Volume 35, Issue 12 | December 2025

Editorial
- - RECOMB 2025 Special Issue
    Sriram Sankararaman
    Bonnie Berger
    First Published December 3, 2025
Methods
- - Graph-based deep reinforcement learning for haplotype assembly with Ralphi
    Enzo Battistella
    Anant Maheshwari
    Barış Ekim
    Bonnie Berger
    Victoria Popic
    First Published November 14, 2025
  - Secure phasing of private genomes in a trusted execution environment with TX-Phase
    Natnatee Dokmai
    Kaiyuan Zhu
    S. Cenk Sahinalp
    Hyunghoon Cho
    First Published November 12, 2025
  - Long-read reconstruction of many diverse haplotypes with devider
    Jim Shaw
    Christina Boucher
    Yun William Yu
    Noelle Noyes
    Heng Li
    First Published September 23, 2025
  - Robust 16S rRNA classification based on a compressed LCA index
    Omar Ahmed
    Christina Boucher
    Ben Langmead
    First Published August 25, 2025
  - Pangenome-based genome inference using integer programming
    Ghanshyam Chandra
    Md Helal Hossen
    Stephan Scholz
    Alexander T. Dilthey
    Daniel Gibney
    First Published August 21, 2025
  - OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
    Siavash Raeisi Dehkordi
    Zhaoyang Jia
    Joey Estabrook
    Jen Hauenstein
    Neil Miller
    Naz Güleray-Lafci Jürgen Neesen Alex Hastie
    ...[+3 authors]...,
    Alka Chaubey
    Andy Wing Chun Pang
    Paul Dremsek
    Vineet Bafna
    First Published November 14, 2025
  - BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
    Antonio Nappi
    Liubov Shilova
    Theofanis Karaletsos
    Na Cai
    Francesco Paolo Casale
    First Published October 24, 2025
  - ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
    Xiran Liu
    Lorin Crawford
    Sohini Ramachandran
    First Published November 19, 2025
  - Estimating the size of long tandem repeat expansions from short reads with ScatTR
    Rashid Al-Abri
    Gamze Gürsoy
    First Published August 21, 2025
  - Accurate detection of tandem repeats from error-prone sequences with EquiRep
    Zhezheng Song
    Tasfia Zahin
    Xiang Li
    Mingfu Shao
    First Published August 21, 2025
  - Unified integration of spatial transcriptomics across platforms with LLOKI
    Ellie Haber
    Ajinkya Deshpande
    Jian Ma
    Spencer Krieger
    First Published November 13, 2025
  - Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
    Hongyu Zheng
    Hirak Sarkar
    Benjamin J. Raphael
    First Published November 17, 2025
  - Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
    An Wang
    Stephanie Hicks
    Donald Geman
    Laurent Younes
    First Published November 12, 2025
  - Interpretable phenotype decoding from multicondition sequencing data with ALPINE
    Wei-Hao Lee
    Lechuan Li
    Ruth Dannenfelser
    Vicky Yao
    First Published October 22, 2025
  - Optimal marker genes for c-separated cell types with SepSolve
    Bartol Borozan
    Tomislav Prusina
    Luka Borozan
    Domagoj Ševerdija
    Francisca Rojas Ringeling
    First Published October 9, 2025
  - ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search
    Haotian Zhang
    Yiming Zhang
    Teng Gao
    Yufeng Wu
    First Published September 3, 2025
List of Reviewers
- - List of Reviewers Volume 35, 2025
    First Published December 3, 2025

Table of Contents

Volume 35, Issue 12 | December 2025

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Editorial

Methods

List of Reviewers