Table of Contents

Research

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Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation
- Amanda J. Price,
- Taeyoung Hwang,
- Ran Tao,
- Emily E. Burke,
- Anandita Rajpurohit,
- Joo Heon Shin,
- Thomas M. Hyde,
- Joel E. Kleinman,
- Andrew E. Jaffe,
- and Daniel R. Weinberger
Genome Res. January 2020 30: 1-11; Published in Advance December 18, 2019, doi:10.1101/gr.250217.119
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Asymmetric repair of UV damage in nucleosomes imposes a DNA strand polarity on somatic mutations in skin cancer
- Peng Mao,
- Michael J. Smerdon,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2020 30: 12-21; Published in Advance December 23, 2019, doi:10.1101/gr.253146.119
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A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis
- Pengfei Cai,
- Auke B.C. Otten,
- Binbin Cheng,
- Mitsuhiro A. Ishii,
- Wen Zhang,
- Beibei Huang,
- Kun Qu,
- and Bryan K. Sun
Genome Res. January 2020 30: 22-34; Published in Advance December 4, 2019, doi:10.1101/gr.251561.119
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Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification
- Megan Rothstein and
- Marcos Simoes-Costa
Genome Res. January 2020 30: 35-48; Published in Advance December 17, 2019, doi:10.1101/gr.249680.119

Methods

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Copolymerization of single-cell nucleic acids into balls of acrylamide gel
- Siran Li,
- Jude Kendall,
- Sarah Park,
- Zihua Wang,
- Joan Alexander,
- Andrea Moffitt,
- Nissim Ranade,
- Cassidy Danyko,
- Bruno Gegenhuber,
- Stephan Fischer,
- Brian D. Robinson,
- Herbert Lepor,
- Jessica Tollkuhn,
- Jesse Gillis,
- Eric Brouzes,
- Alex Krasnitz,
- Dan Levy,
- and Michael Wigler
Genome Res. January 2020 30: 49-61; Published in Advance November 14, 2019, doi:10.1101/gr.253047.119
OPEN ACCESS ARTICLE
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Identification of pathogenic variant enriched regions across genes and gene families
- Eduardo Pérez-Palma,
- Patrick May,
- Sumaiya Iqbal,
- Lisa-Marie Niestroj,
- Juanjiangmeng Du,
- Henrike O. Heyne,
- Jessica A. Castrillon,
- Anne O'Donnell-Luria,
- Peter Nürnberg,
- Aarno Palotie,
- Mark Daly,
- and Dennis Lal
Genome Res. January 2020 30: 62-71; Published in Advance December 23, 2019, doi:10.1101/gr.252601.119
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Quantitative prediction of enhancer–promoter interactions
- Polina S. Belokopytova,
- Miroslav A. Nuriddinov,
- Evgeniy A. Mozheiko,
- Daniil Fishman,
- and Veniamin Fishman
Genome Res. January 2020 30: 72-84; Published in Advance December 2, 2019, doi:10.1101/gr.249367.119
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Predicting transfer RNA gene activity from sequence and genome context
- Bryan P. Thornlow,
- Joel Armstrong,
- Andrew D. Holmes,
- Jonathan M. Howard,
- Russell B. Corbett-Detig,
- and Todd M. Lowe
Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
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CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans
- Ping Wei,
- Wen Xue,
- Yun Zhao,
- Guang Ning,
- and Jiwu Wang
Genome Res. January 2020 30: 95-106; Published in Advance November 13, 2019, doi:10.1101/gr.250811.119
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Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9
- Daniel Agudelo,
- Sophie Carter,
- Minja Velimirovic,
- Alexis Duringer,
- Jean-François Rivest,
- Sébastien Levesque,
- Jeremy Loehr,
- Mathilde Mouchiroud,
- Denis Cyr,
- Paula J. Waters,
- Mathieu Laplante,
- Sylvain Moineau,
- Adeline Goulet,
- and Yannick Doyon
Genome Res. January 2020 30: 107-117; Published in Advance January 3, 2020, doi:10.1101/gr.255414.119

Resources

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Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
- Yonghua Sun,
- Bo Zhang,
- Lingfei Luo,
- De-Li Shi,
- Han Wang,
- Zongbin Cui,
- Honghui Huang,
- Ying Cao,
- Xiaodong Shu,
- Wenqing Zhang,
- Jianfeng Zhou,
- Yun Li,
- Jiulin Du,
- Qingshun Zhao,
- Jun Chen,
- Hanbing Zhong,
- Tao P. Zhong,
- Li Li,
- Jing-Wei Xiong,
- Jinrong Peng,
- Wuhan Xiao,
- Jian Zhang,
- Jihua Yao,
- Zhan Yin,
- Xianming Mo,
- Gang Peng,
- Jun Zhu,
- Yan Chen,
- Yong Zhou,
- Dong Liu,
- Weijun Pan,
- Yiyue Zhang,
- Hua Ruan,
- Feng Liu,
- Zuoyan Zhu,
- Anming Meng,
- and The ZAKOC Consortium
Genome Res. January 2020 30: 118-126; Published in Advance December 12, 2019, doi:10.1101/gr.248559.119
OPEN ACCESS ARTICLE
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Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow–derived stromal stem cells
- Inigo Barrio-Hernandez,
- Abbas Jafari,
- Kristoffer T.G. Rigbolt,
- Philip Hallenborg,
- Virginia Sanchez-Quiles,
- Ida Skovrind,
- Vyacheslav Akimov,
- Irina Kratchmarova,
- Joern Dengjel,
- Moustapha Kassem,
- and Blagoy Blagoev
Genome Res. January 2020 30: 127-137; Published in Advance December 12, 2019, doi:10.1101/gr.248286.119
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The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
- Zhemin Zhou,
- Nabil-Fareed Alikhan,
- Khaled Mohamed,
- Yulei Fan,
- the Agama Study Group,
- and Mark Achtman
Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
OPEN ACCESS ARTICLE

Corrigenda

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Corrigendum: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
- Jacob C. Kimmel,
- Lolita Penland,
- Nimrod D. Rubinstein,
- David G. Hendrickson,
- David R. Kelley,
- and Adam Z. Rosenthal
Genome Res. January 2020 30: 153_1; doi:10.1101/gr.259820.119
OPEN ACCESS ARTICLE
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Corrigendum: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- Michal Pawlak,
- Katarzyna Z. Kedzierska,
- Maciej Migdal,
- Karim Abu Nahia,
- Jordan A. Ramilowski,
- Lukasz Bugajski,
- Kosuke Hashimoto,
- Aleksandra Marconi,
- Katarzyna Piwocka,
- Piero Carninci,
- and Cecilia L. Winata
Genome Res. January 2020 30: 153_2; doi:10.1101/gr.260273.119
OPEN ACCESS ARTICLE

Research

Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation

Asymmetric repair of UV damage in nucleosomes imposes a DNA strand polarity on somatic mutations in skin cancer

A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis

Heterodimerization of TFAP2 pioneer factors drives epigenomic remodeling during neural crest specification

Methods

Copolymerization of single-cell nucleic acids into balls of acrylamide gel

Identification of pathogenic variant enriched regions across genes and gene families

Quantitative prediction of enhancer–promoter interactions

Predicting transfer RNA gene activity from sequence and genome context

CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans

Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9

Resources

Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9

Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow–derived stromal stem cells

The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Corrigenda

Corrigendum: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

Corrigendum: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

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