Volume 34, Issue 10 | October 2024

Mini-Review
- - The chromatin tapestry as a framework for neurodevelopment
    Ben Nolan
    Timothy E. Reznicek
    Christopher T. Cummings
    M. Jordan Rowley
    First Published October 29, 2024
Research
- - AGAP duplicons associate with structural diversity at Chromosome 10q11.22
    Stefania Fornezza
    Vincenza Simona Delvecchio
    William T. Harvey
    Philip C. Dishuck
    Evan E. Eichler
    Giuliana Giannuzzi
    First Published September 25, 2024
  - Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
    Taishan Hu
    Timothy L. Mosbruger
    Nikolaos G. Tairis
    Amalia Dinou
    Pushkala Jayaraman
    Mahdi Sarmady Kingham Brewster
    ...[+2 authors]...,
    Yang Li
    Tristan J. Hayeck
    Jamie L. Duke
    Dimitri S. Monos
    First Published September 26, 2024
  - Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
    Yueqiang Song
    Fuyuan Li
    Shangzi Wang
    Yuntong Wang
    Cong Lai
    Lian Chen Ning Jiang
    ...[+2 authors]...,
    Jin Li
    Xingdong Chen
    Swneke D. Bailey
    Xiaoyang Zhang
    First Published October 18, 2024
  - Evidence for compensatory evolution within pleiotropic regulatory elements
    Zane Kliesmete
    Peter Orchard
    Victor Yan Kin Lee
    Johanna Geuder
    Simon M. Krauß
    Mari Ohnuki
    ...[+1 authors]...,
    Jessica Jocher
    Beate Vieth
    Wolfgang Enard
    Ines Hellmann
    First Published September 10, 2024
  - Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
    James L. Shepherdson
    David M. Granas
    Jie Li
    Zara Shariff
    Stephen P. Plassmeyer
    Alex S. Holehouse
    Michael A. White
    Barak A. Cohen
    First Published September 25, 2024
  - De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
    Basanta Bista
    Laura González-Rodelas
    Lucía Álvarez-González
    Zhi-qiang Wu
    Eugenia E. Montiel
    Ling Sze Lee Daleen B. Badenhorst Srihari Radhakrishnan Robert Literman Beatriz Navarro-Dominguez John B. Iverson
    ...[+6 authors]...,
    Simon Orozco-Arias
    Josefa González
    Aurora Ruiz-Herrera
    Nicole Valenzuela
    First Published October 16, 2024
  - Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
    Marcin P. Sajek
    Danielle Y. Bilodeau
    Michael A. Beer
    Emma Horton
    Yukiko Miyamoto
    Katrina B. Velle
    ...[+1 authors]...,
    Lars Eckmann
    Lillian Fritz-Laylin
    Olivia S. Rissland
    Neelanjan Mukherjee
    First Published September 26, 2024
  - Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
    Shaoqiang Hu
    Xiangguo Zeng
    Yuguo Liu
    Yongping Li
    Minghao Qu
    Wen-Biao Jiao
    Yongchao Han
    Chunying Kang
    First Published October 15, 2024
  - Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
    Valentin-Alvarado Luis E.
    Shi Ling-Dong
    Appler Kathryn E.
    Crits-Christoph Alexander
    De Anda Valerie
    Adler Benjamin A. Cui Michael L. Ly Lynn Leão Pedro Roberts Richard J.
    ...[+5 authors]...,
    Sachdeva Rohan
    Baker Brett J.
    Savage David F.
    Banfield Jillian F.
    First Published October 15, 2024
Methods
- - Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
    Borislav Hrisimirov Hristov
    William Stafford Noble
    Alessandro Bertero
    First Published September 25, 2024
  - Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads
    Seong Woo Han
    San Jewell
    Andrei Thomas-Tikhonenko
    Yoseph Barash
    First Published September 25, 2024
  - Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data
    Alicia Petrany
    Ruoyu Chen
    Shaoqiang Zhang
    Yong Chen
    First Published October 15, 2024
  - Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
    Apurva Narechania
    Dean Bobo
    Kevin Deitz
    Rob DeSalle
    Paul J. Planet
    Barun Mathema
    First Published September 25, 2024
  - Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
    Romain Derelle
    Johanna von Wachsmann
    Tommi Mäklin
    Joel Hellewell
    Timothy Russell
    Ajit Lalvani
    ...[+1 authors]...,
    Leonid Chindelevitch
    Nicholas J. Croucher
    Simon R. Harris
    John A. Lees
    First Published October 15, 2024
Resources
- - PWAS Hub for exploring gene-based associations of common complex diseases
    Guy Kelman
    Roei Zucker
    Nadav Brandes
    Michal Linial
    First Published October 15, 2024
  - Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level
    Wankun Deng
    Citu Citu
    Andi Liu
    Zhongming Zhao
    First Published October 18, 2024

Table of Contents

Volume 34, Issue 10 | October 2024

Mini-Review

The chromatin tapestry as a framework for neurodevelopment

Research

AGAP duplicons associate with structural diversity at Chromosome 10q11.22

Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer

Evidence for compensatory evolution within pleiotropic regulatory elements

Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes

Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists

Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Methods

Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories

Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads

Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data

Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change

Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis

Resources

PWAS Hub for exploring gene-based associations of common complex diseases

Dynamic dysregulation of retrotransposons in neurodegenerative diseases at the single-cell level

Table of Contents

Volume 34, Issue 10 | October 2024

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Mini-Review

Research

Methods

Resources