Searching journal content for articles similar to Gao et al. 32 (6): 1199.

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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
...). In particular, single-cell multi-omics technologies like SHARE-seq (Ma et al. 2020) can simultaneously profile transcriptomic and epigenomic data within individual cells, enabling the interrogation of cellular heterogeneity and molecular hierarchy (Cao et al. 2024). Consequently, numerous methods have emerged...
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Method: Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies
- Jianing Yao,
- Jinglun Yu,
- Brian Caffo,
- Stephanie C. Page,
- Keri Martinowich,
- and Stephanie C. Hicks
Genome Res. July 2025 35: 1621-1632; Published in Advance May 20, 2025, doi:10.1101/gr.279380.124
...demonstrates enhanced accuracy in detecting spatial domains, as evidenced across various benchmark data sets and technological platforms.Spatially resolved multi-omics technologies enable the profiling of multiple omic measurements, such as the transcriptome and proteome, in individual tissue sections, leading...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...) data set because it was primarily designed for short reads. (AUPR) Area under the precision-recall curve.To evaluate the feasibility of PanTax on real metagenomic data, we assessed its performance alongside several leading metagenomic profilers (according to BC distance in our simulated and mock...
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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
...1 Title 1 Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals 2 conserved gene alterations linked to Parkinson’s disease 3 Running title: Substantia nigra aging linked to Parkinson 4 Kangli Wang1, Weikun Xia1, Yingli Gu1, Songpeng Zu1, Qian Yang2, Maria Luisa Amaral1...
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Research: Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis
- Hannah Demond,
- Courtney W. Hanna,
- Juan Castillo-Fernandez,
- Fátima Santos,
- Evangelia K. Papachristou,
- Anne Segonds-Pichon,
- Kamal Kishore,
- Simon Andrews,
- Clive S. D'Santos,
- and Gavin Kelsey
Genome Res. January 2023 33: 18-31; Published in Advance January 23, 2023, doi:10.1101/gr.277046.122
...imaging, multi-omics sequencing, and mass spectrometry (MS)–based proteome analyses in cKO oocytes. Although H3K9me1 was depleted only upon loss of EHMT1, H3K9me2 was decreased, and H3K9me2-enriched domains were eliminated equally upon loss of EHMT1 or EHMT2. Furthermore, there were more significant...
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Method: Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
- Muyoung Lee,
- Qingqing Guo,
- Mijeong Kim,
- Joonhyuk Choi,
- Alia Segura,
- Alper Genceroglu,
- Lucy LeBlanc,
- Nereida Ramirez,
- Yu Jin Jang,
- Yeejin Jang,
- Bum-Kyu Lee,
- Edward M. Marcotte,
- and Jonghwan Kim
Genome Res. March 2024 34: 484-497; Published in Advance April 5, 2024, doi:10.1101/gr.277926.123
...fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem...
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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
..., such as those found in repeat expansion disorders, and for achieving precise haplotype phasing. Enhanced mappability improves variant detection and epigenetic profiling, facilitating a deeper understanding of genetic and epigenetic mechanisms underlying various diseases.Accurate haplotype assignment and phasing...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...in dysregulation of metabolic pathways. We examined the direct effect of glucocorticoid exposure, low-dose dexamethasone (DEX), from embryonic day (E) 4 (before lineage specification) until E7 (blastocyst stage after mural–polar specification has initiated). On E7, we used a single-cell multi-omics approach...
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Resource: dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development
- Xin Huang,
- Xiaohan Tang,
- Xuemei Bai,
- Honglei Li,
- Huan Tao,
- Junting Wang,
- Yaru Li,
- Yu Sun,
- Yang Zheng,
- Xiang Xu,
- Longteng Wang,
- Yang Ding,
- Meisong Lu,
- Pingkun Zhou,
- Xiaochen Bo,
- Hao Li,
- and Hebing Chen
Genome Res. August 2022 32: 1612-1625; Published in Advance August 17, 2022, doi:10.1101/gr.276744.122
...accessibility, and higher-order chromatin structure profiles for human and mouse early embryos. It incorporates customized analysis tools, such as “multi-omics visualization,” “Gene&Peak annotation,” “ZGA gene cluster,” “cis-regulation,” “synergistic regulation,” “promoter signal enrichment,” and “3D .” Users...
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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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