Volume 27, Issue 2 | February 2017

Research
- - APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context
    Vladimir B. Seplyarskiy
    Maria A. Andrianova
    Georgii A. Bazykin
    First Published December 9, 2016
  - Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP
    Maoxiang Qian
    Hui Zhang
    Shirley Kow-Yin Kham
    Shuguang Liu
    Chuang Jiang
    Xujie Zhao Yi Lu Charnise Goodings Ting-Nien Lin Ranran Zhang Takaya Moriyama Zhaohong Yin Zhenhua Li Thuan Chong Quah Hany Ariffin Ah Moy Tan Shuhong Shen Deepa Bhojwani Shaoyan Hu Suning Chen
    ...[+15 authors]...,
    Huyong Zheng
    Ching-Hon Pui
    Allen Eng-Juh Yeoh
    Jun J. Yang
    First Published November 30, 2016
  - Identification of clinically predictive metagenes that encode components of a network coupling cell shape to transcription by image-omics
    Heba Z. Sailem
    Chris Bakal
    First Published November 18, 2016
  - Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes
    Lawlor Nathan
    George Joshy
    Bolisetty Mohan
    Kursawe Romy
    Sun Lili
    Sivakamasundari V.
    Kycia Ina
    Robson Paul
    Stitzel Michael L.
    First Published November 18, 2016
  - Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding
    Guillaume Andrey
    Robert Schöpflin
    Ivana Jerković
    Verena Heinrich
    Daniel M. Ibrahim
    Christina Paliou Myriam Hochradel
    ...[+2 authors]...,
    Bernd Timmermann
    Stefan Haas
    Martin Vingron
    Stefan Mundlos
    First Published December 6, 2016
  - microRNA target prediction programs predict many false positives
    Natalia Pinzón
    Blaise Li
    Laura Martinez
    Anna Sergeeva
    Jessy Presumey
    Florence Apparailly
    Hervé Seitz
    First Published November 15, 2016
  - Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes
    Sakthi D. Moorthy
    Scott Davidson
    Virlana M. Shchuka
    Gurdeep Singh
    Nakisa Malek-Gilani
    Lida Langroudi
    ...[+1 authors]...,
    Alexandre Martchenko
    Vincent So
    Neil N. Macpherson
    Jennifer A. Mitchell
    First Published November 28, 2016
  - Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes
    Yuvia A. Pérez-Rico
    Valentina Boeva
    Allison C. Mallory
    Angelo Bitetti
    Sara Majello
    Emmanuel Barillot
    Alena Shkumatava
    First Published December 13, 2016
  - Nucleosome occupancy as a novel chromatin parameter for replication origin functions
    Jairo Rodriguez
    Laura Lee
    Bryony Lynch
    Toshio Tsukiyama
    First Published November 28, 2016
  - Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1
    Neeman Mohibullah
    Scott Keeney
    First Published December 6, 2016
  - Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism
    Daniel R. Reuß
    Josef Altenbuchner
    Ulrike Mäder
    Hermann Rath
    Till Ischebeck
    Praveen Kumar Sappa Andrea Thürmer Cyprien Guérin Pierre Nicolas Leif Steil Bingyao Zhu Ivo Feussner Stefan Klumpp
    ...[+8 authors]...,
    Rolf Daniel
    Fabian M. Commichau
    Uwe Völker
    Jörg Stülke
    First Published December 13, 2016
Methods
- - Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes
    Dirk D. Dolle
    Zhicheng Liu
    Matthew Cotten
    Jared T. Simpson
    Zamin Iqbal
    Richard Durbin
    Shane A. McCarthy
    Thomas M. Keane
    First Published December 16, 2016
  - Model-based analysis of DNA replication profiles: predicting replication fork velocity and initiation rate by profiling free-cycling cells
    Ariel Gispan
    Miri Carmi
    Naama Barkai
    First Published December 27, 2016
  - Detecting differential growth of microbial populations with Gaussian process regression
    Peter D. Tonner
    Cynthia L. Darnell
    Barbara E. Engelhardt
    Amy K. Schmid
    First Published November 18, 2016
Corrigendum
- - Corrigendum: Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes
    Pierre Chymkowitch
    Aurélie Nguéa P
    Håvard Aanes
    Christian J. Koehler
    Bernd Thiede
    Susanne Lorenz
    Leonardo A. Meza-Zepeda
    Arne Klungland
    Jorrit M. Enserink
    First Published February 1, 2017

Table of Contents

Volume 27, Issue 2 | February 2017

Research

APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context

Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP

Identification of clinically predictive metagenes that encode components of a network coupling cell shape to transcription by image-omics

Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

microRNA target prediction programs predict many false positives

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

Nucleosome occupancy as a novel chromatin parameter for replication origin functions

Numerical and spatial patterning of yeast meiotic DNA breaks by Tel1

Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism

Methods

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

Model-based analysis of DNA replication profiles: predicting replication fork velocity and initiation rate by profiling free-cycling cells

Detecting differential growth of microbial populations with Gaussian process regression

Corrigendum

Corrigendum: Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes

Table of Contents

Volume 27, Issue 2 | February 2017

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Research

Methods

Corrigendum