Volume 23, Issue 11 | November 2013

Research
- - Hominoid fission of chromosome 14/15 and the role of segmental duplications
    Giuliana Giannuzzi
    Michele Pazienza
    John Huddleston
    Francesca Antonacci
    Maika Malig
    First Published September 27, 2013
  - Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins
    Larry D. Mesner
    Veena Valsakumar
    Marcin Cieślik
    Rebecca Pickin
    Joyce L. Hamlin
    First Published July 16, 2013
  - RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA
    Dan Bar-Yaacov
    Gal Avital
    Liron Levin
    Allison L. Richards
    Naomi Hachen
    First Published August 2, 2013
  - Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer
    Sven Bilke
    Raphaela Schwentner
    Fan Yang
    Maximilian Kauer
    Gunhild Jug
    Robert L. Walker Sean Davis
    ...[+2 authors]...,
    Yuelin J. Zhu
    Marbin Pineda
    Paul S. Meltzer
    Heinrich Kovar
    First Published August 12, 2013
  - The evolution of evolvability in microRNA target sites in vertebrates
    Jin Xu
    Rui Zhang
    Yang Shen
    Guojing Liu
    Xuemei Lu
    First Published September 27, 2013
  - Genome-wide evidence for speciation with gene flow in Heliconius butterflies
    Simon H. Martin
    Kanchon K. Dasmahapatra
    Nicola J. Nadeau
    Camilo Salazar
    James R. Walters
    Fraser Simpson
    ...[+1 authors]...,
    Mark Blaxter
    Andrea Manica
    James Mallet
    Chris D. Jiggins
    First Published September 17, 2013
  - High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
    Houssam Hajjoul
    Julien Mathon
    Hubert Ranchon
    Isabelle Goiffon
    Julien Mozziconacci
    Benjamin Albert Pascal Carrivain
    ...[+2 authors]...,
    Jean-Marc Victor
    Olivier Gadal
    Kerstin Bystricky
    Aurélien Bancaud
    First Published September 27, 2013
  - A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen
    Sung Ho Yoon
    Serdar Turkarslan
    David J. Reiss
    Min Pan
    June A. Burn
    Kyle C. Costa Thomas J. Lie Joseph Slagel
    ...[+3 authors]...,
    Robert L. Moritz
    Murray Hackett
    John A. Leigh
    Nitin S. Baliga
    First Published October 2, 2013
Methods
- - Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
    Filipe G. Vieira
    Matteo Fumagalli
    Anders Albrechtsen
    Rasmus Nielsen
    First Published August 15, 2013
  - Defining cell-type specificity at the transcriptional level in human disease
    Wenjun Ju
    Casey S. Greene
    Felix Eichinger
    Viji Nair
    Jeffrey B. Hodgin
    Markus Bitzer Young-suk Lee Qian Zhu Masami Kehata Min Li Song Jiang
    ...[+6 authors]...,
    Maria Pia Rastaldi
    Clemens D. Cohen
    Olga G. Troyanskaya
    Matthias Kretzler
    First Published August 15, 2013
  - Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations
    Rachael J.M. Bashford-Rogers
    Anne L. Palser
    Brian J. Huntly
    Richard Rance
    George S. Vassiliou
    First Published June 6, 2013
  - Analysis and correction of crosstalk effects in pathway analysis
    Michele Donato
    Zhonghui Xu
    Alin Tomoiaga
    James G. Granneman
    Robert G. MacKenzie
    Riyue Bao
    ...[+1 authors]...,
    Nandor Gabor Than
    Peter H. Westfall
    Roberto Romero
    Sorin Draghici
    First Published August 9, 2013
  - Efficient identification of Y chromosome sequences in the human and Drosophila genomes
    Antonio Bernardo Carvalho
    Andrew G. Clark
    First Published August 6, 2013
  - Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants
    Ilaria Mogno
    Jamie C. Kwasnieski
    Barak A. Cohen
    First Published August 6, 2013
  - Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
    Ulrich Omasits
    Maxime Quebatte
    Daniel J. Stekhoven
    Claudia Fortes
    Bernd Roschitzki
    First Published July 22, 2013
Resources
- - Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
    Pablo Meyer
    Geoffrey Siwo
    Danny Zeevi
    Eilon Sharon
    Raquel Norel
    Eran Segal Gustavo Stolovitzky Geoffrey Siwo Andrew K. Rider Asako Tan Richard S. Pinapati Scott Emrich Nitesh Chawla Michael T. Ferdig Yi-An Tung Yong-Syuan Chen Mei-Ju May Chen Chien-Yu Chen Jason M. Knight Sayed Mohammad Ebrahim Sahraeian Mohammad Shahrokh Esfahani Rene Dreos Philipp Bucher Ezekiel Maier Yvan Saeys Ewa Szczurek Alena Myšičková Martin Vingron Holger Klein Szymon M. Kiełbasa Jeff Knisley Jeff Bonnell Debra Knisley Miron B. Kursa Witold R. Rudnicki Madhuchhanda Bhattacharjee Mikko J. Sillanpää James Yeung Pieter Meysman Aminael Sánchez Rodríguez Kristof Engelen Kathleen Marchal Yezhou Huang
    ...[+38 authors]...,
    Fantine Mordelet
    Alexander Hartemink
    Luca Pinello
    Guo-Cheng Yuan
    First Published August 15, 2013
  - Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
    Chirag Nepal
    Yavor Hadzhiev
    Christopher Previti
    Vanja Haberle
    Nan Li
    Hazuki Takahashi Ana Maria M. Suzuki Ying Sheng Rehab F. Abdelhamid Santosh Anand Jochen Gehrig Altuna Akalin Christel E.M. Kockx Antoine A.J. van der Sloot Wilfred F.J. van IJcken Olivier Armant Sepand Rastegar Craig Watson Uwe Strähle
    ...[+14 authors]...,
    Elia Stupka
    Piero Carninci
    Boris Lenhard
    Ferenc Müller
    First Published September 3, 2013
  - Honey bee protein atlas at organ-level resolution
    Queenie W.T. Chan
    Man Yi Chan
    Michelle Logan
    Yuan Fang
    Heather Higo
    First Published July 22, 2013

Table of Contents

Volume 23, Issue 11 | November 2013

Research

Hominoid fission of chromosome 14/15 and the role of segmental duplications

Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins

RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA

Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer

The evolution of evolvability in microRNA target sites in vertebrates

Genome-wide evidence for speciation with gene flow in Heliconius butterflies

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

Methods

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

Defining cell-type specificity at the transcriptional level in human disease

Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations

Analysis and correction of crosstalk effects in pathway analysis

Efficient identification of Y chromosome sequences in the human and Drosophila genomes

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

Resources

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

Honey bee protein atlas at organ-level resolution

Table of Contents

Volume 23, Issue 11 | November 2013

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Research

Methods

Resources