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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
...performance for other tracks. Our results show that current deep learning models perform poorly when presented with novel sequences diverging in certain critical features from their training set. Thus, an iterative approach incorporating profiling of synthetic constructs can improve model generalizability...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...) with default arguments for 20 iterations as conducted in a previous study (Pehrsson et al. 2019). Epigenetic state annotations and subsequent analyses were conducted in the same way as true TEs.TE subfamily enrichment analysisTE subfamily enrichment was calculated as the log odds ratio as previously described...
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Research: Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes
- Yuvia A. Pérez-Rico,
- Valentina Boeva,
- Allison C. Mallory,
- Angelo Bitetti,
- Sara Majello,
- Emmanuel Barillot,
- and Alena Shkumatava
Genome Res. February 2017 27: 259-268; Published in Advance December 13, 2016, doi:10.1101/gr.203679.115
...Comparative analyses of super-enhancers reveal conserved elements in vertebrate s Yuvia A. Pérez-Rico,1,2,3 Valentina Boeva,2,4,5 Allison C. Mallory,1 Angelo Bitetti,1,3 Sara Majello,1 Emmanuel Barillot,2,4 and Alena Shkumatava1 1Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215...
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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...al. 2011; Ernst and Kellis 2012; Day et al. 2007; Zhang et al. 2016) (reviewed in Libbrecht et al. 2 2021 (Libbrecht et al. 2021)). These methods take as input a collection of epigenomic data sets from a given biosample, which may be a primary tissue sample or cell line, and produce an annotation...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
...such as ENCODE (The ENCODE Project Consortium 2012) and Roadmap Epigenomics (Roadmap Epigenomics Consortium et al. 2015) have generated a large amount of genomics data using short-read sequencing technology, but efficient ways for exploring such data in the context of repeat elements have been much less...
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Method: Minimizing reference bias with an imputed personalized reference
- Kavya Vaddadi,
- Mao-Jan Lin,
- Sina Majidian,
- Taher Mun,
- and Ben Langmead
Genome Res. March 5, 2026 gr.280989.125; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
...methods is to reduce the “reference bias” that results when aligning reads to a single reference (Lin et al. 2024). Bias occurs when reads containing non-reference alleles fail to align to their true point of origin, leading to inaccurate results for analyses concerned with hypervariable regions (Brandt...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
..., Yaozhi 5 Wang1, Allen Wang2, Xiang-Dong Fu3, William C. Mobley4, Bing Ren1,2* 6 Department of Cellular and Molecular Medicine, University of California San Diego, School of 7 Medicine, La Jolla, CA 92093, USA 8 Center for Epigenomics, University of California San Diego, School of Medicine, La Jolla, CA 9...
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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
...Corresponding author: chengf@ccf.orgAbstractAlzheimer's disease (AD) is a complex and poorly understood neurodegenerative disorder that lacks sufficiently effective treatments. Computational and integrative analyses that leverage multiomic data provide a promising strategy to uncover disease mechanisms...
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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
...for analyses. The sources of useful data for inferring TFs that might regulate a GOI include – Proximity to experimentally proven TSSs. – Chromatin landscape indicating open chromatin or, more specifically, epigenetic features known to be linked with enhancers. – TF binding to DNA sequences within the GOI...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
.... Comprehensive benchmarking analyses (Fig. 3B) demonstrate that EnDeep4mC's significant outperformance across key evaluation metrics. EnDeep4mC outperformed all baselines with average ACC of 95.28% and AUC of 0.9863, surpassing the suboptimal model EpiTEAmDNA by 2.76% (ACC) and 1.21% (AUC). Notably, EnDeep4m...
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