Table of ContentsVolume 27 Issue 6 March 15, 2011
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DISCOVERY NOTEDATA AND TEXT MINING
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Wai-ki Yip and - Christoph Lange
Quantitative trait prediction based on genetic marker-array data, a simulation study Bioinformatics (2011) 27(6): 745-748 first published online January 31, 2011 doi:10.1093/bioinformatics/btr024
ORIGINAL PAPERSGENOME ANALYSIS
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Jan Fostier, - Sebastian Proost,
- Bart Dhoedt,
- Yvan Saeys,
- Piet Demeester,
- Yves Van de Peer,
- and Klaas Vandepoele
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists Bioinformatics (2011) 27(6): 749-756 first published online January 6, 2011 doi:10.1093/bioinformatics/btr008
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Oliver Keller, - Martin Kollmar,
- Mario Stanke,
- and Stephan Waack
A novel hybrid gene prediction method employing protein multiple sequence alignments Bioinformatics (2011) 27(6): 757-763 first published online January 6, 2011 doi:10.1093/bioinformatics/btr010
SEQUENCE ANALYSIS
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Guillaume Marçais and - Carl Kingsford
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers Bioinformatics (2011) 27(6): 764-770 first published online January 7, 2011 doi:10.1093/bioinformatics/btr011
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Yi Zhang, - Xianhui Wang,
- and Le Kang
A k-mer scheme to predict piRNAs and characterize locust piRNAs Bioinformatics (2011) 27(6): 771-776 first published online January 11, 2011 doi:10.1093/bioinformatics/btr016
OPEN ACCESS 
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Yejun Wang, - Qing Zhang,
- Ming-an Sun,
- and Dianjing Guo
High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles Bioinformatics (2011) 27(6): 777-784 first published online January 13, 2011 doi:10.1093/bioinformatics/btr021
STRUCTURAL BIOINFORMATICS
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Yang Cao, - Lin Song,
- Zhichao Miao,
- Yun Hu,
- Liqing Tian,
- and Taijiao Jiang
Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation Bioinformatics (2011) 27(6): 785-790 first published online January 6, 2011 doi:10.1093/bioinformatics/btr009
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Guy Tsafnat, - Jaron Schaeffer,
- Andrew Clayphan,
- Jon R. Iredell,
- Sally R. Partridge,
- and Enrico Coiera
Computational inference of grammars for larger-than-gene structures from annotated gene sequences Bioinformatics (2011) 27(6): 791-796 first published online January 22, 2011 doi:10.1093/bioinformatics/btr036
GENE EXPRESSION
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Clement Chung, - Jian Liu,
- Andrew Emili,
- and Brendan J. Frey
Computational refinement of post-translational modifications predicted from tandem mass spectrometry Bioinformatics (2011) 27(6): 797-806 first published online January 22, 2011 doi:10.1093/bioinformatics/btr017
OPEN ACCESS
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A. Posekany, - K. Felsenstein,
- and P. Sykacek
Biological assessment of robust noise models in microarray data analysis Bioinformatics (2011) 27(6): 807-814 first published online January 19, 2011 doi:10.1093/bioinformatics/btr018
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GENETICS AND POPULATION ANALYSIS
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V. M. Lourenço, - A. M. Pires,
- and M. Kirst
Robust linear regression methods in association studies Bioinformatics (2011) 27(6): 815-821 first published online January 7, 2011 doi:10.1093/bioinformatics/btr006
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Rick Twee-Hee Ong, - Xuanyao Liu,
- Wan-Ting Poh,
- Xueling Sim,
- Kee-Seng Chia,
- and Yik-Ying Teo
A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies Bioinformatics (2011) 27(6): 822-828 first published online January 6, 2011 doi:10.1093/bioinformatics/btr007
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Christian Rödelsperger, - Peter Krawitz,
- Sebastian Bauer,
- Jochen Hecht,
- Abigail W. Bigham,
- Michael Bamshad,
- Birgit Jonske de Condor,
- Michal R. Schweiger,
- and Peter N. Robinson
Identity-by-descent filtering of exome sequence data for disease–gene identification in autosomal recessive disorders Bioinformatics (2011) 27(6): 829-836 first published online January 28, 2011 doi:10.1093/bioinformatics/btr022
OPEN ACCESS
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Tianqi Zhu, - Yucheng Hu,
- Zhi-Ming Ma,
- De-Xing Zhang,
- Tiejun Li,
- and Ziheng Yang
Efficient simulation under a population genetics model of carcinogenesis Bioinformatics (2011) 27(6): 837-843 first published online January 18, 2011 doi:10.1093/bioinformatics/btr025
SYSTEMS BIOLOGY
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Stuart R. Jefferys and - Morgan C. Giddings
Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data Bioinformatics (2011) 27(6): 844-852 doi:10.1093/bioinformatics/btr027
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Lin Hou, - Lin Wang,
- Minping Qian,
- Dong Li,
- Chao Tang,
- Yunping Zhu,
