Volume 28, Issue 4 | April 2018

Research
- - Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia
    Sanchita Bhattacharya
    Jian Li
    Alexandra Sockell
    Matthew J. Kan
    Felice A. Bava
    Shann-Ching Chen María C. Ávila-Arcos Xuhuai Ji Emery Smith Narges B. Asadi Ralph S. Lachman
    ...[+6 authors]...,
    Hugo Y.K. Lam
    Carlos D. Bustamante
    Atul J. Butte
    Garry P. Nolan
    First Published March 22, 2018
  - Cancer-associated rs6983267 SNP and its accompanying long noncoding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations
    Maitri Y. Shah
    Manuela Ferracin
    Valentina Pileczki
    Baoqing Chen
    Roxana Redis
    Linda Fabris Xinna Zhang Cristina Ivan Masayoshi Shimizu Cristian Rodriguez-Aguayo Mihnea Dragomir Katrien Van Roosbroeck Maria Ines Almeida Maria Ciccone Daniela Nedelcu Maria Angelica Cortez Taghi Manshouri Steliana Calin Muharrem Muftuoglu Pinaki P. Banerjee Mustafa H. Badiwi Jan Parker-Thornburg Asha Multani James William Welsh Marcos Roberto Estecio Hui Ling Ciprian Tomuleasa Delia Dima Hui Yang Hector Alvarez M. James You Milan Radovich Elizabeth Shpall Muller Fabbri Katy Rezvani Leonard Girnita Ioana Berindan-Neagoe Anirban Maitra Srdan Verstovsek Riccardo Fodde
    ...[+35 authors]...,
    Carlos Bueso-Ramos
    Mihai Gagea
    Guillermo Garcia Manero
    George A. Calin
    First Published March 22, 2018
  - Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
    David Thybert
    Maša Roller
    Fábio C.P. Navarro
    Ian Fiddes
    Ian Streeter
    Christine Feig David Martin-Galvez Mikhail Kolmogorov Václav Janoušek Wasiu Akanni Bronwen Aken Sarah Aldridge Varshith Chakrapani William Chow Laura Clarke Carla Cummins Anthony Doran Matthew Dunn Leo Goodstadt Kerstin Howe Matthew Howell Ambre-Aurore Josselin Robert C. Karn Christina M. Laukaitis Lilue Jingtao Fergal Martin Matthieu Muffato Stefanie Nachtweide Michael A. Quail Cristina Sisu Mario Stanke Klara Stefflova Cock Van Oosterhout Frederic Veyrunes Ben Ward Fengtang Yang Golbahar Yazdanifar Amonida Zadissa David J. Adams Alvis Brazma Mark Gerstein Benedict Paten
    ...[+37 authors]...,
    Son Pham
    Thomas M. Keane
    Duncan T. Odom
    Paul Flicek
    First Published March 21, 2018
  - Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
    Antoine Molaro
    Janet M. Young
    Harmit S. Malik
    First Published March 16, 2018
  - Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution
    Sahin Naqvi
    Daniel W. Bellott
    Kathy S. Lin
    David C. Page
    First Published February 15, 2018
  - Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
    Bradford H. Casey
    Rahul K. Kollipara
    Karine Pozo
    Jane E. Johnson
    First Published March 2, 2018
  - Genome-wide determinants of sequence-specific DNA binding of general regulatory factors
    Matthew J. Rossi
    William K.M. Lai
    B. Franklin Pugh
    First Published March 21, 2018
  - Promoter architecture determines cotranslational regulation of mRNA
    Lorena Espinar
    Miquel Àngel Schikora Tamarit
    Júlia Domingo
    Lucas B. Carey
    First Published March 22, 2018
  - Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
    Charles J. Underwood
    Kyuha Choi
    Christophe Lambing
    Xiaohui Zhao
    Heïdi Serra
    Filipe Borges Joe Simorowski
    ...[+2 authors]...,
    Evan Ernst
    Yannick Jacob
    Ian R. Henderson
    Robert A. Martienssen
    First Published March 12, 2018
  - Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
    Kyuha Choi
    Xiaohui Zhao
    Andrew J. Tock
    Christophe Lambing
    Charles J. Underwood
    Thomas J. Hardcastle Heïdi Serra Juhyun Kim Hyun Seob Cho Jaeil Kim Piotr A. Ziolkowski
    ...[+6 authors]...,
    Nataliya E. Yelina
    Ildoo Hwang
    Robert A. Martienssen
    Ian R. Henderson
    First Published March 12, 2018
  - Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
    Ulrike Böhme
    Thomas D. Otto
    James A. Cotton
    Sascha Steinbiss
    Mandy Sanders
    Samuel O. Oyola Antoine Nicot Sylvain Gandon Kailash P. Patra Colin Herd Ellen Bushell Katarzyna K. Modrzynska Oliver Billker
    ...[+8 authors]...,
    Joseph M. Vinetz
    Ana Rivero
    Chris I. Newbold
    Matthew Berriman
    First Published March 2, 2018
  - Selective maternal seeding and environment shape the human gut microbiome
    Katri Korpela
    Paul Costea
    Luis Pedro Coelho
    Stefanie Kandels-Lewis
    Gonneke Willemsen
    First Published March 1, 2018
Methods
- - Genome-reconstruction for eukaryotes from complex natural microbial communities
    Patrick T. West
    Alexander J. Probst
    Igor V. Grigoriev
    Brian C. Thomas
    Jillian F. Banfield
    First Published March 1, 2018
  - SvABA: genome-wide detection of structural variants and indels by local assembly
    Jeremiah A. Wala
    Pratiti Bandopadhayay
    Noah F. Greenwald
    Ryan O'Rourke
    Ted Sharpe
    Chip Stewart Steve Schumacher Yilong Li Joachim Weischenfeldt Xiaotong Yao Chad Nusbaum Peter Campbell Gad Getz
    ...[+8 authors]...,
    Matthew Meyerson
    Cheng-Zhong Zhang
    Marcin Imielinski
    Rameen Beroukhim
    First Published March 13, 2018
  - Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo
    Luca Tosti
    James Ashmore
    Boon Siang Nicholas Tan
    Benedetta Carbone
    Tapan K. Mistri
    First Published March 23, 2018
Corrigenda
- - Corrigendum: Direct determination of diploid genome sequences
    Neil I. Weisenfeld
    Vijay Kumar
    Preyas Shah
    Deanna M. Church
    David B. Jaffe
    First Published April 2, 2018
  - Corrigendum: Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast
    Vahid Aslanzadeh
    Yuanhua Huang
    Guido Sanguinetti
    Jean D. Beggs
    First Published April 2, 2018

Table of Contents

Volume 28, Issue 4 | April 2018

Research

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia

Cancer-associated rs6983267 SNP and its accompanying long noncoding RNA CCAT2 induce myeloid malignancies via unique SNP-specific RNA mutations

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals

Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution

Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors

Genome-wide determinants of sequence-specific DNA binding of general regulatory factors

Promoter architecture determines cotranslational regulation of mRNA

Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation

Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

Selective maternal seeding and environment shape the human gut microbiome

Methods

Genome-reconstruction for eukaryotes from complex natural microbial communities

SvABA: genome-wide detection of structural variants and indels by local assembly

Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo

Corrigenda

Corrigendum: Direct determination of diploid genome sequences

Corrigendum: Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

Table of Contents

Volume 28, Issue 4 | April 2018

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Research

Methods

Corrigenda