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  1. Method: 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
    ..., solving the taxonomic classification problem does not require the full resolution of a locate query. Instead, indexes for taxonomic classification typically support broader queries that either (1) list which in s the query string occurs (“document listing”) or (2) find from which portion of the taxonomic...
  2. Method: Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses
    • Xiuhao Fu,
    • Chao Yang,
    • Chunyan Cui,
    • Aoyun Geng,
    • Yidi Sun,
    • Chao Zha,
    • Feifei Cui,
    • Leyi Wei,
    • Quan Zou,
    • Xin Gao,
    • and Zilong Zhang
    Genome Res. March 26, 2026 gr.281523.125; Published in Advance March 26, 2026, doi:10.1101/gr.281523.125
    ...present an example of combinatorial 109 perturbation response prediction (Figure 1C). The primary inputs to PRIM include a 110 list of genes, a list of perturbation conditions, and the expression profile of an 111 unperturbed cell. The objective is to predict the gene expression profile of this 112...
    ACCEPTED MANUSCRIPT
  3. Research: Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing
    • Kristine Bilgrav Saether,
    • Angelo Salazar Mantero,
    • Marlene Ek,
    • Maria Pettersson,
    • Elisabeth Syk Lundberg,
    • Christopher M. Grochowski,
    • Claudia M.B. Carvalho,
    • Jesper Eisfeldt,
    • and Anna Lindstrand
    Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.281175.125
    ...by enabling more complete capture and interpretation of cytogenetic aberrations with higher resolution and accuracy compared with traditional karyotyping and array-based methods. Methods Ethics approval and consent Ethical approval was given by the regional ethical review board in Stockholm, Sweden (ethical...
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  4. PERSPECTIVE: ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List
    • Michael A. Brasch,
    • James L. Hartley,
    • and Marc Vidal
    Genome Res. October 15, 2004 14: 2001-2009; doi:10.1101/gr.2769804
    ...ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List Michael A. Brasch 1 , James L. Hartley 2 , and Marc Vidal 3 , 4 1 Atto Bioscience, Rockville, Maryland 20850, USA 2 SAIC...
  5. Research: Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases
    • Khang Ma and
    • Rinki Ratnapriya
    Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125
    ...and brain microglia form a separate, closely related cluster, highlighted in a red box, distinct from other cell types. (C) Module scores based on differentially expressed gene lists and our curated marker list are visualized using a dot plot for the annotated microglia, PVMs, and monocyte clusters...
  6. Method: 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
    ...) and 70× faster than SuSiE (∼210 sec). A similar speed advantage was observed on smaller test regions with 1000 variants (ML-MAGES: ∼1 sec; Enet: ∼5 sec; SuSiE: ∼2 sec) (for a full list of times and variance, see Supplemental Table S5). This advantage becomes more significant when analyzing larger...
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  7. Method: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
    • Chen Li,
    • Sijie Chen,
    • Yixin Chen,
    • Haiyang Bian,
    • Minsheng Hao,
    • Lei Wei,
    • and Xuegong Zhang
    Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
    ...) and their combinations that can direct the desired state transition is crucial for the task. Computational methods have been developed to identify such reprogramming TFs. However, most of them can only generate a ranked list of individual TFs and ignore the identification of TF combinations. Even for individual...
  8. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  9. Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
    • Maureen Pittman,
    • Kihyun Lee,
    • Franco Felix,
    • Yu Huang,
    • Adrienne Lam,
    • Mauro W. Costa,
    • Deepak Srivastava,
    • and Katherine S. Pollard
    Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
    ...these difficulties, there are existing methods that scan the for possible oligogenic disease combinations. ORVAL accepts a small list of variants as input and provides gene and variant annotations to a predictor that assesses potential oligogenic combinations (Renaux et al. 2019; Versbraegen et al. 2023). Similarly...
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  10. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...of nonmetabolic genes. Larger-sized structures are shown in Supplemental Figure 7. A complete list of 28 diverse functional families is provided in Supplemental Table 5.The potential role these FIEs might play in neofunctionalization is given in Supplemental Note 3, which presents evidence for moonlighting...
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