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Resource: A single-cell tumor immune atlas for precision oncology
- Paula Nieto,
- Marc Elosua-Bayes,
- Juan L. Trincado,
- Domenica Marchese,
- Ramon Massoni-Badosa,
- Maria Salvany,
- Ana Henriques,
- Juan Nieto,
- Sergio Aguilar-Fernández,
- Elisabetta Mereu,
- Catia Moutinho,
- Sara Ruiz,
- Patricia Lorden,
- Vanessa T. Chin,
- Dominik Kaczorowski,
- Chia-Ling Chan,
- Richard Gallagher,
- Angela Chou,
- Ester Planas-Rigol,
- Carlota Rubio-Perez,
- Ivo Gut,
- Josep M. Piulats,
- Joan Seoane,
- Joseph E. Powell,
- Eduard Batlle,
- and Holger Heyn
Genome Res. October 2021 31: 1913-1926; Published in Advance September 21, 2021, doi:10.1101/gr.273300.120
...comprehensively take into account cell type– or patient-specific peculiarities. Overlapping gene expression signatures, as shown for the proliferation-related transcriptional program, can challenge distinguishing the presence of immune cells from cell types that are not present in the training set. Consequently...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...Institute, University College London, London WC1E 6DD, United Kingdom; 5Cancer Metastasis Laboratory, University College London Cancer Institute, London WC1E 6DD, United Kingdom; 6Department of Oncology, University College London Hospitals, London NW1 2BU, United Kingdom; 7Cancer Genome Evolution Research...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...analysis (miR-10b-5p is downregulated in breast cancer), representing a 75% recall. Considering all of the 14 predicted targets, we also computed a precision of 43% and an accuracy of 64%. If we increase the log2 fold-change threshold to determine which genes are upregulated according to our DGE analysis...
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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
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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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
...Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease Yunxiao Ren1,2, Ming Hu3,4, Yang E. Li5, Andrew A. Pieper6,7,8,9,10,11, Jeffrey Cummings12 and Feixiong Cheng1,2,4,13 1Cleveland Clinic Genome Center, Cleveland Clinic Research...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...accessibility data, and prior GRNs, PRISM-GRN decomposes the observable expression of each gene into latent variables that capture the unobserved contributions of its regulatory factors. This is achieved through a regulation mechanism–informed variational inference process, enabling the precise reconstruction...
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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
...primarily employed RNA sequencing(Jin et al. 2025), which, while 63 informative, does not fully elucidate the complex regulatory mechanisms underlying 64 transcriptional programs. Gene expression is regulated by cis-regulatory elements (CREs) in a 65 spatiotemporal manner through precise gene regulatory...
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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
...in allele frequency between disease cases and healthy controls, these GWAS hits tend to have modest or even minor effects on the phenotype, resulting in limited prediction capability for individuals. In an effort to enhance predictive modeling, various statistical methods have been proposed to aggregate...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
..., STMSC captures intra- and interstage heterogeneity in cancer development, offering novel insights into the complexity of pathological tissue structures.Spatial transcriptomics (ST) technologies have revolutionized biotechnology by enabling precise localization of gene expression within tissues, offering...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
...a prioritization of functionally relevant driver genes. Tissue-specific recalibration increases detection of known disease-relevant processes. Altogether, our method provides a novel view on DE and contributes toward bridging the existing gap between statistical and biological significance. We believe...
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