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Previous Next 		Contents: Volume 24, Number 1, 1 January 2008   [Index by Author] 
       REVIEW
                GENOME ANALYSIS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                GENOME ANALYSIS
                PHYLOGENETICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                DATA AND TEXT MINING
                DATABASE AND ONTOLOGIES
       ERRATUM
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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:

GENOME ANALYSIS:

Christoph Bock and Thomas Lengauer
Computational epigenetics
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 1-10; doi:10.1093/bioinformatics/btm546 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Michael L. Tress, Jan-Jaap Wesselink, Adam Frankish, Gonzalo López, Nick Goldman, Ari Löytynoja, Tim Massingham, Fabio Pardi, Simon Whelan, Jennifer Harrow, and Alfonso Valencia
Determination and validation of principal gene products
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2008 24: 11-17; doi:10.1093/bioinformatics/btm547 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

SEQUENCE ANALYSIS:

Kai Ye, K. Anton Feenstra, Jaap Heringa, Adriaan P. IJzerman, and Elena Marchiori
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 18-25; doi:10.1093/bioinformatics/btm537 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

A.D.J. van Dijk, C.J.F. ter Braak, R.G. Immink, G.C. Angenent, and R.C.H.J. van Ham
Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 26-33; doi:10.1093/bioinformatics/btm539 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

K. Deforche, R. Camacho, K. Van Laethem, P. Lemey, A. Rambaut, Y. Moreau, and A.-M. Vandamme
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 34-41; doi:10.1093/bioinformatics/btm540 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Aleksey V. Zimin, Douglas R. Smith, Granger Sutton, and James A. Yorke
Assembly reconciliation
Bioinformatics Advance Access published on December 5, 2007
Bioinformatics 2008 24: 42-45; doi:10.1093/bioinformatics/btm542 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Kuo-Ching Liang, Xiaodong Wang, and Dimitris Anastassiou
A profile-based deterministic sequential Monte Carlo algorithm for motif discovery
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 46-55; doi:10.1093/bioinformatics/btm543 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

PHYLOGENETICS:

Nicolas Rodrigue, Hervé Philippe, and Nicolas Lartillot
Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models
Bioinformatics Advance Access published on November 14, 2007
Bioinformatics 2008 24: 56-62; doi:10.1093/bioinformatics/btm532 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Dante Mantini, Francesca Petrucci, Piero Del Boccio, Damiana Pieragostino, Marta Di Nicola, Alessandra Lugaresi, Giorgio Federici, Paolo Sacchetta, Carmine Di Ilio, and Andrea Urbani
Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra
Bioinformatics Advance Access published on November 14, 2007
Bioinformatics 2008 24: 63-70; doi:10.1093/bioinformatics/btm533 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Ryan Kelley, Hoda Feizi, and Trey Ideker
Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood
Bioinformatics Advance Access published on July 10, 2007
Bioinformatics 2008 24: 71-77; doi:10.1093/bioinformatics/btm347 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Manuela Hummel, Reinhard Meister, and Ulrich Mansmann
GlobalANCOVA: exploration and assessment of gene group effects
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 78-85; doi:10.1093/bioinformatics/btm531 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENETICS AND POPULATION ANALYSIS:

Guohui Lin, Zhanyong Wang, Lusheng Wang, Yu-Lung Lau, and Wanling Yang
Identification of linked regions using high-density SNP genotype data in linkage analysis
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 86-93; doi:10.1093/bioinformatics/btm552 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

SYSTEMS BIOLOGY:

Meng Wang, Xiaobo Zhou, Fuhai Li, Jeremy Huckins, Randall W. King, and Stephen T.C. Wong
Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy
Bioinformatics Advance Access published on November 7, 2007
Bioinformatics 2008 24: 94-101; doi:10.1093/bioinformatics/btm530 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng, Haixu Tang, Zhiyin Xun, Rong Zeng, and Predrag Radivojac
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics
Bioinformatics Advance Access published on November 22, 2007
Bioinformatics 2008 24: 102-109; doi:10.1093/bioinformatics/btm545 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Michal Draminski, Alvaro Rada-Iglesias, Stefan Enroth, Claes Wadelius, Jacek Koronacki, and Jan Komorowski
Monte Carlo feature selection for supervised classification
Bioinformatics Advance Access published on November 28, 2007
Bioinformatics 2008 24: 110-117; doi:10.1093/bioinformatics/btm486 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Seonho Kim, Juntae Yoon, and Jihoon Yang
Kernel approaches for genic interaction extraction
Bioinformatics Advance Access published on November 14, 2007
Bioinformatics 2008 24: 118-126; doi:10.1093/bioinformatics/btm544 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Cedric Simillion, Koen Janssens, Lieven Sterck, and Yves Van de Peer
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles
Bioinformatics Advance Access published on October 17, 2007
Bioinformatics 2008 24: 127-128; doi:10.1093/bioinformatics/btm449 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Luke J. Harmon, Jason T. Weir, Chad D. Brock, Richard E. Glor, and Wendell Challenger
GEIGER: investigating evolutionary radiations
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2008 24: 129-131; doi:10.1093/bioinformatics/btm538 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

James Long and Mitchell Roth
Synthetic microarray data generation with RANGE and NEMO
Bioinformatics Advance Access published on November 3, 2007
Bioinformatics 2008 24: 132-134; doi:10.1093/bioinformatics/btm529 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Nicola Lama and Mark Girolami
vbmp: Variational Bayesian Multinomial Probit Regression for multi-class classification in R
Bioinformatics Advance Access published on November 14, 2007
Bioinformatics 2008 24: 135-136; doi:10.1093/bioinformatics/btm535 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xiaojiang Xu, Yingdong Zhao, and Richard Simon
Gene Set Expression Comparison kit for BRB-ArrayTools
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2008 24: 137-139; doi:10.1093/bioinformatics/btm541 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENETICS AND POPULATION ANALYSIS:

Chun Li and Mingyao Li
GWAsimulator: a rapid whole-genome simulation program
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2008 24: 140-142; doi:10.1093/bioinformatics/btm549 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Fabien Jourdan, Rainer Breitling, Michael P. Barrett, and David Gilbert
MetaNetter: inference and visualization of high-resolution metabolomic networks
Bioinformatics Advance Access published on November 14, 2007
Bioinformatics 2008 24: 143-145; doi:10.1093/bioinformatics/btm536 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASE AND ONTOLOGIES:

Daniel F. Schwarz, Oliver Hädicke, Jeanette Erdmann, Andreas Ziegler, Daniel Bayer, and Steffen Möller
SNPtoGO: characterizing SNPs by enriched GO terms
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 146-148; doi:10.1093/bioinformatics/btm551 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ERRATUM:

Peng Liu and J.T. Gene Hwang
Gene expression • Quick calculation for sample size while controlling false discovery rate with application to microarray analysis
Bioinformatics Advance Access published on November 14, 2007
Bioinformatics 2008 24: 149; doi:10.1093/bioinformatics/btm534 [Extract] [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.