Volume 35, Issue 5 | May 2025

Research
- - Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
    Hao Zhu
    Jiao Zhang
    Soumya Rao
    Matthew D. Durbin
    Ying Li
    Ruirui Lang Jiqiang Liu Baichuan Xiao Hailin Shan Ziqiu Meng Jinmo Wang Xiaokai Tang Zhenni Shi Liza L. Cox Shouqin Zhao Stephanie M. Ware Tiong Y. Tan Michelle de Silva Lyndon Gallacher Ting Liu Jie Mi Changqing Zeng Hou-Feng Zheng
    ...[+18 authors]...,
    Qingguo Zhang
    Stylianos E. Antonarakis
    Timothy C. Cox
    Yong-Biao Zhang
    First Published April 15, 2025
  - Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
    Reuben M. Buckley
    Nüket Bilgen
    Alexander C. Harris
    Peter Savolainen
    Cafer Tepeli
    Metin Erdoğan Aitor Serres Armero Dayna L. Dreger Frank G. van Steenbeek Marjo K. Hytönen Heidi G. Parker Jessica Hale
    ...[+7 authors]...,
    Hannes Lohi
    Bengi Çınar Kul
    Adam R. Boyko
    Elaine A. Ostrander
    First Published March 24, 2025
  - Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
    Fu Xiang Quah
    Miguel Vasconcelos Almeida
    Moritz Blumer
    Chengwei Ulrika Yuan
    Bettina Fischer
    Kirsten See Ben Jackson Richard Zatha Bosco Rusuwa George F. Turner M. Emília Santos
    ...[+6 authors]...,
    Hannes Svardal
    Martin Hemberg
    Richard Durbin
    Eric Miska
    First Published April 10, 2025
  - Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
    Jun Kim
    Haoyu Wang
    Sevinç Ercan
    First Published April 10, 2025
  - Unexpectedly low recombination rates and presence of hotspots in termite genomes
    Turid Everitt
    Tilman Rönneburg
    Daniel Elsner
    Anna Olsson
    Yuanzhen Liu
    First Published March 20, 2025
  - Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
    Olga M. Sigalova
    Mattia Forneris
    Frosina Stojanovska
    Bingqing Zhao
    Rebecca R. Viales
    Adam Rabinowitz
    ...[+1 authors]...,
    Fayrouz Hammal
    Benoît Ballester
    Judith B. Zaugg
    Eileen E.M. Furlong
    First Published April 15, 2025
Methods
- - An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
    Inswasti Cahyani
    John Tyson
    Nadine Holmes
    Josh Quick
    Chris Moore
    First Published March 24, 2025
  - Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
    Xiaoyue Duan
    Chaolei Chen
    Chang Du
    Liang Guo
    Jun Liu
    Naipeng Hou Pan Li Xiaolan Qi
    ...[+3 authors]...,
    Fei Gao
    Xuguang Du
    Jiangping Song
    Sen Wu
    First Published March 5, 2025
  - Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
    Da-Inn Lee
    Sushmita Roy
    First Published March 20, 2025
  - BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
    Yangyang Liu
    Bingqiang Liu
    Juntao Liu
    First Published March 17, 2025
  - Fast sequence alignment for centromeres with RaMA
    Pinglu Zhang
    Yanming Wei
    Qinzhong Tian
    Quan Zou
    Yansu Wang
    First Published February 12, 2025
  - A unified analysis of atlas single-cell data
    Hao Chen
    Nam D. Nguyen
    Matthew Ruffalo
    Ziv Bar-Joseph
    First Published February 18, 2025
  - k-mer manifold approximation and projection for visualizing DNA sequences
    Chengbo Fu
    Einari A. Niskanen
    Gong-Hong Wei
    Zhirong Yang
    Marta Sanvicente-García
    First Published April 10, 2025
  - Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
    Byron J. Smith
    Chunyu Zhao
    Veronika Dubinkina
    Xiaofan Jin
    Liron Zahavi
    First Published April 10, 2025
Resource
- - Building better genome annotations across the tree of life
    Adam H. Freedman
    Timothy B. Sackton
    First Published April 15, 2025

Table of Contents

Volume 35, Issue 5 | May 2025

Research

Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia

Analysis of canine gene constraint identifies new variants for orofacial clefts and stature

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans

Unexpectedly low recombination rates and presence of hotspots in termite genomes

Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis

Methods

An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride

Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries

Fast sequence alignment for centromeres with RaMA

A unified analysis of atlas single-cell data

k-mer manifold approximation and projection for visualizing DNA sequences

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

Resource

Building better genome annotations across the tree of life

Table of Contents

Volume 35, Issue 5 | May 2025

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Research

Methods

Resource