Bioinformatics

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Get checked abstract Wendy S.W. Wong and Rasmus Nielsen

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models
Bioinformatics Advance Access published on June 5, 2007
Bioinformatics 2007 23: 2031-2037; doi:10.1093/bioinformatics/btm299 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Alessio Ceroni, Fabrizio Costa, and Paolo Frasconi

Classification of small molecules by two- and three-dimensional decomposition kernels
Bioinformatics Advance Access published on June 5, 2007
Bioinformatics 2007 23: 2038-2045; doi:10.1093/bioinformatics/btm298 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Shuichi Hirose, Kana Shimizu, Satoru Kanai, Yutaka Kuroda, and Tamotsu Noguchi

POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions
Bioinformatics Advance Access published on June 1, 2007
Bioinformatics 2007 23: 2046-2053; doi:10.1093/bioinformatics/btm302 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Eva Freyhult, Vincent Moulton, and Peter Clote

Boltzmann probability of RNA structural neighbors and riboswitch detection
Bioinformatics Advance Access published on June 14, 2007
Bioinformatics 2007 23: 2054-2062; doi:10.1093/bioinformatics/btm314 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract R. Maglietta, A. Piepoli, D. Catalano, F. Licciulli, M. Carella, S. Liuni, G. Pesole, F. Perri, and N. Ancona

Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data
Bioinformatics Advance Access published on May 31, 2007
Bioinformatics 2007 23: 2063-2072; doi:10.1093/bioinformatics/btm289 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yiyong Zhou, Corentin Cras-Méneur, Mitsuru Ohsugi, Gary D. Stormo, and M. Alan. Permutt

A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments
Bioinformatics Advance Access published on June 5, 2007
Bioinformatics 2007 23: 2073-2079; doi:10.1093/bioinformatics/btm292 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Yonghong Wang, Ze-Hong Miao, Yves Pommier, Ernest S. Kawasaki, and Audrey Player

Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips
Bioinformatics Advance Access published on June 6, 2007
Bioinformatics 2007 23: 2088-2095; doi:10.1093/bioinformatics/btm306 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Laura L. Elo, Henna Järvenpää, Matej Oresic, Riitta Lahesmaa, and Tero Aittokallio

Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
Bioinformatics Advance Access published on June 6, 2007
Bioinformatics 2007 23: 2096-2103; doi:10.1093/bioinformatics/btm309 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

Get checked abstract James J. Chen, Taewon Lee, Robert R. Delongchamp, Tao Chen, and Chen-An Tsai

Significance analysis of groups of genes in expression profiling studies
Bioinformatics Advance Access published on June 6, 2007
Bioinformatics 2007 23: 2104-2112; doi:10.1093/bioinformatics/btm310 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENETICS AND POPULATION ANALYSIS:

Get checked abstract B.A. McKinney, D.M. Reif, B.C. White, J.E. Crowe, Jr., and J.H. Moore

Evaporative cooling feature selection for genotypic data involving interactions
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2113-2120; doi:10.1093/bioinformatics/btm317 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Zheng Guo, Yongjin Li, Xue Gong, Chen Yao, Wencai Ma, Dong Wang, Yanhui Li, Jing Zhu, Min Zhang, Da Yang, and Jing Wang

Edge-based scoring and searching method for identifying condition-responsive protein–protein interaction sub-network
Bioinformatics Advance Access published on June 1, 2007
Bioinformatics 2007 23: 2121-2128; doi:10.1093/bioinformatics/btm294 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Vachiranee Limviphuvadh, Seigo Tanaka, Susumu Goto, Kunihiro Ueda, and Minoru Kanehisa

The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs)
Bioinformatics Advance Access published on June 6, 2007
Bioinformatics 2007 23: 2129-2138; doi:10.1093/bioinformatics/btm307 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, and Ron Y. Pinter

Constraint-based functional similarity of metabolic genes: going beyond network topology
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2139-2146; doi:10.1093/bioinformatics/btm319 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Minca Mramor, Gregor Leban, Janez Demsar, and Blaz Zupan

Visualization-based cancer microarray data classification analysis
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2147-2154; doi:10.1093/bioinformatics/btm312 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kyu-Won Kim, Hun-Ki Chung, Gyu-Taek Cho, Kyung-Ho Ma, Dorothy Chandrabalan, Jae-Gyun Gwag, Tae-San Kim, Eun-Gi Cho, and Yong-Jin Park

PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2155-2162; doi:10.1093/bioinformatics/btm313 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Long Yang, Gulei Jin, Xiangqian Zhao, Yan Zheng, Zhaohua Xu, and Weiren Wu

PIP: a database of potential intron polymorphism markers
Bioinformatics Advance Access published on June 1, 2007
Bioinformatics 2007 23: 2174-2177; doi:10.1093/bioinformatics/btm296 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Get checked abstract François Enault, Romain Fremez, Eric Baranowski, and Thomas Faraut

Alvira: comparative genomics of viral strains
Bioinformatics Advance Access published on June 5, 2007
Bioinformatics 2007 23: 2178-2179; doi:10.1093/bioinformatics/btm293 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Clément Rezvoy, Delphine Charif, Laurent Guéguen, and Gabriel A.B. Marais

MareyMap: an R-based tool with graphical interface for estimating recombination rates
Bioinformatics Advance Access published on June 22, 2007
Bioinformatics 2007 23: 2188-2189; doi:10.1093/bioinformatics/btm315 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Lukasz Salwinski and David Eisenberg

The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins
Bioinformatics Advance Access published on June 6, 2007
Bioinformatics 2007 23: 2193-2195; doi:10.1093/bioinformatics/btm304 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

DATABASES AND ONTOLOGIES:

Get checked abstract John Day-Richter, Midori A. Harris, Melissa Haendel, The Gene Ontology OBO-Edit Working Group, and Suzanna Lewis

OBO-Edit—an ontology editor for biologists
Bioinformatics Advance Access published on June 1, 2007
Bioinformatics 2007 23: 2198-2200; doi:10.1093/bioinformatics/btm112 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

CORRIGENDUM:

George Nicola and Ilya A. Vakser

A simple shape characteristic of protein–protein recognition
Bioinformatics 2007 23: 2201; doi:10.1093/bioinformatics/btm303 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ERRATUM:

Ross Carlson

Systems biology • Metabolic systems cost-benefit analysis for interpreting network structure and regulation
Bioinformatics 2007 23: 2202; doi:10.1093/bioinformatics/btm318 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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