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Previous Next 		Contents: Volume 22, Number 23, 1 December 2006   [Index by Author] 
       DISCOVERY NOTE
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTE
                GENOME ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
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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.

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Zoë Birtle and Chris P. Ponting
Meisetz and the birth of the KRAB motif
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2006 22: 2841-2845; doi:10.1093/bioinformatics/btl498 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Melissa Da Silva, Ling Shen, Vasily Tcherepanov, Cristalle Watson, and Chris Upton
Predicted function of the vaccinia virus G5R protein
Bioinformatics Advance Access published on October 4, 2006
Bioinformatics 2006 22: 2846-2850; doi:10.1093/bioinformatics/btl506 [Abstract] [FREE Full Text] [Print PDF] [Supplementary material]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Torben Friedrich, Birgit Pils, Thomas Dandekar, Jörg Schultz, and Tobias Müller
Modelling interaction sites in protein domains with interaction profile hidden Markov models
Bioinformatics Advance Access published on September 25, 2006
Bioinformatics 2006 22: 2851-2857; doi:10.1093/bioinformatics/btl486 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Nora Pierstorff, Casey M. Bergman, and Thomas Wiehe
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2006 22: 2858-2864; doi:10.1093/bioinformatics/btl499 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

László Kaján, Attila Kertész-Farkas, Dino Franklin, Neli Ivanova, András Kocsor, and Sándor Pongor
Application of a simple likelihood ratio approximant to protein sequence classification
Bioinformatics Advance Access published on November 7, 2006
Bioinformatics 2006 22: 2865-2869; doi:10.1093/bioinformatics/btl512 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Nak-Kyeong Kim, Kannan Tharakaraman, and John L. Spouge
Adding sequence context to a Markov background model improves the identification of regulatory elements
Bioinformatics Advance Access published on October 26, 2006
Bioinformatics 2006 22: 2870-2875; doi:10.1093/bioinformatics/btl528 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Qifang Xu, Adrian Canutescu, Zoran Obradovic, and Roland L. Dunbrack, Jr
ProtBuD: a database of biological unit structures of protein families and superfamilies
Bioinformatics Advance Access published on October 2, 2006
Bioinformatics 2006 22: 2876-2882; doi:10.1093/bioinformatics/btl490 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

Dong Wang, Yingli Lv, Zheng Guo, Xia Li, Yanhui Li, Jing Zhu, Da Yang, Jianzhen Xu, Chenguang Wang, Shaoqi Rao, and Baofeng Yang
Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules
Bioinformatics Advance Access published on June 29, 2006
Bioinformatics 2006 22: 2883-2889; doi:10.1093/bioinformatics/btl339 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Curtis Huttenhower, Matt Hibbs, Chad Myers, and Olga G. Troyanskaya
A scalable method for integration and functional analysis of multiple microarray datasets
Bioinformatics Advance Access published on September 27, 2006
Bioinformatics 2006 22: 2890-2897; doi:10.1093/bioinformatics/btl492 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Sukjoon Yoon, Young Yang, Jiwon Choi, and Jeeweon Seong
Large scale data mining approach for gene-specific standardization of microarray gene expression data
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2006 22: 2898-2904; doi:10.1093/bioinformatics/btl500 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Alexander Begun
Robust method for detecting differential gene expression in twin studies
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2006 22: 2905-2909; doi:10.1093/bioinformatics/btl501 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Antti Lehmussola, Pekka Ruusuvuori, and Olli Yli-Harja
Evaluating the performance of microarray segmentation algorithms
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2006 22: 2910-2917; doi:10.1093/bioinformatics/btl502 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Chris Sanford, Matthew L.K. Yip, Carl White, and John Parkinson
Cell++—simulating biochemical pathways
Bioinformatics Advance Access published on October 11, 2006
Bioinformatics 2006 22: 2918-2925; doi:10.1093/bioinformatics/btl497 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Jeffrey T. Chang and Joseph R. Nevins
GATHER: a systems approach to interpreting genomic signatures
Bioinformatics Advance Access published on September 25, 2006
Bioinformatics 2006 22: 2926-2933; doi:10.1093/bioinformatics/btl483 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Sorin Draghici, Sivakumar Sellamuthu, and Purvesh Khatri
Babel's tower revisited: a universal resource for cross-referencing across annotation databases
Bioinformatics Advance Access published on October 26, 2006
Bioinformatics 2006 22: 2934-2939; doi:10.1093/bioinformatics/btl372 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Agrawal Shipra, Kumar Chetan, and M. R. S. Rao
CREMOFAC—a database of chromatin remodeling factors
Bioinformatics Advance Access published on October 4, 2006
Bioinformatics 2006 22: 2940-2944; doi:10.1093/bioinformatics/btl509 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Yan V. Sun, Douglas M. Jacobsen, and Sharon L. R. Kardia
ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies
Bioinformatics Advance Access published on October 10, 2006
Bioinformatics 2006 22: 2945-2947; doi:10.1093/bioinformatics/btl503 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Oxana V. Galzitskaya, Sergiy O. Garbuzynskiy, and Michail Yu. Lobanov
FoldUnfold: web server for the prediction of disordered regions in protein chain
Bioinformatics Advance Access published on October 4, 2006
Bioinformatics 2006 22: 2948-2949; doi:10.1093/bioinformatics/btl504 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

James W. MacDonald and Debashis Ghosh
COPA—cancer outlier profile analysis
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2950-2951; doi:10.1093/bioinformatics/btl433 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xiaohui Chen, Ming Chen, and Kaida Ning
BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network
Bioinformatics Advance Access published on September 27, 2006
Bioinformatics 2006 22: 2952-2954; doi:10.1093/bioinformatics/btl491 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xiangfeng Wang, Hang He, Lei Li, Runsheng Chen, Xing Wang Deng, and Songgang Li
NMPP: a user-customized NimbleGen microarray data processing pipeline
Bioinformatics Advance Access published on October 12, 2006
Bioinformatics 2006 22: 2955-2957; doi:10.1093/bioinformatics/btl525 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Nicolas Goffard and Georg Weiller
Extending MapMan: application to legume genome arrays
Bioinformatics Advance Access published on October 17, 2006
Bioinformatics 2006 22: 2958-2959; doi:10.1093/bioinformatics/btl517 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENETICS AND POPULATION ANALYSIS:

Dale R. Nyholt
ssSNPer: identifying statistically similar SNPs to aid interpretation of genetic association studies
Bioinformatics Advance Access published on October 12, 2006
Bioinformatics 2006 22: 2960-2961; doi:10.1093/bioinformatics/btl518 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Boyke Bunk, Martin Kucklick, Rochus Jonas, Richard Münch, Max Schobert, Dieter Jahn, and Karsten Hiller
MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data
Bioinformatics Advance Access published on October 17, 2006
Bioinformatics 2006 22: 2962-2965; doi:10.1093/bioinformatics/btl526 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Anastasia Deckard, Frank T. Bergmann, and Herbert M. Sauro
Supporting the SBML layout extension
Bioinformatics Advance Access published on October 11, 2006
Bioinformatics 2006 22: 2966-2967; doi:10.1093/bioinformatics/btl520 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin Schultz, and Mark Gerstein
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
Bioinformatics Advance Access published on October 4, 2006
Bioinformatics 2006 22: 2968-2970; doi:10.1093/bioinformatics/btl488 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

S. Blair Hedges, Joel Dudley, and Sudhir Kumar
TimeTree: a public knowledge-base of divergence times among organisms
Bioinformatics Advance Access published on October 4, 2006
Bioinformatics 2006 22: 2971-2972; doi:10.1093/bioinformatics/btl505 [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.