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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...score to assign variants to splicing impact categories. We established the quality of SeqSplice results by showing that the splicing impact categories followed the expected trends/results based on (1) variant location; (2) published splicing data from assays using minigenes, whole-gene experimental...
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Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
- Antonio Nappi,
- Liubov Shilova,
- Theofanis Karaletsos,
- Na Cai,
- and Francesco Paolo Casale
Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
...across individuals in a formal gene-level association test (Li and Leal 2008; Madsen and Browning 2009; Brandes et al. 2020; Backman et al. 2021; Jurgens et al. 2022; Karczewski et al. 2022). Likely deleterious variants within a gene are typically identified based on consequence annotations (e.g...
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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...disrupt endogenous gene regulation and 106 compromise genomic stability. Thus, selection cassettes are sometimes placed in 107 intronic regions to mitigate this limitation (Wang et al. 2022); however, these can 108 interfere with splicing and generate aberrant transcripts. Meanwhile, “safe harbor” loci...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...was below the threshold (see Methods).FIE genes showed signals of positive selection, assessed using dN/dS (Fig. 2A; Supplemental Note 4), indicating significant enrichment in missense, nonsense, splice, and truncating mutations compared with synonymous variants. Pancancer FIEs showed positive cancer effect...
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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
.... By integrating transcription factor (TF)–target gene relationships, chromatin accessibility, and genetic variation, this framework aims to elucidate the cell type–specific regulatory mechanisms underlying AD progression, link genetic risk variants to cis-regulatory elements and target genes, and prioritize...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
.... Clustering analysis revealed a group of coregulated genes that increase expression during cell cycle progression, containing cell cycle regulators (Fig. 5D). As expected, ontology analysis confirmed that these variant genes are associated with processes regulating the cell cycle progression (Fig. 5E...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...in the expression of a target gene after enhancer–promoter loop formation (Kim et al. 2019), indicating that loops likely cause increased target gene expression.Such perturbation experiments, combined with newer and higher-resolution 3C variants, have shown that functionally active enhancer–promoter pairs have...
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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
...frame is detected in the Arabidopsis ALP2 gene. The nORF range is highlighted with an orange box in the gene model. (F) A nORF using the blue reading frame is detected in a tomato G protein-coupled receptor beta subunit gene. The nORF range is highlighted with an orange box in the gene model...
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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
...and is susceptible to splice variant “blindness.” Human cancer is especially rich in variations, including coding region mutations of TF genes; these features can sometimes offer similar insights as knockdown/knockout experiments. The Eukaryotic Promoter Database has the SNP2TFBS subdatabase linking genetic variants...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...biological process contains aerobic metabolism genes (e.g., OXPHOS subunits, PPARGC1A, and PPARA), few of those genes are included in the enriched purine metabolism pathway genes in our study, suggesting that the enriched purine metabolic pathway is not caused by aerobic metabolic demands and appears...

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