Table of Contents

Research

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Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays
- Jeremiah H. Li,
- Chase A. Mazur,
- Tomaz Berisa,
- and Joseph K. Pickrell
Genome Res. April 2021 31: 529-537; Published in Advance February 3, 2021, doi:10.1101/gr.266486.120
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AP-1 subunits converge promiscuously at enhancers to potentiate transcription
- Jungkyun Seo,
- D. Dewran Koçak,
- Luke C. Bartelt,
- Courtney A. Williams,
- Alejandro Barrera,
- Charles A. Gersbach,
- and Timothy E. Reddy
Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
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ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
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A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells
- Gurdeep Singh,
- Shanelle Mullany,
- Sakthi D. Moorthy,
- Richard Zhang,
- Tahmid Mehdi,
- Ruxiao Tian,
- Andrew G. Duncan,
- Alan M. Moses,
- and Jennifer A. Mitchell
Genome Res. April 2021 31: 564-575; Published in Advance March 12, 2021, doi:10.1101/gr.272468.120
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Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver
- Ullas V. Chembazhi,
- Sushant Bangru,
- Mikel Hernaez,
- and Auinash Kalsotra
Genome Res. April 2021 31: 576-591; Published in Advance March 1, 2021, doi:10.1101/gr.267013.120
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Genomic analyses provide insights into peach local adaptation and responses to climate change
- Yong Li,
- Ke Cao,
- Nan Li,
- Gengrui Zhu,
- Weichao Fang,
- Changwen Chen,
- Xinwei Wang,
- Jian Guo,
- Qi Wang,
- Tiyu Ding,
- Jiao Wang,
- Liping Guan,
- Junxiu Wang,
- Kuozhan Liu,
- Wenwu Guo,
- Pere Arús,
- Sanwen Huang,
- Zhangjun Fei,
- and Lirong Wang
Genome Res. April 2021 31: 592-606; Published in Advance March 9, 2021, doi:10.1101/gr.261032.120
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Orc4 spatiotemporally stabilizes centromeric chromatin
- Lakshmi Sreekumar,
- Kiran Kumari,
- Krishnendu Guin,
- Asif Bakshi,
- Neha Varshney,
- Bhagya C. Thimmappa,
- Leelavati Narlikar,
- Ranjith Padinhateeri,
- Rahul Siddharthan,
- and Kaustuv Sanyal
Genome Res. April 2021 31: 607-621; Published in Advance January 29, 2021, doi:10.1101/gr.265900.120
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Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature
- Liang Song,
- Jun-Yan Shi,
- Shou-Fu Duan,
- Da-Yong Han,
- Kuan Li,
- Ri-Peng Zhang,
- Peng-Yu He,
- Pei-Jie Han,
- Qi-Ming Wang,
- and Feng-Yan Bai
Genome Res. April 2021 31: 622-634; Published in Advance March 15, 2021, doi:10.1101/gr.262055.120
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SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
- Nicolae Sapoval,
- Medhat Mahmoud,
- Michael D. Jochum,
- Yunxi Liu,
- R.A. Leo Elworth,
- Qi Wang,
- Dreycey Albin,
- Huw A. Ogilvie,
- Michael D. Lee,
- Sonia Villapol,
- Kyle M. Hernandez,
- Irina Maljkovic Berry,
- Jonathan Foox,
- Afshin Beheshti,
- Krista Ternus,
- Kjersti M. Aagaard,
- David Posada,
- Christopher E. Mason,
- Fritz J. Sedlazeck,
- and Todd J. Treangen
Genome Res. April 2021 31: 635-644; Published in Advance February 18, 2021, doi:10.1101/gr.268961.120
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Methods

