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Previous Next 		Contents: Volume 23, Number 24, 15 December 2007   [Index by Author] 
       REVIEW
                SEQUENCE ANALYSIS
       DISCOVERY NOTE
                STRUCTURAL BIOINFORMATICS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTES
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
       CORRIGENDUM
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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:

SEQUENCE ANALYSIS:

Claus Lundegaard, Ole Lund, Can Kesmir, Søren Brunak, and Morten Nielsen
Modeling the adaptive immune system: predictions and simulations
Bioinformatics Advance Access published on November 28, 2007
Bioinformatics 2007 23: 3265-3275; doi:10.1093/bioinformatics/btm471 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

DISCOVERY NOTE:

STRUCTURAL BIOINFORMATICS:

Orly Noivirt-Brik, Ron Unger, and Amnon Horovitz
Low folding propensity and high translation efficiency distinguish in vivo substrates of GroEL from other Escherichia coli proteins
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2007 23: 3276-3279; doi:10.1093/bioinformatics/btm513 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Robin Nunkesser, Thorsten Bernholt, Holger Schwender, Katja Ickstadt, and Ingo Wegener
Detecting high-order interactions of single nucleotide polymorphisms using genetic programming
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2007 23: 3280-3288; doi:10.1093/bioinformatics/btm522 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Shu Wang, Robin R. Gutell, and Daniel P. Miranker
Biclustering as a method for RNA local multiple sequence alignment
Bioinformatics Advance Access published on October 6, 2007
Bioinformatics 2007 23: 3289-3296; doi:10.1093/bioinformatics/btm485 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Holger Dinkel and Heinrich Sticht
A computational strategy for the prediction of functional linear peptide motifs in proteins
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3297-3303; doi:10.1093/bioinformatics/btm524 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Stinus Lindgreen, Paul P. Gardner, and Anders Krogh
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
Bioinformatics Advance Access published on November 15, 2007
Bioinformatics 2007 23: 3304-3311; doi:10.1093/bioinformatics/btm525 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Angelika Fuchs, Antonio J. Martin-Galiano, Matan Kalman, Sarel Fleishman, Nir Ben-Tal, and Dmitrij Frishman
Co-evolving residues in membrane proteins
Bioinformatics 2007 23: 3312-3319; doi:10.1093/bioinformatics/btm515 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Mohammad Tabrez Anwar Shamim, Mohammad Anwaruddin, and H.A. Nagarajaram
Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs
Bioinformatics Advance Access published on November 7, 2007
Bioinformatics 2007 23: 3320-3327; doi:10.1093/bioinformatics/btm527 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Mark M. Gosink, Howard T. Petrie, and Nicholas F. Tsinoremas
Electronically subtracting expression patterns from a mixed cell population
Bioinformatics Advance Access published on October 22, 2007
Bioinformatics 2007 23: 3328-3334; doi:10.1093/bioinformatics/btm508 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Dikla Dotan-Cohen, Avraham A. Melkman, and Simon Kasif
Hierarchical tree snipping: clustering guided by prior knowledge
Bioinformatics Advance Access published on November 7, 2007
Bioinformatics 2007 23: 3335-3342; doi:10.1093/bioinformatics/btm526 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Roy Varshavsky, Assaf Gottlieb, David Horn, and Michal Linial
Unsupervised feature selection under perturbations: meeting the challenges of biological data
Bioinformatics Advance Access published on November 7, 2007
Bioinformatics 2007 23: 3343-3349; doi:10.1093/bioinformatics/btm528 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

F. Castiglione, F. Pappalardo, M. Bernaschi, and S. Motta
Optimization of HAART with genetic algorithms and agent-based models of HIV infection
Bioinformatics Advance Access published on October 17, 2007
Bioinformatics 2007 23: 3350-3355; doi:10.1093/bioinformatics/btm408 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yves Fomekong-Nanfack, Jaap A. Kaandorp, and Joke Blom
Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster
Bioinformatics Advance Access published on September 24, 2007
Bioinformatics 2007 23: 3356-3363; doi:10.1093/bioinformatics/btm433 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Hon Nian Chua, Wing-Kin Sung, and Limsoon Wong
An efficient strategy for extensive integration of diverse biological data for protein function prediction
Bioinformatics Advance Access published on November 28, 2007
Bioinformatics 2007 23: 3364-3373; doi:10.1093/bioinformatics/btm520 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Chung-Chih Lin, Yuh-Show Tsai, Yu-Shi Lin, Tai-Yu Chiu, Chia-Cheng Hsiung, May-I. Lee, Jeremy C. Simpson, and Chun-Nan Hsu
Boosting multiclass learning with repeating codes and weak detectors for protein subcellular localization
Bioinformatics Advance Access published on October 22, 2007
Bioinformatics 2007 23: 3374-3381; doi:10.1093/bioinformatics/btm497 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTES:

