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Previous Next 		Contents: Volume 25, Number 20, 15 October 2009   [Index by Author] 
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down LETTERS TO THE EDITOR
     DATA AND TEXT MINING
     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.

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Sanghamitra Bandyopadhyay and Ramkrishna Mitra
TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples
Bioinformatics Advance Access published on August 19, 2009
Bioinformatics 2009 25: 2625-2631; doi:10.1093/bioinformatics/btp503 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Julien Jorda and Andrey V. Kajava
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm
Bioinformatics Advance Access published on August 11, 2009
Bioinformatics 2009 25: 2632-2638; doi:10.1093/bioinformatics/btp482 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Ami Levy-Moonshine, El-ad David Amir, and Chen Keasar
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential
Bioinformatics Advance Access published on July 23, 2009
Bioinformatics 2009 25: 2639-2645; doi:10.1093/bioinformatics/btp449 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Fenix W. D. Huang, Jing Qin, Christian M. Reidys, and Peter F. Stadler
Partition function and base pairing probabilities for RNA–RNA interaction prediction
Bioinformatics Advance Access published on August 11, 2009
Bioinformatics 2009 25: 2646-2654; doi:10.1093/bioinformatics/btp481 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Qiwen Dong, Shuigeng Zhou, and Jihong Guan
A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation
Bioinformatics Advance Access published on August 25, 2009
Bioinformatics 2009 25: 2655-2662; doi:10.1093/bioinformatics/btp500 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Cristian Micheletti and Henri Orland
MISTRAL: a tool for energy-based multiple structural alignment of proteins
Bioinformatics Advance Access published on August 19, 2009
Bioinformatics 2009 25: 2663-2669; doi:10.1093/bioinformatics/btp506 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Lee Zamparo and Theodore J. Perkins
Statistical lower bounds on protein copy number from fluorescence expression images
Bioinformatics Advance Access published on July 2, 2009
Bioinformatics 2009 25: 2670-2676; doi:10.1093/bioinformatics/btp415 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Kengo Kinoshita and Takeshi Obayashi
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
Bioinformatics Advance Access published on July 20, 2009
Bioinformatics 2009 25: 2677-2684; doi:10.1093/bioinformatics/btp442 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Davide Risso, Maria Sofia Massa, Monica Chiogna, and Chiara Romualdi
A modified LOESS normalization applied to microRNA arrays: a comparative evaluation
Bioinformatics Advance Access published on July 23, 2009
Bioinformatics 2009 25: 2685-2691; doi:10.1093/bioinformatics/btp443 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Guillemette Marot, Jean-Louis Foulley, Claus-Dieter Mayer, and Florence Jaffrézic
Moderated effect size and P-value combinations for microarray meta-analyses
Bioinformatics Advance Access published on July 23, 2009
Bioinformatics 2009 25: 2692-2699; doi:10.1093/bioinformatics/btp444 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Verena Zuber and Korbinian Strimmer
Gene ranking and biomarker discovery under correlation
Bioinformatics Advance Access published on July 30, 2009
Bioinformatics 2009 25: 2700-2707; doi:10.1093/bioinformatics/btp460 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Chen Zhang, Chunguo Wu, Enrico Blanzieri, You Zhou, Yan Wang, Wei Du, and Yanchun Liang
Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model
Bioinformatics Advance Access published on August 6, 2009
Bioinformatics 2009 25: 2708-2714; doi:10.1093/bioinformatics/btp478 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Matthieu Defrance and Jacques van Helden
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling
Bioinformatics Advance Access published on August 18, 2009
Bioinformatics 2009 25: 2715-2722; doi:10.1093/bioinformatics/btp490 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

F. J. Planes and J. E. Beasley
An optimization model for metabolic pathways
Bioinformatics Advance Access published on July 20, 2009
Bioinformatics 2009 25: 2723-2729; doi:10.1093/bioinformatics/btp441 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

John W. Nicol, Gregg A. Helt, Steven G. Blanchard, Jr., Archana Raja, and Ann E. Loraine
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
Bioinformatics Advance Access published on August 4, 2009
Bioinformatics 2009 25: 2730-2731; doi:10.1093/bioinformatics/btp472 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Jacob Almagro-Garcia, Magnus Manske, Celine Carret, Susana Campino, Sarah Auburn, Bronwyn L MacInnis, Gareth Maslen, Arnab Pain, Christopher I Newbold, Dominic P Kwiatkowski, and Taane G Clark
SnoopCGH: software for visualizing comparative genomic hybridization data
Bioinformatics Advance Access published on August 16, 2009
Bioinformatics 2009 25: 2732-2733; doi:10.1093/bioinformatics/btp488 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Paulo C. Carvalho, Tao Xu, Xuemei Han, Daniel Cociorva, Valmir C. Barbosa, and John R. Yates, III
YADA: a tool for taking the most out of high-resolution spectra
Bioinformatics Advance Access published on August 14, 2009
Bioinformatics 2009 25: 2734-2736; doi:10.1093/bioinformatics/btp489 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Erik Kristiansson, Philip Hugenholtz, and Daniel Dalevi
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
Bioinformatics Advance Access published on August 20, 2009
Bioinformatics 2009 25: 2737-2738; doi:10.1093/bioinformatics/btp508 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Olivier Sand, Morgane Thomas-Chollier, and Jacques van Helden
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
Bioinformatics Advance Access published on August 31, 2009
Bioinformatics 2009 25: 2739-2740; doi:10.1093/bioinformatics/btp519 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Filippo Rusconi
massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data
Bioinformatics Advance Access published on September 9, 2009
Bioinformatics 2009 25: 2741-2742; doi:10.1093/bioinformatics/btp504 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

