Table of Contents

Research

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Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation
- Montgomery Blencowe,
- Xuqi Chen,
- Yutian Zhao,
- Yuichiro Itoh,
- Caden N. McQuillen,
- Yanjie Han,
- Benjamin L. Shou,
- Rebecca McClusky,
- Karen Reue,
- Arthur P. Arnold,
- and Xia Yang
Genome Res. May 2022 32: 807-824; Published in Advance April 8, 2022, doi:10.1101/gr.275965.121
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H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
- Haifen Chen,
- Bo Hu,
- Cynthia Horth,
- Eric Bareke,
- Phillip Rosenbaum,
- Sin Young Kwon,
- Jacinthe Sirois,
- Daniel N. Weinberg,
- Faith M. Robison,
- Benjamin A. Garcia,
- Chao Lu,
- William A. Pastor,
- and Jacek Majewski
Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
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Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
- Isabela Gerdes Gyuricza,
- Joel M. Chick,
- Gregory R. Keele,
- Andrew G. Deighan,
- Steven C. Munger,
- Ron Korstanje,
- Steven P. Gygi,
- and Gary A. Churchill
Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
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Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes
- Fan Zhang,
- Hongzhang Xue,
- Xiaorui Dong,
- Min Li,
- Xiaoming Zheng,
- Zhikang Li,
- Jianlong Xu,
- Wensheng Wang,
- and Chaochun Wei
Genome Res. May 2022 32: 853-863; Published in Advance April 8, 2022, doi:10.1101/gr.276015.121
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Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
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Genome-wide promoter assembly in E. coli measured at single-base resolution
- Jordan John,
- Javaid Jabbar,
- Nitika Badjatia,
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121

Methods

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A complete pedigree-based graph workflow for rare candidate variant analysis
- Charles Markello,
- Charles Huang,
- Alex Rodriguez,
- Andrew Carroll,
- Pi-Chuan Chang,
- Jordan Eizenga,
- Thomas Markello,
- David Haussler,
- and Benedict Paten
Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
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A general framework for identifying oligogenic combinations of rare variants in complex disorders
- Vijay Kumar Pounraja and
- Santhosh Girirajan
Genome Res. May 2022 32: 904-915; Published in Advance March 17, 2022, doi:10.1101/gr.276348.121
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A general calculus of fitness landscapes finds genes under selection in cancers
- Teng-Kuei Hsu,
- Jennifer Asmussen,
- Amanda Koire,
- Byung-Kwon Choi,
- Mayur A. Gadhikar,
- Eunna Huh,
- Chih-Hsu Lin,
- Daniel M. Konecki,
- Young Won Kim,
- Curtis R. Pickering,
- Marek Kimmel,
- Lawrence A. Donehower,
- Mitchell J. Frederick,
- Jeffrey N. Myers,
- Panagiotis Katsonis,
- and Olivier Lichtarge
Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
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Chromatin interaction–aware gene regulatory modeling with graph attention networks
- Alireza Karbalayghareh,
- Merve Sahin,
- and Christina S. Leslie
Genome Res. May 2022 32: 930-944; Published in Advance April 8, 2022, doi:10.1101/gr.275870.121
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Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice
- Arikuni Uchimura,
- Hirotaka Matsumoto,
- Yasunari Satoh,
- Yohei Minakuchi,
- Sayaka Wakayama,
- Teruhiko Wakayama,
- Mayumi Higuchi,
- Masakazu Hashimoto,
- Ryutaro Fukumura,
- Atsushi Toyoda,
- Yoichi Gondo,
- and Takeshi Yagi
Genome Res. May 2022 32: 945-955; Published in Advance May 9, 2022, doi:10.1101/gr.276363.121
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Global mapping of RNA homodimers in living cells
- Marta M. Gabryelska,
- Andrew P. Badrock,
- Jian You Lau,
- Raymond T. O'Keefe,
- Yanick J. Crow,
- and Grzegorz Kudla
Genome Res. May 2022 32: 956-967; Published in Advance March 24, 2022, doi:10.1101/gr.275900.121
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Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
- Minjie Zhang,
- Irena T. Hwang,
- Kongpan Li,
- Jianhui Bai,
- Jian-Fu Chen,
- Tsachy Weissman,
- James Y. Zou,
- and Zhipeng Lu
Genome Res. May 2022 32: 968-985; Published in Advance March 24, 2022, doi:10.1101/gr.275979.121
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Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
- Nitan Shalon,
- David A. Relman,
- and Eitan Yaffe
Genome Res. May 2022 32: 986-1003; Published in Advance April 12, 2022, doi:10.1101/gr.275894.121
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Resource

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A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality
- Jane Hawkey,
- Ben Vezina,
- Jonathan M. Monk,
- Louise M. Judd,
- Taylor Harshegyi,
- Sebastián López-Fernández,
- Carla Rodrigues,
- Sylvain Brisse,
- Kathryn E. Holt,
- and Kelly L. Wyres
Genome Res. May 2022 32: 1004-1014; Published in Advance March 11, 2022, doi:10.1101/gr.276289.121
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Corrigendum

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Corrigendum: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
- Qianru Li,
- Haiwang Yang,
- Emily K. Stroup,
- Hongbin Wang,
- and Zhe Ji
Genome Res. May 2022 32: 1015; doi:10.1101/gr.276750.122
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Research

Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation

H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells

Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart

Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes

Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages

Genome-wide promoter assembly in E. coli measured at single-base resolution

Methods

A complete pedigree-based graph workflow for rare candidate variant analysis

A general framework for identifying oligogenic combinations of rare variants in complex disorders

A general calculus of fitness landscapes finds genes under selection in cancers

Chromatin interaction–aware gene regulatory modeling with graph attention networks

Early embryonic mutations reveal dynamics of somatic and germ cell lineages in mice

Global mapping of RNA homodimers in living cells

Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers

Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors

Resource

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

Corrigendum

Corrigendum: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation

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