Bioinformatics

REVIEW:

DATABASES AND ONTOLOGIES:

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Shuichi Takitoh, Shogo Fujii, Yoichi Mase, Junichi Takasaki, Toshimasa Yamazaki, Yozo Ohnishi, Masao Yanagisawa, Yusuke Nakamura, and Naoyuki Kamatani

Accurate automated clustering of two-dimensional data for single-nucleotide polymorphism genotyping by a combination of clustering methods: evaluation by large-scale real data
Bioinformatics 2007 23: 408-413; doi:10.1093/bioinformatics/btl133 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Yvan Saeys, Pierre Rouzé, and Yves Van de Peer

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
Bioinformatics Advance Access published on January 4, 2007
Bioinformatics 2007 23: 414-420; doi:10.1093/bioinformatics/btl639 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Noga Kowalsman and Miriam Eisenstein

Inherent limitations in protein–protein docking procedures
Bioinformatics Advance Access published on October 12, 2006
Bioinformatics 2007 23: 421-426; doi:10.1093/bioinformatics/btl524 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract José Ignacio Garzón, Julio Kovacs, Ruben Abagyan, and Pablo Chacón

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage
Bioinformatics Advance Access published on December 6, 2006
Bioinformatics 2007 23: 427-433; doi:10.1093/bioinformatics/btl625 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai

Robust prediction of consensus secondary structures using averaged base pairing probability matrices
Bioinformatics Advance Access published on December 20, 2006
Bioinformatics 2007 23: 434-441; doi:10.1093/bioinformatics/btl636 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Nitai D. Mukhopadhyay and Snigdhansu Chatterjee

Causality and pathway search in microarray time series experiment
Bioinformatics Advance Access published on December 8, 2006
Bioinformatics 2007 23: 442-449; doi:10.1093/bioinformatics/btl598 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jun Liu, Sanjay Ranka, and Tamer Kahveci

Markers improve clustering of CGH data
Bioinformatics Advance Access published on December 6, 2006
Bioinformatics 2007 23: 450-457; doi:10.1093/bioinformatics/btl624 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jangsun Baek, Young Sook Son, and Geoffrey J. McLachlan

Segmentation and intensity estimation of microarray images using a gamma-t mixture model
Bioinformatics Advance Access published on December 12, 2006
Bioinformatics 2007 23: 458-465; doi:10.1093/bioinformatics/btl630 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Shuangge Ma and Jian Huang

Clustering threshold gradient descent regularization: with applications to microarray studies
Bioinformatics Advance Access published on December 20, 2006
Bioinformatics 2007 23: 466-472; doi:10.1093/bioinformatics/btl632 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Huai Li, Yu Sun, and Ming Zhan

The discovery of transcriptional modules by a two-stage matrix decomposition approach
Bioinformatics Advance Access published on December 22, 2006
Bioinformatics 2007 23: 473-479; doi:10.1093/bioinformatics/btl640 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Orland R. Gonzalez, Christoph Küper, Kirsten Jung, Prospero C. Naval, Jr, and Eduardo Mendoza

Parameter estimation using Simulated Annealing for S-system models of biochemical networks
Bioinformatics Advance Access published on October 11, 2006
Bioinformatics 2007 23: 480-486; doi:10.1093/bioinformatics/btl522 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract M. Doran, D. S. Raicu, J. D. Furst, R. Settimi, M. Schipma, and D. P. Chandler

Oligonucleotide microarray identification of Bacillus anthracis strains using support vector machines
Bioinformatics Advance Access published on January 3, 2007
Bioinformatics 2007 23: 487-492; doi:10.1093/bioinformatics/btl626 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Get checked abstract Matteo Brilli, Renato Fani, and Pietro Lió

MotifScorer: using a compendium of microarrays to identify regulatory motifs
Bioinformatics Advance Access published on November 30, 2006
Bioinformatics 2007 23: 493-495; doi:10.1093/bioinformatics/btl607 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract André Müller, Karlheinz Holzmann, and Hans A. Kestler

Visualization of genomic aberrations using Affymetrix SNP arrays
Bioinformatics Advance Access published on November 30, 2006
Bioinformatics 2007 23: 496-497; doi:10.1093/bioinformatics/btl608 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Thomas Derrien, Catherine André, Francis Galibert, and Christophe Hitte

AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps
Bioinformatics Advance Access published on December 4, 2006
Bioinformatics 2007 23: 498-499; doi:10.1093/bioinformatics/btl618 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Zong Hong Zhang, Judice L. Y. Koh, Guang Lan Zhang, Khar Heng Choo, Martti T. Tammi, and Joo Chuan Tong

AllerTool: a web server for predicting allergenicity and allergic cross-reactivity in proteins
Bioinformatics Advance Access published on December 6, 2006
Bioinformatics 2007 23: 504-506; doi:10.1093/bioinformatics/btl621 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Fang Fang, Jing Ding, Vladimir N. Minin, Marc A. Suchard, and Karin S. Dorman

cBrother: relaxing parental tree assumptions for Bayesian recombination detection
Bioinformatics Advance Access published on December 4, 2006
Bioinformatics 2007 23: 507-508; doi:10.1093/bioinformatics/btl613 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Mahesh Panchal

The automation of Nested Clade Phylogeographic Analysis
Bioinformatics Advance Access published on December 1, 2006
Bioinformatics 2007 23: 509-510; doi:10.1093/bioinformatics/btl614 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Pawel Górecki and Jerzy Tiuryn

URec: a system for unrooted reconciliation
Bioinformatics Advance Access published on December 20, 2006
Bioinformatics 2007 23: 511-512; doi:10.1093/bioinformatics/btl634 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Stefan J. Suhrer, Markus Wiederstein, and Manfred J. Sippl

QSCOP—SCOP quantified by structural relationships
Bioinformatics Advance Access published on November 24, 2006
Bioinformatics 2007 23: 513-514; doi:10.1093/bioinformatics/btl594 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Alessandro Pandini, Laura Bonati, Franca Fraternali, and Jens Kleinjung

MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database
Bioinformatics Advance Access published on January 3, 2007
Bioinformatics 2007 23: 515-516; doi:10.1093/bioinformatics/btl637 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Winston Lau, Tai-Yue Kuo, William Tapper, Simon Cox, and Andrew Collins

Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome
Bioinformatics Advance Access published on December 1, 2006
Bioinformatics 2007 23: 517-519; doi:10.1093/bioinformatics/btl615 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Garrett Hellenthal and Matthew Stephens

msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
Bioinformatics Advance Access published on December 6, 2006
Bioinformatics 2007 23: 520-521; doi:10.1093/bioinformatics/btl622 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Vincent J. Carey, Martin Morgan, Seth Falcon, Ross Lazarus, and Robert Gentleman

GGtools: analysis of genetics of gene expression in bioconductor
Bioinformatics Advance Access published on December 8, 2006
Bioinformatics 2007 23: 522-523; doi:10.1093/bioinformatics/btl628 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

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