Table of Contents

Research

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Thousands of human mutation clusters are explained by short-range template switching
- Ari Löytynoja
Genome Res. August 2022 32: 1437-1447; Published in Advance June 27, 2022, doi:10.1101/gr.276478.121
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Transcriptome innovations in primates revealed by single-molecule long-read sequencing
- Luis Ferrández-Peral,
- Xiaoyu Zhan,
- Marina Alvarez-Estape,
- Cristina Chiva,
- Paula Esteller-Cucala,
- Raquel García-Pérez,
- Eva Julià,
- Esther Lizano,
- Òscar Fornas,
- Eduard Sabidó,
- Qiye Li,
- Tomàs Marquès-Bonet,
- David Juan,
- and Guojie Zhang
Genome Res. August 2022 32: 1448-1462; Published in Advance July 15, 2022, doi:10.1101/gr.276395.121
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High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
- Walter Muskovic,
- Eve Slavich,
- Ben Maslen,
- Dominik C. Kaczorowski,
- Joseph Cursons,
- Edmund Crampin,
- and Maria Kavallaris
Genome Res. August 2022 32: 1463-1473; Published in Advance June 27, 2022, doi:10.1101/gr.276818.122
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Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity
- Conor J. Kelly,
- Carol G. Chitko-McKown,
- and Edward B. Chuong
Genome Res. August 2022 32: 1474-1486; Published in Advance August 10, 2022, doi:10.1101/gr.276241.121
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Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos
- Guowei Bu,
- Wei Zhu,
- Xin Liu,
- Jingjing Zhang,
- Longtao Yu,
- Kai Zhou,
- Shangke Wang,
- Zhekun Li,
- Zhengang Fan,
- Tingting Wang,
- Taotao Hu,
- Ruifeng Hu,
- Zhiting Liu,
- Tao Wang,
- Linhui Wu,
- Xia Zhang,
- Shuhong Zhao,
- and Yi-Liang Miao
Genome Res. August 2022 32: 1487-1501; Published in Advance July 22, 2022, doi:10.1101/gr.276207.121
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ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation
- Lili Tang,
- Fei Huang,
- Wuxin You,
- Ansgar Poetsch,
- Rafael Henrique Nóbrega,
- Deborah Mary Power,
- Tengfei Zhu,
- Kaiqiang Liu,
- Hong-Yan Wang,
- Qian Wang,
- Xiwen Xu,
- Bo Feng,
- Manfred Schartl,
- and Changwei Shao
Genome Res. August 2022 32: 1502-1515; Published in Advance August 12, 2022, doi:10.1101/gr.275962.121
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Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II
- Diyavarshini Gopaul,
- Cyril Denby Wilkes,
- Arach Goldar,
- Nathalie Giordanengo Aiach,
- Marie-Bénédicte Barrault,
- Elizaveta Novikova,
- and Julie Soutourina
Genome Res. August 2022 32: 1516-1528; Published in Advance June 23, 2022, doi:10.1101/gr.276371.121

Methods

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ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
- Tyler J. Hansen and
- Emily Hodges
Genome Res. August 2022 32: 1529-1541; Published in Advance July 20, 2022, doi:10.1101/gr.276766.122
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Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
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An efficient method to identify, date, and describe admixture events using haplotype information
- Pongsakorn Wangkumhang,
- Matthew Greenfield,
- and Garrett Hellenthal
Genome Res. August 2022 32: 1553-1564; Published in Advance July 6, 2022, doi:10.1101/gr.275994.121
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Highly accurate quantification of allelic gene expression for population and disease genetics
- Anna Saukkonen,
- Helena Kilpinen,
- and Alan Hodgkinson
Genome Res. August 2022 32: 1565-1572; Published in Advance July 6, 2022, doi:10.1101/gr.276296.121
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Resources

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Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4
- Honglan Zheng,
- Xinhao Yan,
- Guanluan Li,
- Hengwei Lin,
- Siqi Deng,
- Wenhui Zhuang,
- Fuqiang Yao,
- Yu Lu,
- Xin Xia,
- Huijun Yuan,
- Li Jin,
- and Zhiqiang Yan
Genome Res. August 2022 32: 1573-1584; Published in Advance June 27, 2022, doi:10.1101/gr.276562.122
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Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
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Recent, full-length gene retrocopies are common in canids
- Kevin Batcher,
- Scarlett Varney,
- Daniel York,
- Matthew Blacksmith,
- Jeffrey M. Kidd,
- Robert Rebhun,
- Peter Dickinson,
- and Danika Bannasch
Genome Res. August 2022 32: 1602-1611; Published in Advance August 12, 2022, doi:10.1101/gr.276828.122
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dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
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Corrigendum

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Corrigendum: Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes
- Gilad Barshad,
- Amit Blumberg,
- Tal Cohen,
- and Dan Mishmar
Genome Res. August 2022 32: 1626; doi:10.1101/gr.277125.122
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Research

Thousands of human mutation clusters are explained by short-range template switching

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes

Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity

Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos

ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation

Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II

Methods

ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome

Haplotype and population structure inference using neural networks in whole-genome sequencing data

An efficient method to identify, date, and describe admixture events using haplotype information

Highly accurate quantification of allelic gene expression for population and disease genetics

Resources

Proactive functional classification of all possible missense single-nucleotide variants in KCNQ4

Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history

Recent, full-length gene retrocopies are common in canids

dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development

Corrigendum

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

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