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Contents: Volume 21, Number 21, November 1 2005   [Index by Author]       Other Issues: Previous Next  
       REVIEW
                DATA AND TEXT MINING
       DISCOVERY NOTES
                GENOME ANALYSIS
                STRUCTURAL BIOINFORMATICS
       ORIGINAL PAPERS
                SEQUENCE ANALYSIS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
                DATA AND TEXT MINING
                DATABASES AND ONTOLOGIES
       APPLICATIONS NOTE
                SEQUENCE ANALYSIS
                GENE EXPRESSION
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REVIEW:

DATA AND TEXT MINING:

Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kirsten Roomp, Igor Savenkov, Roman Fischer, Daniel Hoffmann, Joachim Selbig, Klaus Korn, Hauke Walter, Thomas Berg, Patrick Braun, Gerd Fätkenheuer, Mark Oette, Jürgen Rockstroh, Bernd Kupfer, Rolf Kaiser, and Martin Däumer
Computational methods for the design of effective therapies against drug resistant HIV strains
Bioinformatics Advance Access published on September 6, 2005
Bioinformatics 2005 21: 3943-3950; doi:10.1093/bioinformatics/bti654 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

DISCOVERY NOTES:

GENOME ANALYSIS:

Liang Chen and Hongyu Zhao
Negative correlation between compositional symmetries and local recombination rates
Bioinformatics Advance Access published on August 30, 2005
Bioinformatics 2005 21: 3951-3958; doi:10.1093/bioinformatics/bti651 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Iwona A. Cymerman, Gregor Meiss, and Janusz M. Bujnicki
DNase II is a member of the phospholipase D superfamily
Bioinformatics Advance Access published on September 8, 2005
Bioinformatics 2005 21: 3959-3962; doi:10.1093/bioinformatics/bti659 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Chittibabu Guda and Shankar Subramaniam
TARGET: a new method for predicting protein subcellular localization in eukaryotes
Bioinformatics Advance Access published on September 6, 2005
Bioinformatics 2005 21: 3963-3969; doi:10.1093/bioinformatics/bti650 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Yuan Gao and George Church
Improving molecular cancer class discovery through sparse non-negative matrix factorization
Bioinformatics 2005 21: 3970-3975; doi:10.1093/bioinformatics/bti653 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Shin Kawano, Kosuke Hashimoto, Takashi Miyama, Susumu Goto, and Minoru Kanehisa
Prediction of glycan structures from gene expression data based on glycosyltransferase reactions
Bioinformatics Advance Access published on September 13, 2005
Bioinformatics 2005 21: 3976-3982; doi:10.1093/bioinformatics/bti666 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Lei Zhou and David M. Rocke
An expression index for Affymetrix GeneChips based on the generalized logarithm
Bioinformatics Advance Access published on September 13, 2005
Bioinformatics 2005 21: 3983-3989; doi:10.1093/bioinformatics/bti665 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

David M. Rocke, Zelanna Goldberg, Chad Schweitert, and Alison Santana
A method for detection of differential gene expression in the presence of inter-individual variability in response
Bioinformatics Advance Access published on September 13, 2005
Bioinformatics 2005 21: 3990-3992; doi:10.1093/bioinformatics/bti667 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Aurora Torrente, Misha Kapushesky, and Alvis Brazma
A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings
Bioinformatics Advance Access published on September 1, 2005
Bioinformatics 2005 21: 3993-3999; doi:10.1093/bioinformatics/bti644 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Li-yu D. Liu, Naisyin Wang, Joanne R. Lupton, Nancy D. Turner, Robert S. Chapkin, and Laurie A. Davidson
A two-stage normalization method for partially degraded mRNA microarray data
Bioinformatics Advance Access published on September 8, 2005
Bioinformatics 2005 21: 4000-4006; doi:10.1093/bioinformatics/bti661 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Biao Xing and Mark J. van der Laan
A causal inference approach for constructing transcriptional regulatory networks
Bioinformatics Advance Access published on August 30, 2005
Bioinformatics 2005 21: 4007-4013; doi:10.1093/bioinformatics/bti648 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Dongxiao Zhu, Alfred O Hero, Hong Cheng, Ritu Khanna, and Anand Swaroop
Network constrained clustering for gene microarray data
Bioinformatics Advance Access published on September 1, 2005
Bioinformatics 2005 21: 4014-4020; doi:10.1093/bioinformatics/bti655 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Ranadip Pal, Ivan Ivanov, Aniruddha Datta, Michael L. Bittner, and Edward R. Dougherty
Generating Boolean networks with a prescribed attractor structure
Bioinformatics Advance Access published on September 8, 2005
Bioinformatics 2005 21: 4021-4025; doi:10.1093/bioinformatics/bti664 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Florian Markowetz, Jacques Bloch, and Rainer Spang
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference
Bioinformatics Advance Access published on September 13, 2005
Bioinformatics 2005 21: 4026-4032; doi:10.1093/bioinformatics/bti662 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Tianwei Yu and Ker-Chau Li
Inference of transcriptional regulatory network by two-stage constrained space factor analysis
Bioinformatics Advance Access published on September 6, 2005
Bioinformatics 2005 21: 4033-4038; doi:10.1093/bioinformatics/bti656 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Habtom W. Ressom, Rency S. Varghese, Mohamed Abdel-Hamid, Sohair Abdel-Latif Eissa, Daniel Saha, Lenka Goldman, Emanuel F. Petricoin, Thomas P. Conrads, Timothy D. Veenstra, Christopher A. Loffredo, and Radoslav Goldman
Analysis of mass spectral serum profiles for biomarker selection
Bioinformatics Advance Access published on September 13, 2005
Bioinformatics 2005 21: 4039-4045; doi:10.1093/bioinformatics/bti670 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jonathan D. Wren, William H. Hildebrand, Sreedevi Chandrasekaran, and Ulrich Melcher
Markov model recognition and classification of DNA/protein sequences within large text databases
Bioinformatics Advance Access published on September 13, 2005
Bioinformatics 2005 21: 4046-4053; doi:10.1093/bioinformatics/bti657 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xiang Zhang, John M. Asara, Jiri Adamec, Mourad Ouzzani, and Ahmed K. Elmagarmid
Data pre-processing in liquid chromatography–mass spectrometry-based proteomics
Bioinformatics Advance Access published on September 8, 2005
Bioinformatics 2005 21: 4054-4059; doi:10.1093/bioinformatics/bti660 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Christian J. A. Sigrist, Edouard De Castro, Petra S. Langendijk-Genevaux, Virginie Le Saux, Amos Bairoch, and Nicolas Hulo
ProRule: a new database containing functional and structural information on PROSITE profiles
Bioinformatics Advance Access published on August 9, 2005
Bioinformatics 2005 21: 4060-4066; doi:10.1093/bioinformatics/bti614 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

SEQUENCE ANALYSIS:

Christoph Bock, Sabine Reither, Thomas Mikeska, Martina Paulsen, Jörn Walter, and Thomas Lengauer
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
Bioinformatics Advance Access published on September 1, 2005
Bioinformatics 2005 21: 4067-4068; doi:10.1093/bioinformatics/bti652 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

P. Sykacek, R. A. Furlong, and G. Micklem
A friendly statistics package for microarray analysis
Bioinformatics Advance Access published on September 27, 2005
Bioinformatics 2005 21: 4069-4070; doi:10.1093/bioinformatics/bti663 [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.