Volume 23, Issue 5 | May 2013

Research
- - The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes
    Stephen B. Montgomery
    David L. Goode
    Erika Kvikstad
    Cornelis A. Albers
    Zhengdong D. Zhang
    Xinmeng Jasmine Mu Guruprasad Ananda Bryan Howie Konrad J. Karczewski Kevin S. Smith Vanessa Anaya Rhea Richardson Joe Davis Daniel G. MacArthur Arend Sidow Laurent Duret Mark Gerstein
    ...[+12 authors]...,
    Kateryna D. Makova
    Jonathan Marchini
    Gil McVean
    Gerton Lunter
    First Published March 11, 2013
  - Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms
    Ankit Malhotra
    Michael Lindberg
    Gregory G. Faust
    Mitchell L. Leibowitz
    Royden A. Clark
    First Published February 14, 2013
  - Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
    Nathan C. Sheffield
    Robert E. Thurman
    Lingyun Song
    Alexias Safi
    John A. Stamatoyannopoulos
    First Published March 12, 2013
  - DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure
    Sahar Gelfman
    Noa Cohen
    Ahuvi Yearim
    Gil Ast
    First Published March 15, 2013
  - Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
    Pouya Kheradpour
    Jason Ernst
    Alexandre Melnikov
    Peter Rogov
    Li Wang
    First Published March 19, 2013
  - Widespread and extensive lengthening of 3′ UTRs in the mammalian brain
    Pedro Miura
    Sol Shenker
    Celia Andreu-Agullo
    Jakub O. Westholm
    Eric C. Lai
    First Published March 21, 2013
Methods
- - Sequencing of isolated sperm cells for direct haplotyping of a human genome
    Ewen F. Kirkness
    Rashel V. Grindberg
    Joyclyn Yee-Greenbaum
    Christian R. Marshall
    Stephen W. Scherer
    First Published January 2, 2013
  - An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
    Yi Wang
    James Lu
    Jin Yu
    Richard A. Gibbs
    Fuli Yu
    First Published January 7, 2013
  - Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
    Joseph B. Hiatt
    Colin C. Pritchard
    Stephen J. Salipante
    Brian J. O'Roak
    Jay Shendure
    First Published February 4, 2013
  - Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture
    Helena M.B. Seth-Smith
    Simon R. Harris
    Rachel J. Skilton
    Frans M. Radebe
    Daniel Golparian
    Elena Shipitsyna Pham Thanh Duy Paul Scott Lesley T. Cutcliffe Colette O’Neill Surendra Parmar Rachel Pitt Stephen Baker Catherine A. Ison Peter Marsh Hamid Jalal David A. Lewis
    ...[+12 authors]...,
    Magnus Unemo
    Ian N. Clarke
    Julian Parkhill
    Nicholas R. Thomson
    First Published March 22, 2013
  - Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform
    Jeffrey S. McLean
    Mary-Jane Lombardo
    Michael G. Ziegler
    Mark Novotny
    Joyclyn Yee-Greenbaum
    Jonathan H. Badger Glenn Tesler Sergey Nurk Valery Lesin Daniel Brami Adam P. Hall Anna Edlund Lisa Z. Allen Scott Durkin Sharon Reed Francesca Torriani Kenneth H. Nealson
    ...[+12 authors]...,
    Pavel A. Pevzner
    Robert Friedman
    J. Craig Venter
    Roger S. Lasken
    First Published April 5, 2013
  - Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome
    Michael S. Fitzsimons
    Mark Novotny
    Chien-Chi Lo
    Armand E.K. Dichosa
    Joyclyn L. Yee-Greenbaum
    Jeremy P. Snook Wei Gu Olga Chertkov Karen W. Davenport Kim McMurry Krista G. Reitenga Ashlynn R. Daughton Jian He Shannon L. Johnson Cheryl D. Gleasner Patti L. Wills Beverly Parson-Quintana
    ...[+12 authors]...,
    Patrick S. Chain
    John C. Detter
    Roger S. Lasken
    Cliff S. Han
    First Published March 14, 2013
Resource
- - PRISM offers a comprehensive genomic approach to transcription factor function prediction
    Aaron M. Wenger
    Shoa L. Clarke
    Harendra Guturu
    Jenny Chen
    Bruce T. Schaar
    First Published February 4, 2013
Erratum
- - Erratum
    First Published May 1, 2013

Table of Contents

Volume 23, Issue 5 | May 2013

Research

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Widespread and extensive lengthening of 3′ UTRs in the mammalian brain

Methods

Sequencing of isolated sperm cells for direct haplotyping of a human genome

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

Resource

PRISM offers a comprehensive genomic approach to transcription factor function prediction

Erratum

Erratum

Table of Contents

Volume 23, Issue 5 | May 2013

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Research

Methods

Resource

Erratum