Volume 35, Issue 8 | August 2025

Review
- - De novo gene birth and the conundrum of ORFan genes in bacteria
    Md. Hassan uz-Zaman
    Howard Ochman
    First Published July 10, 2025
Research
- - Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
    Benjamin D. Umans
    Yoav Gilad
    First Published June 2, 2025
  - Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
    Anna Nordin
    Chaitali Chakraborty
    Mattias Jonasson
    Orgena Dano
    Gianluca Zambanini
    Pierfrancesco Pagella
    Silvia Remeseiro
    Claudio Cantù
    First Published June 23, 2025
  - Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
    Hiltunen Johannes
    Helminen Laura
    Aaltonen Niina
    Launonen Kaisa-Mari
    Laakso Hanna
    Malinen Marjo
    Niskanen Einari A.
    Palvimo Jorma J.
    Paakinaho Ville
    First Published June 2, 2025
  - Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
    Marlies E. Oomen
    A. Nicole Fox
    Inma Gonzalez
    Amandine Molliex
    Thaleia Papadopoulou
    Pablo Navarro
    Job Dekker
    First Published June 6, 2025
  - Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
    Hadi Rahmaninejad
    Yao Xiao
    Maxime M.C. Tortora
    Geoffrey Fudenberg
    First Published July 8, 2025
  - Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing
    Nora Zidane
    Carla Rodrigues
    Valérie Bouchez
    Martin Rethoret-Pasty
    Virginie Passet
    Sylvain Brisse
    Chiara Crestani
    First Published June 2, 2025
  - Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
    Clarence Zheng
    Sherwood R. Casjens
    Alan R. Davidson
    Susan K. Amundsen
    Gerald R. Smith
    First Published July 10, 2025
Methods
- - Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
    Rachel M. Petersen
    Christopher M. Vockley
    Amanda J. Lea
    First Published July 14, 2025
  - A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
    Daijun Zhang
    Ren Qi
    Xun Lan
    Bin Liu
    First Published July 14, 2025
  - Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq
    Yike Xie
    Abbas Habibalahi
    Ayad G. Anwer
    Kanu Wahi
    Jacqueline Bailey
    Francis Lin Catherine Gatt Emma M.V. Johansson
    ...[+3 authors]...,
    Tatyana Chtanova
    Jeff Holst
    Ewa Goldys
    Fabio Zanini
    First Published July 8, 2025
  - QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data
    Xiaoyu Song
    Yuqing Shang
    Michelle E. Ehrlich
    Panos Roussos
    Guo-Cheng Yuan
    Pei Wang
    First Published June 23, 2025
  - Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
    Sindri Emmanúel Antonsson
    Páll Melsted
    First Published July 7, 2025
  - Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
    Ziyan Rao
    Min Zhang
    Shaodong Huang
    Chenyang Wu
    Yuheng Zhou
    Weijie Zhang
    Xia Lin
    Dongyu Zhao
    First Published May 27, 2025
  - Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
    Jenna Kalleberg
    Jacob Rissman
    Robert D. Schnabel
    First Published June 2, 2025
  - A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
    Zhang Meilin
    Du Heng
    Zhang Yu
    Zhuo Yue
    Liu Zhen
    Xue Yahui
    ...[+1 authors]...,
    Zhou Lei
    Zhou Sixuan
    Li Wanying
    Liu Jian-Feng
    First Published July 15, 2025
Resources
- - A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
    Gaynor-Gillett Sophia C.
    Cheng Lijun
    Shi Manman
    Liu Jason
    Wang Gaoyuan
    Spector Megan Guo Qiuyu Qi Le Flaherty Mary Wall Martha Hwang Ahyeon Gu Mengting Chen Zhanlin Chen Yuhang Moran Jennifer R. Zhang Jing
    ...[+11 authors]...,
    Lee Donghoon
    Gerstein Mark
    Geschwind Daniel
    White Kevin P.
    First Published July 11, 2025
  - CGC1, a new reference genome for Caenorhabditis elegans
    Kazuki Ichikawa
    Massa J. Shoura
    Karen L. Artiles
    Dae-Eun Jeong
    Chie Owa
    Haruka Kobayashi Yoshihiko Suzuki Manami Kanamori Yu Toyoshima Yuichi Iino Ann E. Rougvie
    ...[+6 authors]...,
    Lamia Wahba
    Andrew Z. Fire
    Erich M. Schwarz
    Shinichi Morishita
    First Published July 15, 2025

Table of Contents

Volume 35, Issue 8 | August 2025

Review

De novo gene birth and the conundrum of ORFan genes in bacteria

Research

Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids

Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes

Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells

Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation

Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy

Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing

Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth

Methods

Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes

A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis

Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq

QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data

Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated

Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs

Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain

A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry

Resources

A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq

CGC1, a new reference genome for Caenorhabditis elegans

Table of Contents

Volume 35, Issue 8 | August 2025

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Review

Research

Methods

Resources