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Previous Next 		Contents: Volume 22, Number 20, 15 October 2006   [Index by Author] 
       DISCOVERY NOTE
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTE
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
       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.

DISCOVERY NOTE:

SEQUENCE ANALYSIS:

Sunil Archak and Javaregowda Nagaraju
Eicosapentapeptide repeats (EPRs): novel repeat proteins specific to flowering plants
Bioinformatics Advance Access published on June 29, 2006
Bioinformatics 2006 22: 2455-2458; doi:10.1093/bioinformatics/btl340 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Dapeng Zhang, Christopher J. Martyniuk, and Vance L. Trudeau
SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation
Bioinformatics Advance Access published on July 28, 2006
Bioinformatics 2006 22: 2459-2462; doi:10.1093/bioinformatics/btl414 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Michaël Bekaert, John F Atkins, and Pavel V Baranov
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2463-2465; doi:10.1093/bioinformatics/btl430 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS:

Pekka Marttinen, Jukka Corander, Petri Törönen, and Liisa Holm
Bayesian search of functionally divergent protein subgroups and their function specific residues
Bioinformatics Advance Access published on July 26, 2006
Bioinformatics 2006 22: 2466-2474; doi:10.1093/bioinformatics/btl411 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xijin Ge, Qingfa Wu, Yong-Chul Jung, Jun Chen, and San Ming Wang
A large quantity of novel human antisense transcripts detected by LongSAGE
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2475-2479; doi:10.1093/bioinformatics/btl429 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, and Kiyoshi Asai
Mining frequent stem patterns from unaligned RNA sequences
Bioinformatics Advance Access published on August 14, 2006
Bioinformatics 2006 22: 2480-2487; doi:10.1093/bioinformatics/btl431 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Minoru Kanehisa, and Hiroyuki Toh
Partial correlation coefficient between distance matrices as a new indicator of protein–protein interactions
Bioinformatics Advance Access published on July 31, 2006
Bioinformatics 2006 22: 2488-2492; doi:10.1093/bioinformatics/btl419 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Konrad Scheffler, Darren P. Martin, and Cathal Seoighe
Robust inference of positive selection from recombining coding sequences
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2493-2499; doi:10.1093/bioinformatics/btl427 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

Theodora Manoli, Norbert Gretz, Hermann-Josef Gröne, Marc Kenzelmann, Roland Eils, and Benedikt Brors
Group testing for pathway analysis improves comparability of different microarray datasets
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2500-2506; doi:10.1093/bioinformatics/btl424 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Xin Zhou and K. Z. Mao
The ties problem resulting from counting-based error estimators and its impact on gene selection algorithms
Bioinformatics Advance Access published on August 14, 2006
Bioinformatics 2006 22: 2507-2515; doi:10.1093/bioinformatics/btl438 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Saumyadipta Pyne, Bruce Futcher, and Steve Skiena
Meta-analysis based on control of false discovery rate: combining yeast ChIP-chip datasets
Bioinformatics Advance Access published on August 14, 2006
Bioinformatics 2006 22: 2516-2522; doi:10.1093/bioinformatics/btl439 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Adriano V. Werhli, Marco Grzegorczyk, and Dirk Husmeier
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
Bioinformatics Advance Access published on July 14, 2006
Bioinformatics 2006 22: 2523-2531; doi:10.1093/bioinformatics/btl391 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Quansong Ruan, Debojyoti Dutta, Michael S. Schwalbach, Joshua A. Steele, Jed A. Fuhrman, and Fengzhu Sun
Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors
Bioinformatics Advance Access published on July 31, 2006
Bioinformatics 2006 22: 2532-2538; doi:10.1093/bioinformatics/btl417 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Gautier Stoll, Jacques Rougemont, and Félix Naef
Few crucial links assure checkpoint efficiency in the yeast cell-cycle network
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2539-2546; doi:10.1093/bioinformatics/btl432 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

E. S. Motakis, G. P. Nason, P. Fryzlewicz, and G. A. Rutter
Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
Bioinformatics Advance Access published on July 28, 2006
Bioinformatics 2006 22: 2547-2553; doi:10.1093/bioinformatics/btl412 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENE EXPRESSION:

Max Bylesjö, Andreas Sjödin, Daniel Eriksson, Henrik Antti, Thomas Moritz, Stefan Jansson, and Johan Trygg
MASQOT-GUI: spot quality assessment for the two-channel microarray platform
Bioinformatics Advance Access published on August 9, 2006
Bioinformatics 2006 22: 2554-2555; doi:10.1093/bioinformatics/btl434 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

GENETICS AND POPULATION ANALYSIS:

Frédéric Guillaume and Jacques Rougemont
Nemo: an evolutionary and population genetics programming framework
Bioinformatics Advance Access published on July 31, 2006
Bioinformatics 2006 22: 2556-2557; doi:10.1093/bioinformatics/btl415 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jingwu He and Alexander Zelikovsky
MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2558-2561; doi:10.1093/bioinformatics/btl420 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Qi Zhao, Radka Stoyanova, Shuyan Du, Paul Sajda, and Truman R. Brown
HiRes—a tool for comprehensive assessment and interpretation of metabolomic data
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2562-2564; doi:10.1093/bioinformatics/btl428 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Roger M. Jarvis, David Broadhurst, Helen Johnson, Noel M. O'Boyle, and Royston Goodacre
PYCHEM: a multivariate analysis package for python
Bioinformatics Advance Access published on July 31, 2006
Bioinformatics 2006 22: 2565-2566; doi:10.1093/bioinformatics/btl416 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Julio Bonis, Laura Inés Furlong, and Ferran Sanz
OSIRIS: a tool for retrieving literature about sequence variants
Bioinformatics Advance Access published on July 31, 2006
Bioinformatics 2006 22: 2567-2569; doi:10.1093/bioinformatics/btl421 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Luca Lenzi, Flavia Frabetti, Federica Facchin, Raffaella Casadei, Lorenza Vitale, Silvia Canaider, Paolo Carinci, Maria Zannotti, and Pierluigi Strippoli
UniGene Tabulator: a full parser for the UniGene format
Bioinformatics Advance Access published on August 7, 2006
Bioinformatics 2006 22: 2570-2571; doi:10.1093/bioinformatics/btl425 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Dequan Li, Wen Gao, Charles X. Ling, Xiaobiao Wang, Ruixiang Sun, and Simin He
IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics
Bioinformatics Advance Access published on August 31, 2006
Bioinformatics 2006 22: 2572-2573; doi:10.1093/bioinformatics/btl410 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Igor A. Gariev and Sergey D. Varfolomeev
Hierarchical classification of hydrolases catalytic sites
Bioinformatics Advance Access published on July 28, 2006
Bioinformatics 2006 22: 2574-2576; doi:10.1093/bioinformatics/btl413 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Florian Gnad and John Parsch
Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression
Bioinformatics Advance Access published on July 31, 2006
Bioinformatics 2006 22: 2577-2579; doi:10.1093/bioinformatics/btl422 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

Corrigendum
Bioinformatics 2006 22: 2580; doi:10.1093/bioinformatics/btl436 [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.