Searching journal content for articles similar to Tang et al. 30 (12): 1835.

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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...extra data. For example, GraphReg (Karbalayghareh et al. 2022) introduced a graph attention network that integrates chromatin contact data (Hi-C) to predict gene expression. CREaTor (Li et al. 2023) presented a hierarchical deep learning model based on the self-attention mechanism, which utilizes c...
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Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
- W.H. Adrian Tsui,
- Spencer C. Ding,
- Peiyong Jiang,
- and Y.M. Dennis Lo
Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
...technologies makes it possible to scrutinize the characteristics of cfDNA molecules, opening up the fields of cfDNA genetics, epigenetics, transcriptomics, and fragmentomics, providing a plethora of biomarkers. Machine learning (ML) and/or artificial intelligence (AI) technologies that are known...
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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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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...-Cas9 RE deletionsPaired sgRNAs (5′- and 3′-sgRNAs) were designed to target both ends of selected candidate REs in the human DNAJC9 locus to create a deletion. sgRNA with on-target high predicted cleavage and a low number of off-targets was carefully selected using the UCSC Genome Browser (hg38) (Perez...
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Corrigendum: Corrigendum: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. February 2026 36: 432; doi:10.1101/gr.281294.125
...Milad Razavi-Mohseni, Weitai Huang, Yu A. Guo, Dustin Shigaki, Shamaine Wei Ting Ho, Patrick Tan, Anders J. Skanderup and Michael A. Beer Genome Research 34: 680–695 (2024)Following genotyping analysis from ATAC-seq and RNA-seq reads, the authors found the ATAC-seq sample labeled SNU484...
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Method: Graph-based deep reinforcement learning for haplotype assembly with Ralphi
- Enzo Battistella,
- Anant Maheshwari,
- Barış Ekim,
- Bonnie Berger,
- and Victoria Popic
Genome Res. December 2025 35: 2617-2625; Published in Advance November 14, 2025, doi:10.1101/gr.280569.125
...and an actor-critic RL model to learn the read-to-haplotype assignment algorithm based on the MFC reward. We used a large set of fragment graph topologies derived from s from a diverse set of populations included in the 1000 Genomes Project to train Ralphi. To demonstrate the generalizability and adaptability...
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Method: Modeling and predicting cancer clonal evolution with reinforcement learning
- Stefan Ivanovic and
- Mohammed El-Kebir
Genome Res. July 2023 33: 1078-1088; Published in Advance June 21, 2023, doi:10.1101/gr.277672.123
...generative model of cancer evolution. CloMu uses a two-layer neural network trained via reinforcement learning to determine the probability of new mutations based on the existing mutations on a clone. CloMu supports several prediction tasks, including the determination of evolutionary trajectories, tree...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...contributed equally to this work. Corresponding authors: thomas.near@yale.edu, clad@ihb.ac.cn, yangliandong1987@163.comAbstractGenomic evolution can propel and restrict species diversification. Rapid molecular evolution and genomic rearrangement is often associated with increased species diversification...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...and the International Cancer Research Consortium (ICGC), have facilitated the development of clinical-grade classifiers that leverage machine-learning episignatures for diagnosing brain tumors (Wu et al. 2022) and certain Mendelian disorders (Sadikovic et al. 2020). While clinical implementation requires careful...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...1 assembly. Independently, we predicted 23,249 genomic loci encoding StringTie2 transcripts assembled from ribodepleted RNA-seq data (Wang et al. 2022). These transcripts overlapped with (and thus confirmed) known or predicted N2 or AUGUSTUS protein-coding genes and with known N2 ncRNA genes (Table...
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