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Method: Graph-based self-supervised learning for repeat detection in metagenomic assembly
- Ali Azizpour,
- Advait Balaji,
- Todd J. Treangen,
- and Santiago Segarra
Genome Res. September 2024 34: 1468-1476; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
....In this paper, we propose GraSSRep, a novel graph-based algorithm to identify and detect the repeated sequences in the metagenomic assembly in a self-supervised manner. Our contributions are threefold: (1) By leveraging GNNs, we devise the first method that learns (rather than prespecifies) graph features...
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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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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
...York University Grossman School of Medicine, New York, New York 10016, USA Corresponding author: maurano@nyu.eduAbstractDeep learning models can accurately reconstruct -wide epigenetic tracks from the reference sequence alone. But it is unclear what predictive power they have on sequence diverging from...
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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: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...of intermediary files and making the workflow labor intensive. As more IGH haplotypes become available, pan-locus reference graphs and graph-based variant callers may well replace de novo assembly entirely. Finally, compared with the capture-based PacBio protocol (Rodriguez et al. 2020), our ultra-long ONT...
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Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
- Samuel T. Horsfield,
- Basil C.T. Fok,
- Yuhan Fu,
- Paul Turner,
- John A. Lees,
- and Nicholas J. Croucher
Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
.... To improve performance when detecting novel serotypes, we develop a graph-based bioinformatic method for NAS, named GNASTy (Graph-based Nanopore Adaptive Sampling Typing, pronounced “nasty”), and benchmark it against the current NAS implementation, which uses linear alignment. Overall, we demonstrate...
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Method: Incorporating valuable prior knowledge to improve deep learning prediction of genetic perturbation responses
- Xiuhao Fu,
- Chao Yang,
- Chunyan Cui,
- Aoyun Geng,
- Yidi Sun,
- Chao Zha,
- Feifei Cui,
- Leyi Wei,
- Quan Zou,
- Xin Gao,
- and Zilong Zhang
Genome Res. March 26, 2026 gr.281523.125; Published in Advance March 26, 2026, doi:10.1101/gr.281523.125
....gao@kaust.edu.sa) Abstract 1 Genetic perturbation response prediction plays a critical role in virtual cell research, 2 yet the performance of current deep learning models still leaves room for 3 improvement. In this study, we present a prior-guided response inference model 4 (PRIM) that leverages a valuable priori...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. April 2026 36: 726-739; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...Haplotype-resolved telomere-to-telomere of Aphelenchus avenae implicates P5CS in nematode desiccation stress response Yali Zhang1,2,3,4,7, Yayi Zhou2,3,7, Yangyang Chen2,3, Xueyu Wang2,3, Boyan Hu2,3, Shahid Siddique4, Romnick A. Latina4,5, Veronica I. Casey4, Dexin Bo2,3, Yucheng Liao2,3, Min...
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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
...during Drosophila embryogenesis. Using a combined haplotype test, we identified 9%–18% of TF-bound regions impacted by genetic variation even for essential regulators. By expanding WASP (a tool for allele-specific read mapping) to examine indels, we increased detection of allelically imbalanced peaks...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
..., skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data...
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