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Previous Next 		Contents: Volume 25, Number 18, 15 September 2009   [Index by Author] 
Down DISCOVERY NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
Down ORIGINAL PAPERS
     SEQUENCE ANALYSIS
     STRUCTURAL BIOINFORMATICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
     DATA AND TEXT MINING
     DATABASES AND ONTOLOGIES
Down APPLICATIONS NOTE
     GENOME ANALYSIS
     SEQUENCE ANALYSIS
     PHYLOGENETICS
     GENE EXPRESSION
     GENETICS AND POPULATION ANALYSIS
     SYSTEMS BIOLOGY
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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.

DISCOVERY NOTE Back

GENOME ANALYSIS Back

Hiromi Nishida, Takayuki Motoyama, Shogo Yamamoto, Hiroyuki Aburatani, and Hiroyuki Osada
Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
Bioinformatics Advance Access published on July 1, 2009
Bioinformatics 2009 25: 2295-2297; doi:10.1093/bioinformatics/btp413 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

SEQUENCE ANALYSIS Back

David Langenberger, Clara Bermudez-Santana, Jana Hertel, Steve Hoffmann, Philipp Khaitovich, and Peter F. Stadler
Evidence for human microRNA-offset RNAs in small RNA sequencing data
Bioinformatics Advance Access published on July 6, 2009
Bioinformatics 2009 25: 2298-2301; doi:10.1093/bioinformatics/btp419 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

ORIGINAL PAPERS Back

SEQUENCE ANALYSIS Back

Lauren M. Bragg and Glenn Stone
k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage
Bioinformatics Advance Access published on July 1, 2009
Bioinformatics 2009 25: 2302-2308; doi:10.1093/bioinformatics/btp410 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Zhen Xia, Gulei Jin, Jun Zhu, and Ruhong Zhou
Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus
Bioinformatics Advance Access published on August 25, 2009
Bioinformatics 2009 25: 2309-2317; doi:10.1093/bioinformatics/btp423 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ivan V. Kulakovskiy, Alexander V. Favorov, and Vsevolod J. Makeev
Motif discovery and motif finding from genome-mapped DNase footprint data
Bioinformatics Advance Access published on July 15, 2009
Bioinformatics 2009 25: 2318-2325; doi:10.1093/bioinformatics/btp434 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS Back

Marco Lippi and Paolo Frasconi
Prediction of protein β-residue contacts by Markov logic networks with grounding-specific weights
Bioinformatics Advance Access published on July 9, 2009
Bioinformatics 2009 25: 2326-2333; doi:10.1093/bioinformatics/btp421 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Cenny Taslim, Jiejun Wu, Pearlly Yan, Greg Singer, Jeffrey Parvin, Tim Huang, Shili Lin, and Kun Huang
Comparative study on ChIP-seq data: normalization and binding pattern characterization
Bioinformatics Advance Access published on June 26, 2009
Bioinformatics 2009 25: 2334-2340; doi:10.1093/bioinformatics/btp384 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Pierre Nicolas, Aurélie Leduc, Stéphane Robin, Simon Rasmussen, Hanne Jarmer, and Philippe Bessières
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift
Bioinformatics Advance Access published on June 26, 2009
Bioinformatics 2009 25: 2341-2347; doi:10.1093/bioinformatics/btp395 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Galina V. Glazko and Frank Emmert-Streib
Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets
Bioinformatics Advance Access published on July 2, 2009
Bioinformatics 2009 25: 2348-2354; doi:10.1093/bioinformatics/btp406 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

A. H. M. Mahbub Latif, Frank Bretz, and Edgar Brunner
Robustness considerations in selecting efficient two-color microarray designs
Bioinformatics Advance Access published on July 1, 2009
Bioinformatics 2009 25: 2355-2361; doi:10.1093/bioinformatics/btp407 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xiaofeng Dai, Olli Yli-Harja, and Andre S. Ribeiro
Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources
Bioinformatics Advance Access published on July 1, 2009
Bioinformatics 2009 25: 2362-2368; doi:10.1093/bioinformatics/btp411 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jennifer Toolan Judy and Hongkai Ji
TileProbe: modeling tiling array probe effects using publicly available data
Bioinformatics Advance Access published on July 9, 2009
Bioinformatics 2009 25: 2369-2375; doi:10.1093/bioinformatics/btp425 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

GENETICS AND POPULATION ANALYSIS Back

Øivind Skare, Nuala Sheehan, and Thore Egeland
Identification of distant family relationships
Bioinformatics Advance Access published on July 6, 2009
Bioinformatics 2009 25: 2376-2382; doi:10.1093/bioinformatics/btp418 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY Back

Stefan Jaeger, Qingfeng Song, and Su-Shing Chen
DYNAMIK: a software environment for cell DYNAmics, Motility, and Information tracKing, with an application to Ras pathways
Bioinformatics Advance Access published on July 4, 2009
Bioinformatics 2009 25: 2383-2388; doi:10.1093/bioinformatics/btp405 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Zhihui Wang, Christina M. Birch, Jonathan Sagotsky, and Thomas S. Deisboeck
Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model
Bioinformatics Advance Access published on July 4, 2009
Bioinformatics 2009 25: 2389-2396; doi:10.1093/bioinformatics/btp416 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Kevin Bleakley and Yoshihiro Yamanishi
Supervised prediction of drug–target interactions using bipartite local models
Bioinformatics Advance Access published on July 15, 2009
Bioinformatics 2009 25: 2397-2403; doi:10.1093/bioinformatics/btp433 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

