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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...are therefore likely to impact evolution of gene regulation. Yet, the role of TEs in regulatory evolution after WGDs is not well understood. Here we used Atlantic salmon as a model system to explore how TE activity after the salmonid WGD ∼100 MYA shaped CRE evolution. We identified 55,080 putative TE-CREs using...
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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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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...factors (TFs), and other DNA-associated proteins (Barski et al. 2007; Johnson et al. 2007; Mikkelsen et al. 2007; Furey 2012). The commonly used ChIP-seq method has led to significant insights about principles of gene regulation and function of the epi in both normal and disease conditions (Park 2009...
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Research: A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease
- Sumantra Chatterjee,
- Kameko M. Karasaki,
- Lauren E. Fries,
- Ashish Kapoor,
- and Aravinda Chakravarti
Genome Res. December 2021 31: 2199-2208; Published in Advance November 15, 2021, doi:10.1101/gr.275667.121
...identifies multiscale regulatory element perturbations associated with Hirschsprung disease. Genome Res 30: 1618–1632. doi:10.1101/gr.264473.120 ↵Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, et al. 2002. The structure of haplotype blocks...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
..., such as single-nucleotide variation (SNV), copy number alteration (CNA), and structural variation (SV). The high-throughput sequencing (HTS) technology has revolutionized the way we look at many human diseases, particularly cancer. With its constantly improved capacity and reduced cost, HTS is enabling...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes -wide, providing a deeper, more mechanistic understanding...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...; Porubsky et al. 2022).Consequently, large-scale LRS efforts have enabled the construction of improved reference s, including pangenomic representations of species (Liao et al. 2023) and exploration of the pattern of normal and disease variation across a variety of National Institutes of Health (NIH...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...and ultimately enable functional classification of regulatory variants identified by population studies.Most genetic associations with human diseases and traits lie within noncoding regulatory DNA (Maurano et al. 2012). Genome-scale methods to analyze the function of noncoding regulatory elements within...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
..., reconstructing cell type–specific networks and allowing in silico T perturbations to reveal dynamic regulatory mechanisms. The knowledge-primed model SupirFactor (Tjärnberg et al. 2024) embeds the prior GRN directly into deep learning architectures, enabling biologically interpretable GRN predictions while...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Lê Cao
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...meaningful regulatory variation. For the Perturb-seq data set, which includes perturbations on 5 TFs across different subsets of cells, we again used NNet to measure coexpression between perturbed TFs and 5151 target genes. Subsequently, we calculated ETAS and CoETAS for each of the 5 perturbed TFs across...
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