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Previous Next 		Contents: Volume 22, Number 4, 15 February 2006   [Index by Author] 
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTE
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                GENETICS AND POPULATION ANALYSIS
                SYSTEMS BIOLOGY
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ORIGINAL PAPERS:

GENOME ANALYSIS:

Jiexin Zhang, Li Zhang, and Kevin R. Coombes
Gene sequence signatures revealed by mining the UniGene affiliation network
Bioinformatics Advance Access published on December 8, 2005
Bioinformatics 2006 22: 385-391; doi:10.1093/bioinformatics/bti796 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xiang Guo, Kay Tatsuoka, and Rongxiang Liu
Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae
Bioinformatics Advance Access published on December 8, 2005
Bioinformatics 2006 22: 392-399; doi:10.1093/bioinformatics/bti823 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli S. Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, and Tero Aittokallio
Quality classification of tandem mass spectrometry data
Bioinformatics Advance Access published on December 13, 2005
Bioinformatics 2006 22: 400-406; doi:10.1093/bioinformatics/bti829 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

András Kocsor, Attila Kertész-Farkas, László Kaján, and Sándor Pongor
Application of compression-based distance measures to protein sequence classification: a methodological study
Bioinformatics Advance Access published on November 29, 2005
Bioinformatics 2006 22: 407-412; doi:10.1093/bioinformatics/bti806 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yao-ming Huang and Christopher Bystroff
Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions
Bioinformatics Advance Access published on December 13, 2005
Bioinformatics 2006 22: 413-422; doi:10.1093/bioinformatics/bti828 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kenzie D. MacIsaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, and Ernest Fraenkel
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
Bioinformatics Advance Access published on December 6, 2005
Bioinformatics 2006 22: 423-429; doi:10.1093/bioinformatics/bti815 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tilman Sauer, Ekaterina Shelest, and Edgar Wingender
Evaluating phylogenetic footprinting for human–rodent comparisons
Bioinformatics Advance Access published on December 6, 2005
Bioinformatics 2006 22: 430-437; doi:10.1093/bioinformatics/bti819 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Joseph M. Volpe, Lindsay G. Cowell, and Thomas B. Kepler
SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
Bioinformatics Advance Access published on December 15, 2005
Bioinformatics 2006 22: 438-444; doi:10.1093/bioinformatics/btk004 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zizhen Yao, Zasha Weinberg, and Walter L. Ruzzo
CMfinder—a covariance model based RNA motif finding algorithm
Bioinformatics Advance Access published on December 15, 2005
Bioinformatics 2006 22: 445-452; doi:10.1093/bioinformatics/btk008 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Elodie Duprat, Marie-Paule Lefranc, and Olivier Gascuel
A simple method to predict protein-binding from aligned sequences—application to MHC superfamily and ß2-microglobulin
Bioinformatics Advance Access published on December 13, 2005
Bioinformatics 2006 22: 453-459; doi:10.1093/bioinformatics/bti826 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Simon W. Ginzinger and Johannes Fischer
SimShift: Identifying structural similarities from NMR chemical shifts
Bioinformatics Advance Access published on November 29, 2005
Bioinformatics 2006 22: 460-465; doi:10.1093/bioinformatics/bti805 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Lexin Li
Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information
Bioinformatics Advance Access published on December 8, 2005
Bioinformatics 2006 22: 466-471; doi:10.1093/bioinformatics/bti824 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Baolin Wu
Differential gene expression detection and sample classification using penalized linear regression models
Bioinformatics Advance Access published on December 13, 2005
Bioinformatics 2006 22: 472-476; doi:10.1093/bioinformatics/bti827 [Abstract] [Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

SYSTEMS BIOLOGY:

E. P. van Someren, B. L. T. Vaes, W. T. Steegenga, A. M. Sijbers, K. J. Dechering, and M. J. T. Reinders
Least absolute regression network analysis of the murine osteoblast differentiation network
Bioinformatics Advance Access published on December 6, 2005
Bioinformatics 2006 22: 477-484; doi:10.1093/bioinformatics/bti816 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Siddhartha Basu, Erich Bremer, Chun Zhou, and Daniel F. Bogenhagen
MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation
Bioinformatics Advance Access published on December 20, 2005
Bioinformatics 2006 22: 485-492; doi:10.1093/bioinformatics/btk009 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

APPLICATIONS NOTE:

SEQUENCE ANALYSIS:

Jörg Rothgänger, Markus Weniger, Thomas Weniger, Alexander Mellmann, and Dag Harmsen
Ridom TraceEdit: a DNA trace editor and viewer
Bioinformatics Advance Access published on December 15, 2005
Bioinformatics 2006 22: 493-494; doi:10.1093/bioinformatics/btk002 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Derek Huntley, Angela Baldo, Saurabh Johri, and Marek Sergot
SEAN: SNP prediction and display program utilizing EST sequence clusters
Bioinformatics Advance Access published on December 15, 2005
Bioinformatics 2006 22: 495-496; doi:10.1093/bioinformatics/btk006 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tiziana Castrignanò, Paolo D'Onorio De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano Giuseppe Talamo, and Graziano Pesole
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags
Bioinformatics Advance Access published on November 2, 2005
Bioinformatics 2006 22: 497-499; doi:10.1093/bioinformatics/bti754 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Peter Steffen, Björn Voß, Marc Rehmsmeier, Jens Reeder, and Robert Giegerich
RNAshapes: an integrated RNA analysis package based on abstract shapes
Bioinformatics Advance Access published on December 15, 2005
Bioinformatics 2006 22: 500-503; doi:10.1093/bioinformatics/btk010 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

STRUCTURAL BIOINFORMATICS:

John Eargle, Dan Wright, and Zaida Luthey-Schulten
Multiple Alignment of protein structures and sequences for VMD
Bioinformatics Advance Access published on December 8, 2005
Bioinformatics 2006 22: 504-506; doi:10.1093/bioinformatics/bti825 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, and John D. Storey
EDGE: extraction and analysis of differential gene expression
Bioinformatics Advance Access published on December 15, 2005
Bioinformatics 2006 22: 507-508; doi:10.1093/bioinformatics/btk005 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Michael Mueller, Anuj Goel, Manjula Thimma, Nicholas J Dickens, Timothy J. Aitman, and Jonathan Mangion
eQTL Explorer: integrated mining of combined genetic linkage and expression experiments
Bioinformatics Advance Access published on December 15, 2005
Bioinformatics 2006 22: 509-511; doi:10.1093/bioinformatics/btk007 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

B. L. Browning
FLOSS: flexible ordered subset analysis for linkage mapping of complex traits
Bioinformatics Advance Access published on December 20, 2005
Bioinformatics 2006 22: 512-513; doi:10.1093/bioinformatics/btk012 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Henning Schmidt and Mats Jirstrand
Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
Bioinformatics Advance Access published on November 29, 2005
Bioinformatics 2006 22: 514-515; doi:10.1093/bioinformatics/bti799 [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.