Volume 34, Issue 12 | December 2024

Review
- - Advancements in prospective single-cell lineage barcoding and their applications in research
    Xiaoli Zhang
    Yirui Huang
    Yajing Yang
    Qi-En Wang
    Lang Li
    First Published November 21, 2024
Research
- - Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
    Bertille Montibus
    James A. Cain
    Rocio T. Martinez-Nunez
    Rebecca J. Oakey
    First Published November 22, 2024
  - Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
    Matthew D. Pollard
    Wynn K. Meyer
    Emily E. Puckett
    First Published November 22, 2024
  - Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
    Song Zhang
    Chao Wang
    Shenghua Qin
    Choulin Chen
    Yongzhou Bao
    Yuanyuan Zhang Lingna Xu Qingyou Liu
    ...[+3 authors]...,
    Yunxiang Zhao
    Kui Li
    Zhonglin Tang
    Yuwen Liu
    First Published October 21, 2024
  - A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
    Thiago L. Knittel
    Brooke E. Montgomery
    Alex J. Tate
    Ennis W. Deihl
    Anastasia S. Nawrocki
    First Published December 2, 2024
  - Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
    Arne Sahm
    Konstantin Riege
    Marco Groth
    Martin Bens
    Johann Kraus
    Martin Fischer Hans Kestler
    ...[+2 authors]...,
    Christoph Englert
    Ralf Schaible
    Matthias Platzer
    Steve Hoffmann
    First Published December 4, 2024
  - Characterization of DNA methylation reader proteins in Arabidopsis thaliana
    Jonathan Cahn
    James P.B. Lloyd
    Ino D. Karemaker
    Pascal W.T.C. Jansen
    Jahnvi Pflueger
    Owen Duncan Jakob Petereit
    ...[+2 authors]...,
    Ozren Bogdanovic
    A. Harvey Millar
    Michiel Vermeulen
    Ryan Lister
    First Published December 4, 2024
Methods
- - Inferring ancestry with the hierarchical soft clustering approach tangleGen
    Klara Elisabeth Burger
    Solveig Klepper
    Ulrike von Luxburg
    Franz Baumdicker
    First Published October 21, 2024
  - MCHelper automatically curates transposable element libraries across eukaryotic species
    Simon Orozco-Arias
    Pío Sierra
    Richard Durbin
    Josefa González
    First Published December 9, 2024
  - Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
    Stephanie C. Bohaczuk
    Zachary J. Amador
    Chang Li
    Benjamin J. Mallory
    Elliott G. Swanson
    Jane Ranchalis Mitchell R. Vollger Katherine M. Munson Tom Walsh
    ...[+4 authors]...,
    Morgan O. Hamm
    Yizi Mao
    Andre Lieber
    Andrew B. Stergachis
    First Published December 9, 2024
  - Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
    Irmgard U. Haussmann
    Thomas C. Dix
    David W.J. McQuarrie
    Veronica Dezi
    Abdullah I. Hans
    First Published December 3, 2024
  - Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR
    Artem Mikelov
    George Nefediev
    Alexander Tashkeev
    Oscar L. Rodriguez
    Diego Aguilar Ortmans
    Valeriia Skatova Mark Izraelson Alexey N. Davydov Stanislav Poslavsky Souad Rahmouni
    ...[+5 authors]...,
    Corey T. Watson
    Dmitriy Chudakov
    Scott D. Boyd
    Dmitry Bolotin
    First Published October 21, 2024
Resources
- - An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
    Chong Li
    Marc Jan Bonder
    Sabriya Syed
    Matthew Jensen
    Mark B. Gerstein
    Michael C. Zody Mark J.P. Chaisson Michael E. Talkowski Tobias Marschall
    ...[+4 authors]...,
    Jan O. Korbel
    Evan E. Eichler
    Charles Lee
    Xinghua Shi
    First Published December 5, 2024
  - Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
    Michelle Kudron
    Louis Gevirtzman
    Alec Victorsen
    Bridget C. Lear
    Jiahao Gao
    Jinrui Xu Swapna Samanta Emily Frink Adri Tran-Pearson Chau Huynh Dionne Vafeados Ann Hammonds William Fisher Martha Wall Greg Wesseling Vanessa Hernandez Zhichun Lin Mary Kasparian Kevin White Ravi Allada Mark Gerstein
    ...[+16 authors]...,
    LaDeana Hillier
    Susan E. Celniker
    Valerie Reinke
    Robert H. Waterston
    First Published October 22, 2024
Reviewer Index
- - Reviewer Index, Volume 34, 2024
    First Published December 23, 2024

Table of Contents

Volume 34, Issue 12 | December 2024

Review

Advancements in prospective single-cell lineage barcoding and their applications in research

Research

Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay

Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets

Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development

A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans

Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype

Characterization of DNA methylation reader proteins in Arabidopsis thaliana

Methods

Inferring ancestry with the hierarchical soft clustering approach tangleGen

MCHelper automatically curates transposable element libraries across eukaryotic species

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq

Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR

Resources

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships

Reviewer Index

Reviewer Index, Volume 34, 2024

Table of Contents

Volume 34, Issue 12 | December 2024

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Review

Research

Methods

Resources

Reviewer Index