DATA AND TEXT MINING Back

Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Amy A. Caudy, David C. Hess, and Olga G. Troyanskaya
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction
Bioinformatics Advance Access published on June 26, 2009
Bioinformatics 2009 25: 2404-2410; doi:10.1093/bioinformatics/btp397 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

DATABASES AND ONTOLOGIES Back

David S. DeLuca, Britta Eiz-Vesper, Nektarios Ladas, Barbara Anna-Maria Khattab, and Rainer Blasczyk
High-throughput minor histocompatibility antigen prediction
Bioinformatics Advance Access published on July 1, 2009
Bioinformatics 2009 25: 2411-2417; doi:10.1093/bioinformatics/btp404 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

J. A. Encinar, G. Fernandez-Ballester, I. E. Sánchez, E. Hurtado-Gomez, F. Stricher, P. Beltrao, and L. Serrano
ADAN: a database for prediction of protein–protein interaction of modular domains mediated by linear motifs
Bioinformatics Advance Access published on July 14, 2009
Bioinformatics 2009 25: 2418-2424; doi:10.1093/bioinformatics/btp424 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Xiao-Qin Xia, Michael McClelland, Steffen Porwollik, Wenzhi Song, Xianling Cong, and Yipeng Wang
WebArrayDB: cross-platform microarray data analysis and public data repository
Bioinformatics Advance Access published on July 14, 2009
Bioinformatics 2009 25: 2425-2429; doi:10.1093/bioinformatics/btp430 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

APPLICATIONS NOTE Back

GENOME ANALYSIS Back

Jong Hyun Kim, Woo-Cheol Kim, Michael S. Waterman, Sanghyun Park, and Lei M. Li
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome
Bioinformatics Advance Access published on June 27, 2009
Bioinformatics 2009 25: 2430-2431; doi:10.1093/bioinformatics/btp399 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS Back

Nestor Zaburannyy, Bohdan Ostash, and Victor Fedorenko
TTA Lynx: a web-based service for analysis of actinomycete genes containing rare TTA codon
Bioinformatics Advance Access published on July 2, 2009
Bioinformatics 2009 25: 2432-2433; doi:10.1093/bioinformatics/btp402 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Heinrich Magnus Manske and Dominic P. Kwiatkowski
SNP-o-matic
Bioinformatics Advance Access published on July 2, 2009
Bioinformatics 2009 25: 2434-2435; doi:10.1093/bioinformatics/btp403 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Quan Long, Daniel MacArthur, Zemin Ning, and Chris Tyler-Smith
HI: haplotype improver using paired-end short reads
Bioinformatics Advance Access published on July 1, 2009
Bioinformatics 2009 25: 2436-2437; doi:10.1093/bioinformatics/btp412 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

A. Martínez-Alcántara, E. Ballesteros, C. Feng, M. Rojas, H. Koshinsky, V. Y. Fofanov, P. Havlak, and Y. Fofanov
PIQA: pipeline for Illumina G1 genome analyzer data quality assessment
Bioinformatics Advance Access published on July 14, 2009
Bioinformatics 2009 25: 2438-2439; doi:10.1093/bioinformatics/btp429 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

PHYLOGENETICS Back

Lin Himmelmann and Dirk Metzler
TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
Bioinformatics Advance Access published on July 3, 2009
Bioinformatics 2009 25: 2440-2441; doi:10.1093/bioinformatics/btp417 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION Back

Andrew A. Pohl, Charles W. Sugnet, Tyson A. Clark, Kayla Smith, Pauline A. Fujita, and Melissa S. Cline
Affy exon tissues: exon levels in normal tissues in human, mouse and rat
Bioinformatics Advance Access published on July 1, 2009
Bioinformatics 2009 25: 2442-2443; doi:10.1093/bioinformatics/btp414 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

GENETICS AND POPULATION ANALYSIS Back

David Zamar, Ben Tripp, George Ellis, and Denise Daley
Path: a tool to facilitate pathway-based genetic association analysis
Bioinformatics Advance Access published on July 23, 2009
Bioinformatics 2009 25: 2444-2446; doi:10.1093/bioinformatics/btp431 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

SYSTEMS BIOLOGY Back

Aleksandar Stojmirovic and Yi-Kuo Yu
ITM Probe: analyzing information flow in protein networks
Bioinformatics Advance Access published on June 27, 2009
Bioinformatics 2009 25: 2447-2449; doi:10.1093/bioinformatics/btp398 [Abstract] [FREE Full Text] [Print PDF]   Creative Commons License OPEN ACCESS  

Hong Sun, Karen Lemmens, Tim Van den Bulcke, Kristof Engelen, Bart De Moor, and Kathleen Marchal
ViTraM: visualization of transcriptional modules
Bioinformatics Advance Access published on July 8, 2009
Bioinformatics 2009 25: 2450-2451; doi:10.1093/bioinformatics/btp400 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Lucian P. Smith, Frank T. Bergmann, Deepak Chandran, and Herbert M. Sauro
Antimony: a modular model definition language
Bioinformatics Advance Access published on July 3, 2009
Bioinformatics 2009 25: 2452-2454; doi:10.1093/bioinformatics/btp401 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

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