Bioinformatics

EDITORIALS:

Get checked abstract Hui-Hsien Chou, An-Ping Hsia, Denise L. Mooney, and Patrick S. Schnable

Picky: oligo microarray design for large genomes
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2893-2902; doi:10.1093/bioinformatics/bth347 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

LETTER TO THE EDITORS:

Lisa M. Schilling, Jonathan D. Wren, and Robert P. Dellavalle

Letter to the Editor
Bioinformatics Advance Access published on July 1, 2004
Bioinformatics 2004 20: 2903; doi:10.1093/bioinformatics/bth385 [Print PDF][Screen PDF] [Request Permissions]  

DISCOVERY NOTES:

Get checked abstract Neeraj Pandey, Mythily Ganapathi, Kaushal Kumar, Dipayan Dasgupta, Sushanta Kumar Das Sutar, and Debasis Dash

Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2904-2910; doi:10.1093/bioinformatics/bth344 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Eric Bonnet, Jan Wuyts, Pierre Rouzé, and Yves Van de Peer

Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 2911-2917; doi:10.1093/bioinformatics/bth374 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

ORIGINAL PAPERS:

Get checked abstract Xiaobo Zhou, Xiaodong Wang, Ranadip Pal, Ivan Ivanov, Michael Bittner, and Edward R. Dougherty

A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks
Bioinformatics Advance Access published on May 14, 2004
Bioinformatics 2004 20: 2918-2927; doi:10.1093/bioinformatics/bth318 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Sven Rahmann and Christine Gräfe

Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 2928-2933; doi:10.1093/bioinformatics/bth334 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Iosifina Pournara and Lorenz Wernisch

Reconstruction of gene networks using Bayesian learning and manipulation experiments
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2934-2942; doi:10.1093/bioinformatics/bth337 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Madhuchhanda Bhattacharjee, Colin C. Pritchard, Peter S. Nelson, and Elja Arjas

Bayesian integrated functional analysis of microarray data
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2943-2953; doi:10.1093/bioinformatics/bth338 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Wenqing He

A spline function approach for detecting differentially expressed genes in microarray data analysis
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2954-2963; doi:10.1093/bioinformatics/bth339 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Gábor E. Tusnády, Zsuzsanna Dosztányi, and István Simon

Transmembrane proteins in the Protein Data Bank: identification and classification
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2964-2972; doi:10.1093/bioinformatics/bth340 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Ji-Ping Z. Wang, Bruce G. Lindsay, James Leebens-Mack, Liying Cui, Kerr Wall, Webb C. Miller, and Claude W. dePamphilis

EST clustering error evaluation and correction
Bioinformatics Advance Access published on June 9, 2004
Bioinformatics 2004 20: 2973-2984; doi:10.1093/bioinformatics/bth342 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract C. Baumgartner, C. Böhm, D. Baumgartner, G. Marini, K. Weinberger, B. Olgemöller, B. Liebl, and A. A. Roscher

Supervised machine learning techniques for the classification of metabolic disorders in newborns
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2985-2996; doi:10.1093/bioinformatics/bth343 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Cynthia Sims Parr, Bongshin Lee, Dana Campbell, and Benjamin B. Bederson

Visualizations for taxonomic and phylogenetic trees
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 2997-3004; doi:10.1093/bioinformatics/bth345 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Jörn Lewin, Armin O. Schmitt, Péter Adorján, Thomas Hildmann, and Christian Piepenbrock

Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates
Bioinformatics Advance Access published on July 9, 2004
Bioinformatics 2004 20: 3005-3012; doi:10.1093/bioinformatics/bth346 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract A. D. King, N. Przulj, and I. Jurisica

Protein complex prediction via cost-based clustering
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 3013-3020; doi:10.1093/bioinformatics/bth351 [Abstract] [Print PDF][Screen PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Mark Girolami and Rainer Breitling

Biologically valid linear factor models of gene expression
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3021-3033; doi:10.1093/bioinformatics/bth354 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Scott Soltys, Gongyi Shi, Albert Koong, and Quynh-Thu Le

Sample classification from protein mass spectrometry, by ‘peak probability contrasts’
Bioinformatics Advance Access published on June 29, 2004
Bioinformatics 2004 20: 3034-3044; doi:10.1093/bioinformatics/bth357 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Tom Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Martin Senger, Mark Greenwood, Tim Carver, Kevin Glover, Matthew R. Pocock, Anil Wipat, and Peter Li

Taverna: a tool for the composition and enactment of bioinformatics workflows
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3045-3054; doi:10.1093/bioinformatics/bth361 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Pål Sætrom

Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3055-3063; doi:10.1093/bioinformatics/bth364 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Trees-Juen Chuang, Feng-Chi Chen, and Meng-Yuan Chou

A comparative method for identification of gene structures and alternatively spliced variants
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3064-3079; doi:10.1093/bioinformatics/bth368 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Changyu Hu, Xiang Li, and Jie Liang

Developing optimal non-linear scoring function for protein design
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3080-3098; doi:10.1093/bioinformatics/bth369 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Yan Liu, Jaime Carbonell, Judith Klein-Seetharaman, and Vanathi Gopalakrishnan

Comparison of probabilistic combination methods for protein secondary structure prediction
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3099-3107; doi:10.1093/bioinformatics/bth370 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract A. Hsiao, D. S. Worrall, J. M. Olefsky, and S. Subramaniam

Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3108-3127; doi:10.1093/bioinformatics/bth371 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Glen A. Satten, Somnath Datta, Hercules Moura, Adrian R. Woolfitt, Maria da G. Carvalho, George M. Carlone, Barun K. De, Antonis Pavlopoulos, and John R. Barr

Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3128-3136; doi:10.1093/bioinformatics/bth372 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Jun Sese, Yukinori Kurokawa, Morito Monden, Kikuya Kato, and Shinichi Morishita

Constrained clusters of gene expression profiles with pathological features
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3137-3145; doi:10.1093/bioinformatics/bth373 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Yinglei Lai, Baolin Wu, Liang Chen, and Hongyu Zhao

A statistical method for identifying differential gene–gene co-expression patterns
Bioinformatics Advance Access published on July 1, 2004
Bioinformatics 2004 20: 3146-3155; doi:10.1093/bioinformatics/bth379 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Ben-Yang Liao, Yu-Jung Chang, Jan-Ming Ho, and Ming-Jing Hwang

The UniMarker (UM) method for synteny mapping of large genomes
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3156-3165; doi:10.1093/bioinformatics/bth380 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract J. Wang, K. R. Coombes, W. E. Highsmith, M. J. Keating, and L. V. Abruzzo

Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies
Bioinformatics Advance Access published on July 1, 2004
Bioinformatics 2004 20: 3166-3178; doi:10.1093/bioinformatics/bth381 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Jong Hun Kim, Juyoung Lee, Bermseok Oh, Kuchan Kimm, and InSong Koh

Prediction of phosphorylation sites using SVMs
Bioinformatics Advance Access published on July 1, 2004
Bioinformatics 2004 20: 3179-3184; doi:10.1093/bioinformatics/bth382 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Nathalie Pochet, Frank De Smet, Johan A. K. Suykens, and Bart L. R. De Moor

Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction
Bioinformatics Advance Access published on July 1, 2004
Bioinformatics 2004 20: 3185-3195; doi:10.1093/bioinformatics/bth383 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract David Baird, Peter Johnstone, and Theresa Wilson

Normalization of microarray data using a spatial mixed model analysis which includes splines
Bioinformatics Advance Access published on July 1, 2004
Bioinformatics 2004 20: 3196-3205; doi:10.1093/bioinformatics/bth384 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract David P. A. Corney, Bernard F. Buxton, William B. Langdon, and David T. Jones

BioRAT: extracting biological information from full-length papers
Bioinformatics Advance Access published on July 1, 2004
Bioinformatics 2004 20: 3206-3213; doi:10.1093/bioinformatics/bth386 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract R. Bundschuh

Computational prediction of RNA editing sites
Bioinformatics Advance Access published on July 1, 2004
Bioinformatics 2004 20: 3214-3220; doi:10.1093/bioinformatics/bth387 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Reuben Thomas, Sanjay Mehrotra, Eleftherios T. Papoutsakis, and Vassily Hatzimanikatis

A model-based optimization framework for the inference on gene regulatory networks from DNA array data
Bioinformatics Advance Access published on July 9, 2004
Bioinformatics 2004 20: 3221-3235; doi:10.1093/bioinformatics/bth389 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

APPLICATIONS NOTES:

Get checked abstract Rasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, and Rolf Apweiler

UniProt archive
Bioinformatics Advance Access published on March 25, 2004
Bioinformatics 2004 20: 3236-3237; doi:10.1093/bioinformatics/bth191 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Don Gilbert, Yoshihiro Ugawa, Markus Buchhorn, Tan Tin Wee, Akira Mizushima, Hyunchul Kim, Kilnam Chon, Seyeon Weon, Juncai Ma, Yoshihiro Ichiyanagi, Der-Ming Liou, Somnuk Keretho, and Suhaimi Napis

