Volume 31, Issue 2 | February 2021

Research
- - Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states
    Emily J. Collins
    Mariana P. Cervantes-Silva
    George A. Timmons
    James R. O'Siorain
    Annie M. Curtis
    First Published January 12, 2021
  - KDM1A maintains genome-wide homeostasis of transcriptional enhancers
    Saurabh Agarwal
    Katherine M. Bonefas
    Patricia M. Garay
    Emily Brookes
    Yumie Murata-Nakamura
    First Published January 7, 2021
  - Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals
    Daniel W. Bellott
    David C. Page
    First Published January 21, 2021
  - Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
    Swann Floc'hlay
    Emily S. Wong
    Bingqing Zhao
    Rebecca R. Viales
    Morgane Thomas-Chollier
    First Published December 11, 2020
  - Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
    Todd P. Michael
    Evan Ernst
    Nolan Hartwick
    Philomena Chu
    Douglas Bryant
    Sarah Gilbert Stefan Ortleb Erin L. Baggs K. Sowjanya Sree Klaus J. Appenroth Joerg Fuchs Florian Jupe Justin P. Sandoval Ksenia V. Krasileva Ljudmylla Borisjuk
    ...[+10 authors]...,
    Todd C. Mockler
    Joseph R. Ecker
    Robert A. Martienssen
    Eric Lam
    First Published December 23, 2020
  - Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity
    Alexander Crits-Christoph
    Nicholas Bhattacharya
    Matthew R. Olm
    Yun S. Song
    Jillian F. Banfield
    First Published December 23, 2020
Methods
- - TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes
    Liguo Zhang
    Yang Zhang
    Yu Chen
    Omid Gholamalamdari
    Yuchuan Wang
    First Published December 18, 2020
  - Evidence of widespread, independent sequence signature for transcription factor cobinding
    Manqi Zhou
    Hongyang Li
    Xueqing Wang
    Yuanfang Guan
    First Published December 10, 2020
  - Epigenomic differences in the human and chimpanzee genomes are associated with structural variation
    Xiaoyu Zhuo
    Alan Y. Du
    Erica C. Pehrsson
    Daofeng Li
    Ting Wang
    First Published December 10, 2020
  - Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
    Zhiyi Sun
    Romualdas Vaisvila
    Laura-Madison Hussong
    Bo Yan
    Chloé Baum
    Lana Saleh Mala Samaranayake Shengxi Guan Nan Dai Ivan R. Corrêa
    ...[+5 authors]...,
    Sriharsa Pradhan
    Theodore B. Davis
    Thomas C. Evans
    Laurence M. Ettwiller
    First Published January 19, 2021
  - Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments
    Ales Varabyou
    Steven L. Salzberg
    Mihaela Pertea
    First Published December 23, 2020
  - Contamination detection in sequencing studies using the mitochondrial phylogeny
    Hansi Weissensteiner
    Lukas Forer
    Liane Fendt
    Azin Kheirkhah
    Antonio Salas
    First Published January 15, 2021
  - Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
    Etienne Routhier
    Edgard Pierre
    Ghazaleh Khodabandelou
    Julien Mozziconacci
    First Published December 18, 2020
Resources
- - A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
    Matthew D.C. Neville
    Robin Kohze
    Chaitanya Erady
    Narendra Meena
    Matthew Hayden
    First Published January 19, 2021
  - Modeling molecular development of breast cancer in canine mammary tumors
    Kiley Graim
    Dmitriy Gorenshteyn
    David G. Robinson
    Nicholas J. Carriero
    James A. Cahill
    Rumela Chakrabarti Michael H. Goldschmidt Amy C. Durham Julien Funk John D. Storey
    ...[+5 authors]...,
    Vessela N. Kristensen
    Chandra L. Theesfeld
    Karin U. Sorenmo
    Olga G. Troyanskaya
    First Published December 23, 2020

Table of Contents

Volume 31, Issue 2 | February 2021

Research

Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states

KDM1A maintains genome-wide homeostasis of transcriptional enhancers

Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals

Cis-acting variation is common across regulatory layers but is often buffered during embryonic development

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity

Methods

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

Evidence of widespread, independent sequence signature for transcription factor cobinding

Epigenomic differences in the human and chimpanzee genomes are associated with structural variation

Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments

Contamination detection in sequencing studies using the mitochondrial phylogeny

Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics

Resources

A platform for curated products from novel open reading frames prompts reinterpretation of disease variants

Modeling molecular development of breast cancer in canine mammary tumors

Table of Contents

Volume 31, Issue 2 | February 2021

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Research

Methods

Resources