Volume 27, Issue 6 | June 2017

Perspective
- - Moving beyond Bermuda: sharing data to build a medical information commons
    Robert Cook-Deegan
    Amy L. McGuire
    First Published April 3, 2017
Research
- - A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy
    Ayesha Noorani
    Jan Bornschein
    Andy G. Lynch
    Maria Secrier
    Achilleas Achilleos
    Matthew Eldridge Lawrence Bower Jamie M.J. Weaver Jason Crawte Chin-Ann Ong Nicholas Shannon Shona MacRae Nicola Grehan Barbara Nutzinger Maria O'Donovan Richard Hardwick Simon Tavaré Rebecca C. Fitzgerald Rachael Fels Elliott Paul A.W. Edwards Xiaodun Li Hamza Chettouh Gianmarco Contini Eleanor Gregson Sebastian Zeki Laura Smith Zarah Abdullahi Rachel de la Rue Ahmad Miremadi Shalini Malhotra Mike L. Smith Jim Davies Charles Crichton Nick Carroll Peter Safranek Andrew Hindmarsh Vijayendran Sujendran Richard Turkington Stephen J. Hayes Yeng Ang Shaun R. Preston Sarah Oakes Izhar Bagwan Vicki Save Richard J.E. Skipworth Ted R. Hupp J. Robert O'Neill Olga Tucker Andrew Beggs Philippe Taniere Sonia Puig Timothy J. Underwood Fergus Noble Jack Owsley Hugh Barr Neil Shepherd Oliver Old Jesper Lagergren James Gossage Andrew Davies Fuju Chang Janine Zylstra Grant Sanders Richard Berrisford Catherine Harden David Bunting Mike Lewis Ed Cheong Bhaskar Kumar Simon L. Parsons John Saunders Irshad Soomro Philip Kaye Laurence Lovat Rehan Haidry Victor Eneh Laszlo Igali Ian M. Welch Michael Scott Shamila Sothi Sari Suortamo Suzy Lishman Anna Grabowska
    ...[+78 authors]...,
    Christopher J. Peters
    George B. Hanna
    David Khoo
    Duncan Beardsmore
    First Published May 2, 2017
  - PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX
    Erwan Delbarre
    Kristina Ivanauskiene
    Jane Spirkoski
    Akshay Shah
    Kristin Vekterud
    Jan Øivind Moskaug
    ...[+1 authors]...,
    Stig Ove Bøe
    Lee H. Wong
    Thomas Küntziger
    Philippe Collas
    First Published March 24, 2017
  - Small chromosomal regions position themselves autonomously according to their chromatin class
    Harmen J.G. van de Werken
    Josien C. Haan
    Yana Feodorova
    Dominika Bijos
    An Weuts
    Koen Theunis Sjoerd J.B. Holwerda Wouter Meuleman Ludo Pagie Katharina Thanisch Parveen Kumar Heinrich Leonhardt Peter Marynen Bas van Steensel
    ...[+9 authors]...,
    Thierry Voet
    Wouter de Laat
    Irina Solovei
    Boris Joffe
    First Published March 24, 2017
  - Combinatorial DNA methylation codes at repetitive elements
    Christophe Papin
    Abdulkhaleg Ibrahim
    Stéphanie Le Gras
    Amandine Velt
    Isabelle Stoll
    Bernard Jost
    ...[+1 authors]...,
    Hervé Menoni
    Christian Bronner
    Stefan Dimitrov
    Ali Hamiche
    First Published March 27, 2017
  - Cytosine modifications modulate the chromatin architecture of transcriptional enhancers
    Elise A. Mahé
    Thierry Madigou
    Aurélien A. Sérandour
    Maud Bizot
    Stéphane Avner
    First Published April 10, 2017
  - Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice
    Michael C. Saul
    Christopher H. Seward
    Joseph M. Troy
    Huimin Zhang
    Laura G. Sloofman
    Xiaochen Lu Patricia A. Weisner Derek Caetano-Anolles Hao Sun
    ...[+4 authors]...,
    Sihai Dave Zhao
    Sriram Chandrasekaran
    Saurabh Sinha
    Lisa Stubbs
    First Published March 29, 2017
  - Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock
    François Mange
    Viviane Praz
    Eugenia Migliavacca
    Ian M. Willis
    Frédéric Schütz
    Nouria Hernandez Nouria Hernandez Mauro Delorenzi Bart Deplancke Béatrice Desvergne Nicolas Guex Winship Herr Felix Naef Jacques Rougemont Ueli Schibler Teemu Andersin Pascal Cousin Federica Gilardi Fabienne Lammers François Mange Dominic Villeneuve Fabrice David Roberto Fabbretti Philippe Jacquet Irina Krier Dmitry Kuznetsov Marion Leleu Robin Liechti Olivier Martin Eugenia Migliavacca Aurélien Naldi Viviane Praz
    ...[+27 authors]...,
    Leonor Rib
    Jonathan Sobel
    Volker Vlegel
    Ioannis Xenarios
    First Published March 24, 2017
  - The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions
    Julie Dubois-Chevalier
    Vanessa Dubois
    Hélène Dehondt
    Parisa Mazrooei
    Claire Mazuy
    Aurélien A. Sérandour Céline Gheeraert Penderia Guillaume Eric Baugé Bruno Derudas Nathalie Hennuyer Réjane Paumelle Guillemette Marot Jason S. Carroll
    ...[+9 authors]...,
    Mathieu Lupien
    Bart Staels
    Philippe Lefebvre
    Jérôme Eeckhoute
    First Published April 11, 2017
  - Speciation network in Laurasiatheria: retrophylogenomic signals
    Liliya Doronina
    Gennady Churakov
    Andrej Kuritzin
    Jingjing Shi
    Robert Baertsch
    First Published March 15, 2017
  - Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
    Fan Han
    Sangeet Lamichhaney
    B. Rosemary Grant
    Peter R. Grant
    Leif Andersson
    First Published April 25, 2017
  - Less effective selection leads to larger genomes
    Tristan Lefébure
    Claire Morvan
    Florian Malard
    Clémentine François
    Lara Konecny-Dupré
    Laurent Guéguen Michèle Weiss-Gayet Andaine Seguin-Orlando Luca Ermini Clio Der Sarkissian N. Pierre Charrier David Eme Florian Mermillod-Blondin
    ...[+8 authors]...,
    Laurent Duret
    Cristina Vieira
    Ludovic Orlando
    Christophe Jean Douady
    First Published April 19, 2017
  - Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice
    Hongru Wang
    Filipe G. Vieira
    Jacob E. Crawford
    Chengcai Chu
    Rasmus Nielsen
    First Published April 6, 2017
Methods
- - Short template switch events explain mutation clusters in the human genome
    Ari Löytynoja
    Nick Goldman
    First Published April 6, 2017
  - High-confidence coding and noncoding transcriptome maps
    Bo-Hyun You
    Sang-Ho Yoon
    Jin-Wu Nam
    First Published April 10, 2017
  - RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases
    László Halász
    Zsolt Karányi
    Beáta Boros-Oláh
    Tímea Kuik-Rózsa
    Éva Sipos
    Éva Nagy Ágnes Mosolygó-L
    ...[+2 authors]...,
    Anett Mázló
    Éva Rajnavölgyi
    Gábor Halmos
    Lóránt Székvölgyi
    First Published March 24, 2017
  - Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum
    Heather J. Painter
    Manuela Carrasquilla
    Manuel Llinás
    First Published April 17, 2017
Resource
- - Identification of protein features encoded by alternative exons using Exon Ontology
    Léon-Charles Tranchevent
    Fabien Aubé
    Louis Dulaurier
    Clara Benoit-Pilven
    Amandine Rey
    Arnaud Poret Emilie Chautard Hussein Mortada François-Olivier Desmet Fatima Zahra Chakrama Maira Alejandra Moreno-Garcia Evelyne Goillot
    ...[+7 authors]...,
    Stéphane Janczarski
    Franck Mortreux
    Cyril F. Bourgeois
    Didier Auboeuf
    First Published April 18, 2017

Table of Contents

Volume 27, Issue 6 | June 2017

Perspective

Moving beyond Bermuda: sharing data to build a medical information commons

Research

A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy

PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX

Small chromosomal regions position themselves autonomously according to their chromatin class

Combinatorial DNA methylation codes at repetitive elements

Cytosine modifications modulate the chromatin architecture of transcriptional enhancers

Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice

Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock

The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions

Speciation network in Laurasiatheria: retrophylogenomic signals

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Less effective selection leads to larger genomes

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

Methods

Short template switch events explain mutation clusters in the human genome

High-confidence coding and noncoding transcriptome maps

RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases

Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum

Resource

Identification of protein features encoded by alternative exons using Exon Ontology

Table of Contents

Volume 27, Issue 6 | June 2017

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Perspective

Research

Methods

Resource