Bio-Mirror project for public bio-data distribution
Bioinformatics Advance Access published on April 1, 2004
Bioinformatics 2004 20: 3238-3240; doi:10.1093/bioinformatics/bth219 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Fredrik Pettersson, Oskar Jonsson, and Lon R. Cardon

GOLDsurfer: three dimensional display of linkage disequilibrium
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3241-3243; doi:10.1093/bioinformatics/bth341 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Jaime R. Robles and Edwin J. C. G. van den Oord

lga972: a cross-platform application for optimizing LD studies using a genetic algorithm
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 3244-3245; doi:10.1093/bioinformatics/bth348 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Alok J. Saldanha

Java Treeview—extensible visualization of microarray data
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 3246-3248; doi:10.1093/bioinformatics/bth349 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Ryan T. McDonald, R. Scott Winters, Mark Mandel, Yang Jin, Peter S. White, and Fernando Pereira

An entity tagger for recognizing acquired genomic variations in cancer literature
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 3249-3251; doi:10.1093/bioinformatics/bth350 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Stacia K. Wyman, Robert K. Jansen, and Jeffrey L. Boore

Automatic annotation of organellar genomes with DOGMA
Bioinformatics Advance Access published on June 4, 2004
Bioinformatics 2004 20: 3252-3255; doi:10.1093/bioinformatics/bth352 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract WangSen Feng, Lusheng Wang, and Daming Zhu

CTRD: a fast applet for computing signed translocation distance between genomes
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3256-3257; doi:10.1093/bioinformatics/bth356 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Ioannis C. Spyropoulos, Theodore D. Liakopoulos, Pantelis G. Bagos, and Stavros J. Hamodrakas

TMRPres2D: high quality visual representation of transmembrane protein models
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3258-3260; doi:10.1093/bioinformatics/bth358 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Thomas Mailund and Christian N. S. Pedersen

QuickJoin—fast neighbour-joining tree reconstruction
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3261-3262; doi:10.1093/bioinformatics/bth359 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Tianhua Niu and Zhenjun Hu

SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3263-3265; doi:10.1093/bioinformatics/bth360 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Eugen C. Buehler, Jeffrey R. Sachs, Kui Shao, Ansuman Bagchi, and Lyle H. Ungar

The CRASSS plug-in for integrating annotation data with hierarchical clustering results
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3266-3269; doi:10.1093/bioinformatics/bth362 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Bo Kyeng Hou, Jin Sik Kim, Ji Hoon Jun, Dong-Yup Lee, Yong Wook Kim, Sujin Chae, Mira Roh, Yong-Ho In, and Sang Yup Lee

BioSilico: an integrated metabolic database system
Bioinformatics Advance Access published on June 16, 2004
Bioinformatics 2004 20: 3270-3272; doi:10.1093/bioinformatics/bth363 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Tao-Wei Huang, An-Chi Tien, Wen-Shien Huang, Yuan-Chii G. Lee, Chin-Lin Peng, Huei-Hun Tseng, Cheng-Yan Kao, and Chi-Ying F. Huang

POINT: a database for the prediction of protein–protein interactions based on the orthologous interactome
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3273-3276; doi:10.1093/bioinformatics/bth366 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Patrick May, Stefan Barthel, and Ina Koch

PTGL—a web-based database application for protein topologies
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3277-3279; doi:10.1093/bioinformatics/bth367 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract M. Bahlo, L. Xing, and C. R. Wilkinson

HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3280-3283; doi:10.1093/bioinformatics/bth375 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Alexey V. Antonov, Igor V. Tetko, Volodymyr V. Prokopenko, Denis Kosykh, and Hans W. Mewes

A web portal for classification of expression data using maximal margin linear programming
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3284-3285; doi:10.1093/bioinformatics/bth376 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract J. R. Bilbao-Castro, C. O. S. Sorzano, I. García, and J. J. Fernández

Phan3D: design of biological phantoms in 3D electron microscopy
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3286-3288; doi:10.1093/bioinformatics/bth377 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

Get checked abstract Michael L. Blinov, James R. Faeder, Byron Goldstein, and William S. Hlavacek

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains
Bioinformatics Advance Access published on June 24, 2004
Bioinformatics 2004 20: 3289-3291; doi:10.1093/bioinformatics/bth378 [Abstract] [Print PDF][Screen PDF] [Request Permissions]  

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