Table of Contents

Research

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The landscape of genomic imprinting across diverse adult human tissues
- Yael Baran,
- Meena Subramaniam,
- Anne Biton,
- Taru Tukiainen,
- Emily K. Tsang,
- Manuel A. Rivas,
- Matti Pirinen,
- Maria Gutierrez-Arcelus,
- Kevin S. Smith,
- Kim R. Kukurba,
- Rui Zhang,
- Celeste Eng,
- Dara G. Torgerson,
- Cydney Urbanek,
- the GTEx Consortium,
- Jin Billy Li,
- Jose R. Rodriguez-Santana,
- Esteban G. Burchard,
- Max A. Seibold,
- Daniel G. MacArthur,
- Stephen B. Montgomery,
- Noah A. Zaitlen,
- and Tuuli Lappalainen
Genome Res. July 2015 25: 927-936; Published in Advance May 7, 2015, doi:10.1101/gr.192278.115
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Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis
- Brooke Weckselblatt,
- Karen E. Hermetz,
- and M. Katharine Rudd
Genome Res. July 2015 25: 937-947; Published in Advance June 12, 2015, doi:10.1101/gr.191247.115
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Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders
- Heather Fairfield,
- Anuj Srivastava,
- Guruprasad Ananda,
- Rangjiao Liu,
- Martin Kircher,
- Anuradha Lakshminarayana,
- Belinda S. Harris,
- Son Yong Karst,
- Louise A. Dionne,
- Coleen C. Kane,
- Michelle Curtain,
- Melissa L. Berry,
- Patricia F. Ward-Bailey,
- Ian Greenstein,
- Candice Byers,
- Anne Czechanski,
- Jocelyn Sharp,
- Kristina Palmer,
- Polyxeni Gudis,
- Whitney Martin,
- Abby Tadenev,
- Laurent Bogdanik,
- C. Herbert Pratt,
- Bo Chang,
- David G. Schroeder,
- Gregory A. Cox,
- Paul Cliften,
- Jeffrey Milbrandt,
- Stephen Murray,
- Robert Burgess,
- David E. Bergstrom,
- Leah Rae Donahue,
- Hanan Hamamy,
- Amira Masri,
- Federico A. Santoni,
- Periklis Makrythanasis,
- Stylianos E. Antonarakis,
- Jay Shendure,
- and Laura G. Reinholdt
Genome Res. July 2015 25: 948-957; Published in Advance April 27, 2015, doi:10.1101/gr.186882.114
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Characterization and dynamics of pericentromere-associated domains in mice
- Patrick J. Wijchers,
- Geert Geeven,
- Michael Eyres,
- Atze J. Bergsma,
- Mark Janssen,
- Marjon Verstegen,
- Yun Zhu,
- Yori Schell,
- Carlo Vermeulen,
- Elzo de Wit,
- and Wouter de Laat
Genome Res. July 2015 25: 958-969; Published in Advance April 16, 2015, doi:10.1101/gr.186643.114
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Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
- Mirte Bosse,
- Hendrik-Jan Megens,
- Ole Madsen,
- Richard P.M.A. Crooijmans,
- Oliver A. Ryder,
- Frédéric Austerlitz,
- Martien A.M. Groenen,
- and M. Angeles R. de Cara
Genome Res. July 2015 25: 970-981; Published in Advance June 10, 2015, doi:10.1101/gr.187039.114
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Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites in C. elegans
- James Matthew Ragle,
- Sol Katzman,
- Taylor F. Akers,
- Sergio Barberan-Soler,
- and Alan M. Zahler
Genome Res. July 2015 25: 982-994; Published in Advance April 28, 2015, doi:10.1101/gr.186783.114
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Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
- Yamile Marquez,
- Markus Höpfler,
- Zahra Ayatollahi,
- Andrea Barta,
- and Maria Kalyna
Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
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Core promoter sequence in yeast is a major determinant of expression level
- Shai Lubliner,
- Ifat Regev,
- Maya Lotan-Pompan,
- Sarit Edelheit,
- Adina Weinberger,
- and Eran Segal
Genome Res. July 2015 25: 1008-1017; Published in Advance May 12, 2015, doi:10.1101/gr.188193.114

Methods

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Unraveling determinants of transcription factor binding outside the core binding site
- Michal Levo,
- Einat Zalckvar,
- Eilon Sharon,
- Ana Carolina Dantas Machado,
- Yael Kalma,
- Maya Lotam-Pompan,
- Adina Weinberger,
- Zohar Yakhini,
- Remo Rohs,
- and Eran Segal
Genome Res. July 2015 25: 1018-1029; Published in Advance March 11, 2015, doi:10.1101/gr.185033.114
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High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
- Gaurav K. Varshney,
- Wuhong Pei,
- Matthew C. LaFave,
- Jennifer Idol,
- Lisha Xu,
- Viviana Gallardo,
- Blake Carrington,
- Kevin Bishop,
- MaryPat Jones,
- Mingyu Li,
- Ursula Harper,
- Sunny C. Huang,
- Anupam Prakash,
- Wenbiao Chen,
- Raman Sood,
- Johan Ledin,
- and Shawn M. Burgess
Genome Res. July 2015 25: 1030-1042; Published in Advance June 5, 2015, doi:10.1101/gr.186379.114
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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- Donovan H. Parks,
- Michael Imelfort,
- Connor T. Skennerton,
- Philip Hugenholtz,
- and Gene W. Tyson
Genome Res. July 2015 25: 1043-1055; Published in Advance May 14, 2015, doi:10.1101/gr.186072.114
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Resources

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Using populations of human and microbial genomes for organism detection in metagenomes
- Sasha K. Ames,
- Shea N. Gardner,
- Jose Manuel Marti,
- Tom R. Slezak,
- Maya B. Gokhale,
- and Jonathan E. Allen
Genome Res. July 2015 25: 1056-1067; Published in Advance April 29, 2015, doi:10.1101/gr.184879.114
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The landscape of antisense gene expression in human cancers
- O. Alejandro Balbin,
- Rohit Malik,
- Saravana M. Dhanasekaran,
- John R. Prensner,
- Xuhong Cao,
- Yi-Mi Wu,
- Dan Robinson,
- Rui Wang,
- Guoan Chen,
- David G. Beer,
- Alexey I. Nesvizhskii,
- and Arul M. Chinnaiyan
Genome Res. July 2015 25: 1068-1079; Published in Advance June 10, 2015, doi:10.1101/gr.180596.114

Research

The landscape of genomic imprinting across diverse adult human tissues

Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis

Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders

Characterization and dynamics of pericentromere-associated domains in mice

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites in C. elegans

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity

Core promoter sequence in yeast is a major determinant of expression level

Methods

Unraveling determinants of transcription factor binding outside the core binding site

High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Resources

Using populations of human and microbial genomes for organism detection in metagenomes

The landscape of antisense gene expression in human cancers

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