Bioinformatics

Janet Thornton, David Gilbert, and Cath Brooksbank

ISMB/ECCB 2004
Bioinformatics 2004 20: i1-i2; doi:10.1093/bioinformatics/bth950 [Print PDF][Screen PDF]  

ISMB/ECCB 2004 Organization
Bioinformatics 2004 20: i3-i5; doi:10.1093/bioinformatics/bth951 [Print PDF][Screen PDF]  

Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, and Hiroshi Mamitsuka

Application of a new probabilistic model for recognizing complex patterns in glycans
Bioinformatics 2004 20: i6-i14; doi:10.1093/bioinformatics/bth916 [Abstract] [Print PDF][Screen PDF]  

C. Baral, K. Chancellor, N. Tran, N.L. Tran, A. Joy, and M. Berens

A knowledge based approach for representing and reasoning about signaling networks
Bioinformatics 2004 20: i15-i22; doi:10.1093/bioinformatics/bth918 [Abstract] [Print PDF][Screen PDF]  

Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, and Roni Rosenfeld

Deconvolving cell cycle expression data with complementary information
Bioinformatics 2004 20: i23-i30; doi:10.1093/bioinformatics/bth915 [Abstract] [Print PDF][Screen PDF]  

Tim Beißbarth, Lavinia Hyde, Gordon K. Smyth, Chris Job, Wee-Ming Boon, Seong-Seng Tan, Hamish S. Scott, and Terence P. Speed

Statistical modeling of sequencing errors in SAGE libraries
Bioinformatics 2004 20: i31-i39; doi:10.1093/bioinformatics/bth924 [Abstract] [Print PDF][Screen PDF]  

Gill Bejerano, David Haussler, and Mathieu Blanchette

Into the heart of darkness: large-scale clustering of human non-coding DNA
Bioinformatics 2004 20: i40-i48; doi:10.1093/bioinformatics/bth946 [Abstract] [Print PDF][Screen PDF]  

Marshall Bern, David Goldberg, W. Hayes McDonald, and John R. Yates, III

Automatic Quality Assessment of Peptide Tandem Mass Spectra
Bioinformatics 2004 20: i49-i54; doi:10.1093/bioinformatics/bth947 [Abstract] [Print PDF][Screen PDF]  

Doron Betel, Ruth Isserlin, and Christopher W. V. Hogue

Analysis of domain correlations in yeast protein complexes
Bioinformatics 2004 20: i55-i62; doi:10.1093/bioinformatics/bth903 [Abstract] [Print PDF][Screen PDF]  

Emidio Capriotti, Piero Fariselli, and Rita Casadio

A neural-network-based method for predicting protein stability changes upon single point mutations
Bioinformatics 2004 20: i63-i68; doi:10.1093/bioinformatics/bth928 [Abstract] [Print PDF][Screen PDF]  

Robert Castelo and Roderic Guigó

Splice site identification by idlBNs
Bioinformatics 2004 20: i69-i76; doi:10.1093/bioinformatics/bth932 [Abstract] [Print PDF][Screen PDF]  

Shann-Ching Chen and Ivet Bahar

Mining frequent patterns in protein structures: a study of protease families
Bioinformatics 2004 20: i77-i85; doi:10.1093/bioinformatics/bth912 [Abstract] [Print PDF][Screen PDF]  

Sarah Cohen Boulakia, Séverine Lair, Nicolas Stransky, Stéphane Graziani, François Radvanyi, Emmanuel Barillot, and Christine Froidevaux

Selecting biomedical data sources according to user preferences
Bioinformatics 2004 20: i86-i93; doi:10.1093/bioinformatics/bth949 [Abstract] [Print PDF][Screen PDF]  

L. Coin and R. Durbin

Improved techniques for the identification of pseudogenes
Bioinformatics 2004 20: i94-i100; doi:10.1093/bioinformatics/bth942 [Abstract] [Print PDF][Screen PDF]  

M. J. L. de Hoon, Y. Makita, S. Imoto, K. Kobayashi, N. Ogasawara, K. Nakai, and S. Miyano

Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data
Bioinformatics 2004 20: i101-i108; doi:10.1093/bioinformatics/bth927 [Abstract] [Print PDF][Screen PDF]  

Christoph Dieterich, Sven Rahmann, and Martin Vingron

Functional inference from non-random distributions of conserved predicted transcription factor binding sites
Bioinformatics 2004 20: i109-i115; doi:10.1093/bioinformatics/bth908 [Abstract] [Print PDF][Screen PDF]  

Hernán Dopazo, Javier Santoyo, and Joaquín Dopazo

Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species
Bioinformatics 2004 20: i116-i121; doi:10.1093/bioinformatics/bth902 [Abstract] [Print PDF][Screen PDF]  

