Volume 24, Issue 10 | October 2014

Research
- - Systems consequences of amplicon formation in human breast cancer
    Koichiro Inaki
    Francesca Menghi
    Xing Yi Woo
    Joel P. Wagner
    Pierre-Étienne Jacques
    Yi Fang Lee Phung Trang Shreckengast Wendy WeiJia Soon Ankit Malhotra Audrey S.M. Teo Axel M. Hillmer Alexis Jiaying Khng Xiaoan Ruan Swee Hoe Ong Denis Bertrand
    ...[+10 authors]...,
    Niranjan Nagarajan
    R. Krishna Murthy Karuturi
    Alfredo Hidalgo Miranda
    Edison T. Liu
    First Published September 3, 2014
  - Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate
    Gilad Fuchs
    Dror Hollander
    Yoav Voichek
    Gil Ast
    Moshe Oren
    First Published July 21, 2014
  - The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity
    Kristina Ivanauskiene
    Erwan Delbarre
    James D. McGhie
    Thomas Küntziger
    Lee H. Wong
    First Published July 21, 2014
  - High-throughput functional testing of ENCODE segmentation predictions
    Jamie C. Kwasnieski
    Christopher Fiore
    Hemangi G. Chaudhari
    Barak A. Cohen
    First Published July 17, 2014
  - T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity
    Asaf Madi
    Eric Shifrut
    Shlomit Reich-Zeliger
    Hilah Gal
    Katharine Best
    First Published July 14, 2014
  - Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways
    Weishi Yu
    Carl McIntosh
    Ryan Lister
    Iris Zhu
    Yixing Han
    Jianke Ren David Landsman Eunice Lee Victorino Briones
    ...[+4 authors]...,
    Minoru Terashima
    Robert Leighty
    Joseph R. Ecker
    Kathrin Muegge
    First Published August 28, 2014
  - C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency
    Bettina Meier
    Susanna L. Cooke
    Joerg Weiss
    Aymeric P. Bailly
    Ludmil B. Alexandrov
    John Marshall Keiran Raine Mark Maddison
    ...[+3 authors]...,
    Elizabeth Anderson
    Michael R. Stratton
    Anton Gartner
    Peter J. Campbell
    First Published July 16, 2014
  - RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast
    Dwaipayan Ganguli
    Răzvan V. Chereji
    James R. Iben
    Hope A. Cole
    David J. Clark
    First Published July 11, 2014
  - Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome
    Kyle R. Fowler
    Mariko Sasaki
    Neta Milman
    Scott Keeney
    Gerald R. Smith
    First Published July 14, 2014
  - Differential retention and divergent resolution of duplicate genes following whole-genome duplication
    Casey L. McGrath
    Jean-Francois Gout
    Parul Johri
    Thomas G. Doak
    Michael Lynch
    First Published August 1, 2014
  - Genomic analysis of the causative agents of coccidiosis in domestic chickens
    Adam J. Reid
    Damer P. Blake
    Hifzur R. Ansari
    Karen Billington
    Hilary P. Browne
    Josephine Bryant Matt Dunn Stacy S. Hung Fumiya Kawahara Diego Miranda-Saavedra Tareq B. Malas Tobias Mourier Hardeep Naghra Mridul Nair Thomas D. Otto Neil D. Rawlings Pierre Rivailler Alejandro Sanchez-Flores Mandy Sanders Chandra Subramaniam Yea-Ling Tay Yong Woo Xikun Wu Bart Barrell Paul H. Dear Christian Doerig Arthur Gruber Alasdair C. Ivens John Parkinson Marie-Adèle Rajandream Martin W. Shirley
    ...[+26 authors]...,
    Kiew-Lian Wan
    Matthew Berriman
    Fiona M. Tomley
    Arnab Pain
    First Published July 11, 2014
Methods
- - Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
    Antonio L.C. Gomes
    Thomas Abeel
    Matthew Peterson
    Elham Azizi
    Anna Lyubetskaya
    First Published July 14, 2014
  - Probing the effect of promoters on noise in gene expression using thousands of designed sequences
    Eilon Sharon
    David van Dijk
    Yael Kalma
    Leeat Keren
    Ohad Manor
    First Published July 16, 2014
  - Large-scale identification of chemically induced mutations in Drosophila melanogaster
    Nele A. Haelterman
    Lichun Jiang
    Yumei Li
    Vafa Bayat
    Hector Sandoval
    Berrak Ugur Kai Li Tan Ke Zhang Danqing Bei Bo Xiong Wu-Lin Charng Theodore Busby Adeel Jawaid Gabriela David Manish Jaiswal
    ...[+10 authors]...,
    Koen J.T. Venken
    Shinya Yamamoto
    Rui Chen
    Hugo J. Bellen
    First Published September 25, 2014
Resource
- - OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines
    Jonathan L. Schmid-Burgk
    Tobias Schmidt
    Moritz M. Gaidt
    Karin Pelka
    Eicke Latz
    First Published September 3, 2014

Table of Contents

Volume 24, Issue 10 | October 2014

Research

Systems consequences of amplicon formation in human breast cancer

Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate

The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity

High-throughput functional testing of ENCODE segmentation predictions

T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways

C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency

RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast

Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome

Differential retention and divergent resolution of duplicate genes following whole-genome duplication

Genomic analysis of the causative agents of coccidiosis in domestic chickens

Methods

Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

Large-scale identification of chemically induced mutations in Drosophila melanogaster

Resource

OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines

Table of Contents

Volume 24, Issue 10 | October 2014

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Research

Methods

Resource