SEQUENCE ANALYSIS:

Volker Hollich and Erik L.L. Sonnhammer
PfamAlyzer: domain-centric homology search
Bioinformatics Advance Access published on October 31, 2007
Bioinformatics 2007 23: 3382-3383; doi:10.1093/bioinformatics/btm521 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Thomas Laubach and Arndt von Haeseler
TreeSnatcher: coding trees from images
Bioinformatics Advance Access published on September 24, 2007
Bioinformatics 2007 23: 3384-3385; doi:10.1093/bioinformatics/btm438 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Sanbo Qin and Huan-Xiang Zhou
meta-PPISP: a meta web server for protein-protein interaction site prediction
Bioinformatics Advance Access published on September 25, 2007
Bioinformatics 2007 23: 3386-3387; doi:10.1093/bioinformatics/btm434 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

D. Fusco, B. Bassetti, P. Jona, and M. Cosentino Lagomarsino
DIA-MCIS: an importance sampling network randomizer for network motif discovery and other topological observables in transcription networks
Bioinformatics Advance Access published on September 27, 2007
Bioinformatics 2007 23: 3388-3390; doi:10.1093/bioinformatics/btm454 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

J. R. Bilbao-Castro, I. García, and J. J. Fernández
EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography
Bioinformatics Advance Access published on September 14, 2007
Bioinformatics 2007 23: 3391-3393; doi:10.1093/bioinformatics/btm459 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ted Laderas, Cory Bystrom, Debra McMillen, Guang Fan, and Shannon McWeeney
TandTRAQ: an open-source tool for integrated protein identification and quantitation
Bioinformatics Advance Access published on September 25, 2007
Bioinformatics 2007 23: 3394-3396; doi:10.1093/bioinformatics/btm467 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Surendra S. Negi, Catherine H. Schein, Numan Oezguen, Trevor D. Power, and Werner Braun
InterProSurf: a web server for predicting interacting sites on protein surfaces
Bioinformatics Advance Access published on October 12, 2007
Bioinformatics 2007 23: 3397-3399; doi:10.1093/bioinformatics/btm474 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Min Hu, Junhui Wang, and Qunsheng Peng
Identification and visualization of cage-shaped proteins
Bioinformatics Advance Access published on October 5, 2007
Bioinformatics 2007 23: 3400-3402; doi:10.1093/bioinformatics/btm476 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Lukasz Slabinski, Lukasz Jaroszewski, Leszek Rychlewski, Ian A. Wilson, Scott A. Lesley, and Adam Godzik
XtalPred: a web server for prediction of protein crystallizability
Bioinformatics Advance Access published on October 5, 2007
Bioinformatics 2007 23: 3403-3405; doi:10.1093/bioinformatics/btm477 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

Remo Sanges, Francesca Cordero, and Raffaele A. Calogero
oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language
Bioinformatics Advance Access published on September 17, 2007
Bioinformatics 2007 23: 3406-3408; doi:10.1093/bioinformatics/btm469 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Andre S. Ribeiro, Daniel A. Charlebois, and Jason Lloyd-Price
CellLine, a stochastic cell lineage simulator
Bioinformatics Advance Access published on October 9, 2007
Bioinformatics 2007 23: 3409-3411; doi:10.1093/bioinformatics/btm491 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jean Peccoud, Tod Courtney, and William H. Sanders
Möbius: an integrated discrete-event modeling environment
Bioinformatics Advance Access published on November 28, 2007
Bioinformatics 2007 23: 3412-3414; doi:10.1093/bioinformatics/btm517 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

CORRIGENDUM:

‘ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data’
Bioinformatics 2007 23: 3415; doi:10.1093/bioinformatics/btm419 [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.