, 2005
Bioinformatics 2005 21: 2140-2141; doi:10.1093/bioinformatics/bti269 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Pei Hao, Wei-Zhong He, Yin Huang, Liang-Xiao Ma, Ying Xu, Hong Xi, Chuan Wang, Bo-Shu Liu, Jin-Miao Wang, Yi-Xue Li, and Yang Zhong

MPSS: an integrated database system for surveying a set of proteins
Bioinformatics Advance Access published on February 4, 2005
Bioinformatics 2005 21: 2142-2143; doi:10.1093/bioinformatics/bti306 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 2144; doi:10.1093/bioinformatics/bti446 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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