Bioinformatics

REVIEW:

STRUCTURAL BIOINFORMATICS:

Get checked abstract Svava Ósk Jónsdóttir, Flemming Steen Jørgensen, and Søren Brunak

Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2145-2160; doi:10.1093/bioinformatics/bti314 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

DISCOVERY NOTES:

SEQUENCE ANALYSIS:

Get checked abstract Prachee Prakash, Sailu Yellaboina, Akash Ranjan, and Seyed E. Hasnain

Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2161-2166; doi:10.1093/bioinformatics/bti375 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Akira R. Kinjo and Ken Nishikawa

Recoverable one-dimensional encoding of three-dimensional protein structures
Bioinformatics Advance Access published on February 18, 2005
Bioinformatics 2005 21: 2167-2170; doi:10.1093/bioinformatics/bti330 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract C. Thach Nguyen, Y. C. Tay, and Louxin Zhang

Divide-and-conquer approach for the exemplar breakpoint distance
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2171-2176; doi:10.1093/bioinformatics/bti327 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jayson Falkner and Philip Andrews

Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2177-2184; doi:10.1093/bioinformatics/bti362 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Lei Bao and Yan Cui

Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2185-2190; doi:10.1093/bioinformatics/bti365 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract L. Lancashire, O. Schmid, H. Shah, and G. Ball

Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2191-2199; doi:10.1093/bioinformatics/bti368 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract J. S. Yu, S. Ongarello, R. Fiedler, X. W. Chen, G. Toffolo, C. Cobelli, and Z. Trajanoski

Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry data
Bioinformatics Advance Access published on March 22, 2005
Bioinformatics 2005 21: 2200-2209; doi:10.1093/bioinformatics/bti370 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Halima Bensmail, Jennifer Golek, Michelle M. Moody, John O. Semmes, and Abdelali Haoudi

A novel approach for clustering proteomics data using Bayesian fast Fourier transform
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2210-2224; doi:10.1093/bioinformatics/bti383 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Valerio Freschi and Alessandro Bogliolo

Using sequence compression to speedup probabilistic profile matching
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2225-2229; doi:10.1093/bioinformatics/bti323 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Robert G. Beiko, Cheong Xin Chan, and Mark A. Ragan

A word-oriented approach to alignment validation
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2230-2239; doi:10.1093/bioinformatics/bti335 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract A. V. Favorov, M. S. Gelfand, A. V. Gerasimova, D. A. Ravcheev, A. A. Mironov, and V. J. Makeev

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2240-2245; doi:10.1093/bioinformatics/bti336 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract David H. Mathews

Predicting a set of minimal free energy RNA secondary structures common to two sequences
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2246-2253; doi:10.1093/bioinformatics/bti349 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract R. A. O'Flanagan, G. Paillard, R. Lavery, and A. M. Sengupta

Non-additivity in protein–DNA binding
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2254-2263; doi:10.1093/bioinformatics/bti361 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kyounghwa Bae, Bani K. Mallick, and Christine G. Elsik

Prediction of protein interdomain linker regions by a hidden Markov model
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2264-2270; doi:10.1093/bioinformatics/bti363 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract H. L. Chan, T. W. Lam, W. K. Sung, Prudence W. H. Wong, S. M. Yiu, and X. Fan

The mutated subsequence problem and locating conserved genes
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2271-2278; doi:10.1093/bioinformatics/bti371 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Mikael Bodén and John Hawkins

Prediction of subcellular localization using sequence-biased recurrent networks
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2279-2286; doi:10.1093/bioinformatics/bti372 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Robel Y. Kahsay, Guoli Wang, Guang Gao, Li Liao, and Roland Dunbrack

Quasi-consensus-based comparison of profile hidden Markov models for protein sequences
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2287-2293; doi:10.1093/bioinformatics/bti374 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Ian Holmes

Using evolutionary Expectation Maximization to estimate indel rates
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2294-2300; doi:10.1093/bioinformatics/bti177 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract D. Tsafrir, I. Tsafrir, L. Ein-Dor, O. Zuk, D.A. Notterman, and E. Domany

Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices
Bioinformatics Advance Access published on February 18, 2005
Bioinformatics 2005 21: 2301-2308; doi:10.1093/bioinformatics/bti329 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract George M. Garrity and Timothy G. Lilburn

