Bioinformatics

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Get checked abstract Naum I. Gershenzon and Ilya P. Ioshikhes

Synergy of human Pol II core promoter elements revealed by statistical sequence analysis
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1295-1300; doi:10.1093/bioinformatics/bti172 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Alex Bateman, Matthew T. G. Holden, and Corin Yeats

The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1301-1303; doi:10.1093/bioinformatics/bti206 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Francesca D. Ciccarelli and Peer Bork

The WHy domain mediates the response to desiccation in plants and bacteria
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1304-1307; doi:10.1093/bioinformatics/bti221 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract S. Sri Krishna and Nick V. Grishin

Structural drift: a possible path to protein fold change
Bioinformatics Advance Access published on December 16, 2004
Bioinformatics 2005 21: 1308-1310; doi:10.1093/bioinformatics/bti227 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Antonio del Sol, Hirotomo Fujihashi, and Paul O'Meara

Topology of small-world networks of protein–protein complex structures
Bioinformatics Advance Access published on January 19, 2005
Bioinformatics 2005 21: 1311-1315; doi:10.1093/bioinformatics/bti167 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Tomoyuki Yamada and Shinichi Morishita

Accelerated off-target search algorithm for siRNA
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1316-1324; doi:10.1093/bioinformatics/bti155 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Melissa D. Krebs, Robert D. Tingley, Julie E. Zeskind, Joung-Mo Kang, Maria E. Holmboe, and Cristina E. Davis

Autoregressive modeling of analytical sensor data can yield classifiers in the predictor coefficient parameter space
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1325-1331; doi:10.1093/bioinformatics/bti160 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sven Degroeve, Yvan Saeys, Bernard De Baets, Pierre Rouzé, and Yves Van de Peer

SpliceMachine: predicting splice sites from high-dimensional local context representations
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1332-1338; doi:10.1093/bioinformatics/bti166 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract S. E. Hampson, B. S. Gaut, and P. Baldi

Statistical detection of chromosomal homology using shared-gene density alone
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1339-1348; doi:10.1093/bioinformatics/bti168 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract John R. Rose, William H. Turkett, Jr., Iulia C. Oroian, William W. Laegreid, and John Keele

Correlation of amino acid preference and mammalian viral genome type
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1349-1357; doi:10.1093/bioinformatics/bti174 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yun Lian and Harold R. Garner

Evidence for the regulation of alternative splicing via complementary DNA sequence repeats
Bioinformatics Advance Access published on January 26, 2005
Bioinformatics 2005 21: 1358-1364; doi:10.1093/bioinformatics/bti180 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Eric K. Nordberg

YODA: selecting signature oligonucleotides
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1365-1370; doi:10.1093/bioinformatics/bti182 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ketil Malde, Eivind Coward, and Inge Jonassen

A graph based algorithm for generating EST consensus sequences
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1371-1375; doi:10.1093/bioinformatics/bti184 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Javier Santoyo, Juan M. Vaquerizas, and Joaquín Dopazo

Highly specific and accurate selection of siRNAs for high-throughput functional assays
Bioinformatics Advance Access published on December 10, 2004
Bioinformatics 2005 21: 1376-1382; doi:10.1093/bioinformatics/bti196 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Caroline C. Friedel, Katharina H. V. Jahn, Selina Sommer, Stephen Rudd, Hans W. Mewes, and Igor V. Tetko

Support vector machines for separation of mixed plant–pathogen EST collections based on codon usage
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1383-1388; doi:10.1093/bioinformatics/bti200 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Matthias B. Wahl, Ulrich Heinzmann, and Kenji Imai

LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1389-1392; doi:10.1093/bioinformatics/bti205 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Matthias B. Wahl, Ulrich Heinzmann, and Kenji Imai

LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse
Bioinformatics Advance Access published on December 10, 2004
Bioinformatics 2005 21: 1393-1400; doi:10.1093/bioinformatics/bti207 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xiaochen Bo and Shengqi Wang

TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1401-1402; doi:10.1093/bioinformatics/bti211 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract E. Jacob, R. Sasikumar, and K. N. R. Nair

A fuzzy guided genetic algorithm for operon prediction
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1403-1407; doi:10.1093/bioinformatics/bti156 [Abstract] [Full Text] [Print PDF] [supplementary data] [Request Permissions]  

Get checked abstract Iain M. Wallace, O'Sullivan Orla, and Desmond G. Higgins

Evaluation of iterative alignment algorithms for multiple alignment
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1408-1414; doi:10.1093/bioinformatics/bti159 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract East Zhao, Hsuan-Liang Liu, Chi-Hung Tsai, Huai-Kuang Tsai, Chen-hsiung Chan, and Cheng-Yan Kao

