Volume 34, Issue 3 | March 2024

Review
- - A systematic review on the biochemical threshold of mitochondrial genetic variants
    Karan K. Smith
    Jesse D. Moreira
    Callum R. Wilson
    June O. Padera
    Ashlee N. Lamason
    Liying Xue
    Deepa M. Gopal
    David B. Flynn
    Jessica L. Fetterman
    First Published April 16, 2024
Research
- - Inference of selective forces on house mouse genomes during secondary contact in East Asia
    Kazumichi Fujiwara
    Shunpei Kubo
    Toshinori Endo
    Toyoyuki Takada
    Toshihiko Shiroishi
    Hitoshi Suzuki
    Naoki Osada
    First Published March 20, 2024
  - Systematic identification and characterization of exon–intron circRNAs
    Yinchun Zhong
    Yan Yang
    Xiaolin Wang
    Bingbing Ren
    Xueren Wang
    Ge Shan
    Liang Chen
    First Published April 12, 2024
  - Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation
    Blandine C. Mercier
    Emmanuel Labaronne
    David Cluet
    Laura Guiguettaz
    Nicolas Fontrodona
    Alicia Bicknell Antoine Corbin Mélanie Wencker Fabien Aube Laurent Modolo
    ...[+5 authors]...,
    Karina Jouravleva
    Didier Auboeuf
    Melissa J. Moore
    Emiliano P. Ricci
    First Published March 20, 2024
  - Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
    Selvaraju Divya
    Wierzbicki Filip
    Kofler Robert
    First Published March 15, 2024
  - Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
    Plessy Charles
    Mansfield Michael J.
    Bliznina Aleksandra
    Masunaga Aki
    West Charlotte
    Tan Yongkai Liu Andrew W. Grašič Jan del Río Pisula María Sara Sánchez-Serna Gaspar Fabrega-Torrus Marc Ferrández-Roldán Alfonso Roncalli Vittoria Navratilova Pavla Thompson Eric M.
    ...[+10 authors]...,
    Onuma Takeshi
    Nishida Hiroki
    Cañestro Cristian
    Luscombe Nicholas M.
    First Published April 15, 2024
  - Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
    João L. Reis-Cunha
    Samuel A. Pimenta-Carvalho
    Laila V. Almeida
    Anderson Coqueiro-dos-Santos
    Catarina A. Marques
    Jennifer A. Black
    ...[+1 authors]...,
    Jeziel Damasceno
    Richard McCulloch
    Daniella C. Bartholomeu
    Daniel C. Jeffares
    First Published April 11, 2024
Methods
- - Phased nanopore assembly with Shasta and modular graph phasing with GFAse
    Ryan Lorig-Roach
    Melissa Meredith
    Jean Monlong
    Miten Jain
    Hugh E. Olsen
    Brandy McNulty David Porubsky Tessa G. Montague Julian K. Lucas Chris Condon Jordan M. Eizenga Sissel Juul Sean K. McKenzie Sara E. Simmonds Jimin Park Mobin Asri Sergey Koren Evan E. Eichler Richard Axel
    ...[+14 authors]...,
    Bruce Martin
    Paolo Carnevali
    Karen H. Miga
    Benedict Paten
    First Published April 16, 2024
  - Robust chromatin state annotation
    Mehdi Foroozandeh Shahraki
    Marjan Farahbod
    Maxwell W. Libbrecht
    First Published March 21, 2024
  - Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
    Muyoung Lee
    Qingqing Guo
    Mijeong Kim
    Joonhyuk Choi
    Alia Segura
    Alper Genceroglu Lucy LeBlanc Nereida Ramirez Yu Jin Jang
    ...[+4 authors]...,
    Yeejin Jang
    Bum-Kyu Lee
    Edward M. Marcotte
    Jonghwan Kim
    First Published April 5, 2024
Resource
- - The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
    Christine E. Schnitzler
    E. Sally Chang
    Justin Waletich
    Gonzalo Quiroga-Artigas
    Wai Yee Wong
    Anh-Dao Nguyen Sofia N. Barreira Liam B. Doonan Paul Gonzalez Sergey Koren James M. Gahan Steven M. Sanders Brian Bradshaw Timothy Q. DuBuc Febrimarsa Danielle de Jong Eric P. Nawrocki Alexandra Larson Samantha Klasfeld Sebastian G. Gornik R. Travis Moreland Tyra G. Wolfsberg Adam M. Phillippy James C. Mullikin Oleg Simakov
    ...[+20 authors]...,
    Paulyn Cartwright
    Matthew Nicotra
    Uri Frank
    Andreas D. Baxevanis
    First Published March 20, 2024
Corrigendum
- - Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
    Fei Qin
    Guoshuai Cai
    Christopher I. Amos
    Feifei Xiao
    First Published April 25, 2024

Table of Contents

Volume 34, Issue 3 | March 2024

Review

A systematic review on the biochemical threshold of mitochondrial genetic variants

Research

Inference of selective forces on house mouse genomes during secondary contact in East Asia

Systematic identification and characterization of exon–intron circRNAs

Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation

Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements

Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species

Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites

Methods

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Robust chromatin state annotation

Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches

Resource

The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals

Corrigendum

Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data

Table of Contents

Volume 34, Issue 3 | March 2024

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Review

Research

Methods

Resource

Corrigendum