Bioinformatics

REVIEW:

DATABASES AND ONTOLOGIES:

Get checked abstract Purvesh Khatri and Sorin Draghici

Ontological analysis of gene expression data: current tools, limitations, and open problems
Bioinformatics Advance Access published on June 30, 2005
Bioinformatics 2005 21: 3587-3595; doi:10.1093/bioinformatics/bti565 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Get checked abstract Robert Petryszak, Ernst Kretschmann, Daniela Wieser, and Rolf Apweiler

The predictive power of the CluSTr database
Bioinformatics Advance Access published on June 16, 2005
Bioinformatics 2005 21: 3604-3609; doi:10.1093/bioinformatics/bti542 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, and Yanda Li

MicroRNA identification based on sequence and structure alignment
Bioinformatics Advance Access published on June 30, 2005
Bioinformatics 2005 21: 3610-3614; doi:10.1093/bioinformatics/bti562 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hongyi Zhou and Yaoqi Zhou

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
Bioinformatics Advance Access published on July 14, 2005
Bioinformatics 2005 21: 3615-3621; doi:10.1093/bioinformatics/bti582 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Ashish V. Tendulkar, Milind A. Sohoni, Babatunde Ogunnaike, and Pramod P. Wangikar

A geometric invariant-based framework for the analysis of protein conformational space
Bioinformatics Advance Access published on August 11, 2005
Bioinformatics 2005 21: 3622-3628; doi:10.1093/bioinformatics/bti621 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Xuejun Liu, Marta Milo, Neil D. Lawrence, and Magnus Rattray

A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips
Bioinformatics Advance Access published on July 14, 2005
Bioinformatics 2005 21: 3637-3644; doi:10.1093/bioinformatics/bti583 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Tianwei Yu, Wei Sun, Shinsheng Yuan, and Ker-Chau Li

Study of coordinative gene expression at the biological process level
Bioinformatics Advance Access published on August 2, 2005
Bioinformatics 2005 21: 3651-3657; doi:10.1093/bioinformatics/bti599 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract S. Gaudan, H. Kirsch, and D. Rebholz-Schuhmann

Resolving abbreviations to their senses in Medline
Bioinformatics Advance Access published on July 21, 2005
Bioinformatics 2005 21: 3658-3664; doi:10.1093/bioinformatics/bti586 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract J. C. Abbott, D. M. Aanensen, K. Rutherford, S. Butcher, and B. G. Spratt

WebACT—an online companion for the Artemis Comparison Tool
Bioinformatics Advance Access published on August 2, 2005
Bioinformatics 2005 21: 3665-3666; doi:10.1093/bioinformatics/bti601 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Marcus J. Claesson and Douwe van Sinderen

BlastXtract—a new way of exploring translated searches
Bioinformatics Advance Access published on July 26, 2005
Bioinformatics 2005 21: 3667-3668; doi:10.1093/bioinformatics/bti598 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Elias Zintzaras and John P. A. Ioannidis

HEGESMA: genome search meta-analysis and heterogeneity testing
Bioinformatics Advance Access published on June 14, 2005
Bioinformatics 2005 21: 3672-3673; doi:10.1093/bioinformatics/bti536 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón, and Montserrat Robles

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
Bioinformatics Advance Access published on August 4, 2005
Bioinformatics 2005 21: 3674-3676; doi:10.1093/bioinformatics/bti610 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Alexej Abyzov, Mounir Errami, Chesley M. Leslin, and Valentin A. Ilyin

Friend, an integrated analytical front-end application for bioinformatics
Bioinformatics Advance Access published on August 2, 2005
Bioinformatics 2005 21: 3677-3678; doi:10.1093/bioinformatics/bti602 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract C. Ferrer-Costa, H. P. Shanahan, S. Jones, and J. M. Thornton

HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif
Bioinformatics Advance Access published on July 19, 2005
Bioinformatics 2005 21: 3679-3680; doi:10.1093/bioinformatics/bti575 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Ted Liefeld, Michael Reich, Joshua Gould, Peili Zhang, Pablo Tamayo, and Jill P. Mesirov

GeneCruiser: a web service for the annotation of microarray data
Bioinformatics Advance Access published on July 19, 2005
Bioinformatics 2005 21: 3681-3682; doi:10.1093/bioinformatics/bti587 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Claire L. Wilson and Crispin J. Miller

Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis
Bioinformatics Advance Access published on August 2, 2005
Bioinformatics 2005 21: 3683-3685; doi:10.1093/bioinformatics/bti605 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Bo Peng and Marek Kimmel

simuPOP: a forward-time population genetics simulation environment
Bioinformatics Advance Access published on July 14, 2005
Bioinformatics 2005 21: 3686-3687; doi:10.1093/bioinformatics/bti584 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Vijay Chickarmane, Sri R. Paladugu, Frank Bergmann, and Herbert M. Sauro

Bifurcation discovery tool
Bioinformatics Advance Access published on August 4, 2005
Bioinformatics 2005 21: 3688-3690; doi:10.1093/bioinformatics/bti603 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Quan-Yuan He, Jing Cao, Xiang-Hua Liu, Miao-Xin Li, Yi-Song Liu, Jin-Yun Xie, and Song-Ping Liang

DEPD: a novel database for differentially expressed proteins
Bioinformatics Advance Access published on July 14, 2005
Bioinformatics 2005 21: 3694-3696; doi:10.1093/bioinformatics/bti580 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Min He, John K. Tomfohr, Blythe H. Devlin, Marcella Sarzotti, M. Louise Markert, and Thomas B. Kepler

SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization
Bioinformatics Advance Access published on July 28, 2005
Bioinformatics 2005 21: 3697-3699; doi:10.1093/bioinformatics/bti600 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Erratum
Bioinformatics 2005 21: 3700; doi:10.1093/bioinformatics/bti622 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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