Cysteine separations profiles on protein sequences infer disulfide connectivity
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1415-1420; doi:10.1093/bioinformatics/bti179 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yasuyuki Nozaki and Matthew Bellgard

Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties
Bioinformatics Advance Access published on December 10, 2004
Bioinformatics 2005 21: 1421-1428; doi:10.1093/bioinformatics/bti198 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Volkan Atalay and Rengul Cetin-Atalay

Implicit motif distribution based hybrid computational kernel for sequence classification
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1429-1436; doi:10.1093/bioinformatics/bti212 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract V. Prigent, J. C. Thierry, O. Poch, and F. Plewniak

DbW: automatic update of a functional family-specific multiple alignment
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1437-1442; doi:10.1093/bioinformatics/bti218 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract A. Cavallo and A. C. R. Martin

Mapping SNPs to protein sequence and structure data
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1443-1450; doi:10.1093/bioinformatics/bti220 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Maricel G. Kann, Paul A. Thiessen, Anna R. Panchenko, Alejandro A. Schäffer, Stephen F. Altschul, and Stephen H. Bryant

A structure-based method for protein sequence alignment
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1451-1456; doi:10.1093/bioinformatics/bti233 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Kiyoko F. Aoki, Hiroshi Mamitsuka, Tatsuya Akutsu, and Minoru Kanehisa

A score matrix to reveal the hidden links in glycans
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1457-1463; doi:10.1093/bioinformatics/bti193 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Julian Gough

Convergent evolution of domain architectures (is rare)
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1464-1471; doi:10.1093/bioinformatics/bti204 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Brian Pierce, Weiwei Tong, and Zhiping Weng

M-ZDOCK: a grid-based approach for C_n symmetric multimer docking
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1472-1478; doi:10.1093/bioinformatics/bti229 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hyun S. Moon, Jonghwa Bhak, Kwang H. Lee, and Doheon Lee

Architecture of basic building blocks in protein and domain structural interaction networks
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1479-1486; doi:10.1093/bioinformatics/bti240 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract James R. Bradford and David R. Westhead

Improved prediction of protein–protein binding sites using a support vector machines approach
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1487-1494; doi:10.1093/bioinformatics/bti242 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Ugis Sarkans, Helen Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, Sergio Contrino, Ele Holloway, Philippe Rocca-Serra, Gaurab Mukherjee, Mohammadreza Shojatalab, Misha Kapushesky, Susanna-Assunta Sansone, Anna Farne, Tim Rayner, and Alvis Brazma

The ArrayExpress gene expression database: a software engineering and implementation perspective
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1495-1501; doi:10.1093/bioinformatics/bti157 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Chen-An Tsai, Sue-Jane Wang, Dung-Tsa Chen, and James J. Chen

Sample size for gene expression microarray experiments
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1502-1508; doi:10.1093/bioinformatics/bti162 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jianping Hua, Zixiang Xiong, James Lowey, Edward Suh, and Edward R. Dougherty

Optimal number of features as a function of sample size for various classification rules
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1509-1515; doi:10.1093/bioinformatics/bti171 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rongwei Fu, Dipak K. Dey, and Kent E. Holsinger

Bayesian models for the analysis of genetic structure when populations are correlated
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1516-1529; doi:10.1093/bioinformatics/bti178 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yuhang Wang, Fillia S. Makedon, James C. Ford, and Justin Pearlman

HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1530-1537; doi:10.1093/bioinformatics/bti192 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Qinghua Cui, Bing Liu, Tianzi Jiang, and Songde Ma

Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1538-1541; doi:10.1093/bioinformatics/bti197 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ranadip Pal, Aniruddha Datta, Albert J. Fornace, Jr, Michael L. Bittner, and Edward R. Dougherty

Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1542-1549; doi:10.1093/bioinformatics/bti214 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Céline Lefebvre, Jean-Christophe Aude, Eric Glémet, and Christian Néri

Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1550-1558; doi:10.1093/bioinformatics/bti215 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Xin Zhou and K. Z. Mao

LS Bound based gene selection for DNA microarray data
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1559-1564; doi:10.1093/bioinformatics/bti216 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Baolin Wu

Differential gene expression detection using penalized linear regression models: the improved SAM statistics
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1565-1571; doi:10.1093/bioinformatics/bti217 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ursula Sauer, Claudia Preininger, and Robert Hany-Schmatzberger

Quick and simple: quality control of microarray data
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1572-1578; doi:10.1093/bioinformatics/bti238 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Charles F. Crane and Yan M. Crane

A nearest-neighboring-end algorithm for genetic mapping
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1579-1591; doi:10.1093/bioinformatics/bti164 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hans A. Kestler, André Müller, Thomas M. Gress, and Malte Buchholz

