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Previous Next 		Contents: Volume 25, Number 16, 15 August 2009   [Index by Author] 
Down ORIGINAL PAPERS
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     GENE EXPRESSION
     SYSTEMS BIOLOGY
     DATABASES AND ONTOLOGIES
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down GERMAN CONFERENCE ON BIOINFORMATICS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
Down CORRIGENDUM
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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.

ORIGINAL PAPERS Back

GENOME ANALYSIS Back

E. Andrés Houseman, Brock C. Christensen, Margaret R. Karagas, Margaret R. Wrensch, Heather H. Nelson, Joseph L. Wiemels, Shichun Zheng, John K. Wiencke, Karl T. Kelsey, and Carmen J. Marsit
Copy number variation has little impact on bead-array-based measures of DNA methylation
Bioinformatics Advance Access published on June 19, 2009
Bioinformatics 2009 25: 1999-2005; doi:10.1093/bioinformatics/btp364 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

Yanglan Gan, Jihong Guan, and Shuigeng Zhou
A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles
Bioinformatics Advance Access published on June 10, 2009
Bioinformatics 2009 25: 2006-2012; doi:10.1093/bioinformatics/btp359 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Stan Pounds, Cheng Cheng, Xueyuan Cao, Kristine R. Crews, William Plunkett, Varsha Gandhi, Jeffrey Rubnitz, Raul C. Ribeiro, James R. Downing, and Jatinder Lamba
PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables
Bioinformatics Advance Access published on June 15, 2009
Bioinformatics 2009 25: 2013-2019; doi:10.1093/bioinformatics/btp357 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Chuan Lu and Ross D. King
An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems
Bioinformatics Advance Access published on June 17, 2009
Bioinformatics 2009 25: 2020-2027; doi:10.1093/bioinformatics/btp360 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yuliya Karpievitch, Jeff Stanley, Thomas Taverner, Jianhua Huang, Joshua N. Adkins, Charles Ansong, Fred Heffron, Thomas O. Metz, Wei-Jun Qian, Hyunjin Yoon, Richard D. Smith, and Alan R. Dabney
A statistical framework for protein quantitation in bottom-up MS-based proteomics
Bioinformatics Advance Access published on June 17, 2009
Bioinformatics 2009 25: 2028-2034; doi:10.1093/bioinformatics/btp362 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Kathleen F. Kerr
Comments on the analysis of unbalanced microarray data
Bioinformatics Advance Access published on June 15, 2009
Bioinformatics 2009 25: 2035-2041; doi:10.1093/bioinformatics/btp363 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SYSTEMS BIOLOGY Back

Ritwik Layek, Aniruddha Datta, Ranadip Pal, and Edward R. Dougherty
Adaptive intervention in probabilistic boolean networks
Bioinformatics Advance Access published on June 8, 2009
Bioinformatics 2009 25: 2042-2048; doi:10.1093/bioinformatics/btp349 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Nicola Bonzanni, Elzbieta Krepska, K. Anton Feenstra, Wan Fokkink, Thilo Kielmann, Henri Bal, and Jaap Heringa
Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development
Bioinformatics Advance Access published on June 10, 2009
Bioinformatics 2009 25: 2049-2056; doi:10.1093/bioinformatics/btp355 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Thomas Sütterlin, Simone Huber, Hartmut Dickhaus, and Niels Grabe
Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems
Bioinformatics Advance Access published on June 17, 2009
Bioinformatics 2009 25: 2057-2063; doi:10.1093/bioinformatics/btp361 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

David S. DeLuca, Elena Beisswanger, Joachim Wermter, Peter A. Horn, Udo Hahn, and Rainer Blasczyk
MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining
Bioinformatics Advance Access published on May 7, 2009
Bioinformatics 2009 25: 2064-2070; doi:10.1093/bioinformatics/btp306 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Anna I. Rissman, Bob Mau, Bryan S. Biehl, Aaron E. Darling, Jeremy D. Glasner, and Nicole T. Perna
Reordering contigs of draft genomes using the Mauve Aligner
Bioinformatics Advance Access published on June 10, 2009
Bioinformatics 2009 25: 2071-2073; doi:10.1093/bioinformatics/btp356 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

SEQUENCE ANALYSIS Back

Kathryn E. Holt, Yik Y. Teo, Heng Li, Satheesh Nair, Gordon Dougan, John Wain, and Julian Parkhill
Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA
Bioinformatics Advance Access published on June 3, 2009
Bioinformatics 2009 25: 2074-2075; doi:10.1093/bioinformatics/btp344 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Yong Wang, Ruslan I. Sadreyev, and Nick V. Grishin
PROCAIN server for remote protein sequence similarity search
Bioinformatics Advance Access published on June 3, 2009
Bioinformatics 2009 25: 2076-2077; doi:10.1093/bioinformatics/btp346 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, and 1000 Genome Project Data Processing Subgroup
The Sequence Alignment/Map format and SAMtools
Bioinformatics Advance Access published on June 8, 2009
Bioinformatics 2009 25: 2078-2079; doi:10.1093/bioinformatics/btp352 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Nils Hoffmann and Jens Stoye
ChromA: signal-based retention time alignment for chromatography–mass spectrometry data
Bioinformatics Advance Access published on June 8, 2009
Bioinformatics 2009 25: 2080-2081; doi:10.1093/bioinformatics/btp343 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

