Bioinformatics

EDITORIALS:

Pavel A. Pevzner

Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2159-2161; doi:10.1093/bioinformatics/bth217 [Print PDF][Screen PDF] [Request Permissions]  

DISCOVERY NOTES:

Katherine A. Kantardjieff and Bernhard Rupp

Protein isoelectric point as a predictor for increased crystallization screening efficiency
Bioinformatics Advance Access published on February 10, 2004
Bioinformatics 2004 20: 2162-2168; doi:10.1093/bioinformatics/bth066 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

LETTER TO THE EDITORS:

Thomas Huber and Bostjan Kobe

Comment on ‘Protein isoelectric point as a predictor for increased crystallization screening efficiency’
Bioinformatics Advance Access published on August 18, 2004
Bioinformatics 2004 20: 2169-2170; doi:10.1093/bioinformatics/bth452 [Print PDF][Screen PDF] [Request Permissions]  

REPLY TO THE LETTERS:

Katherine A. Kantardjieff, Mortaza Jamshidian, and Bernhard Rupp

Distributions of pI versus pH provide prior information for the design of crystallization screening experiments: response to comment on ‘Protein isoelectric point as a predictor for increased crystallization screening efficiency’
Bioinformatics Advance Access published on August 18, 2004
Bioinformatics 2004 20: 2171-2174; doi:10.1093/bioinformatics/bth453 [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Bin Qian and Richard A. Goldstein

Performance of an iterated T-HMM for homology detection
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 2175-2180; doi:10.1093/bioinformatics/bth181 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Takaho A. Endo

Probabilistic nucleotide assembling method for sequencing by hybridization
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2181-2188; doi:10.1093/bioinformatics/bth202 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Tuan D. Pham, Denis I. Crane, Tuan H. Tran, and Tam H. Nguyen

Extraction of fluorescent cell puncta by adaptive fuzzy segmentation
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2189-2196; doi:10.1093/bioinformatics/bth213 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

H. P. Shanahan and J. M. Thornton

An examination of the conservation of surface patch polarity for proteins
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2197-2204; doi:10.1093/bioinformatics/bth218 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Guillaume Koum, Augustin Yekel, Bengyella Ndifon, and Frédéric Simard

Design and implementation of a mosquito database through an entomological ontology
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2205-2211; doi:10.1093/bioinformatics/bth221 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ekaterina Poustelnikova, Andrei Pisarev, Maxim Blagov, Maria Samsonova, and John Reinitz

A database for management of gene expression data in situ
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2212-2221; doi:10.1093/bioinformatics/bth222 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Ivo L. Hofacker, Stephan H. F. Bernhart, and Peter F. Stadler

Alignment of RNA base pairing probability matrices
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2222-2227; doi:10.1093/bioinformatics/bth229 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer, and Thomas Lengauer

Arby: automatic protein structure prediction using profile–profile alignment and confidence measures
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2228-2235; doi:10.1093/bioinformatics/bth232 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

C. J. Zheng, H. Zhou, B. Xie, L. Y. Han, C. W. Yap, and Y. Z. Chen

TRMP: a database of therapeutically relevant multiple pathways
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2236-2241; doi:10.1093/bioinformatics/bth233 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Scott L. Carter, Christian M. Brechbühler, Michael Griffin, and Andrew T. Bond

Gene co-expression network topology provides a framework for molecular characterization of cellular state
Bioinformatics Advance Access published on May 6, 2004
Bioinformatics 2004 20: 2242-2250; doi:10.1093/bioinformatics/bth234 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

D. J. Brooks, J. R. Fresco, and M. Singh

A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2251-2257; doi:10.1093/bioinformatics/bth235 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Linyong Mao and Haluk Resat

Probabilistic representation of gene regulatory networks
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2258-2269; doi:10.1093/bioinformatics/bth236 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Claus Thorn Ekstrøm, Søren Bak, Charlotte Kristensen, and Mats Rudemo

Spot shape modelling and data transformations for microarrays
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2270-2278; doi:10.1093/bioinformatics/bth237 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Edward Susko and Andrew J. Roger

Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2279-2287; doi:10.1093/bioinformatics/bth239 [Abstract] [Print PDF][Screen PDF] Supplementary data [Request Permissions]  

James E. Bray, Russell L. Marsden, Stuart C.G. Rison, Alexei Savchenko, Aled M. Edwards, Janet M. Thornton, and Christine A. Orengo

A practical and robust sequence search strategy for structural genomics target selection
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 2288-2295; doi:10.1093/bioinformatics/bth240 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Alejandro Heredia-Langner, William R. Cannon, Kenneth D. Jarman, and Kristin H. Jarman

Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data
Bioinformatics Advance Access published on April 15, 2004
Bioinformatics 2004 20: 2296-2304; doi:10.1093/bioinformatics/bth242 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Markus Ringnér, Srinivas Veerla, Samuel Andersson, Johan Staaf, and Jari Häkkinen

ACID: a database for microarray clone information
Bioinformatics Advance Access published on February 12, 2004
Bioinformatics 2004 20: 2305-2306; doi:10.1093/bioinformatics/bth089 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

R. Ciria, C. Abreu-Goodger, E. Morett, and E. Merino

GeConT: gene context analysis
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2307-2308; doi:10.1093/bioinformatics/bth216 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Yin Te Tsai, Yen Pin Huang, Ching Ta Yu, and Chin Lung Lu

MuSiC: a tool for multiple sequence alignment with constraints
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2309-2311; doi:10.1093/bioinformatics/bth220 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

T. J. Dolinsky, P. M. J. Burgers, K. Karplus, and N. A. Baker

SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2312-2314; doi:10.1093/bioinformatics/bth223 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

M. B. Lanktree, L. VanderBeek, F. M. Macciardi, and J. L. Kennedy

PedSplit: pedigree management for stratified analysis
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2315-2316; doi:10.1093/bioinformatics/bth224 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Thomas Huber, Geoffrey Faulkner, and Philip Hugenholtz

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2317-2319; doi:10.1093/bioinformatics/bth226 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

L. Smith, T. Rindflesch, and W. J. Wilbur

MedPost: a part-of-speech tagger for bioMedical text
Bioinformatics Advance Access published on April 8, 2004
Bioinformatics 2004 20: 2320-2321; doi:10.1093/bioinformatics/bth227 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

George Savva, Jenn Conn, and Jo Dicks

Drawing phylogenetic trees in LATEX and Microsoft Word
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2322-2323; doi:10.1093/bioinformatics/bth228 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Anne Arcade, Aymeric Labourdette, Matthieu Falque, Brigitte Mangin, Fabien Chardon, Alain Charcosset, and Johann Joets

BioMercator: integrating genetic maps and QTL towards discovery of candidate genes
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2324-2326; doi:10.1093/bioinformatics/bth230 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Frank Dudbridge, Tim Carver, and Gary W. Williams

Pelican: pedigree editor for linkage computer analysis
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2327-2328; doi:10.1093/bioinformatics/bth231 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Fran Supek and Kristian Vlahovicek

INCA: synonymous codon usage analysis and clustering by means of self-organizing map
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2329-2330; doi:10.1093/bioinformatics/bth238 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Florian Iragne, Aurélien Barré, Nicolas Goffard, and Antoine de Daruvar

AliasServer: a web server to handle multiple aliases used to refer to proteins
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 2331-2332; doi:10.1093/bioinformatics/bth241 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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