Bioinformatics

EDITORIALS:

Andrew E. Torda and Thomas Lengauer

Editorial
Bioinformatics 2006 22: 1157; doi:10.1093/bioinformatics/btl078 [Extract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Annette Höglund, Pierre Dönnes, Torsten Blum, Hans-Werner Adolph, and Oliver Kohlbacher

MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
Bioinformatics Advance Access published on January 20, 2006
Bioinformatics 2006 22: 1158-1165; doi:10.1093/bioinformatics/btl002 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Ivo L. Hofacker and Peter F. Stadler

Memory efficient folding algorithms for circular RNA secondary structures
Bioinformatics Advance Access published on February 1, 2006
Bioinformatics 2006 22: 1172-1176; doi:10.1093/bioinformatics/btl023 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan H. Bernhart, Peter F. Stadler, and Ivo L. Hofacker

Thermodynamics of RNA–RNA binding
Bioinformatics Advance Access published on January 29, 2006
Bioinformatics 2006 22: 1177-1182; doi:10.1093/bioinformatics/btl024 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Jean-Christophe Nebel

Generation of 3D templates of active sites of proteins with rigid prosthetic groups
Bioinformatics Advance Access published on February 10, 2006
Bioinformatics 2006 22: 1183-1189; doi:10.1093/bioinformatics/btl040 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

SYSTEMS BIOLOGY:

Get checked abstract Ari Rantanen, Taneli Mielikäinen, Juho Rousu, Hannu Maaheimo, and Esko Ukkonen

Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes
Bioinformatics Advance Access published on February 27, 2006
Bioinformatics 2006 22: 1198-1206; doi:10.1093/bioinformatics/btl069 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DISCOVERY NOTE:

STRUCTURAL BIOINFORMATICS:

Get checked abstract Loris Nanni and Alessandra Lumini

An ensemble of K-local hyperplanes for predicting protein–protein interactions
Bioinformatics Advance Access published on February 15, 2006
Bioinformatics 2006 22: 1207-1210; doi:10.1093/bioinformatics/btl055 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Get checked abstract Hideki Nagasaki, Masanori Arita, Tatsuya Nishizawa, Makiko Suwa, and Osamu Gotoh

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns
Bioinformatics Advance Access published on February 24, 2006
Bioinformatics 2006 22: 1211-1216; doi:10.1093/bioinformatics/btl067 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Anton Valouev, Yu Zhang, David C. Schwartz, and Michael S. Waterman

Refinement of optical map assemblies
Bioinformatics Advance Access published on February 24, 2006
Bioinformatics 2006 22: 1217-1224; doi:10.1093/bioinformatics/btl063 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Get checked abstract Faisal Ababneh, Lars S. Jermiin, Chunsheng Ma, and John Robinson

Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences
Bioinformatics Advance Access published on February 21, 2006
Bioinformatics 2006 22: 1225-1231; doi:10.1093/bioinformatics/btl064 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Joo Chuan Tong, Guang Lan Zhang, Tin Wee Tan, J. Thomas August, Vladimir Brusic, and Shoba Ranganathan

Prediction of HLA-DQ3.2ß Ligands: evidence of multiple registers in class II binding peptides
Bioinformatics Advance Access published on March 1, 2006
Bioinformatics 2006 22: 1232-1238; doi:10.1093/bioinformatics/btl071 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Ritesh Agrawal and Gary D. Stormo

Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1239-1244; doi:10.1093/bioinformatics/btl076 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Kristof Engelen, Bart Naudts, Bart De Moor, and Kathleen Marchal

A calibration method for estimating absolute expression levels from microarray data
Bioinformatics Advance Access published on March 7, 2006
Bioinformatics 2006 22: 1251-1258; doi:10.1093/bioinformatics/btl068 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Desheng Huang and Wei Pan

Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data
Bioinformatics Advance Access published on February 24, 2006
Bioinformatics 2006 22: 1259-1268; doi:10.1093/bioinformatics/btl065 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Get checked abstract Tijl De Bie, Nello Cristianini, Jeffery P. Demuth, and Matthew W. Hahn

CAFE: a computational tool for the study of gene family evolution
Bioinformatics Advance Access published on March 16, 2006
Bioinformatics 2006 22: 1269-1271; doi:10.1093/bioinformatics/btl097 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Richard E. Kennedy, Robnet T. Kerns, Xiangrong Kong, Kellie J. Archer, and Michael F. Miles

SScore: an R package for detecting differential gene expression without gene expression summaries
Bioinformatics Advance Access published on March 30, 2006
Bioinformatics 2006 22: 1272-1274; doi:10.1093/bioinformatics/btl108 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Sarah M. Keating, Benjamin J. Bornstein, Andrew Finney, and Michael Hucka

SBMLToolbox: an SBML toolbox for MATLAB users
Bioinformatics Advance Access published on March 30, 2006
Bioinformatics 2006 22: 1275-1277; doi:10.1093/bioinformatics/btl111 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Amanda M. White, Don S. Daly, Susan M. Varnum, Kevin K. Anderson, Nikki Bollinger, and Richard C. Zangar

ProMAT: protein microarray analysis tool
Bioinformatics Advance Access published on April 4, 2006
Bioinformatics 2006 22: 1278-1279; doi:10.1093/bioinformatics/btl093 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Simon Barkow, Stefan Bleuler, Amela Prelic, Philip Zimmermann, and Eckart Zitzler

BicAT: a biclustering analysis toolbox
Bioinformatics Advance Access published on March 21, 2006
Bioinformatics 2006 22: 1282-1283; doi:10.1093/bioinformatics/btl099 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Ge Gao, Yingfu Zhong, Anyuan Guo, Qihui Zhu, Wen Tang, Weimou Zheng, Xiaocheng Gu, Liping Wei, and Jingchu Luo

DRTF: a database of rice transcription factors
Bioinformatics Advance Access published on March 21, 2006
Bioinformatics 2006 22: 1286-1287; doi:10.1093/bioinformatics/btl107 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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