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Previous Next 		Contents: Volume 24, Number 23, 1 December 2008   [Index by Author] 
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATABASES AND ONTOLOGIES
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down LETTER TO THE EDITOR
     SYSTEMS BIOLOGY
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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

Yan Lin, George C. Tseng, Soo Yeon Cheong, Lora J. H. Bean, Stephanie L. Sherman, and Eleanor Feingold
Smarter clustering methods for SNP genotype calling
Bioinformatics Advance Access published on September 29, 2008
Bioinformatics 2008 24: 2665-2671; doi:10.1093/bioinformatics/btn509 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Tim Carver, Matthew Berriman, Adrian Tivey, Chinmay Patel, Ulrike Böhme, Barclay G. Barrell, Julian Parkhill, and Marie-Adèle Rajandream
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
Bioinformatics Advance Access published on October 9, 2008
Bioinformatics 2008 24: 2672-2676; doi:10.1093/bioinformatics/btn529 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Robert K. Bradley, Lior Pachter, and Ian Holmes
Specific alignment of structured RNA: stochastic grammars and sequence annealing
Bioinformatics Advance Access published on September 16, 2008
Bioinformatics 2008 24: 2677-2683; doi:10.1093/bioinformatics/btn495 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Lucie N. Hutchins, Sean M. Murphy, Priyam Singh, and Joel H. Graber
Position-dependent motif characterization using non-negative matrix factorization
Bioinformatics Advance Access published on October 13, 2008
Bioinformatics 2008 24: 2684-2690; doi:10.1093/bioinformatics/btn526 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Ching-Tai Chen, Ei-Wen Yang, Hung-Ju Hsu, Yi-Kun Sun, Wen-Lian Hsu, and An-Suei Yang
Protease substrate site predictors derived from machine learning on multilevel substrate phage display data
Bioinformatics Advance Access published on October 29, 2008
Bioinformatics 2008 24: 2691-2697; doi:10.1093/bioinformatics/btn538 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Mallika Veeramalai and David Gilbert
A novel method for comparing topological models of protein structures enhanced with ligand information
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2698-2705; doi:10.1093/bioinformatics/btn518 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Elmer A. Ferná;ndez, María R. Girotti, Juan A. López del Olmo, Andrea S. Llera, Osvaldo L. Podhajcer, Rodolfo J. C. Cantet, and Mónica Balzarini
Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study
Bioinformatics Advance Access published on September 25, 2008
Bioinformatics 2008 24: 2706-2712; doi:10.1093/bioinformatics/btn508 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Jean-Marie Cornuet, Filipe Santos, Mark A. Beaumont, Christian P. Robert, Jean-Michel Marin, David J. Balding, Thomas Guillemaud, and Arnaud Estoup
Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2713-2719; doi:10.1093/bioinformatics/btn514 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Yuzhong Zhao, Yun Xu, Zhihao Wang, Hong Zhang, and Guoliang Chen
A better block partition and ligation strategy for individual haplotyping
Bioinformatics Advance Access published on October 9, 2008
Bioinformatics 2008 24: 2720-2725; doi:10.1093/bioinformatics/btn519 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY Back

Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, and Alexander Goesmann
MeltDB: a software platform for the analysis and integration of metabolomics experiment data
Bioinformatics Advance Access published on September 2, 2008
Bioinformatics 2008 24: 2726-2732; doi:10.1093/bioinformatics/btn452 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Fergal P. Casey, Gerard Cagney, Nevan J. Krogan, and Denis C. Shields
Optimal stepwise experimental design for pairwise functional interaction studies
Bioinformatics Advance Access published on September 18, 2008
Bioinformatics 2008 24: 2733-2739; doi:10.1093/bioinformatics/btn472 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Gang Liu, Dhananjay D. Marathe, Khushi L. Matta, and Sriram Neelamegham
Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2740-2747; doi:10.1093/bioinformatics/btn515 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Eugenio Cinquemani, Andreas Milias-Argeitis, Sean Summers, and John Lygeros
Stochastic dynamics of genetic networks: modelling and parameter identification
Bioinformatics Advance Access published on October 9, 2008
Bioinformatics 2008 24: 2748-2754; doi:10.1093/bioinformatics/btn527 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jiri Jablonsky, Petr Susila, and Dusan Lazar
Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting
Bioinformatics Advance Access published on October 9, 2008
Bioinformatics 2008 24: 2755-2759; doi:10.1093/bioinformatics/btn530 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

