Table of Contents

Methods

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Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
- Gavin Ha,
- Andrew Roth,
- Daniel Lai,
- Ali Bashashati,
- Jiarui Ding,
- Rodrigo Goya,
- Ryan Giuliany,
- Jamie Rosner,
- Arusha Oloumi,
- Karey Shumansky,
- Suet-Feung Chin,
- Gulisa Turashvili,
- Martin Hirst,
- Carlos Caldas,
- Marco A. Marra,
- Samuel Aparicio,
- and Sohrab P. Shah
Genome Res. October 2012 22: 1995-2007; Published in Advance May 25, 2012, doi:10.1101/gr.137570.112
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Detecting differential usage of exons from RNA-seq data
- Simon Anders,
- Alejandro Reyes,
- and Wolfgang Huber
Genome Res. October 2012 22: 2008-2017; Published in Advance June 21, 2012, doi:10.1101/gr.133744.111
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Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
- J. Omar Yáñez-Cuna,
- Huy Q. Dinh,
- Evgeny Z. Kvon,
- Daria Shlyueva,
- and Alexander Stark
Genome Res. October 2012 22: 2018-2030; Published in Advance April 25, 2012, doi:10.1101/gr.132811.111
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Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution
- Lukas Windhager,
- Thomas Bonfert,
- Kaspar Burger,
- Zsolt Ruzsics,
- Stefan Krebs,
- Stefanie Kaufmann,
- Georg Malterer,
- Anne L'Hernault,
- Markus Schilhabel,
- Stefan Schreiber,
- Philip Rosenstiel,
- Ralf Zimmer,
- Dirk Eick,
- Caroline C. Friedel,
- and Lars Dölken
Genome Res. October 2012 22: 2031-2042; Published in Advance April 26, 2012, doi:10.1101/gr.131847.111

Resources

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Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
- Ozren Bogdanović,
- Ana Fernandez-Miñán,
- Juan J. Tena,
- Elisa de la Calle-Mustienes,
- Carmen Hidalgo,
- Ila van Kruysbergen,
- Simon J. van Heeringen,
- Gert Jan C. Veenstra,
- and José Luis Gómez-Skarmeta
Genome Res. October 2012 22: 2043-2053; Published in Advance May 16, 2012, doi:10.1101/gr.134833.111
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Extensive alternative polyadenylation during zebrafish development
- Igor Ulitsky,
- Alena Shkumatava,
- Calvin H. Jan,
- Alexander O. Subtelny,
- David Koppstein,
- George W. Bell,
- Hazel Sive,
- and David P. Bartel
Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
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Incorporating RNA-seq data into the zebrafish Ensembl genebuild
- John E. Collins,
- Simon White,
- Stephen M.J. Searle,
- and Derek L. Stemple
Genome Res. October 2012 22: 2067-2078; Published in Advance July 12, 2012, doi:10.1101/gr.137901.112
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Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis
- Qiang Tu,
- R. Andrew Cameron,
- Kim C. Worley,
- Richard A. Gibbs,
- and Eric H. Davidson
Genome Res. October 2012 22: 2079-2087; Published in Advance June 18, 2012, doi:10.1101/gr.139170.112

Erratum

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Erratum
Genome Res. October 2012 22: 2088

Research

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia

Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors

Random X inactivation in the mule and horse placenta

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

piRNA-mediated transgenerational inheritance of an acquired trait

Exploring the DNA-recognition potential of homeodomains

Dynamic landscape of tandem 3′ UTRs during zebrafish development

Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity

Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity

Maintaining replication origins in the face of genomic change

Conservation of replication timing reveals global and local regulation of replication origin activity

Natural genetic variation in yeast longevity

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

Methods

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

Detecting differential usage of exons from RNA-seq data

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

Resources

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

Extensive alternative polyadenylation during zebrafish development

Incorporating RNA-seq data into the zebrafish Ensembl genebuild

Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis

Erratum

Erratum

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