Volume 35, Issue 7 | July 2025

Perspective
- - Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
    Jung-Wan Mok
    Shelley B. Gibson
    Haley A. Dostalik
    Shinya Yamamoto
    First Published June 4, 2025
Research
- - Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
    Kevin W. Currin
    Hannah J. Perrin
    Gautam K. Pandey
    Abdalla A. Alkhawaja
    Swarooparani Vadlamudi
    Annie E. Musser Amy S. Etheridge K. Alaine Broadaway Jonathan D. Rosen Arushi Varshney Amarjit S. Chaudhry Paul J. Gallins Fred A. Wright Yi-hui Zhou Stephen C.J. Parker
    ...[+10 authors]...,
    Laura M. Raffield
    Erin G. Schuetz
    Federico Innocenti
    Karen L. Mohlke
    First Published May 20, 2025
  - An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
    Veronica Astro
    Kelly Yojanna Cardona-Londoño
    Lorena Viridiana Cortés-Medina
    Rawan Alghamdi
    Gustavo Ramírez-Calderón
    First Published June 10, 2025
  - Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
    Yichao Zhou
    Venkatasai Rahul Dogiparthi
    Hannah L. Harris
    Suhita Ray
    Avik Choudhuri
    Song Yang
    ...[+1 authors]...,
    Yi Zhou
    Leonard I. Zon
    M. Jordan Rowley
    Kyle J. Hewitt
    First Published June 2, 2025
  - Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    Yanis Zekri
    Sebastian Gregoricchio
    Elif Yapıcı
    Chia-Chi Flora Huang
    Tunç Morova
    First Published June 10, 2025
  - Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
    Liangxi Wang
    Tiegh Taylor
    Kumaragurubaran Rathnakumar
    Nadiya Khyzha
    Minggao Liang
    Azad Alizada Laura F. Campitelli Sara E. Pour Zain M. Patel Lina Antounians Ian C. Tobias Huayun Hou Timothy R. Hughes
    ...[+8 authors]...,
    Sushmita Roy
    Jennifer A. Mitchell
    Jason E. Fish
    Michael D. Wilson
    First Published June 6, 2025
  - Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
    Shelley Reich
    Tobias Loschko
    Julie Jung
    Samantha Nestel
    Ralf J. Sommer
    First Published June 9, 2025
Methods
- - A new compression strategy to reduce the size of nanopore sequencing data
    Kavindu Jayasooriya
    Sasha P. Jenner
    Pasindu Marasinghe
    Udith Senanayake
    Hassaan Saadat
    First Published May 15, 2025
  - Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
    Dmitry Antipov
    Mikko Rautiainen
    Sergey Nurk
    Brian P. Walenz
    Steven J. Solar
    First Published May 19, 2025
  - Highly accurate assembly polishing with DeepPolisher
    Mira Mastoras
    Mobin Asri
    Lucas Brambrink
    Prajna Hebbar
    Alexey Kolesnikov
    Daniel E. Cook Maria Nattestad Julian Lucas Taylor S. Won Pi-Chuan Chang Andrew Carroll Benedict Paten Kishwar Shafin Ahmad Abou Tayoun Derek Albracht Jamie Allen Alawi A. Alsheikh-Ali Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Edward A. Belter Halle D. Bender Andrew P. Blair Silvia Buonaiuto Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Richard Durbin Jana Ebler Evan E Eichler Jordan M. Eizenga Parsa Eskandar Eddie Ferro Anna-Sophie Fiston-Lavier Sarah M. Ford Willard W. Ford Giulio Formenti Adam Frankish Mallory A. Freeberg Qichen Fu Stephanie M. Fullerton Robert S. Fulton Yan Gao Gage H. Garcia Obed A. Garcia Joshua M.V. Gardner Shilpa Garg Erik Garrison Nanibaa' A. Garrison John Garza Mohammadmersad Ghorbani Tina Graves-Lindsay Richard E. Green Cristian Groza Andrea Guarracino Melissa Gymrek Leanne Haggerty Ira M. Hall Nancy F. Hansen Mohammad Amiruddin Hashmi Maximilian Haeussler David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Juan Jiang Jonathan LoTempio Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Ben Langmead Xiaoyu Zhuo Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Juan F. Macias-Velasco Maximillian G. Marin Franco L. Marsico Kateryna D. Makova Christopher Markovic Tobias Marschall Fergal J. Martin Mira Mastoras Capucine Mayoud Brandy McNulty Jack A. Medico Julian M. Menendez Karen H. Miga Anna Minkina Matthew W. Mitchell Saswat K. Mohanty Younes Mokrab Jean Monlong Shabir Moosa Avelina Moreno-Ochando Shinichi Morishita Jonathan M. Mudge Katherine M. Munson Njagi Mwaniki Nasna Nassir Chiara Natali Shloka Negi Lingbin Ni Adam M. Novak Chie Owa Sadye Paez Benedict Paten Hiram Clawson Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Farnaz Salehi Samuel Sacco Michael C. Schatz Laura B. Scheinfeldt Aarushi Sehgal William E. Seligmann Mahsa Shabani Kishwar Shafin Shadi Shahatit Ruhollah Shemirani Vikram S. Shivakumar Swati Sinha Jouni Sirén Linnéa Smeds Steven J. Solar Marco Sollitto Nicole Soranzo Andrew B. Stergachis Marie-Marthe Suner Yoshihiko Suzuki Arda Söylev Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Mitchell R. Vollger Brian P. Walenz Charles Wang Lisa E. Wang Ting Wang Aaron M. Wenger Conor V. Whelan Zilan Xin Zheng Xu Kai Ye DongAhn Yoo
    ...[+196 authors]...,
    Wenjin Zhang
    Ying Zhou
    Ivo Violich
    Giulia Zunino
    First Published May 19, 2025
  - Accurate short-read alignment through r-index-based pangenome indexing
    Rahul Varki
    Massimiliano Rossi
    Eddie Ferro
    Marco Oliva
    Erik Garrison
    First Published June 12, 2025
  - Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
    Jianing Yao
    Jinglun Yu
    Brian Caffo
    Stephanie C. Page
    Keri Martinowich
    First Published May 20, 2025
  - Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
    Maria Grazia Mendoza-Ferri
    Gwendoline Lozachmeur
    Maximilien Duvina
    Laetitia Perret
    Didier Merciris
    First Published May 13, 2025
  - Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics
    Vishvak Raghavan
    Yumin Zheng
    Yue Li
    Jun Ding
    First Published May 2, 2025
Resource
- - Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
    Aliza B. Rubenstein
    Gregory R. Smith
    Zidong Zhang
    Xi Chen
    Toby L. Chambers
    Frederique Ruf-Zamojski Natalia Mendelev Wan Sze Cheng Michel Zamojski Mary Anne S. Amper Venugopalan D. Nair Andrew R. Marderstein Stephen B. Montgomery Olga G. Troyanskaya
    ...[+9 authors]...,
    Elena Zaslavsky
    Todd Trappe
    Scott Trappe
    Stuart C. Sealfon
    First Published May 20, 2025

Table of Contents

Volume 35, Issue 7 | July 2025

Perspective

Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases

Research

Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells

Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors

Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding

Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network

Methods

A new compression strategy to reduce the size of nanopore sequencing data

Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

Highly accurate assembly polishing with DeepPolisher

Accurate short-read alignment through r-index-based pangenome indexing

Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies

Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase

Harnessing agent-based frameworks in CellAgentChat to unravel cell–cell interactions from single-cell and spatial transcriptomics

Resource

Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise

Table of Contents

Volume 35, Issue 7 | July 2025

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Perspective

Research

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Resource