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Previous Next 		Contents: Volume 22, Number 21, 1 November 2006   [Index by Author] 
       DISCOVERY NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
       APPLICATIONS NOTE
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
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DISCOVERY NOTE:

GENOME ANALYSIS:

Kira S. Makarova, Nick V. Grishin, and Eugene V. Koonin
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria
Bioinformatics Advance Access published on August 8, 2006
Bioinformatics 2006 22: 2581-2584; doi:10.1093/bioinformatics/btl418 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

SEQUENCE ANALYSIS:

Yu Wang, Tobias Hindemitt, and Klaus F. X. Mayer
Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs
Bioinformatics Advance Access published on August 10, 2006
Bioinformatics 2006 22: 2585-2589; doi:10.1093/bioinformatics/btl437 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Chunlin Wang, Chris Ding, Richard F. Meraz, and Stephen R. Holbrook
PSoL: a positive sample only learning algorithm for finding non-coding RNA genes
Bioinformatics Advance Access published on August 31, 2006
Bioinformatics 2006 22: 2590-2596; doi:10.1093/bioinformatics/btl441 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

SEQUENCE ANALYSIS:

Levon Budagyan and Ruben Abagyan
Weighted quality estimates in machine learning
Bioinformatics Advance Access published on August 25, 2006
Bioinformatics 2006 22: 2597-2603; doi:10.1093/bioinformatics/btl458 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Guohua Jin, Luay Nakhleh, Sagi Snir, and Tamir Tuller
Maximum likelihood of phylogenetic networks
Bioinformatics Advance Access published on August 23, 2006
Bioinformatics 2006 22: 2604-2611; doi:10.1093/bioinformatics/btl452 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Dominique Douguet, Huei-Chi Chen, Andrey Tovchigrechko, and Ilya A. Vakser
DOCKGROUND resource for studying protein–protein interfaces
Bioinformatics Advance Access published on August 23, 2006
Bioinformatics 2006 22: 2612-2618; doi:10.1093/bioinformatics/btl447 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Eran Eyal, Lee-Wei Yang, and Ivet Bahar
Anisotropic network model: systematic evaluation and a new web interface
Bioinformatics Advance Access published on August 23, 2006
Bioinformatics 2006 22: 2619-2627; doi:10.1093/bioinformatics/btl448 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Fabian Birzele and Stefan Kramer
A new representation for protein secondary structure prediction based on frequent patterns
Bioinformatics Advance Access published on August 29, 2006
Bioinformatics 2006 22: 2628-2634; doi:10.1093/bioinformatics/btl453 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Ronglai Shen, Debashis Ghosh, Arul Chinnaiyan, and Zhaoling Meng
Eigengene-based linear discriminant model for tumor classification using gene expression microarray data
Bioinformatics Advance Access published on August 22, 2006
Bioinformatics 2006 22: 2635-2642; doi:10.1093/bioinformatics/btl442 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Natasa Rajicic, Dianne M. Finkelstein, David A. Schoenfeld, and the Inflammation Host Response to Injury Research Program Investigators
Survival analysis of longitudinal microarrays
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2006 22: 2643-2649; doi:10.1093/bioinformatics/btl450 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Chao Cheng, Xiaotu Ma, Xiting Yan, Fengzhu Sun, and Lei M. Li
MARD: a new method to detect differential gene expression in treatment-control time courses
Bioinformatics Advance Access published on August 23, 2006
Bioinformatics 2006 22: 2650-2657; doi:10.1093/bioinformatics/btl451 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

A. Callegaro, D. Basso, and S. Bicciato
A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions
Bioinformatics Advance Access published on September 1, 2006
Bioinformatics 2006 22: 2658-2666; doi:10.1093/bioinformatics/btl455 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Joe Faith, Robert Mintram, and Maia Angelova
Targeted projection pursuit for visualizing gene expression data classifications
Bioinformatics Advance Access published on September 5, 2006
Bioinformatics 2006 22: 2667-2673; doi:10.1093/bioinformatics/btl463 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

