Bioinformatics

SAC PAPER:

Andrew T. Kwon, Holger H. Hoos, and Raymond Ng

Inference of transcriptional regulation relationships from gene expression data
Bioinformatics 2003 19: 905-912; doi:10.1093/bioinformatics/btg106 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tolga Can, Yujun Wang, Yuan-Fang Wang, and Jianwen Su

FPV: fast protein visualization using Java 3D^TM
Bioinformatics 2003 19: 913-922; doi:10.1093/bioinformatics/btg104 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

See-Kiong Ng, Zhuo Zhang, and Soon-Heng Tan

Integrative approach for computationally inferring protein domain interactions
Bioinformatics 2003 19: 923-929; doi:10.1093/bioinformatics/btg118 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, M. Ozsoyoglu, G. Schaeffer, M. Tasan, and W. Xu

Pathways database system: an integrated system for biological pathways
Bioinformatics 2003 19: 930-937; doi:10.1093/bioinformatics/btg113 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Goran Nenadic, Irena Spasic, and Sophia Ananiadou

Terminology-driven mining of biomedical literature
Bioinformatics 2003 19: 938-943; doi:10.1093/bioinformatics/btg105 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Marcel Brun, David Sabbagh, Seungchan Kim, and Edward R. Dougherty

Corrected small-sample estimation of the Bayes error
Bioinformatics 2003 19: 944-951; doi:10.1093/bioinformatics/btg144 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Howard H. Yang, Ying Hu, Michael Edmonson, Kenneth Buetow, and Maxwell P. Lee

Computation method to identify differential allelic gene expression and novel imprinted genes
Bioinformatics 2003 19: 952-955; doi:10.1093/bioinformatics/btg127 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yudong D. He, Hongyue Dai, Eric E. Schadt, Guy Cavet, Stephen W. Edwards, Sergey B. Stepaniants, Sven Duenwald, Robert Kleinhanz, Allan R. Jones, Daniel D. Shoemaker, and Roland B. Stoughton

Microarray standard data set and figures of merit for comparing data processing methods and experiment designs
Bioinformatics 2003 19: 956-965; doi:10.1093/bioinformatics/btg126 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David M. Rocke and Blythe Durbin

Approximate variance-stabilizing transformations for gene-expression microarray data
Bioinformatics 2003 19: 966-972; doi:10.1093/bioinformatics/btg107 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Doulaye Dembélé and Philippe Kastner

Fuzzy C-means method for clustering microarray data
Bioinformatics 2003 19: 973-980; doi:10.1093/bioinformatics/btg119 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Sorin Draghici, Frank Graziano, Samira Kettoola, Ishwar Sethi, and George Towfic

Mining HIV dynamics using independent component analysis
Bioinformatics 2003 19: 981-986; doi:10.1093/bioinformatics/btg123 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Svetlana Boycheva, Georgi Chkodrov, and Ivan Ivanov

Codon pairs in the genome of Escherichia coli
Bioinformatics 2003 19: 987-998; doi:10.1093/bioinformatics/btg082 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Christopher Lee

Generating consensus sequences from partial order multiple sequence alignment graphs
Bioinformatics 2003 19: 999-1008; doi:10.1093/bioinformatics/btg109 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Harpreet Singh and G.P.S. Raghava

ProPred1: prediction of promiscuous MHC Class-I binding sites
Bioinformatics 2003 19: 1009-1014; doi:10.1093/bioinformatics/btg108 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Krzysztof Ginalski, Arne Elofsson, Daniel Fischer, and Leszek Rychlewski

3D-Jury: a simple approach to improve protein structure predictions
Bioinformatics 2003 19: 1015-1018; doi:10.1093/bioinformatics/btg124 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. Steuer, J. Kurths, O. Fiehn, and W. Weckwerth

Observing and interpreting correlations in metabolomic networks
Bioinformatics 2003 19: 1019-1026; doi:10.1093/bioinformatics/btg120 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Julien Gagneur, David B. Jackson, and Georg Casari

Hierarchical analysis of dependency in metabolic networks
Bioinformatics 2003 19: 1027-1034; doi:10.1093/bioinformatics/btg115 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Apuã C.M. Paquola, Abimael A. Machado, Eduardo M. Reis, Aline M. da Silva, and Sergio Verjovski-Almeida

Zerg: a very fast BLAST parser library
Bioinformatics 2003 19: 1035-1036; doi:10.1093/bioinformatics/btg122 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

David M.A. Martin, Pamela Hill, Geoffrey J. Barton, and Andrew J. Flavell

Visual representation of database search results: the RHIMS Plot
Bioinformatics 2003 19: 1037-1038; doi:10.1093/bioinformatics/btg116 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tao Xie and Leroy Hood

ACGT—a comparative genomics tool
Bioinformatics 2003 19: 1039-1040; doi:10.1093/bioinformatics/btg121 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Marcin von Grotthuss, Jakub Pas, and Leszek Rychlewski

Ligand-Info, searching for similar small compounds using index profiles
Bioinformatics 2003 19: 1041-1042; doi:10.1093/bioinformatics/btg117 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

S. S. Sheik, P. Sundararajan, V. Shanthi, and K. Sekar

CAP: conformation angles package—displaying the conformation angles of side chains in proteins
Bioinformatics 2003 19: 1043-1044; doi:10.1093/bioinformatics/btg125 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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