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Previous Next 		Contents: Volume 22, Number 7, 1 April 2006   [Index by Author] 
       DISCOVERY NOTE
                SEQUENCE ANALYSIS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                GENE EXPRESSION
                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:

Marialuisa Pellegrini-Calace and Anna Tramontano
Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches
Bioinformatics Advance Access published on January 20, 2006
Bioinformatics 2006 22: 775-778; doi:10.1093/bioinformatics/btl006 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Raja Jothi, Elena Zotenko, Asba Tasneem, and Teresa M. Przytycka
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
Bioinformatics Advance Access published on January 24, 2006
Bioinformatics 2006 22: 779-788; doi:10.1093/bioinformatics/btl009 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

Rafael A. Irizarry, Zhijin Wu, and Harris A. Jaffee
Comparison of Affymetrix GeneChip expression measures
Bioinformatics Advance Access published on January 12, 2006
Bioinformatics 2006 22: 789-794; doi:10.1093/bioinformatics/btk046 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Wei Pan
Incorporating gene functions as priors in model-based clustering of microarray gene expression data
Bioinformatics Advance Access published on January 24, 2006
Bioinformatics 2006 22: 795-801; doi:10.1093/bioinformatics/btl011 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

H. P. Piepho, B. Keller, N. Hoecker, and F. Hochholdinger
Combining signals from spotted cDNA microarrays obtained at different scanning intensities
Bioinformatics Advance Access published on January 17, 2006
Bioinformatics 2006 22: 802-807; doi:10.1093/bioinformatics/btk047 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jinwook Seo, Heather Gordish-Dressman, and Eric P. Hoffman
An interactive power analysis tool for microarray hypothesis testing and generation
Bioinformatics Advance Access published on January 17, 2006
Bioinformatics 2006 22: 808-814; doi:10.1093/bioinformatics/btk052 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Mukesh Bansal, Giusy Della Gatta, and Diego di Bernardo
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
Bioinformatics Advance Access published on January 17, 2006
Bioinformatics 2006 22: 815-822; doi:10.1093/bioinformatics/btl003 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, and Mark Gerstein
Predicting interactions in protein networks by completing defective cliques
Bioinformatics Advance Access published on February 2, 2006
Bioinformatics 2006 22: 823-829; doi:10.1093/bioinformatics/btl014 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Zafer Barutcuoglu, Robert E. Schapire, and Olga G. Troyanskaya
Hierarchical multi-label prediction of gene function
Bioinformatics Advance Access published on January 12, 2006
Bioinformatics 2006 22: 830-836; doi:10.1093/bioinformatics/btk048 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Ashish Choudhary, Marcel Brun, Jianping Hua, James Lowey, Ed Suh, and Edward R. Dougherty
Genetic test bed for feature selection
Bioinformatics Advance Access published on January 20, 2006
Bioinformatics 2006 22: 837-842; doi:10.1093/bioinformatics/btl008 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kazumi Hakamada, Masahiro Okamoto, and Taizo Hanai
Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering
Bioinformatics Advance Access published on January 24, 2006
Bioinformatics 2006 22: 843-848; doi:10.1093/bioinformatics/btl016 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

C. Rouveirol, N. Stransky, Ph. Hupé, Ph. La Rosa, E. Viara, E. Barillot, and F. Radvanyi
Computation of recurrent minimal genomic alterations from array-CGH data
Bioinformatics Advance Access published on January 24, 2006
Bioinformatics 2006 22: 849-856; doi:10.1093/bioinformatics/btl004 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Parantu K. Shah and Peer Bork
LSAT: learning about alternative transcripts in MEDLINE
Bioinformatics Advance Access published on January 12, 2006
Bioinformatics 2006 22: 857-865; doi:10.1093/bioinformatics/btk044 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Patricia L. Whetzel, Helen Parkinson, Helen C. Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Laurence Game, Mervi Heiskanen, Norman Morrison, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris Taylor, Joseph White, and Christian J. Stoeckert, Jr
The MGED Ontology: a resource for semantics-based description of microarray experiments
Bioinformatics Advance Access published on January 21, 2006
Bioinformatics 2006 22: 866-873; doi:10.1093/bioinformatics/btl005 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Sandhya Xirasagar, Scott F. Gustafson, Cheng-Cheng Huang, Qinyan Pan, Jennifer Fostel, Paul Boyer, B. Alex Merrick, Kenneth B. Tomer, Denny D. Chan, Kenneth J. Yost, III, Danielle Choi, Nianqing Xiao, Stanley Stasiewicz, Pierre Bushel, and Michael D. Waters
Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application
Bioinformatics Advance Access published on January 12, 2006
Bioinformatics 2006 22: 874-882; doi:10.1093/bioinformatics/btk045 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

APPLICATIONS NOTE:

GENOME ANALYSIS:

E. Ryder, R. Jackson, A. Ferguson-Smith, and S. Russell
MAMMOT—a set of tools for the design, management and visualization of genomic tiling arrays
Bioinformatics Advance Access published on February 1, 2006
Bioinformatics 2006 22: 883-884; doi:10.1093/bioinformatics/btl031 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Payan Canaran, Lincoln Stein, and Doreen Ware
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support
Bioinformatics Advance Access published on February 10, 2006
Bioinformatics 2006 22: 885-886; doi:10.1093/bioinformatics/btl028 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

Weizhong Li and Adam Godzik
VISSA: a program to visualize structural features from structure sequence alignment
Bioinformatics Advance Access published on January 24, 2006
Bioinformatics 2006 22: 887-888; doi:10.1093/bioinformatics/btl019 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Michael Sammeth, Thasso Griebel, Felix Tille, and Jens Stoye
Panta rhei (QAlign2): an open graphical environment for sequence analysis
Bioinformatics Advance Access published on January 17, 2006
Bioinformatics 2006 22: 889-890; doi:10.1093/bioinformatics/btl007 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Avner Schlessinger, Guy Yachdav, and Burkhard Rost
PROFbval: predict flexible and rigid residues in proteins
Bioinformatics Advance Access published on February 2, 2006
Bioinformatics 2006 22: 891-893; doi:10.1093/bioinformatics/btl032 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Fengfeng Zhou, Yu Xue, Xuebiao Yao, and Ying Xu
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)
Bioinformatics Advance Access published on January 24, 2006
Bioinformatics 2006 22: 894-896; doi:10.1093/bioinformatics/btl013 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   OPEN ACCESS ARTICLE  

GENE EXPRESSION:

James M. Wettenhall, Ken M. Simpson, Keith Satterley, and Gordon K. Smyth
affylmGUI: a graphical user interface for linear modeling of single channel microarray data
Bioinformatics Advance Access published on February 2, 2006
Bioinformatics 2006 22: 897-899; doi:10.1093/bioinformatics/btl025 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DATABASES AND ONTOLOGIES:

Sébastien Carrere and Jérôme Gouzy
REMORA: a pilot in the ocean of BioMoby web-services
Bioinformatics Advance Access published on January 19, 2006
Bioinformatics 2006 22: 900-901; doi:10.1093/bioinformatics/btl001 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Pedro Cipriano Feijão, Lissiene Silva Neiva, Ana Maria Lima de Azeredo-Espin, and Ana Cláudia Lessinger
AMiGA: the arthropodan mitochondrial genomes accessible database
Bioinformatics Advance Access published on January 29, 2006
Bioinformatics 2006 22: 902-903; doi:10.1093/bioinformatics/btl021 [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.