T. Aleksiev, R. Potestio, F. Pontiggia, S. Cozzini, and C. Micheletti
PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
Bioinformatics Advance Access published on August 20, 2009
Bioinformatics 2009 25: 2743-2744; doi:10.1093/bioinformatics/btp512 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zsuzsanna Dosztányi, Bálint Mészáros, and István Simon
ANCHOR: web server for predicting protein binding regions in disordered proteins
Bioinformatics Advance Access published on August 28, 2009
Bioinformatics 2009 25: 2745-2746; doi:10.1093/bioinformatics/btp518 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

GENETICS AND POPULATION ANALYSIS Back

Joao S. Lopes, David Balding, and Mark A. Beaumont
PopABC: a program to infer historical demographic parameters
Bioinformatics Advance Access published on August 13, 2009
Bioinformatics 2009 25: 2747-2749; doi:10.1093/bioinformatics/btp487 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Karol Estrada, Anis Abuseiris, Frank G. Grosveld, André G. Uitterlinden, Tobias A. Knoch, and Fernando Rivadeneira
GRIMP: a web- and grid-based tool for high-speed analysis of large-scale genome-wide association using imputed data
Bioinformatics Advance Access published on August 21, 2009
Bioinformatics 2009 25: 2750-2752; doi:10.1093/bioinformatics/btp497 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Steven Maenhout, Bernard De Baets, and Geert Haesaert
CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data
Bioinformatics Advance Access published on August 17, 2009
Bioinformatics 2009 25: 2753-2754; doi:10.1093/bioinformatics/btp499 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY Back

Eva Grafahrend-Belau, Christian Klukas, Björn H. Junker, and Falk Schreiber
FBA-SimVis: interactive visualization of constraint-based metabolic models
Bioinformatics Advance Access published on July 3, 2009
Bioinformatics 2009 25: 2755-2757; doi:10.1093/bioinformatics/btp408 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Magdalena Feldhahn, Pierre Dönnes, Philipp Thiel, and Oliver Kohlbacher
FRED—a framework for T-cell epitope detection
Bioinformatics Advance Access published on July 4, 2009
Bioinformatics 2009 25: 2758-2759; doi:10.1093/bioinformatics/btp409 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Marc Streit, Alexander Lex, Michael Kalkusch, Kurt Zatloukal, and Dieter Schmalstieg
Caleydo: connecting pathways and gene expression
Bioinformatics Advance Access published on July 20, 2009
Bioinformatics 2009 25: 2760-2761; doi:10.1093/bioinformatics/btp432 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Colm O'Dushlaine, Elaine Kenny, Elizabeth A. Heron, Ricardo Segurado, Michael Gill, Derek W. Morris, and Aiden Corvin
The SNP ratio test: pathway analysis of genome-wide association datasets
Bioinformatics Advance Access published on July 20, 2009
Bioinformatics 2009 25: 2762-2763; doi:10.1093/bioinformatics/btp448 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Jan Urban, Jan Vanek, Jirí Soukup, and Dalibor Stys
Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach
Bioinformatics Advance Access published on July 14, 2009
Bioinformatics 2009 25: 2764-2767; doi:10.1093/bioinformatics/btp427 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

Maria Krestyaninova, Andris Zarins, Juris Viksna, Natalja Kurbatova, Peteris Rucevskis, Sudeshna Guha Neogi, Mike Gostev, Teemu Perheentupa, Juha Knuuttila, Amy Barrett, Ilkka Lappalainen, Johan Rung, Karlis Podnieks, Ugis Sarkans, Mark I McCarthy, and Alvis Brazma
A System for Information Management in BioMedical Studies—SIMBioMS
Bioinformatics Advance Access published on July 24, 2009
Bioinformatics 2009 25: 2768-2769; doi:10.1093/bioinformatics/btp420 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

LETTERS TO THE EDITOR Back

DATA AND TEXT MINING Back

Aurélie Névéol, James G. Mork, and Alan R. Aronson
Comment on ‘MeSH-up: effective MeSH text classification for improved document retrieval’
Bioinformatics Advance Access published on August 11, 2009
Bioinformatics 2009 25: 2770-2771; doi:10.1093/bioinformatics/btp483 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Dolf Trieschnigg, Piotr Pezik, Vivian Lee, Franciska de Jong, Wessel Kraaij, and Dietrich Rebholz-Schuhmann
Response to comment on ‘MeSH-up: effective MeSH text classification for improved document retrieval’
Bioinformatics Advance Access published on August 24, 2009
Bioinformatics 2009 25: 2772; doi:10.1093/bioinformatics/btp484 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

Brendan Elliott, Mustafa Kirac, Ali Cakmak, Gokhan Yavas, Stephen Mayes, En Cheng, Yuan Wang, Chirag Gupta, Gultekin Ozsoyoglu, and Zehra Meral Ozsoyoglu
Corrigendum for Elliott,B. et al., ‘PathCase pathways database system’, Bioinformatics, Nov. 2008, 24(21), pp. 2526–2533
Bioinformatics Advance Access published on August 27, 2009
Bioinformatics 2009 25: 2773; doi:10.1093/bioinformatics/btp520 [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.