- Minghua Deng,
- and Fangting Li
Modular analysis of the probabilistic genetic interaction network Bioinformatics (2011) 27(6): 853-859 first published online January 28, 2011 doi:10.1093/bioinformatics/btr031
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APPLICATIONS NOTESEQUENCE ANALYSIS
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Sebastian Deorowicz and - Szymon Grabowski
Compression of DNA sequence reads in FASTQ format Bioinformatics (2011) 27(6): 860-862 first published online January 19, 2011 doi:10.1093/bioinformatics/btr014
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Robert Schmieder and - Robert Edwards
Quality control and preprocessing of metagenomic datasets Bioinformatics (2011) 27(6): 863-864 first published online January 28, 2011 doi:10.1093/bioinformatics/btr026
OPEN ACCESS
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Michael N. Edmonson, - Jinghui Zhang,
- Chunhua Yan,
- Richard P. Finney,
- Daoud M. Meerzaman,
- and Kenneth H. Buetow
Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format Bioinformatics (2011) 27(6): 865-866 first published online January 28, 2011 doi:10.1093/bioinformatics/btr032
GENE EXPRESSION
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Angela Goncalves, - Andrew Tikhonov,
- Alvis Brazma,
- and Misha Kapushesky
A pipeline for RNA-seq data processing and quality assessment Bioinformatics (2011) 27(6): 867-869 first published online January 13, 2011 doi:10.1093/bioinformatics/btr012
OPEN ACCESS
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Qiang Song and - Andrew D. Smith
Identifying dispersed epigenomic domains from ChIP-Seq data Bioinformatics (2011) 27(6): 870-871 first published online February 16, 2011 doi:10.1093/bioinformatics/btr030
OPEN ACCESS
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Andrew T. Magis, - John C. Earls,
- Youn-Hee Ko,
- James A. Eddy,
- and Nathan D. Price
Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup Bioinformatics (2011) 27(6): 872-873 first published online January 20, 2011 doi:10.1093/bioinformatics/btr033
SYSTEMS BIOLOGY
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Yanxiang Zhou, - Juliane Liepe,
- Xia Sheng,
- Michael P. H. Stumpf,
- and Chris Barnes
GPU accelerated biochemical network simulation Bioinformatics (2011) 27(6): 874-876 first published online January 11, 2011 doi:10.1093/bioinformatics/btr015
OPEN ACCESS
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Xuejian Xiong, - Hongyan Song,
- Tuan On,
- Lucas Lochovsky,
- Nicholas J. Provart,
- and John Parkinson
PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya Bioinformatics (2011) 27(6): 877-878 first published online January 19, 2011 doi:10.1093/bioinformatics/btr023
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Xin Wang, - Camille Terfve,
- John C. Rose,
- and Florian Markowetz
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens Bioinformatics (2011) 27(6): 879-880 first published online January 22, 2011 doi:10.1093/bioinformatics/btr028
OPEN ACCESS
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Matthieu Vignes, - Juliette Blanchet,
- Damien Leroux,
- and Florence Forbes
SpaCEM3: a software for biological module detection when data is incomplete, high dimensional and dependent Bioinformatics (2011) 27(6): 881-882 first published online February 3, 2011 doi:10.1093/bioinformatics/btr034
OPEN ACCESS
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Yanqi Hao, - Anna Merkoulovitch,
- James Vlasblom,
- Shuye Pu,
- Andrei L. Turinsky,
- Denitza Roudeva,
- Brian Turner,
- Jack Greenblatt,
- and Shoshana J. Wodak
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms Bioinformatics (2011) 27(6): 883-884 first published online January 20, 2011 doi:10.1093/bioinformatics/btr035
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DATA AND TEXT MINING
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Francesca Chignola, - Silvia Mari,
- Tim J. Stevens,
- Rasmus H. Fogh,
- Valeria Mannella,
- Wayne Boucher,
- and Giovanna Musco
The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR Bioinformatics (2011) 27(6): 885-886 first published online January 6, 2011 doi:10.1093/bioinformatics/btr013
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Riku Louhimo and - Sampsa Hautaniemi
CNAmet: an R package for integrating copy number, methylation and expression data Bioinformatics (2011) 27(6): 887-888 first published online January 12, 2011 doi:10.1093/bioinformatics/btr019
DATABASES AND ONTOLOGIES
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Thomas A. Down, - Matias Piipari,
- and Tim J. P. Hubbard
Dalliance: interactive genome viewing on the web Bioinformatics (2011) 27(6): 889-890 first published online January 19, 2011 doi:10.1093/bioinformatics/btr020
OPEN ACCESS
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Mark Y. Tong, - Christopher A. Cassa,
- and Isaac S. Kohane
Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations Bioinformatics (2011) 27(6): 891-893 first published online January 22, 2011 doi:10.1093/bioinformatics/btr029
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发表于 2011-3-26 23:03:28