Volume 32, Issue 5 | May 2022

Research
- - 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
    ...[+2 authors]...,
    Rebecca McClusky
    Karen Reue
    Arthur P. Arnold
    Xia Yang
    First Published April 8, 2022
  - 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
    ...[+4 authors]...,
    Benjamin A. Garcia
    Chao Lu
    William A. Pastor
    Jacek Majewski
    First Published April 8, 2022
  - 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
    First Published March 11, 2022
  - Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes
    Fan Zhang
    Hongzhang Xue
    Xiaorui Dong
    Min Li
    Xiaoming Zheng
    First Published April 8, 2022
  - 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
    ...[+3 authors]...,
    Chia-Lun Hsieh
    Kuo-Fang Chung
    Gianni Liti
    Isheng Jason Tsai
    First Published March 31, 2022
  - 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
    First Published April 28, 2022
Methods
- - A complete pedigree-based graph workflow for rare candidate variant analysis
    Charles Markello
    Charles Huang
    Alex Rodriguez
    Andrew Carroll
    Pi-Chuan Chang
    First Published April 28, 2022
  - A general framework for identifying oligogenic combinations of rare variants in complex disorders
    Vijay Kumar Pounraja
    Santhosh Girirajan
    First Published March 17, 2022
  - 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
    ...[+7 authors]...,
    Mitchell J. Frederick
    Jeffrey N. Myers
    Panagiotis Katsonis
    Olivier Lichtarge
    First Published March 17, 2022
  - Chromatin interaction–aware gene regulatory modeling with graph attention networks
    Alireza Karbalayghareh
    Merve Sahin
    Christina S. Leslie
    First Published April 8, 2022
  - 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
    ...[+3 authors]...,
    Ryutaro Fukumura
    Atsushi Toyoda
    Yoichi Gondo
    Takeshi Yagi
    First Published May 9, 2022
  - Global mapping of RNA homodimers in living cells
    Marta M. Gabryelska
    Andrew P. Badrock
    Jian You Lau
    Raymond T. O'Keefe
    Yanick J. Crow
    First Published March 24, 2022
  - 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
    First Published March 24, 2022
  - Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
    Nitan Shalon
    David A. Relman
    Eitan Yaffe
    First Published April 12, 2022
Resource
- - 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
    ...[+1 authors]...,
    Carla Rodrigues
    Sylvain Brisse
    Kathryn E. Holt
    Kelly L. Wyres
    First Published March 11, 2022
Corrigendum
- - Corrigendum: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
    Qianru Li
    Haiwang Yang
    Emily K. Stroup
    Hongbin Wang
    Zhe Ji
    First Published May 11, 2022

Table of Contents

Volume 32, Issue 5 | May 2022

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

Table of Contents

Volume 32, Issue 5 | May 2022

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Research

Methods

Resource

Corrigendum