Bioinformatics

Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures
pp. 517-522(6)
Authors: Dalevi, Daniel; Dubhashi, Devdatt; Hermansson, Malte

HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana
pp. 523-526(4)
Authors: Yang, Guojun; Hall, Timothy C.

IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships
pp. 527-531(5)
Authors: D'Auria, Giuseppe; Pushker, Ravindra; Rodriguez-Valera, Francisco

A regularized discriminative model for the prediction of protein-peptide interactions
pp. 532-540(9)
Authors: Lehrach, Wolfgang P.; Husmeier, Dirk; Williams, Christopher K. I.

Accurate prediction of HIV-1 drug response from the reverse transcriptase and protease amino acid sequences using sparse models created by convex optimization
pp. 541-549(9)
Authors: Rabinowitz, Matthew; Myers, Lance; Banjevic, Milena; Chan, Albert; Sweetkind-Singer, Joshua; Haberer, Jessica; McCann, Kelly; Wolkowicz, Roland

Equivalent binding sites reveal convergently evolved interaction motifs
pp. 550-555(6)
Authors: Henschel, Andreas; Kim, Wan Kyu; Schroeder, Michael

Multidimensional local false discovery rate for microarray studies
pp. 556-565(10)
Authors: Ploner, Alexander; Calza, Stefano; Gusnanto, Arief; Pawitan, Yudi

Improving missing value estimation in microarray data with gene ontology
pp. 566-572(7)
Authors: Tuikkala, Johannes; Elo, Laura; Nevalainen, Olli S.; Aittokallio, Tero

Multiple association analysis via simulated annealing (MASSA)
pp. 573-580(8)
Authors: Pérez-Enciso, M.

Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW
pp. 581-588(8)
Authors: Louzoun, Yoram; Muchnik, Lev; Solomon, Sorin

A multi-step approach to time series analysis and gene expression clustering
pp. 589-596(8)
Authors: Amato, R.; Ciaramella, A.; Deniskina, N.; Mondo, C. Del; di Bernardo, D.; Donalek, C.; Longo, G.; Mangano, G.; Miele, G.; Raiconi, G.; Staiano, A.; Tagliaferri, R.

BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature
pp. 597-605(9)
Authors: Kim, Jung-jae; Zhang, Zhuo; Park, Jong C.; Ng, See-Kiong

Inferring global levels of alternative splicing isoforms using a generative model of microarray data
pp. 606-613(8)
Authors: Shai, Ofer; Morris, Quaid D.; Blencowe, Benjamin J.; Frey, Brendan J.

Local RNA base pairing probabilities in large sequences
pp. 614-615(2)
Authors: Bernhart, Stephan H.; Hofacker, Ivo L.; Stadler, Peter F.

GenomeDiagram: a python package for the visualization of large-scale genomic data
pp. 616-617(2)
Authors: Pritchard, Leighton; White, Jennifer A.; Birch, Paul R.J.; Toth, Ian K.

ANDY: a general, fault-tolerant tool for database searching on computer clusters
pp. 618-620(3)
Authors: Smith, Andrew; Chandonia, John-Marc; Brenner, Steven E.

BioShell—a package of tools for structural biology computations
pp. 621-622(2)
Authors: Gront, Dominik; Kolinski, Andrzej

OPM: Orientations of Proteins in Membranes database
pp. 623-625(3)
Authors: Lomize, Mikhail A.; Lomize, Andrei L.; Pogozheva, Irina D.; Mosberg, Henry I.

TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits
pp. 626-627(2)
Authors: Hemminger, Bradley M.; Saelim, Billy; Sullivan, Patrick F.

Tools for the SBML Community
pp. 628-629(2)
Authors: Gillespie, Colin S.; Wilkinson, Darren J.; Proctor, Carole J.; Shanley, Daryl P.; Boys, Richard J.; Kirkwood, Thomas B. L.

VIS-O-BAC: exploratory visualization of functional genome studies from bacteria
pp. 630-631(2)
Authors: Dieterich, Guido; Kärst, Uwe; Wehland, Jürgen; Jänsch, Lothar

ProteomeCommons.org JAF: reference information and tools for proteomics
pp. 632-633(2)
Authors: Falkner, J. A.; Falkner, J. W.; Andrews, P. C.

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data
pp. 634-636(3)
Authors: Katajamaa, Mikko; Miettinen, Jarkko; Orešič, Matej

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
pp. 637-640(4)
Authors: Montgomery, S. B.; Griffith, O. L.; Bergman, C. M.; Bilenky, M.; Pleasance, E. D.; Prychyna, Y.; Zhang, X.; Jones, S. J. M.

BuchneraBASE: a post-genomic resource for Buchnera sp. APS
pp. 641-642(2)
Authors: Prickett, M. Dennis; Page, Matt; Douglas, Angela E.; Thomas, Gavin H.