Bioinformatics

REVIEW:

GENE EXPRESSION:

Get checked abstract Sridhar Hannenhalli

Eukaryotic transcription factor binding sites—modeling and integrative search methods
Bioinformatics Advance Access published on April 21, 2008
Bioinformatics 2008 24: 1325-1331; doi:10.1093/bioinformatics/btn198 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Get checked abstract Daniel Dalevi and Niklas Eriksen

Expected gene-order distances and model selection in bacteria
Bioinformatics Advance Access published on April 1, 2008
Bioinformatics 2008 24: 1332-1338; doi:10.1093/bioinformatics/btn111 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Marianne M. Lee, Michael K. Chan, and Ralf Bundschuh

Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches
Bioinformatics Advance Access published on April 10, 2008
Bioinformatics 2008 24: 1339-1343; doi:10.1093/bioinformatics/btn130 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Takashi Ishida and Kengo Kinoshita

Prediction of disordered regions in proteins based on the meta approach
Bioinformatics Advance Access published on April 20, 2008
Bioinformatics 2008 24: 1344-1348; doi:10.1093/bioinformatics/btn195 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Chunqi Chang, Zhi Ding, Yeung Sam Hung, and Peter Chin Wan Fung

Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data
Bioinformatics Advance Access published on April 9, 2008
Bioinformatics 2008 24: 1349-1358; doi:10.1093/bioinformatics/btn131 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Anindya Bhattacharya and Rajat K. De

Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles
Bioinformatics Advance Access published on April 10, 2008
Bioinformatics 2008 24: 1359-1366; doi:10.1093/bioinformatics/btn133 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Haiyun Wang, Qi Wang, Xia Li, Bairong Shen, Min Ding, and Ziyin Shen

Towards patterns tree of gene coexpression in eukaryotic species
Bioinformatics Advance Access published on April 10, 2008
Bioinformatics 2008 24: 1367-1373; doi:10.1093/bioinformatics/btn134 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY:

Get checked abstract Daniele Santoni, Marco Pedicini, and Filippo Castiglione

Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions
Bioinformatics Advance Access published on April 14, 2008
Bioinformatics 2008 24: 1374-1380; doi:10.1093/bioinformatics/btn135 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Jonathan D. Wren

URL decay in MEDLINE—a 4-year follow-up study
Bioinformatics Advance Access published on April 15, 2008
Bioinformatics 2008 24: 1381-1385; doi:10.1093/bioinformatics/btn127 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

Get checked abstract Michael Hackenberg and Rune Matthiesen

Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists
Bioinformatics Advance Access published on April 23, 2008
Bioinformatics 2008 24: 1386-1393; doi:10.1093/bioinformatics/btn178 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTES:

GENOME ANALYSIS:

Get checked abstract William Ritchie, François-Xavier Théodule, and Daniel Gautheret

Mireval: a web tool for simple microRNA prediction in genome sequences
Bioinformatics Advance Access published on May 3, 2008
Bioinformatics 2008 24: 1394-1396; doi:10.1093/bioinformatics/btn137 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Get checked abstract Claus Lundegaard, Ole Lund, and Morten Nielsen

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers
Bioinformatics Advance Access published on April 14, 2008
Bioinformatics 2008 24: 1397-1398; doi:10.1093/bioinformatics/btn128 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Frédéric Schütz and Mauro Delorenzi

MAMOT: hidden Markov modeling tool
Bioinformatics Advance Access published on April 25, 2008
Bioinformatics 2008 24: 1399-1400; doi:10.1093/bioinformatics/btn201 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

GENETICS AND POPULATION ANALYSIS:

Get checked abstract Thibaut Jombart

adegenet: a R package for the multivariate analysis of genetic markers
Bioinformatics Advance Access published on April 8, 2008
Bioinformatics 2008 24: 1403-1405; doi:10.1093/bioinformatics/btn129 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Gilles Guillot, Filipe Santos, and Arnaud Estoup

Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface
Bioinformatics Advance Access published on April 14, 2008
Bioinformatics 2008 24: 1406-1407; doi:10.1093/bioinformatics/btn136 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Bo Peng and Christopher I. Amos

Forward-time simulations of non-random mating populations using simuPOP
Bioinformatics Advance Access published on April 15, 2008
Bioinformatics 2008 24: 1408-1409; doi:10.1093/bioinformatics/btn179 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

Get checked abstract Soyang Ha, Young-Ju Seo, Min-Seok Kwon, Byung-Ha Chang, Cheol-Kyu Han, and Jeong-Hyeok Yoon

IDMap: facilitating the detection of potential leads with therapeutic targets
Bioinformatics Advance Access published on April 15, 2008
Bioinformatics 2008 24: 1413-1415; doi:10.1093/bioinformatics/btn138 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Andreas Quandt, Patricia Hernandez, Alexandre Masselot, Céline Hernandez, Sergio Maffioletti, Cesare Pautasso, Ron D. Appel, and Frederique Lisacek

swissPIT: a novel approach for pipelined analysis of mass spectrometry data
Bioinformatics Advance Access published on April 23, 2008
Bioinformatics 2008 24: 1416-1417; doi:10.1093/bioinformatics/btn139 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES:

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