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Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data
- Matthew D. Parker,
- Benjamin B. Lindsey,
- Shay Leary,
- Silvana Gaudieri,
- Abha Chopra,
- Matthew Wyles,
- Adrienn Angyal,
- Luke R. Green,
- Paul Parsons,
- Rachel M. Tucker,
- Rebecca Brown,
- Danielle Groves,
- Katie Johnson,
- Laura Carrilero,
- Joe Heffer,
- David G. Partridge,
- Cariad Evans,
- Mohammad Raza,
- Alexander J. Keeley,
- Nikki Smith,
- Ana Da Silva Filipe,
- James G. Shepherd,
- Chris Davis,
- Sahan Bennett,
- Vattipally B. Sreenu,
- Alain Kohl,
- Elihu Aranday-Cortes,
- Lily Tong,
- Jenna Nichols,
- Emma C. Thomson,
- The COVID-19 Genomics UK (COG-UK) Consortium,
- Dennis Wang,
- Simon Mallal,
- and Thushan I. de Silva
Genome Res. April 2021 31: 645-658; Published in Advance March 15, 2021, doi:10.1101/gr.268110.120
OPEN ACCESS ARTICLE
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Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus
- Bharat Panwar,
- Benjamin J. Schmiedel,
- Shu Liang,
- Brandie White,
- Enrique Rodriguez,
- Kenneth Kalunian,
- Andrew J. McKnight,
- Rachel Soloff,
- Gregory Seumois,
- Pandurangan Vijayanand,
- and Ferhat Ay
Genome Res. April 2021 31: 659-676; Published in Advance March 5, 2021, doi:10.1101/gr.265249.120
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Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
- Van Hoan Do,
- Francisca Rojas Ringeling,
- and Stefan Canzar
Genome Res. April 2021 31: 677-688; Published in Advance February 24, 2021, doi:10.1101/gr.267906.120
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Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data
- Krishan Gupta,
- Manan Lalit,
- Aditya Biswas,
- Chad D. Sanada,
- Cassandra Greene,
- Kyle Hukari,
- Ujjwal Maulik,
- Sanghamitra Bandyopadhyay,
- Naveen Ramalingam,
- Gaurav Ahuja,
- Abhik Ghosh,
- and Debarka Sengupta
Genome Res. April 2021 31: 689-697; Published in Advance March 5, 2021, doi:10.1101/gr.267070.120
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Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching
- Mengjie Chen,
- Qi Zhan,
- Zepeng Mu,
- Lili Wang,
- Zhaohui Zheng,
- Jinlin Miao,
- Ping Zhu,
- and Yang I. Li
Genome Res. April 2021 31: 698-712; Published in Advance March 19, 2021, doi:10.1101/gr.261115.120
OPEN ACCESS ARTICLE
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Ultrafast functional profiling of RNA-seq data for nonmodel organisms
- Peng Liu,
- Jessica Ewald,
- Jose Hector Galvez,
- Jessica Head,
- Doug Crump,
- Guillaume Bourque,
- Niladri Basu,
- and Jianguo Xia
Genome Res. April 2021 31: 713-720; Published in Advance March 17, 2021, doi:10.1101/gr.269894.120
OPEN ACCESS ARTICLE
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Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
- Hongyang Li and
- Yuanfang Guan
Genome Res. April 2021 31: 721-731; Published in Advance March 19, 2021, doi:10.1101/gr.269613.120

Resource

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Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
- Daniel E. Goszczynski,
- Michelle M. Halstead,
- Alma D. Islas-Trejo,
- Huaijun Zhou,
- and Pablo J. Ross
Genome Res. April 2021 31: 732-744; Published in Advance March 15, 2021, doi:10.1101/gr.267336.120

Corrigendum

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Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities
- Luz Garcia-Alonso,
- Christian H. Holland,
- Mahmoud M. Ibrahim,
- Denes Turei,
- and Julio Saez-Rodriguez
Genome Res. April 2021 31: 745; doi:10.1101/gr.275408.121
OPEN ACCESS ARTICLE

Research

Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays

AP-1 subunits converge promiscuously at enhancers to potentiate transcription

ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters

A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells

Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver

Genomic analyses provide insights into peach local adaptation and responses to climate change

Orc4 spatiotemporally stabilizes centromeric chromatin

Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature

SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission

Methods

Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data

Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus

Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data

Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data

Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching

Ultrafast functional profiling of RNA-seq data for nonmodel organisms

Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution

Resource

Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage

Corrigendum

Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities

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