DATA AND TEXT MINING Back

Raul Rodriguez-Esteban and Ivan Iossifov
Figure mining for biomedical research
Bioinformatics Advance Access published on May 13, 2009
Bioinformatics 2009 25: 2082-2084; doi:10.1093/bioinformatics/btp318 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Woonghee Lee, William M. Westler, Arash Bahrami, Hamid R. Eghbalnia, and John L. Markley
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy
Bioinformatics Advance Access published on June 3, 2009
Bioinformatics 2009 25: 2085-2087; doi:10.1093/bioinformatics/btp345 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

DATABASES AND ONTOLOGIES Back

Claudia Andreini, Ivano Bertini, Gabriele Cavallaro, Gemma L. Holliday, and Janet M. Thornton
Metal-MACiE: a database of metals involved in biological catalysis
Bioinformatics Advance Access published on April 15, 2009
Bioinformatics 2009 25: 2088-2089; doi:10.1093/bioinformatics/btp256 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J. C. Bryne, T. Hupponen, D. Mowbray, and G. Vriend
An active registry for bioinformatics web services
Bioinformatics Advance Access published on May 21, 2009
Bioinformatics 2009 25: 2090-2091; doi:10.1093/bioinformatics/btp329 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Audrey Kauffmann, Tim F. Rayner, Helen Parkinson, Misha Kapushesky, Margus Lukk, Alvis Brazma, and Wolfgang Huber
Importing ArrayExpress datasets into R/Bioconductor
Bioinformatics Advance Access published on June 8, 2009
Bioinformatics 2009 25: 2092-2094; doi:10.1093/bioinformatics/btp354 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

GERMAN CONFERENCE ON BIOINFORMATICS Back

SEQUENCE ANALYSIS Back

Steffen Heyne, Sebastian Will, Michael Beckstette, and Rolf Backofen
Lightweight comparison of RNAs based on exact sequence–structure matches
Bioinformatics Advance Access published on February 2, 2009
Bioinformatics 2009 25: 2095-2102; doi:10.1093/bioinformatics/btp065 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

Utz J. Pape, Holger Klein, and Martin Vingron
Statistical detection of cooperative transcription factors with similarity adjustment
Bioinformatics Advance Access published on March 13, 2009
Bioinformatics 2009 25: 2103-2109; doi:10.1093/bioinformatics/btp143 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

STRUCTURAL BIOINFORMATICS Back

Thomas Fober, Marco Mernberger, Gerhard Klebe, and Eyke Hüllermeier
Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules
Bioinformatics Advance Access published on March 13, 2009
Bioinformatics 2009 25: 2110-2117; doi:10.1093/bioinformatics/btp144 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

GENE EXPRESSION Back

Michael Seifert, Jens Keilwagen, Marc Strickert, and Ivo Grosse
Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data
Bioinformatics Advance Access published on April 28, 2009
Bioinformatics 2009 25: 2118-2125; doi:10.1093/bioinformatics/btp276 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Sebastian J. Schultheiss, Wolfgang Busch, Jan U. Lohmann, Oliver Kohlbacher, and Gunnar Rätsch
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences
Bioinformatics Advance Access published on April 23, 2009
Bioinformatics 2009 25: 2126-2133; doi:10.1093/bioinformatics/btp278 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

GENETICS AND POPULATION ANALYSIS Back

Markus Riester, Peter F. Stadler, and Konstantin Klemm
FRANz: reconstruction of wild multi-generation pedigrees
Bioinformatics Advance Access published on February 8, 2009
Bioinformatics 2009 25: 2134-2139; doi:10.1093/bioinformatics/btp064 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Caroline C. Friedel and Ralf Zimmer
Identifying the topology of protein complexes from affinity purification assays
Bioinformatics Advance Access published on June 8, 2009
Bioinformatics 2009 25: 2140-2146; doi:10.1093/bioinformatics/btp353 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data]   Creative Commons License OPEN ACCESS  

CORRIGENDUM Back

Lee-Wei Yang, Eran Eyal, Ivet Bahar, and Akio Kitao
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics
Bioinformatics 2009 25: 2147; doi:10.1093/bioinformatics/btp396 [Extract] [Full Text] [Print PDF] [Request Permissions]  

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.