Table of Contents

Research

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Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains
- Ying-Tao Zhao,
- Deborah Y. Kwon,
- Brian S. Johnson,
- Maria Fasolino,
- Janine M. Lamonica,
- Yoon Jung Kim,
- Boxuan Simen Zhao,
- Chuan He,
- Golnaz Vahedi,
- Tae Hoon Kim,
- and Zhaolan Zhou
Genome Res. July 2018 28: 933-942; Published in Advance May 30, 2018, doi:10.1101/gr.233775.117
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A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations
- Adam Yongxin Ye,
- Yanmei Dou,
- Xiaoxu Yang,
- Sheng Wang,
- August Yue Huang,
- and Liping Wei
Genome Res. July 2018 28: 943-951; Published in Advance June 6, 2018, doi:10.1101/gr.230003.117
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Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes
- Gilad Barshad,
- Amit Blumberg,
- Tal Cohen,
- and Dan Mishmar
Genome Res. July 2018 28: 952-967; Published in Advance June 14, 2018, doi:10.1101/gr.226324.117
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Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides
- Sidi Zhang,
- Kaitlin E. Samocha,
- Manuel A. Rivas,
- Konrad J. Karczewski,
- Emma Daly,
- Ben Schmandt,
- Benjamin M. Neale,
- Daniel G. MacArthur,
- and Mark J. Daly
Genome Res. July 2018 28: 968-974; Published in Advance June 1, 2018, doi:10.1101/gr.231902.117
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Human long intrinsically disordered protein regions are frequent targets of positive selection
- Arina Afanasyeva,
- Mathias Bockwoldt,
- Christopher R. Cooney,
- Ines Heiland,
- and Toni I. Gossmann
Genome Res. July 2018 28: 975-982; Published in Advance June 1, 2018, doi:10.1101/gr.232645.117
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Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- Nathan H. Lazar,
- Kimberly A. Nevonen,
- Brendan O'Connell,
- Christine McCann,
- Rachel J. O'Neill,
- Richard E. Green,
- Thomas J. Meyer,
- Mariam Okhovat,
- and Lucia Carbone
Genome Res. July 2018 28: 983-997; Published in Advance June 18, 2018, doi:10.1101/gr.233874.117
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Inherited DNA methylation primes the establishment of accessible chromatin during genome activation
- Guifen Liu,
- Wen Wang,
- Shengen Hu,
- Xiangxiu Wang,
- and Yong Zhang
Genome Res. July 2018 28: 998-1007; Published in Advance May 29, 2018, doi:10.1101/gr.228833.117
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Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
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Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
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Methods

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Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
- Ian T. Fiddes,
- Joel Armstrong,
- Mark Diekhans,
- Stefanie Nachtweide,
- Zev N. Kronenberg,
- Jason G. Underwood,
- David Gordon,
- Dent Earl,
- Thomas Keane,
- Evan E. Eichler,
- David Haussler,
- Mario Stanke,
- and Benedict Paten
Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
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Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq
- Yu Kong,
- Esther R. Berko,
- Anthony Marcketta,
- Shahina B. Maqbool,
- Claudia A. Simões-Pires,
- David F. Kronn,
- Kenny Q. Ye,
- Masako Suzuki,
- Adam Auton,
- and John M. Greally
Genome Res. July 2018 28: 1039-1052; Published in Advance May 17, 2018, doi:10.1101/gr.226282.117
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Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations
- Quan H. Nguyen,
- Samuel W. Lukowski,
- Han Sheng Chiu,
- Anne Senabouth,
- Timothy J.C. Bruxner,
- Angelika N. Christ,
- Nathan J. Palpant,
- and Joseph E. Powell
Genome Res. July 2018 28: 1053-1066; Published in Advance May 11, 2018, doi:10.1101/gr.223925.117
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Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing
- Shijia Zhu,
- John Beaulaurier,
- Gintaras Deikus,
- Tao P. Wu,
- Maya Strahl,
- Ziyang Hao,
- Guanzheng Luo,
- James A. Gregory,
- Andrew Chess,
- Chuan He,
- Andrew Xiao,
- Robert Sebra,
- Eric E. Schadt,
- and Gang Fang
Genome Res. July 2018 28: 1067-1078; Published in Advance May 15, 2018, doi:10.1101/gr.231068.117
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Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
- Alexandre Lomsadze,
- Karl Gemayel,
- Shiyuyun Tang,
- and Mark Borodovsky
Genome Res. July 2018 28: 1079-1089; Published in Advance May 17, 2018, doi:10.1101/gr.230615.117

Resource

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EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow
- Wagner C.S. Magalhães,
- Nathalia M. Araujo,
- Thiago P. Leal,
- Gilderlanio S. Araujo,
- Paula J.S. Viriato,
- Fernanda S. Kehdy,
- Gustavo N. Costa,
- Mauricio L. Barreto,
- Bernardo L. Horta,
- Maria Fernanda Lima-Costa,
- Alexandre C. Pereira,
- Eduardo Tarazona-Santos,
- Maíra R. Rodrigues,
- and The Brazilian EPIGEN Consortium
Genome Res. July 2018 28: 1090-1095; Published in Advance June 14, 2018, doi:10.1101/gr.225458.117

Corrigendum

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Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. July 2018 28: 1096; doi:10.1101/gr.239137.118
OPEN ACCESS ARTICLE

Research

Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domains

A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations

Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes

Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides

Human long intrinsically disordered protein regions are frequent targets of positive selection

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome

Inherited DNA methylation primes the establishment of accessible chromatin during genome activation

Long-read sequencing of nascent RNA reveals coupling among RNA processing events

Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize

Methods

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq

Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes

Resource

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

Corrigendum

Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

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