Volume 31, Issue 4 | April 2021

Research
- - 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
    Joseph K. Pickrell
    First Published February 3, 2021
  - AP-1 subunits converge promiscuously at enhancers to potentiate transcription
    Jungkyun Seo
    D. Dewran Koçak
    Luke C. Bartelt
    Courtney A. Williams
    Alejandro Barrera
    First Published March 5, 2021
  - 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
    ...[+1 authors]...,
    Fred T.G. White
    Marc D. Galland
    Marten P. Smidt
    Frank M.J. Jacobs
    First Published March 15, 2021
  - 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
    First Published March 12, 2021
  - Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver
    Ullas V. Chembazhi
    Sushant Bangru
    Mikel Hernaez
    Auinash Kalsotra
    First Published March 1, 2021
  - 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
    ...[+10 authors]...,
    Pere Arús
    Sanwen Huang
    Zhangjun Fei
    Lirong Wang
    First Published March 9, 2021
  - Orc4 spatiotemporally stabilizes centromeric chromatin
    Lakshmi Sreekumar
    Kiran Kumari
    Krishnendu Guin
    Asif Bakshi
    Neha Varshney
    Bhagya C. Thimmappa
    ...[+1 authors]...,
    Leelavati Narlikar
    Ranjith Padinhateeri
    Rahul Siddharthan
    Kaustuv Sanyal
    First Published January 29, 2021
  - 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
    ...[+1 authors]...,
    Peng-Yu He
    Pei-Jie Han
    Qi-Ming Wang
    Feng-Yan Bai
    First Published March 15, 2021
  - 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
    ...[+11 authors]...,
    David Posada
    Christopher E. Mason
    Fritz J. Sedlazeck
    Todd J. Treangen
    First Published February 18, 2021
Methods
- - 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
    ...[+24 authors]...,
    Emma C. Thomson
    Dennis Wang
    Simon Mallal
    Thushan I. de Silva
    First Published March 15, 2021
  - 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
    ...[+2 authors]...,
    Rachel Soloff
    Gregory Seumois
    Pandurangan Vijayanand
    Ferhat Ay
    First Published March 5, 2021
  - Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
    Van Hoan Do
    Francisca Rojas Ringeling
    Stefan Canzar
    First Published February 24, 2021
  - 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
    ...[+3 authors]...,
    Naveen Ramalingam
    Gaurav Ahuja
    Abhik Ghosh
    Debarka Sengupta
    First Published March 5, 2021
  - Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching
    Mengjie Chen
    Qi Zhan
    Zepeng Mu
    Lili Wang
    Zhaohui Zheng
    First Published March 19, 2021
  - Ultrafast functional profiling of RNA-seq data for nonmodel organisms
    Peng Liu
    Jessica Ewald
    Jose Hector Galvez
    Jessica Head
    Doug Crump
    First Published March 17, 2021
  - Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
    Hongyang Li
    Yuanfang Guan
    First Published March 19, 2021
Resource
- - 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
    Pablo J. Ross
    First Published March 15, 2021
Corrigendum
- - 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
    Julio Saez-Rodriguez
    First Published April 1, 2021

Table of Contents

Volume 31, Issue 4 | April 2021

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

Table of Contents

Volume 31, Issue 4 | April 2021

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Research

Methods

Resource

Corrigendum