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Previous Next 		Contents: Volume 25, Number 6, 15 March 2009   [Index by Author] 
Down EDITORIAL
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
Down APPLICATIONS NOTE
     SEQUENCE ANALYSIS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
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To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

EDITORIAL Back

David M. Rocke, Trey Ideker, Olga Troyanskaya, John Quackenbush, and Joaquin Dopazo
Papers on normalization, variable selection, classification or clustering of microarray data
Bioinformatics Advance Access published on February 9, 2009
Bioinformatics 2009 25: 701-702; doi:10.1093/bioinformatics/btp038 [Extract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

Eva Budinska, Eva Gelnarova, and Michael G. Schimek
MSMAD: a computationally efficient method for the analysis of noisy array CGH data
Bioinformatics Advance Access published on January 15, 2009
Bioinformatics 2009 25: 703-713; doi:10.1093/bioinformatics/btp022 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Tong Tong Wu, Yi Fang Chen, Trevor Hastie, Eric Sobel, and Kenneth Lange
Genome-wide association analysis by lasso penalized logistic regression
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 714-721; doi:10.1093/bioinformatics/btp041 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Thomas LaFramboise, Wendy Winckler, and Roman K. Thomas
A flexible rank-based framework for detecting copy number aberrations from array data
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 722-728; doi:10.1093/bioinformatics/btp063 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Inkyung Jung and Dongsup Kim
SIMPRO: simple protein homology detection method by using indirect signals
Bioinformatics Advance Access published on January 22, 2009
Bioinformatics 2009 25: 729-735; doi:10.1093/bioinformatics/btp048 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS Back

Thomas Pommier, Björn Canbäck, Per Lundberg, Åke Hagström, and Anders Tunlid
RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities
Bioinformatics Advance Access published on February 17, 2009
Bioinformatics 2009 25: 736-742; doi:10.1093/bioinformatics/btp051 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Supplementary Data]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

Jinyan Li and Qian Liu
‘Double water exclusion’: a hypothesis refining the O-ring theory for the hot spots at protein interfaces
Bioinformatics Advance Access published on January 29, 2009
Bioinformatics 2009 25: 743-750; doi:10.1093/bioinformatics/btp058 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

GENE EXPRESSION Back

Yang Xie, Xinlei Wang, and Michael Story
Statistical methods of background correction for Illumina BeadArray data
Bioinformatics Advance Access published on February 4, 2009
Bioinformatics 2009 25: 751-757; doi:10.1093/bioinformatics/btp040 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Katharina Podwojski, Arno Fritsch, Daniel C. Chamrad, Wolfgang Paul, Barbara Sitek, Kai Stühler, Petra Mutzel, Christian Stephan, Helmut E. Meyer, Wolfgang Urfer, Katja Ickstadt, and Jörg Rahnenführer
Retention time alignment algorithms for LC/MS data must consider non-linear shifts
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 758-764; doi:10.1093/bioinformatics/btp052 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Davis J. McCarthy and Gordon K. Smyth
Testing significance relative to a fold-change threshold is a TREAT
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 765-771; doi:10.1093/bioinformatics/btp053 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

David R. Bickel, Zahra Montazeri, Pei-Chun Hsieh, Mary Beatty, Shai J. Lawit, and Nicholas J. Bate
Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: a case for the second derivative
Bioinformatics Advance Access published on February 13, 2009
Bioinformatics 2009 25: 772-779; doi:10.1093/bioinformatics/btp028 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Peter Gennemark and Dag Wedelin
Benchmarks for identification of ordinary differential equations from time series data
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 780-786; doi:10.1093/bioinformatics/btp050 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

V. V. Mihaleva, H. A. Verhoeven, R. C. H. de Vos, R. D. Hall, and R. C. H. J. van Ham
Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 787-794; doi:10.1093/bioinformatics/btp056 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zhirong Sun, Jie Luo, Yun Zhou, Junjie Luo, Ke Liu, and Wenting Li
Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework
Bioinformatics Advance Access published on January 29, 2009
Bioinformatics 2009 25: 795-800; doi:10.1093/bioinformatics/btp057 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Brian C. Haynes and Michael R. Brent
Benchmarking regulatory network reconstruction with GRENDEL
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 801-807; doi:10.1093/bioinformatics/btp068 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATA AND TEXT MINING Back

Shuo Chen, Ming Li, Don Hong, Dean Billheimer, Huiming Li, Baogang J. Xu, and Yu Shyr
A novel comprehensive wave-form MS data processing method
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 808-814; doi:10.1093/bioinformatics/btp060 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Joachim Wermter, Katrin Tomanek, and Udo Hahn
High-performance gene name normalization with GENO
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 815-821; doi:10.1093/bioinformatics/btp071 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE Back

SEQUENCE ANALYSIS Back

Lucian Ilie and Silvana Ilie
Fast computation of neighbor seeds
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 822-823; doi:10.1093/bioinformatics/btp054 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jacques Lagnel, Costas S. Tsigenopoulos, and Ioannis Iliopoulos
NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results
Bioinformatics Advance Access published on January 29, 2009
Bioinformatics 2009 25: 824-826; doi:10.1093/bioinformatics/btp067 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Christine Porzelius, Harald Binder, and Martin Schumacher
Parallelized prediction error estimation for evaluation of high-dimensional models
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 827-829; doi:10.1093/bioinformatics/btp062 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Sabine Dietmann, Elisabeth Georgii, Alexey Antonov, Koji Tsuda, and Hans-Werner Mewes
The DICS repository: module-assisted analysis of disease-related gene lists
Bioinformatics Advance Access published on January 28, 2009
Bioinformatics 2009 25: 830-831; doi:10.1093/bioinformatics/btp055 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

X. Wu and M Watson
CORNA: testing gene lists for regulation by microRNAs
Bioinformatics Advance Access published on January 29, 2009
Bioinformatics 2009 25: 832-833; doi:10.1093/bioinformatics/btp059 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Armando Reyes-Palomares, Raul Montañez, Alejando Real-Chicharro, Othmane Chniber, Amine Kerzazi, Ismael Navas-Delgado, Miguel Ángel Medina, José F. Aldana-Montes, and Francisca Sánchez-Jiménez
Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 834-835; doi:10.1093/bioinformatics/btp061 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

J. Vanlier, F. Wu, F. Qi, K. C. Vinnakota, Y. Han, R. K. Dash, F. Yang, and D. A. Beard
BISEN: Biochemical Simulation Environment
Bioinformatics Advance Access published on February 25, 2009
Bioinformatics 2009 25: 836-837; doi:10.1093/bioinformatics/btp069 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

DATA AND TEXT MINING Back

Junguk Hur, Adam D. Schuyler, David J. States, and Eva L. Feldman
SciMiner: web-based literature mining tool for target identification and functional enrichment analysis
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 838-840; doi:10.1093/bioinformatics/btp049 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.