Volume 22, Issue 11 | November 2012

Perspectives
- - Genetic basis of kidney cancer: Role of genomics for the development of disease-based therapeutics
    W. Marston Linehan
    First Published October 4, 2012
  - Translating genomic information into clinical medicine: Lung cancer as a paradigm
    Mia A. Levy
    Christine M. Lovly
    William Pao
    First Published September 27, 2012
Research
- - The transcriptional landscape and mutational profile of lung adenocarcinoma
    Jeong-Sun Seo
    Young Seok Ju
    Won-Chul Lee
    Jong-Yeon Shin
    June Koo Lee
    Thomas Bleazard Junho Lee Yoo Jin Jung Jung-Oh Kim Jung-Young Shin Saet-Byeol Yu Jihye Kim Eung-Ryoung Lee Chang-Hyun Kang In-Kyu Park Hwanseok Rhee
    ...[+11 authors]...,
    Se-Hoon Lee
    Jong-Il Kim
    Jin-Hyoung Kang
    Young Tae Kim
    First Published September 13, 2012
  - Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer
    Han Liang
    Lydia W.T. Cheung
    Jie Li
    Zhenlin Ju
    Shuangxing Yu
    Katherine Stemke-Hale Turgut Dogruluk Yiling Lu Xiuping Liu Chao Gu Wei Guo Steven E. Scherer Hannah Carter Shannon N. Westin Mary D. Dyer Roeland G.W. Verhaak Fan Zhang Rachel Karchin Chang-Gong Liu Karen H. Lu
    ...[+15 authors]...,
    Russell R. Broaddus
    Kenneth L. Scott
    Bryan T. Hennessy
    Gordon B. Mills
    First Published October 1, 2012
  - A functional methylome map of ulcerative colitis
    Robert Häsler
    Zhe Feng
    Liselotte Bäckdahl
    Martina E. Spehlmann
    Andre Franke
    Andrew Teschendorff Vardhman K. Rakyan Thomas A. Down Gareth A. Wilson
    ...[+4 authors]...,
    Andrew Feber
    Stephan Beck
    Stefan Schreiber
    Philip Rosenstiel
    First Published July 23, 2012
  - Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans
    Huriya Beyan
    Thomas A. Down
    Sreeram V. Ramagopalan
    Kristina Uvebrant
    Anita Nilsson
    Michelle L. Holland Carolina Gemma Gavin Giovannoni Bernhard O. Boehm George C. Ebers
    ...[+5 authors]...,
    Åke Lernmark
    Corrado M. Cilio
    R. David Leslie
    Vardhman K. Rakyan
    First Published August 23, 2012
  - Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood
    Simone S. Stahringer
    Jose C. Clemente
    Robin P. Corley
    John Hewitt
    Dan Knights
    First Published October 12, 2012
  - Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner
    Jason Gertz
    Timothy E. Reddy
    Katherine E. Varley
    Michael J. Garabedian
    Richard M. Myers
    First Published September 26, 2012
  - Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
    Andre J. Faure
    Dominic Schmidt
    Stephen Watt
    Petra C. Schwalie
    Michael D. Wilson
    First Published July 10, 2012
  - Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains
    Kevin Van Bortle
    Edward Ramos
    Naomi Takenaka
    Jingping Yang
    Jessica E. Wahi
    First Published June 21, 2012
  - Nature and function of insulator protein binding sites in the Drosophila genome
    Yuri B. Schwartz
    Daniela Linder-Basso
    Peter V. Kharchenko
    Michael Y. Tolstorukov
    Maria Kim
    Hua-Bing Li Andrey A. Gorchakov Aki Minoda Gregory Shanower Artyom A. Alekseyenko Nicole C. Riddle Youngsook L. Jung Tingting Gu Annette Plachetka Sarah C.R. Elgin Mitzi I. Kuroda
    ...[+11 authors]...,
    Peter J. Park
    Mikhail Savitsky
    Gary H. Karpen
    Vincenzo Pirrotta
    First Published July 5, 2012
  - The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species
    Jingping Yang
    Edward Ramos
    Victor G. Corces
    First Published August 15, 2012
  - Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
    Claudia Fritsch
    Alexander Herrmann
    Michael Nothnagel
    Karol Szafranski
    Klaus Huse
    Frank Schumann Stefan Schreiber
    ...[+2 authors]...,
    Matthias Platzer
    Michael Krawczak
    Jochen Hampe
    Mario Brosch
    First Published August 9, 2012
Methods
- - Observation of dually decoded regions of the human genome using ribosome profiling data
    Audrey M. Michel
    Kingshuk Roy Choudhury
    Andrew E. Firth
    Nicholas T. Ingolia
    John F. Atkins
    First Published May 16, 2012
  - Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease
    Snehit Prabhu
    Itsik Pe'er
    First Published July 5, 2012
  - Paired-end sequencing of Fosmid libraries by Illumina
    Louise J.S. Williams
    Diana G. Tabbaa
    Na Li
    Aaron M. Berlin
    Terrance P. Shea
    Iain MacCallum Michael S. Lawrence Yotam Drier Gad Getz
    ...[+4 authors]...,
    Sarah K. Young
    David B. Jaffe
    Chad Nusbaum
    Andreas Gnirke
    First Published July 16, 2012
  - nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
    Andrew McPherson
    Chunxiao Wu
    Alexander W. Wyatt
    Sohrab Shah
    Colin Collins
    First Published June 28, 2012
  - Spark: A navigational paradigm for genomic data exploration
    Cydney B. Nielsen
    Hamid Younesy
    Henriette O'Geen
    Xiaoqin Xu
    Andrew R. Jackson
    Aleksandar Milosavljevic Ting Wang
    ...[+2 authors]...,
    Joseph F. Costello
    Martin Hirst
    Peggy J. Farnham
    Steven J.M. Jones
    First Published September 7, 2012
  - Finished bacterial genomes from shotgun sequence data
    Filipe J. Ribeiro
    Dariusz Przybylski
    Shuangye Yin
    Ted Sharpe
    Sante Gnerre
    Amr Abouelleil Aaron M. Berlin Anna Montmayeur Terrance P. Shea Bruce J. Walker Sarah K. Young
    ...[+6 authors]...,
    Carsten Russ
    Chad Nusbaum
    Iain MacCallum
    David B. Jaffe
    First Published July 24, 2012
  - Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control
    Grzegorz M. Burzynski
    Xylena Reed
    Leila Taher
    Zachary E. Stine
    Takeshi Matsui
    First Published July 3, 2012
  - Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
    David U. Gorkin
    Dongwon Lee
    Xylena Reed
    Christopher Fletez-Brant
    Seneca L. Bessling
    First Published September 27, 2012
Resource
- - A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers
    Christopher L. Plaisier
    Min Pan
    Nitin S. Baliga
    First Published June 28, 2012

Table of Contents

Volume 22, Issue 11 | November 2012

Perspectives

Genetic basis of kidney cancer: Role of genomics for the development of disease-based therapeutics

Translating genomic information into clinical medicine: Lung cancer as a paradigm

Research

The transcriptional landscape and mutational profile of lung adenocarcinoma

Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer

A functional methylome map of ulcerative colitis

Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

Nature and function of insulator protein binding sites in the Drosophila genome

The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

Methods

Observation of dually decoded regions of the human genome using ribosome profiling data

Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease

Paired-end sequencing of Fosmid libraries by Illumina

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

Spark: A navigational paradigm for genomic data exploration

Finished bacterial genomes from shotgun sequence data

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes

Resource

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

Table of Contents

Volume 22, Issue 11 | November 2012

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Perspectives

Research

Methods

Resource