Bioinformatics

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Teemu Kivioja, Mikko Arvas, Markku Saloheimo, Merja Penttilä, and Esko Ukkonen

Optimization of cDNA-AFLP experiments using genomic sequence data
Bioinformatics Advance Access published on March 17, 2005
Bioinformatics 2005 21: 2573-2579; doi:10.1093/bioinformatics/bti393 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Yan Zhang and Vadim N. Gladyshev

An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2580-2589; doi:10.1093/bioinformatics/bti400 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract D. R. Clutterbuck, A. Leroy, M. A. O'Connell, and C. A. M. Semple

A bioinformatic screen for novel A–I RNA editing sites reveals recoding editing in BC10
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2590-2595; doi:10.1093/bioinformatics/bti411 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Jean-François Dufayard, Laurent Duret, Simon Penel, Manolo Gouy, François Rechenmann, and Guy Perrière

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
Bioinformatics Advance Access published on February 15, 2005
Bioinformatics 2005 21: 2596-2603; doi:10.1093/bioinformatics/bti325 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hadas Leonov and Isaiah T. Arkin

A periodicity analysis of transmembrane helices
Bioinformatics Advance Access published on March 3, 2005
Bioinformatics 2005 21: 2604-2610; doi:10.1093/bioinformatics/bti369 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hiroshi Matsui, Kengo Sato, and Yasubumi Sakakibara

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
Bioinformatics Advance Access published on March 22, 2005
Bioinformatics 2005 21: 2611-2617; doi:10.1093/bioinformatics/bti385 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Victor Kunin, Sarah A. Teichmann, Martijn A. Huynen, and Christos A. Ouzounis

The properties of protein family space depend on experimental design
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2618-2622; doi:10.1093/bioinformatics/bti386 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Rajesh Chowdhary, R. Ayesha Ali, Werner Albig, Detlef Doenecke, and Vladimir B Bajic

Promoter modeling: the case study of mammalian histone promoters
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2623-2628; doi:10.1093/bioinformatics/bti387 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jason E. Donald and Eugene I. Shakhnovich

Determining functional specificity from protein sequences
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2629-2635; doi:10.1093/bioinformatics/bti396 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Pengyu Hong, X. Shirley Liu, Qing Zhou, Xin Lu, Jun S. Liu, and Wing H. Wong

A boosting approach for motif modeling using ChIP-chip data
Bioinformatics Advance Access published on April 7, 2005
Bioinformatics 2005 21: 2636-2643; doi:10.1093/bioinformatics/bti402 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Zheng Rong Yang

Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2644-2650; doi:10.1093/bioinformatics/bti404 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Moti Zviling, Hadas Leonov, and Isaiah T. Arkin

Genetic algorithm-based optimization of hydrophobicity tables
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2651-2656; doi:10.1093/bioinformatics/bti405 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract I. Ben-Gal, A. Shani, A. Gohr, J. Grau, S. Arviv, A. Shmilovici, S. Posch, and I. Grosse

Identification of transcription factor binding sites with variable-order Bayesian networks
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2657-2666; doi:10.1093/bioinformatics/bti410 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Sangjo Han, Byung-chul Lee, Seung Taek Yu, Chan-seok Jeong, Soyoung Lee, and Dongsup Kim

Fold recognition by combining profile–profile alignment and support vector machine
Bioinformatics Advance Access published on March 15, 2005
Bioinformatics 2005 21: 2667-2673; doi:10.1093/bioinformatics/bti384 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract A. L. Tarca and J. E. K. Cooke

A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray data
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2674-2683; doi:10.1093/bioinformatics/bti397 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Gregory R. Grant, Junmin Liu, and Christian J. Stoeckert, Jr.

A practical false discovery rate approach to identifying patterns of differential expression in microarray data
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2684-2690; doi:10.1093/bioinformatics/bti407 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Jane Jijun Liu, Gene Cutler, Wuxiong Li, Zheng Pan, Sihua Peng, Tim Hoey, Liangbiao Chen, and Xuefeng Bruce Ling

Multiclass cancer classification and biomarker discovery using GA-based algorithms
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2691-2697; doi:10.1093/bioinformatics/bti419 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Bor-Sen Chen, Yu-Chao Wang, Wei-Sheng Wu, and Wen-Hsiung Li

A new measure of the robustness of biochemical networks
Bioinformatics Advance Access published on February 24, 2005
Bioinformatics 2005 21: 2698-2705; doi:10.1093/bioinformatics/bti348 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Svetlana Bulashevska and Roland Eils

