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Table of Contents

Volume 28 Issue 11 June 1, 2012

To see an article, click its [Full Text] or [PDF] 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.

HITSEQ PAPERS

GENOME ANALYSIS

    • Anthony J. Cox,
    • Markus J. Bauer,
    • Tobias Jakobi,
    • and Giovanna Rosone

    Large-scale compression of genomic sequence databases with the Burrows–Wheeler transform

    Bioinformatics (2012) 28(11): 1415-1419 first published online May 3, 2012 doi:10.1093/bioinformatics/bts173

SEQUENCE ANALYSIS

    • Yu Peng,
    • Henry C. M. Leung,
    • S. M. Yiu,
    • and Francis Y. L. Chin

    IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

    Bioinformatics (2012) 28(11): 1420-1428 first published online April 11, 2012 doi:10.1093/bioinformatics/bts174
    • Alexey A. Gritsenko,
    • Jurgen F. Nijkamp,
    • Marcel J.T. Reinders,
    • and Dick de Ridder

    GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

    Bioinformatics (2012) 28(11): 1429-1437 first published online April 6, 2012 doi:10.1093/bioinformatics/bts175

ORIGINAL PAPERS

GENOME ANALYSIS

    • Matthieu Chartier,
    • Francis Gaudreault,
    • and Rafael Najmanovich

    Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

    Bioinformatics (2012) 28(11): 1438-1445 first published online March 30, 2012 doi:10.1093/bioinformatics/bts149
    • Anton Aboukhalil and
    • Martha L. Bulyk

    LOESS correction for length variation in gene set-based genomic sequence analysis

    Bioinformatics (2012) 28(11): 1446-1454 first published online April 5, 2012 doi:10.1093/bioinformatics/bts155
    • Binbin Lai,
    • Ruogu Ding,
    • Yang Li,
    • Liping Duan,
    • and Huaiqiu Zhu

    A de novo metagenomic assembly program for shotgun DNA reads

    Bioinformatics (2012) 28(11): 1455-1462 first published online April 11, 2012 doi:10.1093/bioinformatics/bts162

STRUCTURAL BIOINFORMATICS

    • Valéry Ozenne,
    • Frédéric Bauer,
    • Loïc Salmon,
    • Jie-rong Huang,
    • Malene Ringkjøbing Jensen,
    • Stéphane Segard,
    • Pau Bernadó,
    • Céline Charavay,
    • and Martin Blackledge

    Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables

    Bioinformatics (2012) 28(11): 1463-1470 doi:10.1093/bioinformatics/bts172

GENE EXPRESSION

    • Christian Otto,
    • Kristin Reiche,
    • and Jörg Hackermüller

    Detection of differentially expressed segments in tiling array data

    Bioinformatics (2012) 28(11): 1471-1479 first published online April 6, 2012 doi:10.1093/bioinformatics/bts142
    • Haroon Naeem,
    • Ralf Zimmer,
    • Pegah Tavakkolkhah,
    • and Robert Küffner

    Rigorous assessment of gene set enrichment tests

    Bioinformatics (2012) 28(11): 1480-1486 first published online April 5, 2012 doi:10.1093/bioinformatics/bts164
    • Andrew E. Teschendorff and
    • Martin Widschwendter

    Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions

    Bioinformatics (2012) 28(11): 1487-1494 first published online April 6, 2012 doi:10.1093/bioinformatics/bts170

SYSTEMS BIOLOGY

    • Jochen Weile,
    • Katherine James,
    • Jennifer Hallinan,
    • Simon J. Cockell,
    • Phillip Lord,
    • Anil Wipat,
    • and Darren J. Wilkinson

    Bayesian integration of networks without gold standards

    Bioinformatics (2012) 28(11): 1495-1500 first published online April 6, 2012 doi:10.1093/bioinformatics/bts154
    OPEN ACCESS
    • Xin Liu and
    • Mahesan Niranjan

    State and parameter estimation of the heat shock response system using Kalman and particle filters

    Bioinformatics (2012) 28(11): 1501-1507 first published online April 26, 2012 doi:10.1093/bioinformatics/bts161
    • Bing Liu,
    • Andrei Hagiescu,
    • Sucheendra K. Palaniappan,
    • Bipasa Chattopadhyay,
    • Zheng Cui,
    • Weng-Fai Wong,
    • and P. S. Thiagarajan

    Approximate probabilistic analysis of biopathway dynamics

    Bioinformatics (2012) 28(11): 1508-1516 first published online April 5, 2012 doi:10.1093/bioinformatics/bts166
    • Nicolae Radu Zabet and
    • Boris Adryan

    A comprehensive computational model of facilitated diffusion in prokaryotes

    Bioinformatics (2012) 28(11): 1517-1524 first published online April 6, 2012 doi:10.1093/bioinformatics/bts178
    OPEN ACCESS

APPLICATIONS NOTE

GENOME ANALYSIS

    • Simon P. Sadedin,
    • Bernard Pope,
    • and Alicia Oshlack

    Bpipe: a tool for running and managing bioinformatics pipelines

    Bioinformatics (2012) 28(11): 1525-1526 first published online April 12, 2012 doi:10.1093/bioinformatics/bts167
    • Vikas R. Pejaver,
    • Jaehyun An,
    • SungMin Rhee,
    • Ankita Bhan,
    • Jeong-Hyeon Choi,
    • Boshu Liu,
    • Heewook Lee,
    • Pamela J. Brown,
    • David Kysela,
    • Yves V. Brun,
    • and Sun Kim

    GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis

    Bioinformatics (2012) 28(11): 1527-1529 first published online April 11, 2012 doi:10.1093/bioinformatics/bts177
    • David S. DeLuca,
    • Joshua Z. Levin,
    • Andrey Sivachenko,
    • Timothy Fennell,
    • Marc-Danie Nazaire,
    • Chris Williams,
    • Michael Reich,
    • Wendy Winckler,
    • and Gad Getz

    RNA-SeQC: RNA-seq metrics for quality control and process optimization

    Bioinformatics (2012) 28(11): 1530-1532 first published online April 25, 2012 doi:10.1093/bioinformatics/bts196
    OPEN ACCESS

SEQUENCE ANALYSIS

    • Xuesong Hu,
    • Jianying Yuan,
    • Yujian Shi,
    • Jianliang Lu,
    • Binghang Liu,
    • Zhenyu Li,
    • Yanxiang Chen,
    • Desheng Mu,
    • Hao Zhang,
    • Nan Li,
    • Zhen Yue,
    • Fan Bai,
    • Heng Li,
    • and Wei Fan

    pIRS: Profile-based Illumina pair-end reads simulator

    Bioinformatics (2012) 28(11): 1533-1535 first published online April 15, 2012 doi:10.1093/bioinformatics/bts187

PHYLOGENETICS

    • Andrei-Alin Popescu,
    • Katharina T. Huber,
    • and Emmanuel Paradis

    ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

    Bioinformatics (2012) 28(11): 1536-1537 first published online April 11, 2012 doi:10.1093/bioinformatics/bts184

STRUCTURAL BIOINFORMATICS

    • Osvaldo A. Martin,
    • Jorge A. Vila,
    • and Harold A. Scheraga

    CheShift-2: graphic validation of protein structures

    Bioinformatics (2012) 28(11): 1538-1539 first published online April 11, 2012 doi:10.1093/bioinformatics/bts179
    OPEN ACCESS
    • Emilie Pihan,
    • Lionel Colliandre,
    • Jean-François Guichou,
    • and Dominique Douguet

    e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design

    Bioinformatics (2012) 28(11): 1540-1541 first published online April 26, 2012 doi:10.1093/bioinformatics/bts186

GENE EXPRESSION

    • Laurent Jourdren,
    • Maria Bernard,
    • Marie-Agnès Dillies,
    • and Stéphane Le Crom

    Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses

    Bioinformatics (2012) 28(11): 1542-1543 first published online April 5, 2012 doi:10.1093/bioinformatics/bts165
    • Jian-Bo Pan,
    • Shi-Chang Hu,
    • Hao Wang,
    • Quan Zou,
    • and Zhi-Liang Ji

    PaGeFinder: quantitative identification of spatiotemporal pattern genes

    Bioinformatics (2012) 28(11): 1544-1545 first published online April 6, 2012 doi:10.1093/bioinformatics/bts169
    OPEN ACCESS
    • Daryl Waggott,
    • Kenneth Chu,
    • Shaoming Yin,
    • Bradly G. Wouters,
    • Fei-Fei Liu,
    • and Paul C. Boutros

    NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data

    Bioinformatics (2012) 28(11): 1546-1548 first published online April 17, 2012 doi:10.1093/bioinformatics/bts188
    OPEN ACCESS

SYSTEMS BIOLOGY

    • Gábor Szederkényi,
    • Julio R. Banga,
    • and Antonio A. Alonso

    CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks

    Bioinformatics (2012) 28(11): 1549-1550 first published online April 6, 2012 doi:10.1093/bioinformatics/bts171

DATABASES AND ONTOLOGIES

    • Feng Gao,
    • Hao Luo,
    • and Chun-Ting Zhang

    DeOri: a database of eukaryotic DNA replication origins

    Bioinformatics (2012) 28(11): 1551-1552 first published online March 30, 2012 doi:10.1093/bioinformatics/bts151

GENETICS AND POPULATION ANALYSIS

    • Stephen A. Stanhope and
    • Mark Abney

    GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations

    Bioinformatics (2012) 28(11): 1553-1554 first published online April 19, 2012 doi:10.1093/bioinformatics/bts190

To see an article, click its [Full Text] or [PDF] 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.

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This Issue

June 1, 2012 28 (11)
Bioinformatics
  1. HITSEQ PAPERS
    1. GENOME ANALYSIS
    2. SEQUENCE ANALYSIS
  3. ORIGINAL PAPERS
    1. GENOME ANALYSIS
    2. STRUCTURAL BIOINFORMATICS
    3. GENE EXPRESSION
    4. SYSTEMS BIOLOGY
  5. APPLICATIONS NOTE
    1. GENOME ANALYSIS
    2. SEQUENCE ANALYSIS
    3. PHYLOGENETICS
    4. STRUCTURAL BIOINFORMATICS
    5. GENE EXPRESSION
    6. SYSTEMS BIOLOGY
    7. DATABASES AND ONTOLOGIES
    8. GENETICS AND POPULATION ANALYSIS

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