Table of Contents

Research

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Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation
- Clara Y. Cheong,
- Keefe Chng,
- Shilen Ng,
- Siew Boom Chew,
- Louiza Chan,
- and Anne C. Ferguson-Smith
Genome Res. May 2015 25: 611-623; Published in Advance April 10, 2015, doi:10.1101/gr.183301.114
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Evidence for widespread subfunctionalization of splice forms in vertebrate genomes
- Matthew J. Lambert,
- Wayne O. Cochran,
- Brandon M. Wilde,
- Kyle G. Olsen,
- and Cynthia D. Cooper
Genome Res. May 2015 25: 624-632; Published in Advance March 19, 2015, doi:10.1101/gr.184473.114
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Global variability in gene expression and alternative splicing is modulated by mitochondrial content
- Raul Guantes,
- Alberto Rastrojo,
- Ricardo Neves,
- Ana Lima,
- Begoña Aguado,
- and Francisco J. Iborra
Genome Res. May 2015 25: 633-644; Published in Advance March 23, 2015, doi:10.1101/gr.178426.114
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Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans
- Éric Zampini,
- Étienne Lepage,
- Samuel Tremblay-Belzile,
- Sébastien Truche,
- and Normand Brisson
Genome Res. May 2015 25: 645-654; Published in Advance March 23, 2015, doi:10.1101/gr.188573.114
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Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells
- Jennifer Y. Tan,
- Tamara Sirey,
- Frantisek Honti,
- Bryony Graham,
- Allison Piovesan,
- Matthias Merkenschlager,
- Caleb Webber,
- Chris P. Ponting,
- and Ana C. Marques
Genome Res. May 2015 25: 655-666; Published in Advance March 19, 2015, doi:10.1101/gr.181974.114
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Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
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New signaling pathways govern the host response to C. albicans infection in various niches
- Yaoping Liu,
- Amol C. Shetty,
- Jennifer A. Schwartz,
- L. Latey Bradford,
- Wenjie Xu,
- Qyunh T. Phan,
- Priti Kumari,
- Anup Mahurkar,
- Aaron P. Mitchell,
- Jacques Ravel,
- Claire M. Fraser,
- Scott G. Filler,
- and Vincent M. Bruno
Genome Res. May 2015 25: 679-689; Published in Advance April 9, 2015, doi:10.1101/gr.187427.114

Methods

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Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation
- Ezekiel J. Maier,
- Brian C. Haynes,
- Stacey R. Gish,
- Zhuo A. Wang,
- Michael L. Skowyra,
- Alyssa L. Marulli,
- Tamara L. Doering,
- and Michael R. Brent
Genome Res. May 2015 25: 690-700; Published in Advance February 2, 2015, doi:10.1101/gr.184101.114
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Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity
- Martin Stroedicke,
- Yacine Bounab,
- Nadine Strempel,
- Konrad Klockmeier,
- Sargon Yigit,
- Ralf P. Friedrich,
- Gautam Chaurasia,
- Shuang Li,
- Franziska Hesse,
- Sean-Patrick Riechers,
- Jenny Russ,
- Cecilia Nicoletti,
- Annett Boeddrich,
- Thomas Wiglenda,
- Christian Haenig,
- Sigrid Schnoegl,
- David Fournier,
- Rona K. Graham,
- Michael R. Hayden,
- Stephan Sigrist,
- Gillian P. Bates,
- Josef Priller,
- Miguel A. Andrade-Navarro,
- Matthias E. Futschik,
- and Erich E. Wanker
Genome Res. May 2015 25: 701-713; Published in Advance April 23, 2015, doi:10.1101/gr.182444.114
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Optimizing sparse sequencing of single cells for highly multiplex copy number profiling
- Timour Baslan,
- Jude Kendall,
- Brian Ward,
- Hilary Cox,
- Anthony Leotta,
- Linda Rodgers,
- Michael Riggs,
- Sean D'Italia,
- Guoli Sun,
- Mao Yong,
- Kristy Miskimen,
- Hannah Gilmore,
- Michael Saborowski,
- Nevenka Dimitrova,
- Alexander Krasnitz,
- Lyndsay Harris,
- Michael Wigler,
- and James Hicks
Genome Res. May 2015 25: 714-724; Published in Advance April 9, 2015, doi:10.1101/gr.188060.114
OPEN ACCESS ARTICLE
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Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins
- Michael S. Foulk,
- John M. Urban,
- Cinzia Casella,
- and Susan A. Gerbi
Genome Res. May 2015 25: 725-735; Published in Advance February 18, 2015, doi:10.1101/gr.183848.114
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Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
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MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
- Keisha D. Carlson,
- Peter H. Sudmant,
- Maximilian O. Press,
- Evan E. Eichler,
- Jay Shendure,
- and Christine Queitsch
Genome Res. May 2015 25: 750-761; Published in Advance February 6, 2015, doi:10.1101/gr.182212.114

Resource

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The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen
- Pooja K. Strope,
- Daniel A. Skelly,
- Stanislav G. Kozmin,
- Gayathri Mahadevan,
- Eric A. Stone,
- Paul M. Magwene,
- Fred S. Dietrich,
- and John H. McCusker
Genome Res. May 2015 25: 762-774; Published in Advance April 3, 2015, doi:10.1101/gr.185538.114

Research

Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation

Evidence for widespread subfunctionalization of splice forms in vertebrate genomes

Global variability in gene expression and alternative splicing is modulated by mitochondrial content

Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans

Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis

New signaling pathways govern the host response to C. albicans infection in various niches

Methods

Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation

Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling

Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

Resource

The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

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