Bioinformatics

REVIEW PAPER

DATA AND TEXT MINING

ORIGINAL PAPERS

GENOME ANALYSIS

Get checked abstract Gyan P. Srivastava, Juyuan Guo, Huidong Shi, and Dong Xu

PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands
Bioinformatics Advance Access published on June 25, 2008
Bioinformatics 2008 24: 1837-1842; doi:10.1093/bioinformatics/btn320 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jie Wu, Douglas H. Sieglaff, Joshua Gervin, and Xiaohui S. Xie

Discovering regulatory motifs in the Plasmodium genome using comparative genomics
Bioinformatics Advance Access published on July 8, 2008
Bioinformatics 2008 24: 1843-1849; doi:10.1093/bioinformatics/btn348 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS

Get checked abstract Jiajian Liu and Gary D. Stormo

Context-dependent DNA recognition code for C₂H₂ zinc-finger transcription factors
Bioinformatics Advance Access published on June 27, 2008
Bioinformatics 2008 24: 1850-1857; doi:10.1093/bioinformatics/btn331 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract James Lara, Robert M. Wohlhueter, Zoya Dimitrova, and Yury E. Khudyakov

Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein
Bioinformatics Advance Access published on July 15, 2008
Bioinformatics 2008 24: 1858-1864; doi:10.1093/bioinformatics/btn339 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract David W. Ritchie, Dima Kozakov, and Sandor Vajda

Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions
Bioinformatics Advance Access published on June 30, 2008
Bioinformatics 2008 24: 1865-1873; doi:10.1093/bioinformatics/btn334 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Shuiwang Ji, Liang Sun, Rong Jin, Sudhir Kumar, and Jieping Ye

Automated annotation of Drosophila gene expression patterns using a controlled vocabulary
Bioinformatics Advance Access published on July 16, 2008
Bioinformatics 2008 24: 1881-1888; doi:10.1093/bioinformatics/btn347 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Blaise Hanczar and Edward R. Dougherty

Classification with reject option in gene expression data
Bioinformatics Advance Access published on July 10, 2008
Bioinformatics 2008 24: 1889-1895; doi:10.1093/bioinformatics/btn349 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Nils Homer, Waibhav D. Tembe, Szabolcs Szelinger, Margot Redman, Dietrich A. Stephan, John V. Pearson, Stanley F. Nelson, and David Craig

Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies
Bioinformatics Advance Access published on July 10, 2008
Bioinformatics 2008 24: 1896-1902; doi:10.1093/bioinformatics/btn333 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract M.A. Marchisio and J. Stelling

Computational design of synthetic gene circuits with composable parts
Bioinformatics Advance Access published on June 25, 2008
Bioinformatics 2008 24: 1903-1910; doi:10.1093/bioinformatics/btn330 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Yung-Keun Kwon and Kwang-Hyun Cho

Coherent coupling of feedback loops: a design principle of cell signaling networks
Bioinformatics Advance Access published on July 2, 2008
Bioinformatics 2008 24: 1926-1932; doi:10.1093/bioinformatics/btn337 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Vladislav Vyshemirsky and Mark Girolami

BioBayes: A software package for Bayesian inference in systems biology
Bioinformatics Advance Access published on July 16, 2008
Bioinformatics 2008 24: 1933-1934; doi:10.1093/bioinformatics/btn338 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract T. Theodosiou, N. Darzentas, L. Angelis, and C. A. Ouzounis

PuReD-MCL: a graph-based PubMed document clustering methodology
Bioinformatics Advance Access published on July 1, 2008
Bioinformatics 2008 24: 1935-1941; doi:10.1093/bioinformatics/btn318 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Han Zhang, Hsin-Chou Yang, and Yaning Yang

PoooL: an efficient method for estimating haplotype frequencies from large DNA pools
Bioinformatics Advance Access published on June 23, 2008
Bioinformatics 2008 24: 1942-1948; doi:10.1093/bioinformatics/btn324 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE

SEQUENCE ANALYSIS

Get checked abstract Art F. Y. Poon, Fraser I. Lewis, Simon D. W. Frost, and Sergei L. Kosakovsky Pond

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
Bioinformatics Advance Access published on June 18, 2008
Bioinformatics 2008 24: 1949-1950; doi:10.1093/bioinformatics/btn313 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS

Get checked abstract Shantanu Sharma, Feng Ding, and Nikolay V. Dokholyan

iFoldRNA: three-dimensional RNA structure prediction and folding
Bioinformatics Advance Access published on June 25, 2008
Bioinformatics 2008 24: 1951-1952; doi:10.1093/bioinformatics/btn328 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Paolo Marcatili, Alessandra Rosi, and Anna Tramontano

PIGS: automatic prediction of antibody structures
Bioinformatics Advance Access published on July 19, 2008
Bioinformatics 2008 24: 1953-1954; doi:10.1093/bioinformatics/btn341 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION

Get checked abstract Eoghan D. Harrington and Peer Bork

Sircah: a tool for the detection and visualization of alternative transcripts
Bioinformatics Advance Access published on July 17, 2008
Bioinformatics 2008 24: 1959-1960; doi:10.1093/bioinformatics/btn361 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS

Get checked abstract Dominik Heider, Daniel Kessler, and Angelika Barnekow

Watermarking sexually reproducing diploid organisms
Bioinformatics Advance Access published on July 3, 2008
Bioinformatics 2008 24: 1961-1962; doi:10.1093/bioinformatics/btn342 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY

Get checked abstract Frank T. Bergmann and Herbert M. Sauro

Comparing simulation results of SBML capable simulators
Bioinformatics Advance Access published on June 25, 2008
Bioinformatics 2008 24: 1963-1965; doi:10.1093/bioinformatics/btn319 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Garrett M. Dancik and Karin S. Dorman

mlegp: statistical analysis for computer models of biological systems using R
Bioinformatics Advance Access published on July 17, 2008
Bioinformatics 2008 24: 1966-1967; doi:10.1093/bioinformatics/btn329 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING

Get checked abstract Songhua Xu, James McCusker, and Michael Krauthammer

Yale Image Finder (YIF): a new search engine for retrieving biomedical images
Bioinformatics Advance Access published on July 9, 2008
Bioinformatics 2008 24: 1968-1970; doi:10.1093/bioinformatics/btn340 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES

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