Volume 29, Issue 5 | May 2019

Research
- - Interplay between coding and exonic splicing regulatory sequences
    Nicolas Fontrodona
    Fabien Aubé
    Jean-Baptiste Claude
    Hélène Polvèche
    Sébastien Lemaire
    Léon-Charles Tranchevent
    ...[+1 authors]...,
    Laurent Modolo
    Franck Mortreux
    Cyril F. Bourgeois
    Didier Auboeuf
    First Published April 8, 2019
  - Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state
    Connor Rogerson
    Edward Britton
    Sarah Withey
    Neil Hanley
    Yeng S. Ang
    Andrew D. Sharrocks
    First Published April 8, 2019
  - Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin
    Kez Cleal
    Rhiannon E. Jones
    Julia W. Grimstead
    Eric A. Hendrickson
    Duncan M. Baird
    First Published March 14, 2019
  - DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
    Laura Wiehle
    Graeme J. Thorn
    Günter Raddatz
    Christopher T. Clarkson
    Karsten Rippe
    Frank Lyko
    Achim Breiling
    Vladimir B. Teif
    First Published April 4, 2019
  - Brown rat demography reveals pre-commensal structure in eastern Asia before expansion into Southeast Asia
    Emily E. Puckett
    Jason Munshi-South
    First Published March 25, 2019
  - ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm
    Marta Bozek
    Roberto Cortini
    Andrea Ennio Storti
    Ulrich Unnerstall
    Ulrike Gaul
    Nicolas Gompel
    First Published April 8, 2019
  - Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
    Joana Sequeira-Mendes
    Zaida Vergara
    Ramon Peiró
    Jordi Morata
    Irene Aragüez
    Celina Costas
    ...[+1 authors]...,
    Raul Mendez-Giraldez
    Josep M. Casacuberta
    Ugo Bastolla
    Crisanto Gutierrez
    First Published March 7, 2019
Methods
- - Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
    Ou Wang
    Robert Chin
    Xiaofang Cheng
    Michelle Ka Yan Wu
    Qing Mao
    Jingbo Tang Yuhui Sun Ellis Anderson Han K. Lam Dan Chen Yujun Zhou Linying Wang Fei Fan Yan Zou Yinlong Xie Rebecca Yu Zhang Snezana Drmanac Darlene Nguyen Chongjun Xu Christian Villarosa Scott Gablenz Nina Barua Staci Nguyen Wenlan Tian Jia Sophie Liu Jingwan Wang Xiao Liu Xiaojuan Qi Ao Chen He Wang Yuliang Dong Wenwei Zhang Andrei Alexeev Huanming Yang Jian Wang
    ...[+30 authors]...,
    Karsten Kristiansen
    Xun Xu
    Radoje Drmanac
    Brock A. Peters
    First Published April 2, 2019
  - A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS
    Sahar Gelfman
    Sarah Dugger
    Cristiane de Araujo Martins Moreno
    Zhong Ren
    Charles J. Wolock
    Neil A. Shneider Hemali Phatnani Elizabeth T. Cirulli Brittany N. Lasseigne Tim Harris Tom Maniatis Guy A. Rouleau Robert H. Brown Aaron D. Gitler Richard M. Myers
    ...[+10 authors]...,
    Slavé Petrovski
    Andrew Allen
    David B. Goldstein
    Matthew B. Harms
    First Published April 2, 2019
  - A virome-wide clonal integration analysis platform for discovering cancer viral etiology
    Xun Chen
    Jason Kost
    Arvis Sulovari
    Nathalie Wong
    Winnie S. Liang
    Jian Cao
    Dawei Li
    First Published March 14, 2019
  - Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
    Steve Miller
    Samia N. Naccache
    Erik Samayoa
    Kevin Messacar
    Shaun Arevalo
    Scot Federman Doug Stryke Elizabeth Pham Becky Fung William J. Bolosky Danielle Ingebrigtsen Walter Lorizio Sandra M. Paff John A. Leake
    ...[+9 authors]...,
    Rick Pesano
    Roberta DeBiasi
    Samuel Dominguez
    Charles Y. Chiu
    First Published April 16, 2019
  - Accurate analysis of genuine CRISPR editing events with ampliCan
    Kornel Labun
    Xiaoge Guo
    Alejandro Chavez
    George Church
    James A. Gagnon
    Eivind Valen
    First Published March 8, 2019
Resources
- - Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony
    Jacqueline A. Robinson
    Saurabh Belsare
    Shifra Birnbaum
    Deborah E. Newman
    Jeannie Chan
    Jeremy P. Glenn
    Betsy Ferguson
    Laura A. Cox
    Jeffrey D. Wall
    First Published March 29, 2019
  - The accessible chromatin landscape of the murine hippocampus at single-cell resolution
    John R. Sinnamon
    Kristof A. Torkenczy
    Michael W. Linhoff
    Sarah A. Vitak
    Ryan M. Mulqueen
    Hannah A. Pliner
    ...[+1 authors]...,
    Cole Trapnell
    Frank J. Steemers
    Gail Mandel
    Andrew C. Adey
    First Published April 1, 2019
  - Structural variants in 3000 rice genomes
    Fuentes Roven Rommel
    Chebotarov Dmytro
    Duitama Jorge
    Smith Sean
    De la Hoz Juan Fernando
    Mohiyuddin Marghoob Wing Rod A. McNally Kenneth L.
    ...[+3 authors]...,
    Tatarinova Tatiana
    Grigoriev Andrey
    Mauleon Ramil
    Alexandrov Nickolai
    First Published April 16, 2019
Erratum
- - Erratum: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
    Jaaved Mohammed
    Alex S. Flynt
    Alexandra M. Panzarino
    Md Mosharrof Hossain Mondal
    Matthew DeCruz
    Adam Siepel
    Eric C. Lai
    First Published May 1, 2019

Table of Contents

Volume 29, Issue 5 | May 2019

Research

Interplay between coding and exonic splicing regulatory sequences

Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state

Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries

Brown rat demography reveals pre-commensal structure in eastern Asia before expansion into Southeast Asia

ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm

Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins

Methods

Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly

A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS

A virome-wide clonal integration analysis platform for discovering cancer viral etiology

Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid

Accurate analysis of genuine CRISPR editing events with ampliCan

Resources

Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony

The accessible chromatin landscape of the murine hippocampus at single-cell resolution

Structural variants in 3000 rice genomes

Erratum

Erratum: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus

Table of Contents

Volume 29, Issue 5 | May 2019

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Research

Methods

Resources

Erratum