Generalized Venn diagrams: a new method of visualizing complex genetic set relations
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1592-1595; doi:10.1093/bioinformatics/bti169 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Matthew Holford, Naixin Li, Prakash Nadkarni, and Hongyu Zhao

VitaPad: visualization tools for the analysis of pathway data
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1596-1602; doi:10.1093/bioinformatics/bti153 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Vassily Hatzimanikatis, Chunhui Li, Justin A. Ionita, Christopher S. Henry, Matthew D. Jankowski, and Linda J. Broadbelt

Exploring the diversity of complex metabolic networks
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1603-1609; doi:10.1093/bioinformatics/bti213 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract A. Beyer and T. Wilhelm

Dynamic simulation of protein complex formation on a genomic scale
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1610-1616; doi:10.1093/bioinformatics/bti223 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Marc Daniel Haunschild, Bernd Freisleben, Ralf Takors, and Wolfgang Wiechert

Investigating the dynamic behavior of biochemical networks using model families
Bioinformatics Advance Access published on December 16, 2004
Bioinformatics 2005 21: 1617-1625; doi:10.1093/bioinformatics/bti225 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Reinhard Guthke, Ulrich Möller, Martin Hoffmann, Frank Thies, and Susanne Töpfer

Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1626-1634; doi:10.1093/bioinformatics/bti226 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Joachim Kopka, Nicolas Schauer, Stephan Krueger, Claudia Birkemeyer, Björn Usadel, Eveline Bergmüller, Peter Dörmann, Wolfram Weckwerth, Yves Gibon, Mark Stitt, Lothar Willmitzer, Alisdair R. Fernie, and Dirk Steinhauser

GMD@CSB.DB: the Golm Metabolome Database
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1635-1638; doi:10.1093/bioinformatics/bti236 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract P. Tieri, S. Valensin, V. Latora, G. C. Castellani, M. Marchiori, D. Remondini, and C. Franceschi

Quantifying the relevance of different mediators in the human immune cell network
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1639-1643; doi:10.1093/bioinformatics/bti239 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Patrick Kemmeren, Thessa T. J. P. Kockelkorn, Theo Bijma, Rogier Donders, and Frank C. P. Holstege

Predicting gene function through systematic analysis and quality assessment of high-throughput data
Bioinformatics Advance Access published on November 5, 2004
Bioinformatics 2005 21: 1644-1652; doi:10.1093/bioinformatics/bti103 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Carlos Santos, Daniela Eggle, and David. J. States

Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1653-1658; doi:10.1093/bioinformatics/bti165 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ying Tao, Carol Friedman, and Yves A. Lussier

Visualizing information across multidimensional post-genomic structured and textual databases
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1659-1667; doi:10.1093/bioinformatics/bti210 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andrea L. Knorr and Ranjan Srivastava

Evaluation of HIV-1 kinetic models using quantitative discrimination analysis
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1668-1677; doi:10.1093/bioinformatics/bti230 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rasmus H. Fogh, Wayne Boucher, Wim F. Vranken, Anne Pajon, Tim J. Stevens, T. N. Bhat, John Westbrook, John M. C. Ionides, and Ernest D. Laue

A framework for scientific data modeling and automated software development
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1678-1684; doi:10.1093/bioinformatics/bti234 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract K. Wolstencroft, R. McEntire, R. Stevens, L. Tabernero, and A. Brass

Constructing ontology-driven protein family databases
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1685-1692; doi:10.1093/bioinformatics/bti158 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Jin Billy Li, Miao Zhang, Susan K. Dutcher, and Gary D. Stormo

Procom: a web-based tool to compare multiple eukaryotic proteomes
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1693-1694; doi:10.1093/bioinformatics/bti161 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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

TERMINUS—Telomeric End-Read Mining IN Unassembled Sequences
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1695-1698; doi:10.1093/bioinformatics/bti181 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Tae-Hyung Kim, Yeo-Jin Jeon, Woo-Yeon Kim, and Heui-Soo Kim

HESAS: HERVs Expression and Structure Analysis System
Bioinformatics Advance Access published on December 10, 2004
Bioinformatics 2005 21: 1699-1700; doi:10.1093/bioinformatics/bti194 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Lauris Kaplinski, Reidar Andreson, Tarmo Puurand, and Maido Remm

MultiPLX: automatic grouping and evaluation of PCR primers
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1701-1702; doi:10.1093/bioinformatics/bti219 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Simon de Givry, Martin Bouchez, Patrick Chabrier, Denis Milan, and Thomas Schiex

CAR_H^TA GENE: multipopulation integrated genetic and radiation hybrid mapping
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1703-1704; doi:10.1093/bioinformatics/bti222 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract T. M. Keane and T. J. Naughton

