Bioinformatics

DISCOVERY NOTE:

SYSTEMS BIOLOGY:

Get checked abstract Niels Grabe and Karsten Neuber

Simulating psoriasis by altering transit amplifying cells
Bioinformatics Advance Access published on February 18, 2007
Bioinformatics 2007 23: 1309-1312; doi:10.1093/bioinformatics/btm042 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

SEQUENCE ANALYSIS:

Get checked abstract Edmund S. Jackson and William J. Fitzgerald

A sequential Monte Carlo EM approach to the transcription factor binding site identification problem
Bioinformatics Advance Access published on March 25, 2007
Bioinformatics 2007 23: 1313-1320; doi:10.1093/bioinformatics/btm054 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Kwang Loong Stanley Ng and Santosh K. Mishra

De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
Bioinformatics Advance Access published on January 31, 2007
Bioinformatics 2007 23: 1321-1330; doi:10.1093/bioinformatics/btm026 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Shuoyong Shi, Yi Zhong, Indraneel Majumdar, S. Sri Krishna, and Nick V. Grishin

Searching for three-dimensional secondary structural patterns in proteins with ProSMoS
Bioinformatics Advance Access published on March 24, 2007
Bioinformatics 2007 23: 1331-1338; doi:10.1093/bioinformatics/btm121 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Xiuwen Zheng, Hung-Chung Huang, Wenyuan Li, Peng Liu, Quan-Zhen Li, and Ying Liu

Modeling nonlinearity in dilution design microarray data
Bioinformatics Advance Access published on January 19, 2007
Bioinformatics 2007 23: 1339-1347; doi:10.1093/bioinformatics/btm002 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract George Vasmatzis, Eric W. Klee, Dagmar M. Kube, Terry M. Therneau, and Farhad Kosari

Quantitating tissue specificity of human genes to facilitate biomarker discovery
Bioinformatics Advance Access published on March 23, 2007
Bioinformatics 2007 23: 1348-1355; doi:10.1093/bioinformatics/btm102 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Get checked abstract Daniel M. Kemp, N. R. Nirmala, and Joseph D. Szustakowski

Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation
Bioinformatics Advance Access published on March 28, 2007
Bioinformatics 2007 23: 1356-1362; doi:10.1093/bioinformatics/btm116 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Ian A. Wood, Peter M. Visscher, and Kerrie L. Mengersen

Classification based upon gene expression data: bias and precision of error rates
Bioinformatics Advance Access published on March 28, 2007
Bioinformatics 2007 23: 1363-1370; doi:10.1093/bioinformatics/btm117 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

DATA AND TEXT MINING:

Get checked abstract Peicheng Du, Rajagopalan Sudha, Michael B. Prystowsky, and Ruth Hogue Angeletti

Data reduction of isotope-resolved LC-MS spectra
Bioinformatics Advance Access published on May 11, 2007
Bioinformatics 2007 23: 1394-1400; doi:10.1093/bioinformatics/btm083 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Martin Sköld, Tobias Rydén, Viktoria Samuelsson, Charlotte Bratt, Lars Ekblad, Håkan Olsson, and Bo Baldetorp

Regression analysis and modelling of data acquisition for SELDI-TOF mass spectrometry
Bioinformatics Advance Access published on March 25, 2007
Bioinformatics 2007 23: 1401-1409; doi:10.1093/bioinformatics/btm104 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Get checked abstract Hagit Shatkay, Annette Höglund, Scott Brady, Torsten Blum, Pierre Dönnes, and Oliver Kohlbacher

SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
Bioinformatics Advance Access published on March 28, 2007
Bioinformatics 2007 23: 1410-1417; doi:10.1093/bioinformatics/btm115 [Abstract] [Full Text] [Print PDF] [Supplementary data] [Request Permissions]  

DATABASES AND ONTOLOGIES:

APPLICATIONS NOTES:

GENOME ANALYSIS:

SEQUENCE ANALYSIS:

Get checked abstract Reed A. Cartwright

Ngila: global pairwise alignments with logarithmic and affine gap costs
Bioinformatics Advance Access published on March 25, 2007
Bioinformatics 2007 23: 1427-1428; doi:10.1093/bioinformatics/btm095 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Get checked abstract Michal J. Pietal, Irina Tuszynska, and Janusz M. Bujnicki

PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure
Bioinformatics Advance Access published on March 30, 2007
Bioinformatics 2007 23: 1429-1430; doi:10.1093/bioinformatics/btm124 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Get checked abstract Joachim L. Schultze and Daniela Eggle

IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform
Bioinformatics Advance Access published on March 23, 2007
Bioinformatics 2007 23: 1431-1433; doi:10.1093/bioinformatics/btm101 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING:

DATABASES AND ONTOLOGIES:

Get checked abstract Maxim V. Shapovalov, Adrian A. Canutescu, and Roland L. Dunbrack, Jr.

BioDownloader: bioinformatics downloads and updates in a few clicks
Bioinformatics Advance Access published on May 5, 2007
Bioinformatics 2007 23: 1437-1439; doi:10.1093/bioinformatics/btm120 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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