Inferring genetic regulatory logic from expression data
Bioinformatics Advance Access published on March 22, 2005
Bioinformatics 2005 21: 2706-2713; doi:10.1093/bioinformatics/bti388 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Thierry Emonet, Charles M. Macal, Michael J. North, Charles E. Wickersham, and Philippe Cluzel

AgentCell: a digital single-cell assay for bacterial chemotaxis
Bioinformatics Advance Access published on March 17, 2005
Bioinformatics 2005 21: 2714-2721; doi:10.1093/bioinformatics/bti391 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract Luonan Chen, Ruiqi Wang, Tianshou Zhou, and Kazuyuki Aihara

Noise-induced cooperative behavior in a multicell system
Bioinformatics Advance Access published on March 17, 2005
Bioinformatics 2005 21: 2722-2729; doi:10.1093/bioinformatics/bti392 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Nitin Bhardwaj and Hui Lu

Correlation between gene expression profiles and protein–protein interactions within and across genomes
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2730-2738; doi:10.1093/bioinformatics/bti398 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Phil Hyoun Lee and Doheon Lee

Modularized learning of genetic interaction networks from biological annotations and mRNA expression data
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2739-2747; doi:10.1093/bioinformatics/bti406 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Irena Spasic, Sophia Ananiadou, and Junichi Tsujii

MaSTerClass: a case-based reasoning system for the classification of biomedical terms
Bioinformatics Advance Access published on February 22, 2005
Bioinformatics 2005 21: 2748-2758; doi:10.1093/bioinformatics/bti338 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Z. Z. Hu, M. Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, and C. H. Wu

Literature mining and database annotation of protein phosphorylation using a rule-based system
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2759-2765; doi:10.1093/bioinformatics/bti390 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract René Korn, Sascha Röhrig, Steffen Schulze-Kremer, and Ulrich Brinkmann

Common denominator procedure: a novel approach to gene-expression data mining for identification of phenotype-specific genes
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2766-2772; doi:10.1093/bioinformatics/bti416 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Stuart Aitken

Formalizing concepts of species, sex and developmental stage in anatomical ontologies
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2773-2779; doi:10.1093/bioinformatics/bti409 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Chin Lung Lu, Tsui Ching Wang, Ying Chih Lin, and Chuan Yi Tang

ROBIN: a tool for genome rearrangement of block-interchanges
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2780-2782; doi:10.1093/bioinformatics/bti412 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Vincent Miele, Pierre-Yves Bourguignon, David Robelin, Grégory Nuel, and Hugues Richard

seq++: analyzing biological sequences with a range of Markov-related models
Bioinformatics Advance Access published on March 17, 2005
Bioinformatics 2005 21: 2783-2784; doi:10.1093/bioinformatics/bti389 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Daniel Schober, Ulf Leser, Martin Zenke, and Jens Reich

GandrKB—ontological microarray annotation and visualization
Bioinformatics Advance Access published on March 31, 2005
Bioinformatics 2005 21: 2785-2786; doi:10.1093/bioinformatics/bti401 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Taner Z. Sen, Robert L. Jernigan, Jean Garnier, and Andrzej Kloczkowski

GOR V server for protein secondary structure prediction
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2787-2788; doi:10.1093/bioinformatics/bti408 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Aedín C. Culhane, Jean Thioulouse, Guy Perrière, and Desmond G. Higgins

MADE4: an R package for multivariate analysis of gene expression data
Bioinformatics Advance Access published on March 29, 2005
Bioinformatics 2005 21: 2789-2790; doi:10.1093/bioinformatics/bti394 [Abstract] [Full Text] [Print PDF] [Supplementary Data - index.htslp] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Albert J. Vilella, Angel Blanco-Garcia, Stephan Hutter, and Julio Rozas

VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2791-2793; doi:10.1093/bioinformatics/bti403 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Yu Song, Eunju Kim, Gary Geunbae Lee, and Byoung-kee Yi

POSBIOTM—NER: a trainable biomedical named-entity recognition system
Bioinformatics Advance Access published on April 6, 2005
Bioinformatics 2005 21: 2794-2796; doi:10.1093/bioinformatics/bti414 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Guillaume Koum, Augustin Yekel, Bengyella Ndifon, and Frédéric Simard

Erratum
Bioinformatics 2005 21: 2797-2802; doi:10.1093/bioinformatics/bti399 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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