Bioinformatics

ORIGINAL PAPERS:

Rajeev K. Azad and Mark Borodovsky

Effects of choice of DNA sequence model structure on gene identification accuracy
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 993-1005; doi:10.1093/bioinformatics/bth028 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Robert J. Clifford, Michael N. Edmonson, Cu Nguyen, and Kenneth H. Buetow

Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 1006-1014; doi:10.1093/bioinformatics/bth029 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

N. Krasnogor and D. A. Pelta

Measuring the similarity of protein structures by means of the universal similarity metric
Bioinformatics Advance Access published on January 29, 2004
Bioinformatics 2004 20: 1015-1021; doi:10.1093/bioinformatics/bth031 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Adele A. Mitchell, Michael E. Zwick, Aravinda Chakravarti, and David J. Cutler

Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1022-1032; doi:10.1093/bioinformatics/bth034 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Jorge Lepre, J. Jeremy Rice, Yuhai Tu, and Gustavo Stolovitzky

Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1033-1044; doi:10.1093/bioinformatics/bth035 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Zeyar Aung and Kian-Lee Tan

Rapid 3D protein structure database searching using information retrieval techniques
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 1045-1052; doi:10.1093/bioinformatics/bth036 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Kwok Pui Choi, Fanfan Zeng, and Louxin Zhang

Good spaced seeds for homology search
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1053-1059; doi:10.1093/bioinformatics/bth037 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Andrew C. James, Jim G. Veitch, Ali R. Zareh, and Timothy Triche

Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarrays
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1060-1065; doi:10.1093/bioinformatics/bth038 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Werner G. Krebs and Philip E. Bourne

Statistically rigorous automated protein annotation
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1066-1073; doi:10.1093/bioinformatics/bth039 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ramakant Sharma, Jitendra Kumar Maheshwari, Tulika Prakash, Debasis Dash, and Samir K. Brahmachari

Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1074-1080; doi:10.1093/bioinformatics/bth041 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Lida Zhang, Dejun Yuan, Shunwu Yu, Zhugang Li, Youfang Cao, Zhiqi Miao, Hongmei Qian, and Kexuan Tang

Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1081-1086; doi:10.1093/bioinformatics/bth043 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Adrian K. Arakaki, Yang Zhang, and Jeffrey Skolnick

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1087-1096; doi:10.1093/bioinformatics/bth044 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yohei Minakuchi, Masahiro Ito, and Yuji Kohara

SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1097-1109; doi:10.1093/bioinformatics/bth045 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ross D. King, Paul H. Wise, and Amanda Clare

Confirmation of data mining based predictions of protein function
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1110-1118; doi:10.1093/bioinformatics/bth047 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Goro Terai and Toshihisa Takagi

Predicting rules on organization of cis-regulatory elements, taking the order of elements into account
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1119-1128; doi:10.1093/bioinformatics/bth049 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

J. A. Izaguirre, R. Chaturvedi, C. Huang, T. Cickovski, J. Coffland, G. Thomas, G. Forgacs, M. Alber, G. Hentschel, S. A. Newman, and J. A. Glazier

COMPUCELL, a multi-model framework for simulation of morphogenesis
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1129-1137; doi:10.1093/bioinformatics/bth050 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Wan K. Kim, Dan M. Bolser, and Jong H. Park

Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1138-1150; doi:10.1093/bioinformatics/bth053 [Abstract] [Print PDF][Screen PDF] Supplementary Data [Request Permissions]  

Yu-Dong Cai and Kuo-Chen Chou

Predicting subcellular localization of proteins in a hybridization space
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1151-1156; doi:10.1093/bioinformatics/bth054 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Volker Brendel, Liqun Xing, and Wei Zhu

Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1157-1169; doi:10.1093/bioinformatics/bth058 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yong Wang and Frederick C.C. Leung

An evaluation of new criteria for CpG islands in the human genome as gene markers
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1170-1177; doi:10.1093/bioinformatics/bth059 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

GuoDong Zhou, Jie Zhang, Jian Su, Dan Shen, and ChewLim Tan

Recognizing names in biomedical texts: a machine learning approach
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1178-1190; doi:10.1093/bioinformatics/bth060 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Jihoon Kim, Hee-Joon Chung, Chan Hee Park, Woong-Yang Park, and Ju Han Kim

ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1191-1192; doi:10.1093/bioinformatics/bth052 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Justin Ebedes and Amitava Datta

Multiple sequence alignment in parallel on a workstation cluster
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1193-1195; doi:10.1093/bioinformatics/bth055 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

N.H. Shah and N.V. Fedoroff

CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1196-1197; doi:10.1093/bioinformatics/bth056 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Han Yu, Andrew S. Yoo, and Iva Greenwald

Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites
Bioinformatics Advance Access published on February 5, 2004
Bioinformatics 2004 20: 1198-1200; doi:10.1093/bioinformatics/bth057 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Nigel I. Kirby, Eugene F. DeRose, Robert E. London, and Geoffrey A. Mueller

NvAssign: protein NMR spectral assignment with NMRView
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 1201-1203; doi:10.1093/bioinformatics/bth064 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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