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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
...the potential design for iterative improvement of such models by integrating synthetic regulatory data set. Our work suggests a key role for synthetic regulatory genomics in training future genomic deep learning models.ResultsEnformer performance predicting synthetic payloadsTo probe the varied performance...
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Method: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...Geometric deep learning framework for de novo assembly Lovro Vrček1,2, Xavier Bresson3, Thomas Laurent4, Martin Schmitz1,3, Kenji Kawaguchi3 and Mile Šikić1,2 1Genome Institute of Singapore, A*STAR, Singapore 138672; 2Faculty of Electrical Engineering and Computing, University of Zagreb, 10000...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...address this issue by developing deep learning models to deconvolute degenerate cis-regulatory elements and quantify their positional importance in mediating yeast poly(A) site formation, cleavage heterogeneity, and strength. In S. cerevisiae, cleavage heterogeneity is promoted by the depletion of U...
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Method: Modeling gene interactions in polygenic prediction via geometric deep learning
- Han Li,
- Jianyang Zeng,
- Michael P. Snyder,
- and Sai Zhang
Genome Res. January 2025 35: 178-187; Published in Advance November 19, 2024, doi:10.1101/gr.279694.124
...-Net, an interpretable geometric deep learning–based framework that effectively models the nonlinearity of biological systems for enhanced disease prediction and biological discovery. PRS-Net begins by deconvoluting the -wide PRS at the single-gene resolution and then explicitly encapsulates gene–gene interactions...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...(Fisher's test odds ratios 0.24–0.72) (Fig. 2G) and more generally (using a large collection of ChIP data from the ModERN database) (Supplemental Fig. S3D; Kudron et al. 2018). This suggests that the effect of genetic perturbation is buffered through redundant binding of other factors to the same element...
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Resource: Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes
- Wenjuan Yu,
- Haohui Luo,
- Jinbao Yang,
- Shengchen Zhang,
- Heling Jiang,
- Xianjia Zhao,
- Xingqi Hui,
- Da Sun,
- Liang Li,
- Xiu-qing Wei,
- Stefano Lonardi,
- and Weihua Pan
Genome Res. February 2024 34: 326-340; Published in Advance March 1, 2024, doi:10.1101/gr.278232.123
...Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic s and metas Wenjuan Yu1,6, Haohui Luo1,6, Jinbao Yang1,5,6, Shengchen Zhang1,5,6, Heling Jiang1,6, Xianjia Zhao1,4, Xingqi Hui1,4, Da Sun1, Liang Li2, Xiu-qing Wei2, Stefano Lonardi3 and Weihua Pan1 1Shenzhen Branch...
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Method: Polishing copy number variant calls on exome sequencing data via deep learning
- Furkan Özden,
- Can Alkan,
- and A. Ercüment Çiçek
Genome Res. June 2022 32: 1170-1182; Published in Advance June 13, 2022, doi:10.1101/gr.274845.120
..., and sample batching during sequencing. Here, we present a novel deep learning model, DECoNT, which uses the matched WES and WGS data, and learns to correct the copy number variations reported by any off-the-shelf WES-based germline CNV caller. We train DECoNT on the 1000 Genomes Project data, and we show...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
.... These structures have demonstrably shaped organismal evolution. However, a comprehensive, organism-wide G-quadruplex map encompassing the diversity of life has remained elusive. Here, we introduce Quadrupia, the most extensive and well-characterized G-quadruplex database to date, facilitating the exploration of G...
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Method: MCHelper automatically curates transposable element libraries across eukaryotic species
- Simon Orozco-Arias,
- Pío Sierra,
- Richard Durbin,
- and Josefa González
Genome Res. December 2024 34: 2256-2268; Published in Advance December 9, 2024, doi:10.1101/gr.278821.123
.... Genome-wide TE annotations are also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy-to-install and easy-to-use tool.After two decades of sequencing projects, reference s for thousands of eukaryotic species are already available and many more are currently being sequenced...
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Method: Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
...Although motif enrichment can predict candidate regulators, we sought to build a more comprehensive model of the MEL enhancers, which would allow cross-species predictions and in-depth analysis of enhancer architecture. To this end, we trained a deep learning (DL) model on the human ATAC-seq data. First...
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