Volume 35, Issue 2 | February 2025

Review
- - k-mer approaches for biodiversity genomics
    Jenike Katharine M.
    Campos-Domínguez Lucía
    Boddé Marilou
    Cerca José
    Hodson Christina N.
    Schatz Michael C.
    Jaron Kamil S.
    First Published January 31, 2025
Research
- - Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
    Dahl-Jessen Mikkel
    Terkelsen Thorkild
    Bak Rasmus O.
    Jensen Uffe Birk
    First Published January 13, 2025
  - Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
    Yiqiao Zheng
    Gary D. Stormo
    Shiming Chen
    First Published December 23, 2024
  - Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
    Benjamin Morledge-Hampton
    Kathiresan Selvam
    Manish Chauhan
    Alan G. Goodman
    John J. Wyrick
    First Published January 6, 2025
  - Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
    Liu Yang
    Botelho João
    Iranzo Jaime
    First Published January 10, 2025
Methods
- - Identification of the shortest species-specific oligonucleotide sequences
    Ioannis Mouratidis
    Maxwell A. Konnaris
    Nikol Chantzi
    Candace S.Y. Chan
    Michail Patsakis
    Kimonas Provatas Austin Montgomery Fotis A. Baltoumas Congzhou M. Sha
    ...[+4 authors]...,
    Manvita Mareboina
    Georgios A. Pavlopoulos
    Dionysios V. Chartoumpekis
    Ilias Georgakopoulos-Soares
    First Published January 2, 2025
  - Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
    Zepu Miao
    Jia-Xing Yue
    First Published January 13, 2025
  - Combining DNA and protein alignments to improve genome annotation with LiftOn
    Kuan-Hao Chao
    Jakob M. Heinz
    Celine Hoh
    Alan Mao
    Alaina Shumate
    Mihaela Pertea
    Steven L. Salzberg
    First Published December 27, 2024
  - Proxy panels enable privacy-aware outsourcing of genotype imputation
    Degui Zhi
    Xiaoqian Jiang
    Arif Harmanci
    First Published January 10, 2025
  - Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
    Chuanyuan Wang
    Zhi-Ping Liu
    First Published December 18, 2024
  - Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains
    Hang Zhang
    Yi Zhang
    Kai Ming Ting
    Jie Zhang
    Qiuran Zhao
    First Published February 5, 2025
  - Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
    Ming Yan
    Thea O. Andersen
    Phillip B. Pope
    Zhongtang Yu
    First Published December 27, 2024

Table of Contents

Volume 35, Issue 2 | February 2025

Review

k-mer approaches for biodiversity genomics

Research

Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations

Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models

Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency

Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer

Methods

Identification of the shortest species-specific oligonucleotide sequences

Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration

Combining DNA and protein alignments to improve genome annotation with LiftOn

Proxy panels enable privacy-aware outsourcing of genotype imputation

Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet

Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains

Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases

Table of Contents

Volume 35, Issue 2 | February 2025

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Review

Research

Methods