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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Res 27: 38–52. Johnson GD, Barrera A, McDowell IC, D’Ippolito AM, Majoros WH, Vockley CM, Wang X, Allen AS, Reddy TE. 2018. Human -wide measurement of drug-responsive regulatory activity. Nat Commun 9...
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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
...insights into the accessibility of a GOI. Chromatin compaction measured by FRET-FISH was shown to correlate strongly with chromatin accessibility data obtained from ATAC-seq (Mota et al. 2022). FRET-FISH can also detect changes in chromatin compaction in response to drug treatments, during different phases...
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Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...). An example of this is the pharmacological rescue of GABA transport deficiency seen with overexpression of the p.A288V variant in GAT1 (Kasture et al. 2023). This study provided valuable in vivo functional data on drug treatments that could improve the individual's symptoms and set up assays that can be used...
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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 Le Cao
Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...-inflammatory 367 CD8+ T cells, driving tumour growth, metastasis, and immunosuppression (Qi et al., 2022; Bill 368 et al., 2023). While the roles of SRB1, SRC, and ENO1 in TAM have been independently reported, 369 their interaction in promoting SPP1 expression presents a potential regulatory mechanism that 370...
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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
..., et al. 2004. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22: 1001–5. Li Q, Gloudemans MJ, Geisinger JM, Fan B, Aguet F, Sun T, Ramaswami G, Li YI, Ma JB, Pritchard JK, et al. 2022. RNA editing underlies genetic risk of common inflammatory...
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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
...with the Connectivity Map (CMap) database and the drug–target interactome (Fig. 1C). This approach facilitated the identification of candidate repurposable drugs for each major brain cell type across AD progression.Overview of snRNA-seq and snATAC-seq data across ADNC progressionAD progression staging based on ADNC...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...Systematic identification and characterization of exon–intron circRNAs Yinchun Zhong1,6, Yan Yang2,6, Xiaolin Wang2, Bingbing Ren3, Xueren Wang4,5, Ge Shan2 and Liang Chen1 1Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science...
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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
...Wit et al. 2013; Ito et al. 2016), the systematic discovery of functional trans interactions is currently very challenging.View larger version: In this window In a new window Figure 1. The trans-C algorithm. (A) Schematic of typical interchromosomal organization in mammals. Interchromosomal (trans...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...neurological disorders had the strongest associations, including schizophrenia, bipolar disorder, intellectual disability, drug abuse, and autism (Fig. 5B–D; Supplemental Fig. 6). Specifically, we report that 198 schizophrenia-associated genes and 113 bipolar disorder–associated genes are also quasi...
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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
...assay and their tendency to appear in homotypic clusters throughout the . Overall, our study systematically assays the elements that drive expression in core and proximal promoter regions and sheds light on organization principles of regulatory regions in the human .In contrast to the significant...

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