Searching journal content for articles similar to Lozupone et al. 22 (10): 1974.

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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...of 22 RNA editing in gut-brain interactions remains unexplored. Comparative transcriptomic 23 analyses were performed between heads of germ-free (GF) versus conventional (CV) 24 honey bees. A total of 1,528 A-to-I editing sites are identified in honey bee heads, among 25 which nonsynonymous editing...
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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. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
..., it often 24 struggles with interpretability because of its black-box nature. We evaluate 12 ML models 25 alongside GBLUP and BayesR to identify key factors influencing genomic prediction 26 performance across traits with different genetic architectures in multiple agricultural species, 27 including pigs...
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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
...and regression are based on dimensionality reduction and clustering techniques (Tan and Atkinson 2023). Genomic sequences from known and unknown origins are jointly analyzed—unknown samples are assigned to the nearest labeled cluster of the feature space (e.g., PCA space). Yet there are some caveats (Baran et al...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...undergone to colonize a wide variety of animal guts.The herbivorous tortoise isolates of Blastocystis diverged substantially from the human isolated Blastocystis and have many genomic features not seen in the human isolates. We found substantial changes in size, with human isolates possessing significantly...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...DongAhn Yoo1, Katherine M. Munson1 and Evan E. Eichler1,2 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA; 2Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA Corresponding author: ee3@uw...
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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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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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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
...progeny of both sexes (Woodruff et al. 2010; Xie et al. 2022, 2024). This parallel asymmetry in sizes and gene flow suggests that unique genomic components in C. nigoni underlie the numerous HI phenotypes observed between these species (Bi et al. 2015, 2019; Xie et al. 2024). Transcriptomic analyses have...
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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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