Angela Enosh, Sarel J. Fleishman, Nir Ben-Tal, and Dan Halperin

Assigning transmembrane segments to helices in intermediate-resolution structures
Bioinformatics 2004 20: i122-i129; doi:10.1093/bioinformatics/bth939 [Abstract] [Print PDF][Screen PDF]  

Richard A. George, Ruth V. Spriggs, Janet M. Thornton, Bissan Al-Lazikani, and Mark B. Swindells

SCOPEC: a database of protein catalytic domains
Bioinformatics 2004 20: i130-i136; doi:10.1093/bioinformatics/bth948 [Abstract] [Print PDF][Screen PDF]  

G. Greenspan and D. Geiger

High density linkage disequilibrium mapping using models of haplotype block variation
Bioinformatics 2004 20: i137-i144; doi:10.1093/bioinformatics/bth907 [Abstract] [Print PDF][Screen PDF]  

Cigdem Gunduz, Bülent Yener, and S. Humayun Gultekin

The cell graphs of cancer
Bioinformatics 2004 20: i145-i151; doi:10.1093/bioinformatics/bth933 [Abstract] [Print PDF][Screen PDF]  

Naohiko Heida, Yoshikazu Hasegawa, Yoshiki Mochizuki, Katsura Hirosawa, Akihiko Konagaya, and Tetsuro Toyoda

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks
Bioinformatics 2004 20: i152-i160; doi:10.1093/bioinformatics/bth940 [Abstract] [Print PDF][Screen PDF]  

Vladimir Jojic, Nebojsa Jojic, Chris Meek, Dan Geiger, Adam Siepel, David Haussler, and D. Heckerman

Efficient approximations for learning phylogenetic HMM models from data
Bioinformatics 2004 20: i161-i168; doi:10.1093/bioinformatics/bth917 [Abstract] [Print PDF][Screen PDF]  

Cliff A. Joslyn, Susan M. Mniszewski, Andy Fulmer, and Gary Heaton

The Gene Ontology Categorizer
Bioinformatics 2004 20: i169-i177; doi:10.1093/bioinformatics/bth921 [Abstract] [Print PDF][Screen PDF]  

Peter Kharchenko, Dennis Vitkup, and George M. Church

Filling gaps in a metabolic network using expression information
Bioinformatics 2004 20: i178-i185; doi:10.1093/bioinformatics/bth930 [Abstract] [Print PDF][Screen PDF]  

Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, and Knut Reinert

Optimal robust non-unique probe selection using Integer Linear Programming
Bioinformatics 2004 20: i186-i193; doi:10.1093/bioinformatics/bth936 [Abstract] [Print PDF][Screen PDF]  

Dennis Kostka and Rainer Spang

Finding disease specific alterations in the co-expression of genes
Bioinformatics 2004 20: i194-i199; doi:10.1093/bioinformatics/bth909 [Abstract] [Print PDF][Screen PDF]  

Mehmet Koyutürk, Ananth Grama, and Wojciech Szpankowski

An efficient algorithm for detecting frequent subgraphs in biological networks
Bioinformatics 2004 20: i200-i207; doi:10.1093/bioinformatics/bth919 [Abstract] [Print PDF][Screen PDF]  

Hongzhe Li and Jiang Gui

Partial Cox regression analysis for high-dimensional microarray gene expression data
Bioinformatics 2004 20: i208-i215; doi:10.1093/bioinformatics/bth900 [Abstract] [Print PDF][Screen PDF]  

Gerton Lunter and Jotun Hein

A nucleotide substitution model with nearest-neighbour interactions
Bioinformatics 2004 20: i216-i223; doi:10.1093/bioinformatics/bth901 [Abstract] [Print PDF][Screen PDF]  

Robert M. MacCallum

Striped sheets and protein contact prediction
Bioinformatics 2004 20: i224-i231; doi:10.1093/bioinformatics/bth913 [Abstract] [Print PDF][Screen PDF]  

Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, and Christina Leslie

Predicting genetic regulatory response using classification
Bioinformatics 2004 20: i232-i240; doi:10.1093/bioinformatics/bth923 [Abstract] [Print PDF][Screen PDF]  

Sven Mika and Burkhard Rost

Protein names precisely peeled off free text
Bioinformatics 2004 20: i241-i247; doi:10.1093/bioinformatics/bth904 [Abstract] [Print PDF][Screen PDF]  

I. Nachman, A. Regev, and N. Friedman

Inferring quantitative models of regulatory networks from expression data
Bioinformatics 2004 20: i248-i256; doi:10.1093/bioinformatics/bth941 [Abstract] [Print PDF][Screen PDF]  

S. A. Racunas, N. H. Shah, I. Albert, and N. V. Fedoroff

HyBrow: a prototype system for computer-aided hypothesis evaluation
Bioinformatics 2004 20: i257-i264; doi:10.1093/bioinformatics/bth905 [Abstract] [Print PDF][Screen PDF]  

