Volume 31, Issue 5 | May 2021

Research
- - DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
    Brian Giacopelli
    Min Wang
    Ada Cleary
    Yue-Zhong Wu
    Anna Reister Schultz
    Maximilian Schmutz James S. Blachly Ann-Kathrin Eisfeld Bethany Mundy-Bosse Sebastian Vosberg Philipp A. Greif Rainer Claus Lars Bullinger Ramiro Garzon Kevin R. Coombes Clara D. Bloomfield
    ...[+11 authors]...,
    Brian J. Druker
    Jeffrey W. Tyner
    John C. Byrd
    Christopher C. Oakes
    First Published March 11, 2021
  - Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
    Aitor Serres-Armero
    Brian W. Davis
    Inna S. Povolotskaya
    Carlos Morcillo-Suarez
    Jocelyn Plassais
    First Published April 16, 2021
  - Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
    Vinay Tripuraneni
    Gonen Memisoglu
    Heather K. MacAlpine
    Trung Q. Tran
    Wei Zhu
    First Published April 2, 2021
  - The Enterprise, a massive transposon carrying Spok meiotic drive genes
    Aaron A. Vogan
    S. Lorena Ament-Velásquez
    Eric Bastiaans
    Ola Wallerman
    Sven J. Saupe
    First Published April 19, 2021
  - The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
    Yue Hao
    Makenzie E. Mabry
    Patrick P. Edger
    Michael Freeling
    Chunfang Zheng
    Lingling Jin Robert VanBuren Marivi Colle Hong An R. Shawn Abrahams Jacob D. Washburn Xinshuai Qi Kerrie Barry Christopher Daum Shengqiang Shu Jeremy Schmutz David Sankoff
    ...[+12 authors]...,
    Michael S. Barker
    Eric Lyons
    J. Chris Pires
    Gavin C. Conant
    First Published April 16, 2021
  - Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
    Xiaoli Ma
    Tom Denyer
    Marie Javelle
    Antje Feller
    Marja C.P. Timmermans
    First Published April 16, 2021
  - Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements
    Luisa Berná
    Pablo Marquez
    Andrés Cabrera
    Gonzalo Greif
    María E. Francia
    First Published April 27, 2021
  - Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants
    Jing Xia
    Aarthi Venkat
    Rachel E. Bainbridge
    Michael L. Reese
    Karine G. Le Roch
    First Published April 27, 2021
  - A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
    Sivaranjani Namasivayam
    Rodrigo P. Baptista
    Wenyuan Xiao
    Erica M. Hall
    Joseph S. Doggett
    First Published April 27, 2021
  - Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
    Brian S. Roberts
    E. Christopher Partridge
    Bryan A. Moyers
    Vikram Agarwal
    Kimberly M. Newberry
    First Published April 20, 2021
Methods
- - Correcting signal biases and detecting regulatory elements in STARR-seq data
    Young-Sook Kim
    Graham D. Johnson
    Jungkyun Seo
    Alejandro Barrera
    Thomas N. Cowart
    First Published March 15, 2021
  - Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
    Meng Chen
    Ran Wei
    Gang Wei
    Mingqing Xu
    Zhixi Su
    First Published April 19, 2021
  - A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor
    Hengxing Lu
    Jun Liu
    Tao Feng
    Zihang Guo
    Yunjun Yin
    First Published April 1, 2021
  - Optimized sample selection for cost-efficient long-read population sequencing
    T. Rhyker Ranallo-Benavidez
    Zachary Lemmon
    Sebastian Soyk
    Sergey Aganezov
    William J. Salerno
    First Published April 2, 2021
  - A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation
    René A.M. Dirks
    Peter C. Thomas
    Haoyu Wu
    Robert C. Jones
    Hendrik G. Stunnenberg
    First Published March 11, 2021
Erratum
- - Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
    Zhoutao Chen
    Long Pham
    Tsai-Chin Wu
    Guoya Mo
    Yu Xia
    Peter L. Chang Devin Porter Tan Phan Huu Che Hao Tran Vikas Bansal Justin Shaffer Pedro Belda-Ferre Greg Humphrey Rob Knight
    ...[+10 authors]...,
    Pavel Pevzner
    Son Pham
    Yong Wang
    Ming Lei
    First Published May 3, 2021

Table of Contents

Volume 31, Issue 5 | May 2021

Research

DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia

Copy number variation underlies complex phenotypes in domestic dog breeds and other canids

Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication

The Enterprise, a massive transposon carrying Spok meiotic drive genes

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts

Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants

A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

Methods

Correcting signal biases and detecting regulatory elements in STARR-seq data

Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes

A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor

Optimized sample selection for cost-efficient long-read population sequencing

A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation

Erratum

Erratum: Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

Table of Contents

Volume 31, Issue 5 | May 2021

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Research

Methods

Erratum