Table of Contents

Research

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A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes
- Lily Bazak,
- Ami Haviv,
- Michal Barak,
- Jasmine Jacob-Hirsch,
- Patricia Deng,
- Rui Zhang,
- Farren J. Isaacs,
- Gideon Rechavi,
- Jin Billy Li,
- Eli Eisenberg,
- and Erez Y. Levanon
Genome Res. March 2014 24: 365-376; Published in Advance December 17, 2013, doi:10.1101/gr.164749.113
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The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages
- Musa A. Hassan,
- Vincent Butty,
- Kirk D.C. Jensen,
- and Jeroen P.J. Saeij
Genome Res. March 2014 24: 377-389; Published in Advance November 18, 2013, doi:10.1101/gr.166033.113
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Functional and topological characteristics of mammalian regulatory domains
- Orsolya Symmons,
- Veli Vural Uslu,
- Taro Tsujimura,
- Sandra Ruf,
- Sonya Nassari,
- Wibke Schwarzer,
- Laurence Ettwiller,
- and François Spitz
Genome Res. March 2014 24: 390-400; Published in Advance January 7, 2014, doi:10.1101/gr.163519.113
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Principles of nucleation of H3K27 methylation during embryonic development
- Simon J. van Heeringen,
- Robert C. Akkers,
- Ila van Kruijsbergen,
- M. Asif Arif,
- Lars L.P. Hanssen,
- Nilofar Sharifi,
- and Gert Jan C. Veenstra
Genome Res. March 2014 24: 401-410; Published in Advance December 11, 2013, doi:10.1101/gr.159608.113
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Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
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Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
- C. Joel McManus,
- Gemma E. May,
- Pieter Spealman,
- and Alan Shteyman
Genome Res. March 2014 24: 422-430; Published in Advance December 6, 2013, doi:10.1101/gr.164996.113
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Regulatory modules controlling maize inflorescence architecture
- Andrea L. Eveland,
- Alexander Goldshmidt,
- Michael Pautler,
- Kengo Morohashi,
- Christophe Liseron-Monfils,
- Michael W. Lewis,
- Sunita Kumari,
- Susumu Hiraga,
- Fang Yang,
- Erica Unger-Wallace,
- Andrew Olson,
- Sarah Hake,
- Erik Vollbrecht,
- Erich Grotewold,
- Doreen Ware,
- and David Jackson
Genome Res. March 2014 24: 431-443; Published in Advance December 4, 2013, doi:10.1101/gr.166397.113
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Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
- Huan Wang,
- Pil Joong Chung,
- Jun Liu,
- In-Cheol Jang,
- Michelle J. Kean,
- Jun Xu,
- and Nam-Hai Chua
Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113

Methods

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Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
- Jakob Skou Pedersen,
- Eivind Valen,
- Amhed M. Vargas Velazquez,
- Brian J. Parker,
- Morten Rasmussen,
- Stinus Lindgreen,
- Berit Lilje,
- Desmond J. Tobin,
- Theresa K. Kelly,
- Søren Vang,
- Robin Andersson,
- Peter A. Jones,
- Cindi A. Hoover,
- Alexei Tikhonov,
- Egor Prokhortchouk,
- Edward M. Rubin,
- Albin Sandelin,
- M. Thomas P. Gilbert,
- Anders Krogh,
- Eske Willerslev,
- and Ludovic Orlando
Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
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A fine-scale recombination map of the human–chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion
- Kasper Munch,
- Thomas Mailund,
- Julien Y. Dutheil,
- and Mikkel Heide Schierup
Genome Res. March 2014 24: 467-474; Published in Advance November 4, 2013, doi:10.1101/gr.158469.113
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Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
- Yi-Chieh Wu,
- Matthew D. Rasmussen,
- Mukul S. Bansal,
- and Manolis Kellis
Genome Res. March 2014 24: 475-486; Published in Advance December 5, 2013, doi:10.1101/gr.161968.113
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A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates
- José Bessa,
- Mario Luengo,
- Solangel Rivero-Gil,
- Ana Ariza-Cosano,
- António H.F. Maia,
- Francisco J. Ruiz-Ruano,
- Pablo Caballero,
- Silvia Naranjo,
- Jaime J. Carvajal,
- and José Luis Gómez-Skarmeta
Genome Res. March 2014 24: 487-495; Published in Advance November 25, 2013, doi:10.1101/gr.165654.113
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From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
- Georgi K. Marinov,
- Brian A. Williams,
- Ken McCue,
- Gary P. Schroth,
- Jason Gertz,
- Richard M. Myers,
- and Barbara J. Wold
Genome Res. March 2014 24: 496-510; Published in Advance December 3, 2013, doi:10.1101/gr.161034.113
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Resources

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Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin
- Pierre Mallinjoud,
- Jean-Philippe Villemin,
- Hussein Mortada,
- Micaela Polay Espinoza,
- François-Olivier Desmet,
- Samaan Samaan,
- Emilie Chautard,
- Léon-Charles Tranchevent,
- and Didier Auboeuf
Genome Res. March 2014 24: 511-521; Published in Advance December 4, 2013, doi:10.1101/gr.162933.113
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A biochemical landscape of A-to-I RNA editing in the human brain transcriptome
- Masayuki Sakurai,
- Hiroki Ueda,
- Takanori Yano,
- Shunpei Okada,
- Hideki Terajima,
- Toutai Mitsuyama,
- Atsushi Toyoda,
- Asao Fujiyama,
- Hitomi Kawabata,
- and Tsutomu Suzuki
Genome Res. March 2014 24: 522-534; Published in Advance January 9, 2014, doi:10.1101/gr.162537.113
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An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa
- Rosaria Scozzari,
- Andrea Massaia,
- Beniamino Trombetta,
- Giovanna Bellusci,
- Natalie M. Myres,
- Andrea Novelletto,
- and Fulvio Cruciani
Genome Res. March 2014 24: 535-544; Published in Advance January 6, 2014, doi:10.1101/gr.160788.113

Research

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

Functional and topological characteristics of mammalian regulatory domains

Principles of nucleation of H3K27 methylation during embryonic development

Evolution at two levels of gene expression in yeast

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

Regulatory modules controlling maize inflorescence architecture

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

Methods

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

A fine-scale recombination map of the human–chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

Resources

Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin

A biochemical landscape of A-to-I RNA editing in the human brain transcriptome

An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

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