DSEARCH: sensitive database searching using distributed computing
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1705-1706; doi:10.1093/bioinformatics/bti163 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Richard J. D. Rouse, Jesus Castagnetto, and Roland H. Niedner

PatGen—a consolidated resource for searching genetic patent sequences
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 1707-1708; doi:10.1093/bioinformatics/bti202 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Kai M. A. Chan and Brian R. Moore

SYMMETREE: whole-tree analysis of differential diversification rates
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1709-1710; doi:10.1093/bioinformatics/bti175 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Søren Besenbacher, Thomas Mailund, Lasse Westh-Nielsen, and Christian N. S. Pedersen

RBT—a tool for building refined Buneman trees
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1711-1712; doi:10.1093/bioinformatics/bti195 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xun Gu, Wei Huang, Dongping Xu, and Hongmei Zhang

GeneContent: software for whole-genome phylogenetic analysis
Bioinformatics Advance Access published on December 14, 2004
Bioinformatics 2005 21: 1713-1714; doi:10.1093/bioinformatics/bti208 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Franck Dupuis, Jean-François Sadoc, Rémi Jullien, Borislav Angelov, and Jean-Paul Mornon

Voro3D: 3D Voronoi tessellations applied to protein structures
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2005 21: 1715-1716; doi:10.1093/bioinformatics/bth365 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Norihiro Kikuchi, Akihiko Kameyama, Shuuichi Nakaya, Hiromi Ito, Takashi Sato, Toshihide Shikanai, Yoriko Takahashi, and Hisashi Narimatsu

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1717-1718; doi:10.1093/bioinformatics/bti152 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Gianluca Pollastri and Aoife McLysaght

Porter: a new, accurate server for protein secondary structure prediction
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1719-1720; doi:10.1093/bioinformatics/bti203 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yuko Tsuchiya, Kengo Kinoshita, and Haruki Nakamura

PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1721-1723; doi:10.1093/bioinformatics/bti232 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Matthias E. Futschik and Toni Crompton

OLIN: optimized normalization, visualization and quality testing of two-channel microarray data
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1724-1726; doi:10.1093/bioinformatics/bti199 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Christian Schwager and Jonathon Blake

Bloader—a batch loader application for MIAMExpress
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1727-1729; doi:10.1093/bioinformatics/bti231 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Holger Thiele and Peter Nürnberg

HaploPainter: a tool for drawing pedigrees with complex haplotypes
Bioinformatics Advance Access published on September 17, 2004
Bioinformatics 2005 21: 1730-1732; doi:10.1093/bioinformatics/bth488 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Christian N. K. Anderson, Uma Ramakrishnan, Yvonne L. Chan, and Elizabeth A. Hadly

Serial SimCoal: A population genetics model for data from multiple populations and points in time
Bioinformatics Advance Access published on November 25, 2004
Bioinformatics 2005 21: 1733-1734; doi:10.1093/bioinformatics/bti154 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract S. I. Ao, Kevin Yip, Michael Ng, David Cheung, Pui-Yee Fong, Ian Melhado, and Pak C. Sham

CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs
Bioinformatics Advance Access published on December 7, 2004
Bioinformatics 2005 21: 1735-1736; doi:10.1093/bioinformatics/bti201 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Pablo Serrano-Fernández, Saleh M. Ibrahim, Dirk Koczan, Uwe K. Zettl, and Steffen Möller

In silico fine-mapping: narrowing disease-associated loci by intergenomics
Bioinformatics Advance Access published on December 10, 2004
Bioinformatics 2005 21: 1737-1738; doi:10.1093/bioinformatics/bti209 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Steven L. Bell and Bernhard Ø. Palsson

expa: a program for calculating extreme pathways in biochemical reaction networks
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1739-1740; doi:10.1093/bioinformatics/bti228 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Aaron N. Chang, Jason McDermott, and Ram Samudrala

An enhanced Java graph applet interface for visualizing interactomes
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1741-1742; doi:10.1093/bioinformatics/bti237 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Violaine Pillet, Marc Zehnder, Alexander K. Seewald, Anne-Lise Veuthey, and Johann Petrak

GPSDB: a new database for synonyms expansion of gene and protein names
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 1743-1744; doi:10.1093/bioinformatics/bti235 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract G. Finak, N. Godin, M. Hallett, F. Pepin, Z. Rajabi, V. Srivastava, and Z. Tang

BIAS: Bioinformatics Integrated Application Software
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1745-1746; doi:10.1093/bioinformatics/bti170 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Casey M. Bergman, Joseph W. Carlson, and Susan E. Celniker

Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
Bioinformatics Advance Access published on November 30, 2004
Bioinformatics 2005 21: 1747-1749; doi:10.1093/bioinformatics/bti173 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 1750; doi:10.1093/bioinformatics/bti395 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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