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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
...applied distinct approaches both to the identification of drivers (i.e., by predicting FIEs) and to their analysis with respect to gene duplication.FunVar was designed to detect mutations with impacts on functional sites, predict rare drivers, and provide insights into the structural and functional...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...for highly expressed genes.Although Noureen et al. (2022) investigated the robustness of various signature scoring methods for bulk and single-cell RNA-seq, focusing on sensitivity and specificity across in silico data sets, the study did not address score range comparability, which is necessary for accurate...
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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
...in silico perturbation methods for drug repurposing. Network proximity analysis identifies potential drugs by assessing the proximity between the drug target set and AD-related gene set. Drug efficacy is evaluated based on the proximity distance and Z-score. GSEA leverages drug–gene signatures from the CMap...
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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
...sitesA eukaryotic gene typically consists of regulatory elements such as distal enhancers, which can act over long distances; a proximal promoter containing key TF binding sites; a core promoter surrounding the transcription start site (TSS) where the preinitiation complex assembles, followed...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...and proceeds along the gene body to transcribe RNA (Jonkers and Lis 2015; Core and Adelman 2019; Noe Gonzalez et al. 2021; Aoi and Shilatifard 2023). As with all steps in the transcription process, elongation is tightly regulated to ensure that RNAPII travels along the gene at a proper speed (i.e., elongation...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...(SINEs), which are believed to play a role in Xist spreading, coating, and X-linked gene silencing (Fig. 2A; Lyon 1998; Chaumeil et al. 2006; Chow et al. 2010; Loda et al. 2017). Additionally, it has been shown that this region contains the P0 Xist promoter, although the existence of the P0 promoter...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...nucleic acids, so as to maximize the efficacy and specificity of their processing (Fig. 5A; Bertero 2021). We specifically propose that, as in the case of RBM20, “RNA factories” arise from the clustered binding of trans-acting factors to one or more core coregulated genes and/or their encoded transcripts...
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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
...et al. 2004; Deng and Roberts 2005; Sandelin et al. 2007; Juven-Gershon and Kadonaga 2010; Kadonaga 2012). Hence, in the analysis of gene expression, it is necessary to understand and to incorporate the specific components of the core promoter (Juven-Gershon and Kadonaga 2010; Kadonaga 2012...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...-1, (UN2) unknown-2. (D) Genome browser views showing the aggregated and normalized snATAC-seq signals at promoter regions (±1 kb from transcription start site) of selected cell-type marker genes. Tracks are colored with the same color code as in B and C.After quality control, a total of 83,281 high...
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Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
- Kathleen Zeglinski,
- Christian Montellese,
- Matthew E. Ritchie,
- Monther Alhamdoosh,
- Cédric Vonarburg,
- Rory Bowden,
- Monika Jordi,
- Quentin Gouil,
- Florian Aeschimann,
- and Arthur Hsu
Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
...(Cavazzana-Calvo et al. 2010; De Ravin et al. 2022) also present in the Globin LV, and an additional splice acceptor site predicted in silico using NetGene2 (Brunak et al. 1991), located outside the core region and thus specific to the 650 bp insulator version. Vector “WAS LV3” contains an additional...

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