Self-organizing and self-correcting classifications of biological data
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2309-2314; doi:10.1093/bioinformatics/bti346 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andrew J. Bordner and Ruben Abagyan

REVCOM: a robust Bayesian method for evolutionary rate estimation
Bioinformatics Advance Access published on March 4, 2005
Bioinformatics 2005 21: 2315-2321; doi:10.1093/bioinformatics/bti347 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Peter F. Arndt and Terence Hwa

Identification and measurement of neighbor-dependent nucleotide substitution processes
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2322-2328; doi:10.1093/bioinformatics/bti376 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Stefan R. Henz, Daniel H. Huson, Alexander F. Auch, Kay Nieselt-Struwe, and Stephan C. Schuster

Whole-genome prokaryotic phylogeny
Bioinformatics Advance Access published on May 27, 2004
Bioinformatics 2005 21: 2329-2335; doi:10.1093/bioinformatics/bth324 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract F. Ferrè and P. Clote

Disulfide connectivity prediction using secondary structure information and diresidue frequencies
Bioinformatics Advance Access published on March 1, 2005
Bioinformatics 2005 21: 2336-2346; doi:10.1093/bioinformatics/bti328 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Richard J. Morris, Rafael J. Najmanovich, Abdullah Kahraman, and Janet M. Thornton

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2347-2355; doi:10.1093/bioinformatics/bti337 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jacek Blazewicz, Marta Szachniuk, and Adam Wojtowicz

RNA tertiary structure determination: NOE pathways construction by tabu search
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2356-2361; doi:10.1093/bioinformatics/bti351 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yuzhen Ye and Adam Godzik

Multiple flexible structure alignment using partial order graphs
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2362-2369; doi:10.1093/bioinformatics/bti353 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Qidong Zhang, Sukjoon Yoon, and William J. Welsh

Improved method for predicting ß-turn using support vector machine
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2370-2374; doi:10.1093/bioinformatics/bti358 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Markus Leber, Lars Kaderali, Alexander Schönhuth, and Rainer Schrader

A fractional programming approach to efficient DNA melting temperature calculation
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2375-2382; doi:10.1093/bioinformatics/bti379 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Ö. Carlborg, D. J. De Koning, K. F. Manly, E. Chesler, R. W. Williams, and C. S. Haley

Methodological aspects of the genetic dissection of gene expression
Bioinformatics Advance Access published on December 21, 2004
Bioinformatics 2005 21: 2383-2393; doi:10.1093/bioinformatics/bti241 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ka Yee Yeung, Roger E. Bumgarner, and Adrian E. Raftery

Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2394-2402; doi:10.1093/bioinformatics/bti319 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hongzhe Li and Yihui Luan

Boosting proportional hazards models using smoothing splines, with applications to high-dimensional microarray data
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2403-2409; doi:10.1093/bioinformatics/bti324 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Wotao Yin, Terrence Chen, Sean Xiang Zhou, and Amit Chakraborty

Background correction for cDNA microarray images using the TV+L¹ model
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2410-2416; doi:10.1093/bioinformatics/bti341 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Muhammad Shoaib B. Sehgal, Iqbal Gondal, and Laurence S. Dooley

Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2417-2423; doi:10.1093/bioinformatics/bti345 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Christian H. Busold, Stefan Winter, Nicole Hauser, Andrea Bauer, Jürgen Dippon, Jörg D. Hoheisel, and Kurt Fellenberg

Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2424-2429; doi:10.1093/bioinformatics/bti367 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract K. K. Dobbin, E. S. Kawasaki, D. W. Petersen, and R. M. Simon

Characterizing dye bias in microarray experiments
Bioinformatics Advance Access published on March 17, 2005
Bioinformatics 2005 21: 2430-2437; doi:10.1093/bioinformatics/bti378 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Jörg Rahnenführer, Niko Beerenwinkel, Wolfgang A. Schulz, Christian Hartmann, Andreas von Deimling, Bernd Wullich, and Thomas Lengauer

Estimating cancer survival and clinical outcome based on genetic tumor progression scores
Bioinformatics Advance Access published on February 10, 2005
Bioinformatics 2005 21: 2438-2446; doi:10.1093/bioinformatics/bti312 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yuehua Cui and Rongling Wu

