Volume 25, Issue 11 | November 2015

Research
- - Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
    Tugce Bilgin Sonay
    Tiago Carvalho
    Mark D. Robinson
    Maja P. Greminger
    Michael Krützen
    David Comas Gareth Highnam
    ...[+2 authors]...,
    David Mittelman
    Andrew Sharp
    Tomàs Marques-Bonet
    Andreas Wagner
    First Published August 19, 2015
  - GC skew defines distinct RNA polymerase pause sites in CpG island promoters
    Wendy A. Kellner
    Joshua S.K. Bell
    Paula M. Vertino
    First Published August 14, 2015
  - Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
    Can Cenik
    Elif Sarinay Cenik
    Gun W. Byeon
    Fabian Grubert
    Sophie I. Candille
    Damek Spacek Bilal Alsallakh Hagen Tilgner
    ...[+3 authors]...,
    Carlos L. Araya
    Hua Tang
    Emiliano Ricci
    Michael P. Snyder
    First Published August 21, 2015
  - DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts
    Teresa Szczepińska
    Katarzyna Kalisiak
    Rafal Tomecki
    Anna Labno
    Lukasz S. Borowski
    First Published August 20, 2015
  - Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background
    Ingegerd Elvers
    Jason Turner-Maier
    Ross Swofford
    Michele Koltookian
    Jeremy Johnson
    Chip Stewart Cheng-Zhong Zhang Steven E. Schumacher Rameen Beroukhim Mara Rosenberg Rachael Thomas Evan Mauceli Gad Getz Federica Di Palma
    ...[+9 authors]...,
    Jaime F. Modiano
    Matthew Breen
    Kerstin Lindblad-Toh
    Jessica Alföldi
    First Published September 16, 2015
  - Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor
    Brennan Decker
    Brian W. Davis
    Maud Rimbault
    Adrienne H. Long
    Eric Karlins
    Vidhya Jagannathan Rebecca Reiman Heidi G. Parker Cord Drögemüller Jason J. Corneveaux Erica S. Chapman Jeffery M. Trent Tosso Leeb
    ...[+8 authors]...,
    Matthew J. Huentelman
    Robert K. Wayne
    Danielle M. Karyadi
    Elaine A. Ostrander
    First Published July 31, 2015
  - Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
    Reto Burri
    Alexander Nater
    Takeshi Kawakami
    Carina F. Mugal
    Pall I. Olason
    Linnea Smeds Alexander Suh Ludovic Dutoit Stanislav Bureš Laszlo Z. Garamszegi Silje Hogner Juan Moreno Anna Qvarnström Milan Ružić
    ...[+9 authors]...,
    Stein-Are Sæther
    Glenn-Peter Sætre
    Janos Török
    Hans Ellegren
    First Published September 9, 2015
  - An extended family of novel vertebrate photopigments is widely expressed and displays a diversity of function
    Wayne I.L. Davies
    T. Katherine Tamai
    Lei Zheng
    Josephine K. Fu
    Jason Rihel
    First Published October 8, 2015
  - Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans
    Deni Subasic
    Anneke Brümmer
    Yibo Wu
    Sérgio Morgado Pinto
    Jochen Imig
    Martin Keller Marko Jovanovic Helen Louise Lightfoot Sara Nasso Sandra Goetze Erich Brunner
    ...[+6 authors]...,
    Jonathan Hall
    Ruedi Aebersold
    Mihaela Zavolan
    Michael O. Hengartner
    First Published July 31, 2015
  - Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila
    Marcus H. Stoiber
    Sara Olson
    Gemma E. May
    Michael O. Duff
    Jan Manent
    Robert Obar K.G. Guruharsha Peter J. Bickel
    ...[+3 authors]...,
    Spyros Artavanis-Tsakonas
    James B. Brown
    Brenton R. Graveley
    Susan E. Celniker
    First Published August 20, 2015
  - Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
    Yujia Sun
    Chung-Yi Nien
    Kai Chen
    Hsiao-Yun Liu
    Jeff Johnston
    First Published September 2, 2015
  - Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo
    Katharine N. Schulz
    Eliana R. Bondra
    Arbel Moshe
    Jacqueline E. Villalta
    Jason D. Lieb
    First Published September 2, 2015
  - DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome
    Leslie Y. Beh
    Manuel M. Müller
    Tom W. Muir
    Noam Kaplan
    Laura F. Landweber
    First Published September 1, 2015
  - Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
    Rob W. Ness
    Andrew D. Morgan
    Radhakrishnan B. Vasanthakrishnan
    Nick Colegrave
    Peter D. Keightley
    First Published August 10, 2015
Methods
- - Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
    Sara Goodwin
    James Gurtowski
    Scott Ethe-Sayers
    Panchajanya Deshpande
    Michael C. Schatz
    First Published October 7, 2015
  - Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
    Alicia N. Schep
    Jason D. Buenrostro
    Sarah K. Denny
    Katja Schwartz
    Gavin Sherlock
    First Published August 27, 2015
Resource
- - Regulation of alternative splicing in Drosophila by 56 RNA binding proteins
    Angela N. Brooks
    Michael O. Duff
    Gemma May
    Li Yang
    Mohan Bolisetty
    Jane Landolin Ken Wan Jeremy Sandler
    ...[+3 authors]...,
    Benjamin W. Booth
    Susan E. Celniker
    Brenton R. Graveley
    Steven E. Brenner
    First Published August 20, 2015

Table of Contents

Volume 25, Issue 11 | November 2015

Research

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

GC skew defines distinct RNA polymerase pause sites in CpG island promoters

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts

Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background

Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers

An extended family of novel vertebrate photopigments is widely expressed and displays a diversity of function

Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans

Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii

Methods

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

Resource

Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

Table of Contents

Volume 25, Issue 11 | November 2015

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Research

Methods

Resource