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Previous Next 		Contents: Volume 24, Number 5, 1 March 2008   [Index by Author] 
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
       APPLICATIONS NOTES
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
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ORIGINAL PAPERS:

GENOME ANALYSIS:

Qian Liu, Aaron J. Mackey, David S. Roos, and Fernando C. N. Pereira
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction
Bioinformatics Advance Access published on January 10, 2008
Bioinformatics 2008 24: 597-605; doi:10.1093/bioinformatics/btn004 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Onur Sakarya, Kenneth S. Kosik, and Todd H. Oakley
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony
Bioinformatics Advance Access published on January 9, 2008
Bioinformatics 2008 24: 606-612; doi:10.1093/bioinformatics/btn005 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

J. D. Fischer, C. E. Mayer, and J. Söding
Prediction of protein functional residues from sequence by probability density estimation
Bioinformatics Advance Access published on January 2, 2008
Bioinformatics 2008 24: 613-620; doi:10.1093/bioinformatics/btm626 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Igor V. Tetko, Igor V. Rodchenkov, Mathias C. Walter, Thomas Rattei, and Hans-Werner Mewes
Beyond the ‘best’ match: machine learning annotation of protein sequences by integration of different sources of information
Bioinformatics Advance Access published on January 3, 2008
Bioinformatics 2008 24: 621-628; doi:10.1093/bioinformatics/btm633 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Leping Li, Robert L. Bass, and Yu Liang
fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control
Bioinformatics Advance Access published on February 22, 2008
Bioinformatics 2008 24: 629-636; doi:10.1093/bioinformatics/btn009 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Mario Stanke, Mark Diekhans, Robert Baertsch, and David Haussler
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Bioinformatics Advance Access published on January 24, 2008
Bioinformatics 2008 24: 637-644; doi:10.1093/bioinformatics/btn013 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Arun S. Konagurthu, Peter J. Stuckey, and Arthur M. Lesk
Structural search and retrieval using a tableau representation of protein folding patterns
Bioinformatics Advance Access published on January 5, 2008
Bioinformatics 2008 24: 645-651; doi:10.1093/bioinformatics/btm641 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Julie Bernauer, Ranjit Prasad Bahadur, Francis Rodier, Joël Janin, and Anne Poupon
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions
Bioinformatics Advance Access published on January 19, 2008
Bioinformatics 2008 24: 652-658; doi:10.1093/bioinformatics/btn022 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Changjun Chen and Yi Xiao
Observation of multiple folding pathways of β-hairpin trpzip2 from independent continuous folding trajectories
Bioinformatics Advance Access published on January 23, 2008
Bioinformatics 2008 24: 659-665; doi:10.1093/bioinformatics/btn029 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Yinglei Lai
Genome-wide co-expression based prediction of differential expressions
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2008 24: 666-673; doi:10.1093/bioinformatics/btm507 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jainab Khatun, Eric Hamlett, and Morgan C. Giddings
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification
Bioinformatics Advance Access published on January 10, 2008
Bioinformatics 2008 24: 674-681; doi:10.1093/bioinformatics/btn011 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Laurent Bréhélin, Olivier Gascuel, and Olivier Martin
Using repeated measurements to validate hierarchical gene clusters
Bioinformatics Advance Access published on January 19, 2008
Bioinformatics 2008 24: 682-688; doi:10.1093/bioinformatics/btn017 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Ramazan Saeed and Charlotte Deane
An assessment of the uses of homologous interactions
Bioinformatics Advance Access published on November 27, 2007
Bioinformatics 2008 24: 689-695; doi:10.1093/bioinformatics/btm576 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Nicolas Thierry-Mieg and Gilles Bailly
Interpool: interpreting smart-pooling results
Bioinformatics Advance Access published on January 9, 2008
Bioinformatics 2008 24: 696-703; doi:10.1093/bioinformatics/btn001 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

A. Kremling, K. Bettenbrock, and E. D. Gilles
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake
Bioinformatics Advance Access published on January 10, 2008
Bioinformatics 2008 24: 704-710; doi:10.1093/bioinformatics/btn010 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Simon Gog, Martin Bader, and Enno Ohlebusch
GENESIS: genome evolution scenarios
Bioinformatics Advance Access published on January 19, 2008
Bioinformatics 2008 24: 711-712; doi:10.1093/bioinformatics/btn026 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Ruiqiang Li, Yingrui Li, Karsten Kristiansen, and Jun Wang
SOAP: short oligonucleotide alignment program
Bioinformatics Advance Access published on January 28, 2008
Bioinformatics 2008 24: 713-714; doi:10.1093/bioinformatics/btn025 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Stephen A. Smith and Casey W. Dunn
Phyutility: a phyloinformatics tool for trees, alignments and molecular data
Bioinformatics Advance Access published on January 28, 2008
Bioinformatics 2008 24: 715-716; doi:10.1093/bioinformatics/btm619 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

J. D. Moore and R. G. Allaby
TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism
Bioinformatics Advance Access published on January 19, 2008
Bioinformatics 2008 24: 717-718; doi:10.1093/bioinformatics/btn027 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Peter Langfelder, Bin Zhang, and Steve Horvath
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
Bioinformatics Advance Access published on November 16, 2007
Bioinformatics 2008 24: 719-720; doi:10.1093/bioinformatics/btm563 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Jian Yang, Chengcheng Hu, Han Hu, Rongdong Yu, Zhen Xia, Xiuzi Ye, and Jun Zhu
QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations
Bioinformatics Advance Access published on January 17, 2008
Bioinformatics 2008 24: 721-723; doi:10.1093/bioinformatics/btm494 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Mario Falchi and Christian Fuchsberger
Jenti: an efficient tool for mining complex inbred genealogies
Bioinformatics Advance Access published on January 24, 2008
Bioinformatics 2008 24: 724-726; doi:10.1093/bioinformatics/btm617 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Martijn J. Schuemie and Jan A. Kors
Jane: suggesting journals, finding experts
Bioinformatics Advance Access published on January 28, 2008
Bioinformatics 2008 24: 727-728; doi:10.1093/bioinformatics/btn006 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Giorgio Valentini and Nicolò Cesa-Bianchi
HCGene: a software tool to support the hierarchical classification of genes
Bioinformatics Advance Access published on January 18, 2008
Bioinformatics 2008 24: 729-731; doi:10.1093/bioinformatics/btn015 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Alexander Luedemann, Katrin Strassburg, Alexander Erban, and Joachim Kopka
TagFinder for the quantitative analysis of gas chromatography—mass spectrometry (GC-MS)-based metabolite profiling experiments
Bioinformatics Advance Access published on January 19, 2008
Bioinformatics 2008 24: 732-737; doi:10.1093/bioinformatics/btn023 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Sorin Draghici, Adi L. Tarca, Longfei Yu, Stephen Ethier, and Roberto Romero
KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours
Bioinformatics Advance Access published on November 17, 2007
Bioinformatics 2008 24: 738-740; doi:10.1093/bioinformatics/btm559 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

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.