Mapping genome–genome epistasis: a high-dimensional model
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2447-2455; doi:10.1093/bioinformatics/bti342 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rui-Sheng Wang, Ling-Yun Wu, Zhen-Ping Li, and Xiang-Sun Zhang

Haplotype reconstruction from SNP fragments by minimum error correction
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2456-2462; doi:10.1093/bioinformatics/bti352 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dmitry A. Konovalov, Bruce Litow, and Nigel Bajema

Partition-distance via the assignment problem
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2463-2468; doi:10.1093/bioinformatics/bti373 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Wei Zhao, Ying Q. Chen, George Casella, James M. Cheverud, and Rongling Wu

A non-stationary model for functional mapping of complex traits
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2469-2477; doi:10.1093/bioinformatics/bti382 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Nobukazu Ohki and Masatoshi Hagiwara

Bio-Object, a stochastic simulator for post-transcriptional regulation
Bioinformatics Advance Access published on February 10, 2005
Bioinformatics 2005 21: 2478-2487; doi:10.1093/bioinformatics/bti316 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Tsuyoshi Kato, Koji Tsuda, and Kiyoshi Asai

Selective integration of multiple biological data for supervised network inference
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2488-2495; doi:10.1093/bioinformatics/bti339 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract I. Res, I. Mihalek, and O. Lichtarge

An evolution based classifier for prediction of protein interfaces without using protein structures
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2496-2501; doi:10.1093/bioinformatics/bti340 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Daniel Shegogue and W. Jim Zheng

Object-oriented biological system integration: a SARS coronavirus example
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2502-2509; doi:10.1093/bioinformatics/bti344 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Feng-Chi Chen and Trees-Juen Chuang

ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants
Bioinformatics Advance Access published on February 18, 2005
Bioinformatics 2005 21: 2510-2513; doi:10.1093/bioinformatics/bti332 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kwangmin Choi, Yu Ma, Jeong-Heyon Choi, and Sun Kim

PLATCOM: a Platform for Computational Comparative Genomics
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2514-2516; doi:10.1093/bioinformatics/bti350 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Fengkai Zhang and Zhongming Zhao

SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2517-2519; doi:10.1093/bioinformatics/bti377 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Igor V. Tetko, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Gisela Fobo, Andreas Ruepp, Alexey V. Antonov, Dimitrij Surmeli, and Hans-Wernen Mewes

MIPS bacterial genomes functional annotation benchmark dataset
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2520-2521; doi:10.1093/bioinformatics/bti380 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Manoj Bhasin, Aarti Garg, and G. P. S. Raghava

PSLpred: prediction of subcellular localization of bacterial proteins
Bioinformatics Advance Access published on February 4, 2005
Bioinformatics 2005 21: 2522-2524; doi:10.1093/bioinformatics/bti309 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Dariusz Plewczynski, Adrian Tkacz, Lucjan Stanislaw Wyrwicz, and Leszek Rychlewski

AutoMotif server: prediction of single residue post-translational modifications in proteins
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2525-2527; doi:10.1093/bioinformatics/bti333 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Per Unneberg, Michael Strömberg, and Fredrik Sterky

SNP discovery using advanced algorithms and neural networks
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2528-2530; doi:10.1093/bioinformatics/bti354 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Sergei L. Kosakovsky Pond and Simon D. W. Frost

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2531-2533; doi:10.1093/bioinformatics/bti320 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Carlos J. Camacho and Chao Zhang

FastContact: rapid estimate of contact and binding free energies
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2534-2536; doi:10.1093/bioinformatics/bti322 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract G. M. Torrance, D. R. Gilbert, I. Michalopoulos, and D. W. Westhead

Protein structure topological comparison, discovery and matching service
Bioinformatics Advance Access published on March 1, 2005
Bioinformatics 2005 21: 2537-2538; doi:10.1093/bioinformatics/bti331 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jason E. Donald, Isaac A. Hubner, Veronica M. Rotemberg, Eugene I. Shakhnovich, and Leonid A. Mirny

CoC: a database of universally conserved residues in protein folds
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2539-2540; doi:10.1093/bioinformatics/bti360 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sungsam Gong, Giseok Yoon, Insoo Jang, Dan Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, and Jonghwa Bhak

