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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...and categorical variables, underlying sparse network structures, and, importantly, the block structure introduced by redundant variables (simulating multiple peptides per protein) alongside unique variables (simulating other omics or phenotypes).PriOmics improves on network inference in settings with redundant...
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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
...-GRN was further validated by its strong performance with limited prior knowledge and unpaired omics data. Additionally, downstream biological analyses were conducted to highlight PRISM-GRN's real-world efficacy in improving the understanding of gene functions and finding GRNs.More specifically, for a given cell...
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Method: A new framework for exploratory network mediator analysis in omics data
- Qingpo Cai,
- Yinghao Fu,
- Cheng Lyu,
- Zihe Wang,
- Shun Rao,
- Jessica A. Alvarez,
- Yun Bai,
- Jian Kang,
- and Tianwei Yu
Genome Res. April 2024 34: 642-654; Published in Advance May 7, 2024, doi:10.1101/gr.278684.123
..., University of Michigan, Ann Arbor, Michigan 48109, USA ↵6 These authors contributed equally to this work. Corresponding authors: jiankang@umich.edu, yutianwei@cuhk.edu.cnAbstractOmics methods are widely used in basic biology and translational medicine research. More and more omics data are collected...
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Resource: Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
- Peng Gao,
- Xiaotao Shen,
- Xinyue Zhang,
- Chao Jiang,
- Sai Zhang,
- Xin Zhou,
- Sophia Miryam Schüssler-Fiorenza Rose,
- and Michael Snyder
Genome Res. June 2022 32: 1199-1214; Published in Advance June 6, 2022, doi:10.1101/gr.276521.121
.... 2018; Schüssler-Fiorenza Rose et al. 2019; Zhou et al. 2019). Specifically, this study (1) improved the annotation of biological and chemical exposures in the external exposome and human blood; (2) integrated the external exposome with internal multi-omics to investigate the effect of the exposome...
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Resource: Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes
- Andrea Halaburkova,
- Vincent Cahais,
- Alexei Novoloaca,
- Mariana Gomes da Silva Araujo,
- Rita Khoueiry,
- Akram Ghantous,
- and Zdenko Herceg
Genome Res. October 2020 30: 1517-1532; Published in Advance September 22, 2020, doi:10.1101/gr.268292.120
...and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far...
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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
...expression. This is followed by a cascade of RNA processing and protein translation, allowing for the newly expressed protein to execute its function, which in turn may contribute to cell signaling. Consequently, one of the main questions that often arises in research is what transcription factors (TFs...
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Method: Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
- Pratibha Jagannatha,
- Alexandra T. Tankka,
- Daniel A. Lorenz,
- Tao Yu,
- Brian A. Yee,
- Kristopher W. Brannan,
- Cathy J. Zhou,
- Jason G. Underwood,
- and Gene W. Yeo
Genome Res. November 2024 34: 2012-2024; Published in Advance June 21, 2024, doi:10.1101/gr.279176.124
...Methodist Research Institute, Houston, TX 77030, USA Corresponding author: geneyeo@ucsd.eduAbstractTranscription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...Medical University (Naval Medical University), Shanghai 200433, China; 2Center for Translational Medicine, Second Military Medical University (Naval Medical University), Shanghai 200433, China; 3National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University...
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Method: STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
- Congcong Hu,
- Nana Wei,
- Jiyuan Yang,
- Hua-Jun Wu,
- and Xiaoqi Zheng
Genome Res. June 2025 35: 1415-1428; Published in Advance May 12, 2025, doi:10.1101/gr.280031.124
...Congcong Hu1, Nana Wei2,3, Jiyuan Yang1, Hua-Jun Wu2,4,5 and Xiaoqi Zheng1 1Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; 2Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education...
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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
...occur through alterations in cell-signaling and regulatory processes, with post-translational modifications (PTMs) via phosphorylation of serine, threonine, or tyrosine residues used in intracellular signaling pathways, which are among the most widely studied examples (Hunter 1995). However, a large...
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