Benjamin J. Raphael and Pavel A. Pevzner

Reconstructing tumor amplisomes
Bioinformatics 2004 20: i265-i273; doi:10.1093/bioinformatics/bth931 [Abstract] [Print PDF][Screen PDF]  

David J. Reiss and Benno Schwikowski

Predicting protein–peptide interactions via a network-based motif sampler
Bioinformatics 2004 20: i274-i282; doi:10.1093/bioinformatics/bth922 [Abstract] [Print PDF][Screen PDF]  

Alexander Schliep, Christine Steinhoff, and Alexander Schönhuth

Robust inference of groups in gene expression time-courses using mixtures of HMMs
Bioinformatics 2004 20: i283-i289; doi:10.1093/bioinformatics/bth937 [Abstract] [Print PDF][Screen PDF]  

Padmini Srinivasan and Bisharah Libbus

Mining MEDLINE for implicit links between dietary substances and diseases
Bioinformatics 2004 20: i290-i296; doi:10.1093/bioinformatics/bth914 [Abstract] [Print PDF][Screen PDF]  

K.N. Srinivasan, G.L. Zhang, A.M. Khan, J.T. August, and V. Brusic

Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens
Bioinformatics 2004 20: i297-i302; doi:10.1093/bioinformatics/bth943 [Abstract] [Print PDF][Screen PDF]  

R. D. Stevens, H. J. Tipney, C. J. Wroe, T. M. Oinn, M. Senger, P. W. Lord, C. A. Goble, A. Brass, and M. Tassabehji

Exploring Williams–Beuren syndrome using ^myGrid
Bioinformatics 2004 20: i303-i310; doi:10.1093/bioinformatics/bth944 [Abstract] [Print PDF][Screen PDF]  

Radek Szklarczyk and Jaap Heringa

Tracking repeats using significance and transitivity
Bioinformatics 2004 20: i311-i317; doi:10.1093/bioinformatics/bth911 [Abstract] [Print PDF][Screen PDF]  

Phil Trinh, Aoife McLysaght, and David Sankoff

Genomic features in the breakpoint regions between syntenic blocks
Bioinformatics 2004 20: i318-i325; doi:10.1093/bioinformatics/bth934 [Abstract] [Print PDF][Screen PDF]  

Koji Tsuda and William Stafford Noble

Learning kernels from biological networks by maximizing entropy
Bioinformatics 2004 20: i326-i333; doi:10.1093/bioinformatics/bth906 [Abstract] [Print PDF][Screen PDF]  

Zasha Weinberg and Walter L. Ruzzo

Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy
Bioinformatics 2004 20: i334-i341; doi:10.1093/bioinformatics/bth925 [Abstract] [Print PDF][Screen PDF]  

D. Wieser, E. Kretschmann, and R. Apweiler

Filtering erroneous protein annotation
Bioinformatics 2004 20: i342-i347; doi:10.1093/bioinformatics/bth938 [Abstract] [Print PDF][Screen PDF]  

M. D. Woodhams and M. D. Hendy

Reconstructing phylogeny by Quadratically Approximated Maximum Likelihood
Bioinformatics 2004 20: i348-i354; doi:10.1093/bioinformatics/bth926 [Abstract] [Print PDF][Screen PDF]  

Weijia Xu, Willard J. Briggs, Joanna Padolina, Ruth E. Timme, Wenguo Liu, C. Randal Linder, and Daniel P. Miranker

Using MoBIoS' scalable genome join to find conserved primer pair candidates between two genomes
Bioinformatics 2004 20: i355-i362; doi:10.1093/bioinformatics/bth929 [Abstract] [Print PDF][Screen PDF]  

Y. Yamanishi, J.-P. Vert, and M. Kanehisa

Protein network inference from multiple genomic data: a supervised approach
Bioinformatics 2004 20: i363-i370; doi:10.1093/bioinformatics/bth910 [Abstract] [Print PDF][Screen PDF]  

Changhui Yan, Drena Dobbs, and Vasant Honavar

A two-stage classifier for identification of protein–protein interface residues
Bioinformatics 2004 20: i371-i378; doi:10.1093/bioinformatics/bth920 [Abstract] [Print PDF][Screen PDF]  

Mehdi Yousfi Monod, Véronique Giudicelli, Denys Chaume, and Marie-Paule Lefranc

IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V–J and V–D–J JUNCTIONs
Bioinformatics 2004 20: i379-i385; doi:10.1093/bioinformatics/bth945 [Abstract] [Print PDF][Screen PDF]  

Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, and Chris Bystroff

Predicting protein folding pathways
Bioinformatics 2004 20: i386-i393; doi:10.1093/bioinformatics/bth935 [Abstract] [Print PDF][Screen PDF]  

Author Index
Bioinformatics 2004 20: i394-i395; doi:10.1093/bioinformatics/bth952 [Print PDF][Screen PDF]  

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