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Previous Next 		Contents: Volume 22, Number 12, 15 June 2006   [Index by Author] 
       EDITORIALS
       DISCOVERY NOTES
                GENOME ANALYSIS
                SYSTEMS BIOLOGY
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
       APPLICATIONS NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                GENE EXPRESSION
                DATA AND TEXT MINING
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EDITORIALS:

Alfonso Valencia and Alex Bateman
Software patents in Bioinformatics
Bioinformatics 2006 22: 1415; doi:10.1093/bioinformatics/btl166 [Extract] [Full Text] [Print PDF] [Request Permissions]  

John Quackenbush and Steven L. Salzberg
It is time to end the patenting of software
Bioinformatics 2006 22: 1416-1417; doi:10.1093/bioinformatics/btl167 [Extract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTES:

GENOME ANALYSIS:

Sophie Pasek, Jean-Loup Risler, and Pierre Brézellec
Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
Bioinformatics Advance Access published on April 6, 2006
Bioinformatics 2006 22: 1418-1423; doi:10.1093/bioinformatics/btl135 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Martin G. Grigorov
Global dynamics of biological systems from time-resolved omics experiments
Bioinformatics Advance Access published on April 3, 2006
Bioinformatics 2006 22: 1424-1430; doi:10.1093/bioinformatics/btl119 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Radek Szklarczyk and Jaap Heringa
AuberGene—a sensitive genome alignment tool
Bioinformatics Advance Access published on April 10, 2006
Bioinformatics 2006 22: 1431-1436; doi:10.1093/bioinformatics/btl112 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John Karro, Paul M. Harrison, and Mark Gerstein
PseudoPipe: an automated pseudogene identification pipeline
Bioinformatics Advance Access published on March 30, 2006
Bioinformatics 2006 22: 1437-1439; doi:10.1093/bioinformatics/btl116 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SEQUENCE ANALYSIS:

Florencio Pazos, Antonio Rausell, and Alfonso Valencia
Phylogeny-independent detection of functional residues
Bioinformatics Advance Access published on March 21, 2006
Bioinformatics 2006 22: 1440-1448; doi:10.1093/bioinformatics/btl104 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

Francesco Ortuso, Thierry Langer, and Stefano Alcaro
GBPM: GRID-based pharmacophore model: concept and application studies to protein–protein recognition
Bioinformatics Advance Access published on March 27, 2006
Bioinformatics 2006 22: 1449-1455; doi:10.1093/bioinformatics/btl115 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jianlin Cheng and Pierre Baldi
A machine learning information retrieval approach to protein fold recognition
Bioinformatics Advance Access published on March 17, 2006
Bioinformatics 2006 22: 1456-1463; doi:10.1093/bioinformatics/btl102 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Alison L. Cuff, Robert W. Janes, and Andrew C.R. Martin
Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins
Bioinformatics Advance Access published on April 6, 2006
Bioinformatics 2006 22: 1464-1470; doi:10.1093/bioinformatics/btl120 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

S. E. Ahnert, K. Willbrand, F. C. S. Brown, and T. M. A. Fink
Unbiased pattern detection in microarray data series
Bioinformatics Advance Access published on April 3, 2006
Bioinformatics 2006 22: 1471-1476; doi:10.1093/bioinformatics/btl121 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Philippe Broët, Vladimir A. Kuznetsov, Jonas Bergh, Edison T. Liu, and Lance D. Miller
Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients
Bioinformatics Advance Access published on March 21, 2006
Bioinformatics 2006 22: 1477-1485; doi:10.1093/bioinformatics/btl110 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xin Gao
Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments
Bioinformatics Advance Access published on March 30, 2006
Bioinformatics 2006 22: 1486-1494; doi:10.1093/bioinformatics/btl109 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Lars Kaderali, Thomas Zander, Ulrich Faigle, Jürgen Wolf, Joachim L. Schultze, and Rainer Schrader
CASPAR: a hierarchical bayesian approach to predict survival times in cancer from gene expression data
Bioinformatics Advance Access published on March 22, 2006
Bioinformatics 2006 22: 1495-1502; doi:10.1093/bioinformatics/btl103 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Wentian Li, Mingyi Wang, Patricia Irigoyen, and Peter K. Gregersen
Inferring causal relationships among intermediate phenotypes and biomarkers: a case study of rheumatoid arthritis
Bioinformatics Advance Access published on March 21, 2006
Bioinformatics 2006 22: 1503-1507; doi:10.1093/bioinformatics/btl100 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, and Fengzhu Sun
A dynamic programming algorithm for binning microbial community profiles
Bioinformatics Advance Access published on March 27, 2006
Bioinformatics 2006 22: 1508-1514; doi:10.1093/bioinformatics/btl114 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Chuen Seng Tan, Alexander Ploner, Andreas Quandt, Janne Lehtiö, and Yudi Pawitan
Finding regions of significance in SELDI measurements for identifying protein biomarkers
Bioinformatics Advance Access published on March 27, 2006
Bioinformatics 2006 22: 1515-1523; doi:10.1093/bioinformatics/btl106 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Smriti R. Ramakrishnan, Rui Mao, Aleksey A. Nakorchevskiy, John T. Prince, Willard S. Willard, Weijia Xu, Edward M. Marcotte, and Daniel P. Miranker
A fast coarse filtering method for peptide identification by mass spectrometry
Bioinformatics Advance Access published on April 3, 2006
Bioinformatics 2006 22: 1524-1531; doi:10.1093/bioinformatics/btl118 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Boris Adryan and Sarah A. Teichmann
FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
Bioinformatics Advance Access published on April 13, 2006
Bioinformatics 2006 22: 1532-1533; doi:10.1093/bioinformatics/btl143 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

SEQUENCE ANALYSIS:

Yann Ponty, Michel Termier, and Alain Denise
GenRGenS: software for generating random genomic sequences and structures
Bioinformatics Advance Access published on March 30, 2006
Bioinformatics 2006 22: 1534-1535; doi:10.1093/bioinformatics/btl113 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Vladimir Vacic, Lilia M. Iakoucheva, and Predrag Radivojac
Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 1536-1537; doi:10.1093/bioinformatics/btl151 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto, and Satoru Miyano
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles
Bioinformatics Advance Access published on April 10, 2006
Bioinformatics 2006 22: 1538-1539; doi:10.1093/bioinformatics/btl129 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATA AND TEXT MINING:

Ryota Suzuki and Hidetoshi Shimodaira
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1540-1542; doi:10.1093/bioinformatics/btl117 [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.