Searching journal content for articles similar to Lowe and Reddy 25 (10): 1432.

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Method: Automated interpretable artificial intelligence genomic prediction with AlGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...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 prediction; however, it often struggles...
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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. February 3, 2026 ; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...) spRefine as a pretraining framework for representing phenotype information. spRefine is capable of performing survival prediction, identifying spot-level phenotype information, and predicting disease states. spRefine imputes and denoises ST data Genome Research 3 www..org commonly used tools...
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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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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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Method: Genetics-driven risk predictions leveraging the Mendelian randomization framework
- Daniel Sens,
- Liubov Shilova,
- Ludwig Gräf,
- Maria Grebenshchikova,
- Bjoern M. Eskofier,
- and Francesco Paolo Casale
Genome Res. September 2024 34: 1276-1285; Published in Advance September 27, 2024, doi:10.1101/gr.279252.124
...health outcomes are limited. To overcome this challenge, we introduce a novel framework, Predictive Risk modeling using Mendelian Randomization (PRiMeR), which utilizes genetic effects as supervisory signals to learn disease risk predictors without relying on longitudinal data. To do so, PRiMeR leverages...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease Yunxiao Ren1,2, Ming Hu3,4, Yang E. Li5, Andrew A. Pieper6,7,8,9,10,11, Jeffrey Cummings12 and Feixiong Cheng1,2,4,13 1Cleveland Clinic Genome Center, Cleveland Clinic Research...
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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: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...in PD (Hindle 2010; Reeve et al. 2014; Collier et al. 2017). In addition, genetic susceptibility and environmental exposures are believed to interact with age-related cellular decline to influence disease onset and progression (Pang et al. 2019). Despite aging being the greatest risk factor...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...and enabling the exploration of the diversity from complex genomic regions (Miga and Wang 2021). This is particularly valuable for detecting links between genetic markers and diseases, facilitating the genetic study of more prevalent pathologies in different populations. Combining long-read sequencing...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...The paradox of R-loops: guardians of the or drivers of disease? Shachinthaka D. Dissanayaka Mudiyanselage1,2, Phillip Wulfridge1,2 and Kavitha Sarma1,2 1The Wistar Institute, Philadelphia, Pennsylvania 19104, USA; 2Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104...

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