SYSTEMS BIOLOGY:

Nicole Radde, Jutta Gebert, and Christian V. Forst
Systematic component selection for gene-network refinement
Bioinformatics Advance Access published on August 22, 2006
Bioinformatics 2006 22: 2674-2680; doi:10.1093/bioinformatics/btl440 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Visakan Kadirkamanathan, Jing Yang, Stephen A. Billings, and Phillip C. Wright
Markov Chain Monte Carlo Algorithm based metabolic flux distribution analysis on Corynebacterium glutamicum
Bioinformatics Advance Access published on August 29, 2006
Bioinformatics 2006 22: 2681-2687; doi:10.1093/bioinformatics/btl445 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

PHYLOGENETICS:

Alexandros Stamatakis
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Bioinformatics Advance Access published on August 23, 2006
Bioinformatics 2006 22: 2688-2690; doi:10.1093/bioinformatics/btl446 [Abstract] [FREE Full Text] [Print PDF] [Supplementary data]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Brajesh K. Rai, Carlos J. Madrid-Aliste, J. Eduardo Fajardo, and András Fiser
MMM: a sequence-to-structure alignment protocol
Bioinformatics Advance Access published on August 23, 2006
Bioinformatics 2006 22: 2691-2692; doi:10.1093/bioinformatics/btl449 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Shantanu Sharma, Feng Ding, Huifen Nie, Daniel Watson, Aditya Unnithan, Jameson Lopp, Diane Pozefsky, and Nikolay V. Dokholyan
iFold: a platform for interactive folding simulations of proteins
Bioinformatics Advance Access published on August 29, 2006
Bioinformatics 2006 22: 2693-2694; doi:10.1093/bioinformatics/btl460 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Barry J. Grant, Ana P. C. Rodrigues, Karim M. ElSawy, J. Andrew McCammon, and Leo S. D. Caves
Bio3d: an R package for the comparative analysis of protein structures
Bioinformatics Advance Access published on August 29, 2006
Bioinformatics 2006 22: 2695-2696; doi:10.1093/bioinformatics/btl461 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

Tsun-Po Yang, Ting-Yu Chang, Chi-Hung Lin, Ming-Ta Hsu, and Hsei-Wei Wang
ArrayFusion: a web application for multi-dimensional analysis of CGH, SNP and microarray data
Bioinformatics Advance Access published on August 25, 2006
Bioinformatics 2006 22: 2697-2698; doi:10.1093/bioinformatics/btl457 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kellie J. Archer and Tobias Guennel
An application for assessing quality of RNA hybridized to Affymetrix GeneChips
Bioinformatics Advance Access published on August 25, 2006
Bioinformatics 2006 22: 2699-2701; doi:10.1093/bioinformatics/btl459 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Grégory Deceliere, Yann Letrillard, Sandrine Charles, and Christian Biémont
TESD: a transposable element dynamics simulation environment
Bioinformatics Advance Access published on August 23, 2006
Bioinformatics 2006 22: 2702-2703; doi:10.1093/bioinformatics/btl454 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Zhike Zi and Edda Klipp
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool
Bioinformatics Advance Access published on August 22, 2006
Bioinformatics 2006 22: 2704-2705; doi:10.1093/bioinformatics/btl443 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ronald C. Taylor, Anuj Shah, Charles Treatman, and Meridith Blevins
SEBINI: Software Environment for BIological Network Inference
Bioinformatics Advance Access published on September 5, 2006
Bioinformatics 2006 22: 2706-2708; doi:10.1093/bioinformatics/btl444 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Markus Ulrich, Constantin Kappel, Joel Beaudouin, Stefan Hezel, Jochen Ulrich, and Roland Eils
Tropical—parameter estimation and simulation of reaction–diffusion models based on spatio-temporal microscopy images
Bioinformatics Advance Access published on August 29, 2006
Bioinformatics 2006 22: 2709-2710; doi:10.1093/bioinformatics/btl456 [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.