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Previous Next 		Contents: Volume 23, Number 19, 1 October 2007   [Index by Author] 
       REVIEW
                GENE EXPRESSION
       DISCOVERY NOTES
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
       APPLICATIONS NOTES
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
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To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

REVIEW:

GENE EXPRESSION:

Yvan Saeys, Iñaki Inza, and Pedro Larrañaga
A review of feature selection techniques in bioinformatics
Bioinformatics Advance Access published on August 24, 2007
Bioinformatics 2007 23: 2507-2517; doi:10.1093/bioinformatics/btm344 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTES:

SEQUENCE ANALYSIS:

Kirill Borziak and Igor B. Zhulin
FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes
Bioinformatics Advance Access published on September 12, 2007
Bioinformatics 2007 23: 2518-2521; doi:10.1093/bioinformatics/btm384 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Andrzej Kolinski and Dominik Gront
Comparative modeling without implicit sequence alignments
Bioinformatics Advance Access published on July 27, 2007
Bioinformatics 2007 23: 2522-2527; doi:10.1093/bioinformatics/btm380 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Karin Noy and Daniel Fasulo
Improved model-based, platform-independent feature extraction for mass spectrometry
Bioinformatics Advance Access published on August 13, 2007
Bioinformatics 2007 23: 2528-2535; doi:10.1093/bioinformatics/btm385 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Pawel Smialowski, Antonio J. Martin-Galiano, Aleksandra Mikolajka, Tobias Girschick, Tad A. Holak, and Dmitrij Frishman
Protein solubility: sequence based prediction and experimental verification
Bioinformatics Advance Access published on December 6, 2006
Bioinformatics 2007 23: 2536-2542; doi:10.1093/bioinformatics/btl623 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

J. Zucko, N. Skunca, T. Curk, B. Zupan, P.F. Long, J. Cullum, R.H. Kessin, and D. Hranueli
Polyketide synthase genes and the natural products potential of Dictyostelium discoideum
Bioinformatics Advance Access published on July 27, 2007
Bioinformatics 2007 23: 2543-2549; doi:10.1093/bioinformatics/btm381 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Cécile Militon, Sébastien Rimour, Mohieddine Missaoui, Corinne Biderre, Vincent Barra, David Hill, Anne Moné, Geneviève Gagne, Harald Meier, Eric Peyretaillade, and Pierre Peyret
PhylArray: phylogenetic probe design algorithm for microarray
Bioinformatics Advance Access published on August 12, 2007
Bioinformatics 2007 23: 2550-2557; doi:10.1093/bioinformatics/btm392 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Narcis Fernandez-Fuentes, Brajesh K. Rai, Carlos J. Madrid-Aliste, J. Eduardo Fajardo, and András Fiser
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
Bioinformatics Advance Access published on September 6, 2007
Bioinformatics 2007 23: 2558-2565; doi:10.1093/bioinformatics/btm377 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Chunlei Wu, Haitao Zhao, Keith Baggerly, Roberto Carta, and Li Zhang
Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays
Bioinformatics Advance Access published on May 30, 2007
Bioinformatics 2007 23: 2566-2572; doi:10.1093/bioinformatics/btm271 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Thomas Dhollander, Qizheng Sheng, Karen Lemmens, Bart De Moor, Kathleen Marchal, and Yves Moreau
Query-driven module discovery in microarray data
Bioinformatics Advance Access published on August 8, 2007
Bioinformatics 2007 23: 2573-2580; doi:10.1093/bioinformatics/btm387 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Fred A. Wright, Hanwen Huang, Xiaojun Guan, Kevin Gamiel, Clark Jeffries, William T. Barry, Fernando Pardo-Manuel de Villena, Patrick F. Sullivan, Kirk C. Wilhelmsen, and Fei Zou
Simulating association studies: a data-based resampling method for candidate regions or whole genome scans
Bioinformatics Advance Access published on September 4, 2007
Bioinformatics 2007 23: 2581-2588; doi:10.1093/bioinformatics/btm386 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Seung Yeoun Lee, Yujin Chung, Robert C. Elston, Youngchul Kim, and Taesung Park
Log-linear model-based multifactor dimensionality reduction method to detect gene–gene interactions
Bioinformatics Advance Access published on September 14, 2007
Bioinformatics 2007 23: 2589-2595; doi:10.1093/bioinformatics/btm396 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Elizabeth A. Heron, Bärbel Finkenstädt, and David A. Rand
Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study
Bioinformatics Advance Access published on July 28, 2007
Bioinformatics 2007 23: 2596-2603; doi:10.1093/bioinformatics/btm367 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zachary M. Saul and Vladimir Filkov
Exploring biological network structure using exponential random graph models
Bioinformatics Advance Access published on July 20, 2007
Bioinformatics 2007 23: 2604-2611; doi:10.1093/bioinformatics/btm370 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

