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  Graph-based deep reinforcement learning for haplotype assembly with Ralphi

  • Enzo Battistella,
  • Anant Maheshwari,
  • Barış Ekim,
  • Bonnie Berger,
  • and Victoria Popic

  Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
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  Secure phasing of private genomes in a trusted execution environment with TX-Phase

  • Natnatee Dokmai,
  • Kaiyuan Zhu,
  • S. Cenk Sahinalp,
  • and Hyunghoon Cho

  Genome Res. December 2025 35: 2626-2636; Published in Advance November 12, 2025, doi:10.1101/gr.280558.125
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  Long-read reconstruction of many diverse haplotypes with devider

  • Jim Shaw,
  • Christina Boucher,
  • Yun William Yu,
  • Noelle Noyes,
  • and Heng Li

  Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
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  Robust 16S rRNA classification based on a compressed LCA index

  • Omar Ahmed,
  • Christina Boucher,
  • and Ben Langmead

  Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
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  Pangenome-based genome inference using integer programming

  • Ghanshyam Chandra,
  • Md Helal Hossen,
  • Stephan Scholz,
  • Alexander T. Dilthey,
  • Daniel Gibney,
  • and Chirag Jain

  Genome Res. December 2025 35: 2661-2670; Published in Advance August 21, 2025, doi:10.1101/gr.280567.125
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  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,
  • Alka Chaubey,
  • Andy Wing Chun Pang,
  • Paul Dremsek,
  • and Vineet Bafna

  Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
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  BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations

  • Antonio Nappi,
  • Liubov Shilova,
  • Theofanis Karaletsos,
  • Na Cai,
  • and Francesco Paolo Casale

  Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
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  ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage

  • Xiran Liu,
  • Lorin Crawford,
  • and Sohini Ramachandran

  Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
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  Estimating the size of long tandem repeat expansions from short reads with ScatTR

  • Rashid Al-Abri and
  • Gamze Gürsoy

  Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
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  Accurate detection of tandem repeats from error-prone sequences with EquiRep

  • Zhezheng Song,
  • Tasfia Zahin,
  • Xiang Li,
  • and Mingfu Shao

  Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
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  Unified integration of spatial transcriptomics across platforms with LLOKI

  • Ellie Haber,
  • Ajinkya Deshpande,
  • Jian Ma,
  • and Spencer Krieger

  Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
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  Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms

  • Hongyu Zheng,
  • Hirak Sarkar,
  • and Benjamin J. Raphael

  Genome Res. December 2025 35: 2734-2743; Published in Advance November 17, 2025, doi:10.1101/gr.280555.125
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  Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover

  • An Wang,
  • Stephanie Hicks,
  • Donald Geman,
  • and Laurent Younes

  Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
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  Interpretable phenotype decoding from multicondition sequencing data with ALPINE

  • Wei-Hao Lee,
  • Lechuan Li,
  • Ruth Dannenfelser,
  • and Vicky Yao

  Genome Res. December 2025 35: 2756-2769; Published in Advance October 22, 2025, doi:10.1101/gr.280566.125
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  Optimal marker genes for c-separated cell types with SepSolve

  • Bartol Borozan,
  • Tomislav Prusina,
  • Luka Borozan,
  • Domagoj Ševerdija,
  • Francisca Rojas Ringeling,
  • Domagoj Matijević,
  • and Stefan Canzar

  Genome Res. December 2025 35: 2770-2780; Published in Advance October 9, 2025, doi:10.1101/gr.280637.125
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  ScisTree2 enables large-scale inference of cell lineage trees and genotype calling using efficient local search

  • Haotian Zhang,
  • Yiming Zhang,
  • Teng Gao,
  • and Yufeng Wu

  Genome Res. December 2025 35: 2781-2791; Published in Advance September 3, 2025, doi:10.1101/gr.280542.125
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