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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
...their relevant context would improve our ability for direct assessment of disease-associated variation. Profiling of allelic transcription factor (TF) activity across multiple cell and tissue types has shown that both genomic and tissue contexts modulate the penetrance of noncoding variants (Halow et al. 2021...
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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. April 2026 36: 785-801; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...Yidi Deng1,2, Jiadong Mao1,4, Jarny Choi3,4 and Kim-Anh Lê Cao1,4 1Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia; 2Research School of Finance, Actuarial Studies & Statistics, The Australian National University...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...and to associated organs including the liver and pancreas. We used functional genomic approaches to identify highly conserved endodermal cis-regulatory modules (CRMs) functioning across the 400 million years of evolution separating zebrafish and humans. Our analyses suggest that there are few endoderm-specific CRMs...
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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
.... Their main use is for generating experimentally testable hypotheses for further research.Experimentally validating TFs by measuring transcription from the GOIWhen dissecting transcriptional regulation, the first experimental point of interest is the process of transcription itself and its immediate product...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...enriched for genomic regions that contained bivalent domains, similar to prior findings (Thudium et al. 2022). These findings suggest that instances of specific genomic features identified in ASD risk genes (King et al. 2013; Zhao et al. 2018) are also common features of transcriptional disruptions...
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Method: TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
- Chen Li,
- Sijie Chen,
- Yixin Chen,
- Haiyang Bian,
- Minsheng Hao,
- Lei Wei,
- and Xuegong Zhang
Genome Res. June 2025 35: 1429-1439; Published in Advance April 10, 2025, doi:10.1101/gr.279955.124
...of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China Corresponding author: weilei92@tsinghua.edu.cnAbstractReprogramming cell state transitions provides the potential for cell engineering and regenerative therapy. Finding the reprogramming transcription factors (TFs...
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Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
- Howard J. Womersley,
- Daniel Muliaditan,
- Ramanuj DasGupta,
- and Lih Feng Cheow
Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
...Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression Howard J. Womersley1,4, Daniel Muliaditan2,3,4, Ramanuj DasGupta3 and Lih Feng Cheow1,2 1Institute for Health Innovation and Technology, National University...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage s publicly available. Importantly, as the number of sequenced s increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior...
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Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
- Alexander Morin,
- Eric Ching-Pan Chu,
- Aman Sharma,
- Alex Adrian-Hamazaki,
- and Paul Pavlidis
Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
...Columbia V6T 1Z4, Canada; 3Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Corresponding author: paul@msl.ubc.caAbstractMapping the gene targets of chromatin-associated transcription regulators (TRs) is a major goal of genomics research. Ch...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...transcriptionally distinct subpopulations, as well as cell type–specific disease-associated gene expression changes from 80,660 cells. Notably, they found that female cells were overrepresented in disease-associated subpopulations and that transcriptional responses were substantially different between sexes...
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