Sirarat Sarntivijai, Alexander S. Ade, Brian D. Athey, and David J. States
A bioinformatics analysis of the cell line nomenclature
Bioinformatics Advance Access published on October 10, 2008
Bioinformatics 2008 24: 2760-2766; doi:10.1093/bioinformatics/btn502 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Gabrielle A. Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A. Harris, Sandra Orchard, Rafael C. Jimenez, Andreas Prlic, Tim J. P. Hubbard, Henning Hermjakob, and Janet M. Thornton
The Protein Feature Ontology: a tool for the unification of protein feature annotations
Bioinformatics Advance Access published on October 20, 2008
Bioinformatics 2008 24: 2767-2772; doi:10.1093/bioinformatics/btn528 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Peng-An Chen, Hsiao-Fei Liu, and Kun-Mao Chao
CNVDetector: locating copy number variations using array CGH data
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2773-2775; doi:10.1093/bioinformatics/btn517 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Brian D. Ondov, Anjana Varadarajan, Karla D. Passalacqua, and Nicholas H. Bergman
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2776-2777; doi:10.1093/bioinformatics/btn512 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

PHYLOGENETICS Back

Thorhildur Juliusdottir, Fredrik Pettersson, and Richard R. Copley
POPE—a tool to aid high-throughput phylogenetic analysis
Bioinformatics Advance Access published on October 10, 2008
Bioinformatics 2008 24: 2778-2779; doi:10.1093/bioinformatics/btn533 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

L. Holm, S. Kääriäinen, P. Rosenström, and A. Schenkel
Searching protein structure databases with DaliLite v.3
Bioinformatics Advance Access published on September 25, 2008
Bioinformatics 2008 24: 2780-2781; doi:10.1093/bioinformatics/btn507 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Michaël Heymann, David Paramelle, Gilles Subra, Eric Forest, Jean Martinez, Christophe Geourjon, and Gilbert Deléage
MSX-3D: a tool to validate 3D protein models using mass spectrometry
Bioinformatics Advance Access published on September 30, 2008
Bioinformatics 2008 24: 2782-2783; doi:10.1093/bioinformatics/btn510 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS Back

Marit Holden, Shiwei Deng, Leszek Wojnowski, and Bettina Kulle
GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies
Bioinformatics Advance Access published on October 14, 2008
Bioinformatics 2008 24: 2784-2785; doi:10.1093/bioinformatics/btn516 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ryan D. Hernandez
A flexible forward simulator for populations subject to selection and demography
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2786-2787; doi:10.1093/bioinformatics/btn522 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Roby Joehanes and James C. Nelson
QGene 4.0, an extensible Java QTL-analysis platform
Bioinformatics Advance Access published on October 21, 2008
Bioinformatics 2008 24: 2788-2789; doi:10.1093/bioinformatics/btn523 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Anna Ramírez-Soriano and Francesc Calafell
FABSIM: a software for generating FST distributions with various ascertainment biases
Bioinformatics Advance Access published on October 9, 2008
Bioinformatics 2008 24: 2790-2791; doi:10.1093/bioinformatics/btn531 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Josselin Noirel, Guido Sanguinetti, and Phillip C. Wright
Identifying differentially expressed subnetworks with MMG
Bioinformatics Advance Access published on September 25, 2008
Bioinformatics 2008 24: 2792-2793; doi:10.1093/bioinformatics/btn499 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tom S. Price, Julie E. Baggs, Anne M. Curtis, Garret A. FitzGerald, and John B. Hogenesch
WAVECLOCK: wavelet analysis of circadian oscillation
Bioinformatics Advance Access published on October 17, 2008
Bioinformatics 2008 24: 2794-2795; doi:10.1093/bioinformatics/btn521 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

John T. Prince and Edward M. Marcotte
mspire: mass spectrometry proteomics in Ruby
Bioinformatics Advance Access published on October 16, 2008
Bioinformatics 2008 24: 2796-2797; doi:10.1093/bioinformatics/btn513 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Yuelin Zhu, Sean Davis, Robert Stephens, Paul S. Meltzer, and Yidong Chen
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2798-2800; doi:10.1093/bioinformatics/btn520 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

Dihui Lu, Richard Z. Liu, Victoria Izumi, David Fenstermacher, Eric B. Haura, John Koomen, and Steven A. Eschrich
IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2801-2802; doi:10.1093/bioinformatics/btn511 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Geoffrey L. Winsor, Bhavjinder Khaira, Thea Van Rossum, Raymond Lo, Matthew D. Whiteside, and Fiona S. L. Brinkman
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses
Bioinformatics Advance Access published on October 7, 2008
Bioinformatics 2008 24: 2803-2804; doi:10.1093/bioinformatics/btn524 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

LETTER TO THE EDITOR Back

SYSTEMS BIOLOGY Back

Faruck Morcos, Charles Lamanna, Marcin Sikora, and Jesús Izaguirre
Addendum. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference
Bioinformatics Advance Access published on October 9, 2008
Bioinformatics 2008 24: 2805; doi:10.1093/bioinformatics/btn532 [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.