Volume 23, Issue 1 | January 2013

Research
- - Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing
    Gaetano Ivan Dellino
    Davide Cittaro
    Rossana Piccioni
    Lucilla Luzi
    Stefania Banfi
    Simona Segalla
    ...[+1 authors]...,
    Matteo Cesaroni
    Ramiro Mendoza-Maldonado
    Mauro Giacca
    Pier Giuseppe Pelicci
    First Published November 27, 2012
  - GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility
    Vasiliki Theodorou
    Rory Stark
    Suraj Menon
    Jason S. Carroll
    First Published November 21, 2012
  - Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder
    Przemyslaw Szafranski
    Avinash V. Dharmadhikari
    Erwin Brosens
    Priyatansh Gurha
    Katarzyna E. Kołodziejska
    Ou Zhishuo Piotr Dittwald Tadeusz Majewski K. Naga Mohan Bo Chen Richard E. Person Dick Tibboel Annelies de Klein Jason Pinner Maya Chopra Girvan Malcolm Gregory Peters Susan Arbuckle Sixto F. Guiang Virginia A. Hustead Jose Jessurun Russel Hirsch David P. Witte Isabelle Maystadt Neil Sebire
    ...[+20 authors]...,
    Richard Fisher
    Claire Langston
    Partha Sen
    Paweł Stankiewicz
    First Published October 3, 2012
  - Birth and expression evolution of mammalian microRNA genes
    Julien Meunier
    Frédéric Lemoine
    Magali Soumillon
    Angélica Liechti
    Manuela Weier
    First Published October 3, 2012
  - Evolutionary dynamism of the primate LRRC37 gene family
    Giuliana Giannuzzi
    Priscillia Siswara
    Maika Malig
    Tomas Marques-Bonet
    James C. Mullikin
    First Published October 11, 2012
  - Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
    Phil Arnold
    Anne Schöler
    Mikhail Pachkov
    Piotr J. Balwierz
    Helle Jørgensen
    First Published September 10, 2012
  - Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions
    Marina Naval-Sánchez
    Delphine Potier
    Lotte Haagen
    Máximo Sánchez
    Sebastian Munck
    First Published October 15, 2012
  - A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
    Tina T. Hu
    Michael B. Eisen
    Kevin R. Thornton
    Peter Andolfatto
    First Published August 30, 2012
  - Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
    Viola Nolte
    Ram Vinay Pandey
    Robert Kofler
    Christian Schlötterer
    First Published October 10, 2012
  - Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
    Itai Sharon
    Michael J. Morowitz
    Brian C. Thomas
    Elizabeth K. Costello
    David A. Relman
    First Published August 30, 2012
Methods
- - Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene
    Erick W. Loomis
    John S. Eid
    Paul Peluso
    Jun Yin
    Luke Hickey
    David Rank
    ...[+1 authors]...,
    Sarah McCalmon
    Randi J. Hagerman
    Flora Tassone
    Paul J. Hagerman
    First Published October 11, 2012
  - Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
    Eric E. Schadt
    Onureena Banerjee
    Gang Fang
    Zhixing Feng
    Wing H. Wong
    Xuegong Zhang Andrey Kislyuk Tyson A. Clark Khai Luong Alona Keren-Paz Andrew Chess Vipin Kumar
    ...[+7 authors]...,
    Alice Chen-Plotkin
    Neal Sondheimer
    Jonas Korlach
    Andrew Kasarskis
    First Published October 23, 2012
  - Genotype calling and haplotyping in parent-offspring trios
    Wei Chen
    Bingshan Li
    Zhen Zeng
    Serena Sanna
    Carlo Sidore
    First Published October 11, 2012
  - Haplotype-based profiling of subtle allelic imbalance with SNP arrays
    Selina Vattathil
    Paul Scheet
    First Published October 1, 2012
  - Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases
    Christine Merlin
    Lauren E. Beaver
    Orley R. Taylor
    Scot A. Wolfe
    Steven M. Reppert
    First Published September 25, 2012
  - High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
    Philippe Batut
    Alexander Dobin
    Charles Plessy
    Piero Carninci
    Thomas R. Gingeras
    First Published August 30, 2012
  - P-value-based regulatory motif discovery using positional weight matrices
    Holger Hartmann
    Eckhart W. Guthöhrlein
    Matthias Siebert
    Sebastian Luehr
    Johannes Söding
    First Published September 18, 2012
Resources
- - SOAPindel: Efficient identification of indels from short paired reads
    Shengting Li
    Ruiqiang Li
    Heng Li
    Jianliang Lu
    Yingrui Li
    First Published September 12, 2012
  - RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development
    Meng How Tan
    Kin Fai Au
    Arielle L. Yablonovitch
    Andrea E. Wills
    Jason Chuang
    First Published September 7, 2012

Table of Contents

Volume 23, Issue 1 | January 2013

Research

Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder

Birth and expression evolution of mammalian microRNA genes

Evolutionary dynamism of the primate LRRC37 gene family

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

Methods

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

Genotype calling and haplotyping in parent-offspring trios

Haplotype-based profiling of subtle allelic imbalance with SNP arrays

Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

P-value-based regulatory motif discovery using positional weight matrices

Resources

SOAPindel: Efficient identification of indels from short paired reads

RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

Table of Contents

Volume 23, Issue 1 | January 2013

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Research

Methods

Resources