Volume 24, Issue 2 | February 2014

Research
- - Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization
    Kasper D. Hansen
    Sarven Sabunciyan
    Ben Langmead
    Noemi Nagy
    Rebecca Curley
    First Published September 25, 2013
  - Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
    Keiko Akagi
    Jingfeng Li
    Tatevik R. Broutian
    Hesed Padilla-Nash
    Weihong Xiao
    Bo Jiang James W. Rocco Theodoros N. Teknos Bhavna Kumar Danny Wangsa
    ...[+5 authors]...,
    Dandan He
    Thomas Ried
    David E. Symer
    Maura L. Gillison
    First Published November 7, 2013
  - Genomic and transcriptomic plasticity in treatment-naïve ovarian cancer
    Marlous Hoogstraat
    Mirjam S. de Pagter
    Geert A. Cirkel
    Markus J. van Roosmalen
    Timothy T. Harkins
    Karen Duran Jennifer Kreeftmeijer Ivo Renkens Petronella O. Witteveen Clarence C. Lee Isaac J. Nijman Tanisha Guy Ruben van ’t Slot Trudy N. Jonges Martijn P. Lolkema Marco J. Koudijs
    ...[+11 authors]...,
    Ronald P. Zweemer
    Emile E. Voest
    Edwin Cuppen
    Wigard P. Kloosterman
    First Published November 12, 2013
  - Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
    Pedro G. Ferreira
    Pedro Jares
    Daniel Rico
    Gonzalo Gómez-López
    Alejandra Martínez-Trillos
    Neus Villamor Simone Ecker Abel González-Pérez David G. Knowles Jean Monlong Rory Johnson Victor Quesada Sarah Djebali Panagiotis Papasaikas Mónica López-Guerra Dolors Colomer Cristina Royo Maite Cazorla Magda Pinyol Guillem Clot Marta Aymerich Maria Rozman Marta Kulis David Tamborero Anaïs Gouin Julie Blanc Marta Gut Ivo Gut Xose S. Puente David G. Pisano José Ignacio Martin-Subero Nuria López-Bigas Armando López-Guillermo
    ...[+28 authors]...,
    Alfonso Valencia
    Carlos López-Otín
    Elías Campo
    Roderic Guigó
    First Published November 21, 2013
  - An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease
    Farhoud Faraji
    Ying Hu
    Gang Wu
    Natalie E. Goldberger
    Renard C. Walker
    First Published December 9, 2013
  - Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
    Jeremy M. Simon
    Kathryn E. Hacker
    Darshan Singh
    A. Rose Brannon
    Joel S. Parker
    Matthew Weiser Thai H. Ho Pei-Fen Kuan Eric Jonasch Terrence S. Furey
    ...[+5 authors]...,
    Jan F. Prins
    Jason D. Lieb
    W. Kimryn Rathmell
    Ian J. Davis
    First Published October 24, 2013
  - The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed
    Brittany S. Sexton
    Denis Avey
    Brooke R. Druliner
    Justin A. Fincher
    Daniel L. Vera
    Daniel J. Grau Mark L. Borowsky Shobhit Gupta Senthil B. Girimurugan Eric Chicken Jinfeng Zhang
    ...[+6 authors]...,
    William S. Noble
    Fanxiu Zhu
    Robert E. Kingston
    Jonathan H. Dennis
    First Published December 5, 2013
  - Canonical nucleosome organization at promoters forms during genome activation
    Yong Zhang
    Nadine L. Vastenhouw
    Jianxing Feng
    Kai Fu
    Chenfei Wang
    Ying Ge
    ...[+1 authors]...,
    Andrea Pauli
    Paul van Hummelen
    Alexander F. Schier
    X. Shirley Liu
    First Published November 27, 2013
  - Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells
    Timothy J. Looney
    Li Zhang
    Chih-Hsin Chen
    Jae Hyun Lee
    Sheila Chari
    Frank Fuxiang Mao Mattia Pelizzola Lu Zhang Ryan Lister Samuel W. Baker Croydon J. Fernandes Jedidiah Gaetz Kara M. Foshay Kayla L. Clift Zhenyu Zhang Wei-Qiang Li Eric J. Vallender Ulrich Wagner Jane Yuxia Qin Katelyn J. Michelini Branimir Bugarija Donghyun Park Emmanuel Aryee Thomas Stricker Jie Zhou Kevin P. White Bing Ren
    ...[+22 authors]...,
    Gary P. Schroth
    Joseph R. Ecker
    Andy Peng Xiang
    Bruce T. Lahn
    First Published December 5, 2013
  - Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network
    Marcos Simões-Costa
    Joanne Tan-Cabugao
    Igor Antoshechkin
    Tatjana Sauka-Spengler
    Marianne E. Bronner
    First Published January 3, 2014
  - Genomic analysis of primordial dwarfism reveals novel disease genes
    Ranad Shaheen
    Eissa Faqeih
    Shinu Ansari
    Ghada Abdel-Salam
    Zuhair N. Al-Hassnan
    First Published January 3, 2014
Methods
- - Discovery of recurrent structural variants in nasopharyngeal carcinoma
    Anton Valouev
    Ziming Weng
    Robert T. Sweeney
    Sushama Varma
    Quynh-Thu Le
    First Published November 8, 2013
  - TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
    Ken Chen
    Lei Chen
    Xian Fan
    John Wallis
    Li Ding
    First Published December 4, 2013
  - Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations
    Anand Patel
    Richard Schwab
    Yu-Tsueng Liu
    Vineet Bafna
    First Published December 4, 2013
  - Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma
    Nancy H. Nabilsi
    Loic P. Deleyrolle
    Russell P. Darst
    Alberto Riva
    Brent A. Reynolds
    First Published October 8, 2013
Resources
- - Improved exome prioritization of disease genes through cross-species phenotype comparison
    Peter N. Robinson
    Sebastian Köhler
    Anika Oellrich
    Kai Wang
    Christopher J. Mungall
    Suzanna E. Lewis Nicole Washington Sebastian Bauer Dominik Seelow
    ...[+4 authors]...,
    Peter Krawitz
    Christian Gilissen
    Melissa Haendel
    Damian Smedley
    First Published October 25, 2013
  - Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster
    Federico A. Santoni
    Periklis Makrythanasis
    Sergey Nikolaev
    Michel Guipponi
    Daniel Robyr
    First Published January 3, 2014
  - Variation Ontology for annotation of variation effects and mechanisms
    Mauno Vihinen
    First Published October 25, 2013

Table of Contents

Volume 24, Issue 2 | February 2014

Research

Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalization

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

Genomic and transcriptomic plasticity in treatment-naïve ovarian cancer

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease

Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects

The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed

Canonical nucleosome organization at promoters forms during genome activation

Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells

Transcriptome analysis reveals novel players in the cranial neural crest gene regulatory network

Genomic analysis of primordial dwarfism reveals novel disease genes

Methods

Discovery of recurrent structural variants in nasopharyngeal carcinoma

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations

Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma

Resources

Improved exome prioritization of disease genes through cross-species phenotype comparison

Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster

Variation Ontology for annotation of variation effects and mechanisms

Table of Contents

Volume 24, Issue 2 | February 2014

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Research

Methods

Resources