Volume 24, Issue 12 | December 2014

Research
- - Genome-wide map of regulatory interactions in the human genome
    Nastaran Heidari
    Douglas H. Phanstiel
    Chao He
    Fabian Grubert
    Fereshteh Jahanbani
    First Published September 16, 2014
  - Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia
    Stephen N. Sansom
    Noriko Shikama-Dorn
    Saule Zhanybekova
    Gretel Nusspaumer
    Iain C. Macaulay
    First Published September 15, 2014
  - Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis
    Maxim Pimkin
    Andrew V. Kossenkov
    Tejaswini Mishra
    Christapher S. Morrissey
    Weisheng Wu
    Cheryl A. Keller Gerd A. Blobel
    ...[+2 authors]...,
    Dongwon Lee
    Michael A. Beer
    Ross C. Hardison
    Mitchell J. Weiss
    First Published October 15, 2014
  - Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
    Weisheng Wu
    Christapher S. Morrissey
    Cheryl A. Keller
    Tejaswini Mishra
    Maxim Pimkin
    First Published October 15, 2014
  - Widespread contribution of transposable elements to the innovation of gene regulatory networks
    Vasavi Sundaram
    Yong Cheng
    Zhihai Ma
    Daofeng Li
    Xiaoyun Xing
    First Published October 15, 2014
  - Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures
    Yuliya A. Sytnikova
    Reazur Rahman
    Gung-wei Chirn
    Josef P. Clark
    Nelson C. Lau
    First Published September 29, 2014
  - Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
    Danny Zeevi
    Shai Lubliner
    Maya Lotan-Pompan
    Eran Hodis
    Rita Vesterman
    First Published October 7, 2014
  - Heritable variation of mRNA decay rates in yeast
    Jennifer M. Andrie
    Jon Wakefield
    Joshua M. Akey
    First Published September 25, 2014
  - Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation
    Carlo G. Artieri
    Hunter B. Fraser
    First Published October 7, 2014
Methods
- - DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly
    Ilari Scheinin
    Daoud Sie
    Henrik Bengtsson
    Mark A. van de Wiel
    Adam B. Olshen
    Hinke F. van Thuijl Hendrik F. van Essen Paul P. Eijk François Rustenburg Gerrit A. Meijer Jaap C. Reijneveld
    ...[+6 authors]...,
    Pieter Wesseling
    Daniel Pinkel
    Donna G. Albertson
    Bauke Ylstra
    First Published September 18, 2014
  - Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
    Simone Picelli
    Åsa K. Björklund
    Björn Reinius
    Sven Sagasser
    Gösta Winberg
    First Published July 30, 2014
  - In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
    Andrew Adey
    Jacob O. Kitzman
    Joshua N. Burton
    Riza Daza
    Akash Kumar
    Lena Christiansen Mostafa Ronaghi
    ...[+2 authors]...,
    Sasan Amini
    Kevin L. Gunderson
    Frank J. Steemers
    Jay Shendure
    First Published October 19, 2014
  - A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness
    Panagiotis Katsonis
    Olivier Lichtarge
    First Published September 12, 2014
  - Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line
    Patrick Essletzbichler
    Tomasz Konopka
    Federica Santoro
    Doris Chen
    Bianca V. Gapp
    First Published November 4, 2014
Resources
- - Single haplotype assembly of the human genome from a hydatidiform mole
    Karyn Meltz Steinberg
    Valerie A. Schneider
    Tina A. Graves-Lindsay
    Robert S. Fulton
    Richa Agarwala
    John Huddleston Sergey A. Shiryev Aleksandr Morgulis Urvashi Surti
    ...[+4 authors]...,
    Wesley C. Warren
    Deanna M. Church
    Evan E. Eichler
    Richard K. Wilson
    First Published November 4, 2014
  - Alignathon: a competitive assessment of whole-genome alignment methods
    Dent Earl
    Ngan Nguyen
    Glenn Hickey
    Robert S. Harris
    Stephen Fitzgerald
    Kathryn Beal Igor Seledtsov Vladimir Molodtsov Brian J. Raney Hiram Clawson Jaebum Kim Carsten Kemena Jia-Ming Chang Ionas Erb Alexander Poliakov Minmei Hou Javier Herrero William James Kent Victor Solovyev Aaron E. Darling Jian Ma Cedric Notredame
    ...[+17 authors]...,
    Michael Brudno
    Inna Dubchak
    David Haussler
    Benedict Paten
    First Published October 1, 2014
Author Index
- - Author Index, Volume 24, 2014
    First Published December 1, 2014
Reviewer Index
- - Reviewer Index, Volume 24, 2014
    First Published December 1, 2014

Table of Contents

Volume 24, Issue 12 | December 2014

Research

Genome-wide map of regulatory interactions in the human genome

Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis

Widespread contribution of transposable elements to the innovation of gene regulatory networks

Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures

Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters

Heritable variation of mRNA decay rates in yeast

Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

Methods

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line

Resources

Single haplotype assembly of the human genome from a hydatidiform mole

Alignathon: a competitive assessment of whole-genome alignment methods

Author Index

Author Index, Volume 24, 2014

Reviewer Index

Reviewer Index, Volume 24, 2014

Table of Contents

Volume 24, Issue 12 | December 2014

Share this issue

Research

Methods

Resources

Author Index

Reviewer Index