Bioinformatics

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Tao Huang, Baolin Wu, Paul Lizardi, and Hongyu Zhao

Detection of DNA copy number alterations using penalized least squares regression
Bioinformatics Advance Access published on August 30, 2005
Bioinformatics 2005 21: 3811-3817; doi:10.1093/bioinformatics/bti646 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Onkar C. Kulkarni, R. Vigneshwar, Valadi K. Jayaraman, and Bhaskar D. Kulkarni

Identification of coding and non-coding sequences using local Hölder exponent formalism
Bioinformatics Advance Access published on August 23, 2005
Bioinformatics 2005 21: 3818-3823; doi:10.1093/bioinformatics/bti639 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Shane T. Jensen, Lei Shen, and Jun S. Liu

Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes
Bioinformatics Advance Access published on August 16, 2005
Bioinformatics 2005 21: 3832-3839; doi:10.1093/bioinformatics/bti628 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Jesús S. Aguilar-Ruiz

Shifting and scaling patterns from gene expression data
Bioinformatics Advance Access published on September 6, 2005
Bioinformatics 2005 21: 3840-3845; doi:10.1093/bioinformatics/bti641 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract L. Diambra and L. da F. Costa

Complex networks approach to gene expression driven phenotype imaging
Bioinformatics Advance Access published on August 16, 2005
Bioinformatics 2005 21: 3846-3851; doi:10.1093/bioinformatics/bti625 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Xinping Cui, Jin Xu, Rehana Asghar, Pascal Condamine, Jan T. Svensson, Steve Wanamaker, Nils Stein, Mikeal Roose, and Timothy J. Close

Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit
Bioinformatics Advance Access published on August 23, 2005
Bioinformatics 2005 21: 3852-3858; doi:10.1093/bioinformatics/bti640 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

Get checked abstract Karen Willbrand, Francois Radvanyi, Jean-Pierre Nadal, Jean-Paul Thiery, and Thomas M. A. Fink

Identifying genes from up–down properties of microarray expression series
Bioinformatics 2005 21: 3859-3864; doi:10.1093/bioinformatics/bti549 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yudi Pawitan, Karuturi R. Krishna Murthy, Stefan Michiels, and Alexander Ploner

Bias in the estimation of false discovery rate in microarray studies
Bioinformatics Advance Access published on August 16, 2005
Bioinformatics 2005 21: 3865-3872; doi:10.1093/bioinformatics/bti626 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kavitha Bhasi, Alan Forrest, and Murali Ramanathan

SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles
Bioinformatics Advance Access published on August 11, 2005
Bioinformatics 2005 21: 3873-3879; doi:10.1093/bioinformatics/bti624 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract David Meintrup and Ellen Reisinger

A statistical model providing comprehensive predictions for the mRNA differential display
Bioinformatics Advance Access published on August 18, 2005
Bioinformatics 2005 21: 3880-3886; doi:10.1093/bioinformatics/bti636 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Supplementary Data] [Request Permissions]  

Get checked abstract Aik Choon Tan, Daniel Q. Naiman, Lei Xu, Raimond L. Winslow, and Donald Geman

Simple decision rules for classifying human cancers from gene expression profiles
Bioinformatics Advance Access published on August 16, 2005
Bioinformatics 2005 21: 3896-3904; doi:10.1093/bioinformatics/bti631 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Lei Xu, Aik Choon Tan, Daniel Q. Naiman, Donald Geman, and Raimond L. Winslow

Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data
Bioinformatics Advance Access published on August 30, 2005
Bioinformatics 2005 21: 3905-3911; doi:10.1093/bioinformatics/bti647 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Dmitry A. Konovalov, Nigel Bajema, and Bruce Litow

Modified SIMPSON O(n³) algorithm for the full sibship reconstruction problem
Bioinformatics Advance Access published on August 23, 2005
Bioinformatics 2005 21: 3912-3917; doi:10.1093/bioinformatics/bti642 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Sreenivas Chavali, Anubha Mahajan, Rubina Tabassum, Souvik Maiti, and Dwaipayan Bharadwaj

Oligonucleotide properties determination and primer designing: a critical examination of predictions
Bioinformatics Advance Access published on August 16, 2005
Bioinformatics 2005 21: 3918-3925; doi:10.1093/bioinformatics/bti633 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE:

STRUCTURAL BIOINFORMATICS:

Get checked abstract Chi Yu Chan, Charles E. Lawrence, and Ye Ding

Structure clustering features on the Sfold Web server
Bioinformatics Advance Access published on August 18, 2005
Bioinformatics 2005 21: 3926-3928; doi:10.1093/bioinformatics/bti632 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Martin Jambon, Olivier Andrieu, Christophe Combet, Gilbert Deléage, François Delfaud, and Christophe Geourjon

The SuMo server: 3D search for protein functional sites
Bioinformatics Advance Access published on September 1, 2005
Bioinformatics 2005 21: 3929-3930; doi:10.1093/bioinformatics/bti645 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Nir Kalisman, Ami Levi, Tetyana Maximova, Dan Reshef, Sharon Zafriri-Lynn, Yan Gleyzer, and Chen Keasar

MESHI: a new library of Java classes for molecular modeling
Bioinformatics Advance Access published on August 16, 2005
Bioinformatics 2005 21: 3931-3932; doi:10.1093/bioinformatics/bti630 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract S. Peddada, S. Harris, J. Zajd, and E. Harvey

ORIOGEN: order restricted inference for ordered gene expression data
Bioinformatics Advance Access published on August 18, 2005
Bioinformatics 2005 21: 3933-3934; doi:10.1093/bioinformatics/bti637 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Derek Gordon, Chad Haynes, Jon Blumenfeld, and Stephen J. Finch

PAWE-3D: visualizing power for association with error in case–control genetic studies of complex traits
Bioinformatics Advance Access published on August 25, 2005
Bioinformatics 2005 21: 3935-3937; doi:10.1093/bioinformatics/bti643 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Sheng Gu, Andrew J. Pakstis, and Kenneth K. Kidd

HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations
Bioinformatics Advance Access published on August 30, 2005
Bioinformatics 2005 21: 3938-3939; doi:10.1093/bioinformatics/bti649 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Tobias Sing, Oliver Sander, Niko Beerenwinkel, and Thomas Lengauer

ROCR: visualizing classifier performance in R
Bioinformatics Advance Access published on August 11, 2005
Bioinformatics 2005 21: 3940-3941; doi:10.1093/bioinformatics/bti623 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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