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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
...et al., 2008, 2010), the regulatory basis of the IFN 89 system, and more generally antiviral transcriptional responses, remains poorly understood. 90 To tackle this knowledge gap, we investigated the genomic regulatory mechanisms driving 91 core ISG expression responses in the head kidney of Atlantic...
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Method: spRefine denoises and imputes spatial transcriptomics 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 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...spRefine denoises and imputes spatial1 transcriptomics with a reference-free framework2 powered by genomic language model3 Tianyu Liu1,2, Tinglin Huang3, Wengong Jin4,5, Tinyi Chu2, Rex4 Ying3, Hongyu Zhao1,2*5 1Interdepartmental Program in Computational Biology &6 Bioinformatics, Yale University...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...is able to uncover more genetic effects and methylation-dependent genetic effects, highlighting the importance of including diverse s in assays that aim to understand gene regulatory processes.A major goal in evolutionary biology, human genomics, and biomedicine is to understand how the generates complex...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
..., but characterization of their roles in phage lifecycles is limited, and their impact on phage replication is controversial. To address these issues, we have searched for phages whose growth is impacted by the major recombination-promoting helicase-nuclease of Escherichia coli, the RecBCD enzyme. Although no phages...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
.... The first relates to comparative genomics of MGEs across the Asgard archaea and beyond, including investigations across diverse environments and temporal studies. Using enrichments of Asgard archaea or, if they become available, pure cultures, experimental studies could test the adaptive significance...
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Method: Memory-bound k-mer selection for large and evolutionarily diverse reference libraries
- Ali Osman Berk Şapcı and
- Siavash Mirarab
Genome Res. September 2024 34: 1455-1467; Published in Advance August 29, 2024, doi:10.1101/gr.279339.124
...ultra-large genomic reference sets (e.g., Parks et al. 2018; McDonald et al. 2024), often used with marker genes (Asnicar et al. 2020; Balaban et al. 2024). Using these data sets with k-mers-based methods, however, runs into a mundane but key limitation—the memory needed to use these s as reference...
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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
..., controlled by many genes as well as their response to the environment (Mackay et al. 2009). In fact, the recently proposed omnigenic model suggests that a large proportion of all genes play at least some role in controlling every phenotype through trans regulation of the expression of core genes...
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Research: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
- Kaia Mattioli,
- Pieter-Jan Volders,
- Chiara Gerhardinger,
- James C. Lee,
- Philipp G. Maass,
- Marta Melé,
- and John L. Rinn
Genome Res. March 2019 29: 344-355; Published in Advance January 25, 2019, doi:10.1101/gr.242222.118
..., Colorado 80301, USA ↵12 These authors contributed equally to this work. Corresponding author: marta.mele.messeguer@gmail.comAbstractTranscription initiates at both coding and noncoding genomic elements, including mRNA and long noncoding RNA (lncRNA) core promoters and enhancer RNAs (eRNAs). However, each...
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Research: Systematic interrogation of human promoters
- Shira Weingarten-Gabbay,
- Ronit Nir,
- Shai Lubliner,
- Eilon Sharon,
- Yael Kalma,
- Adina Weinberger,
- and Eran Segal
Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
...are structurally and functionally diverse regulatory sequences composed of a variety of DNA elements, including CpG islands, TATA-box, initiator (Inr), upstream and downstream TFIIB recognition elements (BREu and BREd), motif ten element (MTE), and downstream core promoter element (DPE) (Lagrange et al. 1998; Lim...
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Research: Genomic insights into metabolic flux in hummingbirds
- Ariel Gershman,
- Quinn Hauck,
- Morag Dick,
- Jerrica M. Jamison,
- Michael Tassia,
- Xabier Agirrezabala,
- Saad Muhammad,
- Raafay Ali,
- Rachael E. Workman,
- Mikel Valle,
- G. William Wong,
- Kenneth C. Welch, Jr.,
- and Winston Timp
Genome Res. May 2023 33: 703-714; Published in Advance May 8, 2023, doi:10.1101/gr.276779.122
...diversity of repetitive elements (International Chicken Genome Sequencing Consortium 2004; Dalloul et al. 2010; Warren et al. 2010; Sotero-Caio et al. 2017), with the exception of the woodpecker (Picoides pubescens), whose is 22.2% TEs, mostly contributed by the LINE/CR1 (Zhang et al. 2014). In A. colubris...

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