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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., Barcelona 08034, Spain; 3Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, California 94720, USA; 4Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95060, USA; 5Institute for Computational and Mathematical Engineering...
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Method: Automated interpretable artificial intelligence genomic prediction with AIGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
....edu.cnAbstractPredicting phenotypes from genomic mutations remains a major genetic challenge. Traditional statistical methods (such as GBLUP and BayesR) have limitations, including reliance on artificial prior assumptions, and hard to capture epistatic effects. Machine learning (ML) has emerged as a powerful alternative for genomic...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...expression. To gain insights into the mechanistic aspects controlling the genomic occupancy of ACTB and how this phenomenon is regulated by SETD3, we performed a proteomic experiment to identify overlapping interacting proteins with ACTB and SETD3. Biological process GO enrichment and STRING analysis...
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Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
- Shuai Wang,
- Merritt Khaipho-Burch,
- Lynn C. Johnson,
- Zachary R. Miller,
- Peter J. Bradbury,
- Doug Speed,
- William J. Allen,
- M. Cinta Romay,
- Jiquan Xue,
- Edward S. Buckler,
- Guillaume P. Ramstein,
- and Baoxing Song
Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
...University, Ithaca, New York 14853, USA; 4Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA; 5Agricultural Research Service, United States Department of Agriculture, Ithaca, New York 14853, USA; 6Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000...
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Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. April 2026 36: 754-768; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...transcriptomic data is hindered by high noise levels and missing gene measurements, challenges that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome this challenge, we introduce spRefine, a deep learning framework that leverages genomic language...
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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
...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
...Ruhollah Shemirani1, Gillian M. Belbin1,9, Sinead Cullina1,2, Christa Caggiano1, Christopher R. Gignoux3,4, Noah Zaitlen5,6,7 and Eimear E. Kenny1,2,8 1Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; 2Department of Genetics and Genomic Sciences...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; 3State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...provide examples of multiomic comparisons that reveal insights that connect the transcriptome, translatome, and degradome. In summary, ggRibo is an advanced single-gene viewer that offers a valuable resource for studying gene expression regulation through its intuitive and flexible platform...
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