S. Hengl, C. Kreutz, J. Timmer, and T. Maiwald
Data-based identifiability analysis of non-linear dynamical models
Bioinformatics Advance Access published on July 28, 2007
Bioinformatics 2007 23: 2612-2618; doi:10.1093/bioinformatics/btm382 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

APPLICATIONS NOTES:

SEQUENCE ANALYSIS:

Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, and Sun Kim
dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
Bioinformatics Advance Access published on June 5, 2007
Bioinformatics 2007 23: 2619-2621; doi:10.1093/bioinformatics/btm288 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Matthew N. Bainbridge, René L. Warren, An He, Mikhail Bilenky, A. Gordon Robertson, and Steven J.M. Jones
THOR: targeted high-throughput ortholog reconstructor
Bioinformatics Advance Access published on October 11, 2006
Bioinformatics 2007 23: 2622-2624; doi:10.1093/bioinformatics/btl513 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, and Amedeo Caflisch
Wordom: a program for efficient analysis of molecular dynamics simulations
Bioinformatics Advance Access published on August 23, 2007
Bioinformatics 2007 23: 2625-2627; doi:10.1093/bioinformatics/btm378 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Haitao Cheng, Taner Z. Sen, Robert L. Jernigan, and Andrzej Kloczkowski
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM)
Bioinformatics Advance Access published on July 27, 2007
Bioinformatics 2007 23: 2628-2630; doi:10.1093/bioinformatics/btm379 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Duccio Cavalieri, Cinzia Castagnini, Simona Toti, Karolina Maciag, Thomas Kelder, Luca Gambineri, Samuele Angioli, and Piero Dolara
Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases
Bioinformatics Advance Access published on June 28, 2007
Bioinformatics 2007 23: 2631-2632; doi:10.1093/bioinformatics/btm333 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Peter J. Bradbury, Zhiwu Zhang, Dallas E. Kroon, Terry M. Casstevens, Yogesh Ramdoss, and Edward S. Buckler
TASSEL: software for association mapping of complex traits in diverse samples
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2633-2635; doi:10.1093/bioinformatics/btm308 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Heiko A. Schmidt, Arndt von Haeseler, and Jutta Buschbom
pIPHULA—parallel inference of population parameters using a likelihood approach
Bioinformatics Advance Access published on August 12, 2007
Bioinformatics 2007 23: 2636-2637; doi:10.1093/bioinformatics/btm391 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Julio Vera, Cheng Sun, Yvonne Oertel, and Olaf Wolkenhauer
PLMaddon: a power-law module for the MatlabTM SBToolbox
Bioinformatics Advance Access published on May 11, 2007
Bioinformatics 2007 23: 2638-2640; doi:10.1093/bioinformatics/btm245 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Joanna Jakubowska, Ela Hunt, Matthew Chalmers, Martin McBride, and Anna F. Dominiczak
VisGenome: visualization of single and comparative genome representations
Bioinformatics 2007 23: 2641-2642; doi:10.1093/bioinformatics/btm394 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Dominik Seelow, Katrin Hoffmann, and Tom H. Lindner
AssociationDB: web-based exploration of genomic association
Bioinformatics Advance Access published on July 27, 2007
Bioinformatics 2007 23: 2643-2644; doi:10.1093/bioinformatics/btm376 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Milind Misra and Catherine H. Schein
Flavitrack: an annotated database of flavivirus sequences
Bioinformatics Advance Access published on July 28, 2007
Bioinformatics 2007 23: 2645-2647; doi:10.1093/bioinformatics/btm383 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Hyrum Carroll, Wesley Beckstead, Timothy O'Connor, Mark Ebbert, Mark Clement, Quinn Snell, and David McClellan
DNA reference alignment benchmarks based on tertiary structure of encoded proteins
Bioinformatics Advance Access published on August 8, 2007
Bioinformatics 2007 23: 2648-2649; doi:10.1093/bioinformatics/btm389 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.