PSIbase: a database of Protein Structural Interactome map (PSIMAP)
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2541-2543; doi:10.1093/bioinformatics/bti366 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Ivan G. Costa, Alexander Schönhuth, and Alexander Schliep

The Graphical Query Language: a tool for analysis of gene expression time-courses
Bioinformatics Advance Access published on February 8, 2005
Bioinformatics 2005 21: 2544-2545; doi:10.1093/bioinformatics/bti311 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Nadia Bolshakova, Francisco Azuaje, and Pádraig Cunningham

A knowledge-driven approach to cluster validity assessment
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2546-2547; doi:10.1093/bioinformatics/bti317 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Alexei A. Sharov, Dawood B. Dudekula, and Minoru S. H. Ko

A web-based tool for principal component and significance analysis of microarray data
Bioinformatics Advance Access published on February 25, 2005
Bioinformatics 2005 21: 2548-2549; doi:10.1093/bioinformatics/bti343 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract John Boyle

Gene-Expression Omnibus integration and clustering Tools in SeqExpress
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2550-2551; doi:10.1093/bioinformatics/bti355 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hui Sun Leong, Tim Yates, Claire Wilson, and Crispin J. Miller

ADAPT: a database of affymetrix probesets and transcripts
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2552-2553; doi:10.1093/bioinformatics/bti359 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Su Young Kim, Suk Woo Nam, Sug Hyung Lee, Won Sang Park, Nam Jin Yoo, Jung Young Lee, and Yeun-Jun Chung

ArrayCyGHt: a web application for analysis and visualization of array-CGH data
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2554-2555; doi:10.1093/bioinformatics/bti357 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill, and Daniel E. Weeks

Mega2: data-handling for facilitating genetic linkage and association analyses
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2556-2557; doi:10.1093/bioinformatics/bti364 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Shailesh V. Date and Edward M. Marcotte

Protein function prediction using the Protein Link EXplorer (PLEX)
Bioinformatics Advance Access published on February 8, 2005
Bioinformatics 2005 21: 2558-2559; doi:10.1093/bioinformatics/bti313 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract J. Ding, K. Viswanathan, D. Berleant, L. Hughes, E. S. Wurtele, D. Ashlock, J. A. Dickerson, A. Fulmer, and P. S. Schnable

Using the biological taxonomy to access biological literature with PathBinderH
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2560-2562; doi:10.1093/bioinformatics/bti381 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Pierre-Étienne Jacques, Alain L. Gervais, Mathieu Cantin, Jean-Francois Lucier, Guillaume Dallaire, Geneviève Drouin, Luc Gaudreau, Jean Goulet, and Ryszard Brzezinski

MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis
Bioinformatics Advance Access published on February 18, 2005
Bioinformatics 2005 21: 2563-2565; doi:10.1093/bioinformatics/bti321 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ana Tereza R. de Vasconcelos, Ana Carolina R. Guimarães, Carlos Henrique M. Castelletti, Célia S. Caruso, Cristina Ribeiro, Fabiano Yokaichiya, Geraldo R. G. Armôa, Gislaine da Silva P. Pereira, Israel T. da Silva, Carlos G. Schrago, Adélia L. V. Fernandes, Aline R. da Silveira, André G. Carneiro, Bruno M. Carvalho, Carlos J. M. Viana, Daniel Gramkow, Franklin J. Lima, Luiz G. G. Corrêa, Maurício de A. Mudado, Pablo Nehab-Hess, Rangel de Souza, Régis L. Corrêa, and Claudia A. M. Russo

MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2566-2567; doi:10.1093/bioinformatics/bti326 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Anyuan Guo, Kun He, Di Liu, Shunong Bai, Xiaocheng Gu, Liping Wei, and Jingchu Luo

DATF: a database of Arabidopsis transcription factors
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2568-2569; doi:10.1093/bioinformatics/bti334 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Tariq Riaz, Hen Ley Hor, Arun Krishnan, Francis Tang, and Kuo-Bin Li

WebAllergen: a web server for predicting allergenic proteins
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2570-2571; doi:10.1093/bioinformatics/bti356 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 2572; doi:10.1093/bioinformatics/bti472 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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