Searching journal content for articles similar to Hanson et al. 28 (8): 1207.

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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
..., and interpretable exploration of causal GRNs with prior knowledge and multi-omics data.Gene regulatory networks (GRNs), which encapsulate the complex interactions among transcription factors (TFs), target genes, and various regulatory elements, constitute the core machinery of gene regulation (Levine and Davidson...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33...
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Research: Diploid genome architecture revealed by multi-omic data of hybrid mice
- Zhijun Han,
- Kairong Cui,
- Katarzyna Placek,
- Ni Hong,
- Chengqi Lin,
- Wei Chen,
- Keji Zhao,
- and Wenfei Jin
Genome Res. August 2020 30: 1097-1106; Published in Advance August 5, 2020, doi:10.1101/gr.257568.119
...Diploid architecture revealed by multi-omic data of hybrid mice Zhijun Han1,2, Kairong Cui3, Katarzyna Placek3, Ni Hong1, Chengqi Lin2, Wei Chen1, Keji Zhao3 and Wenfei Jin1 1Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; 2Institute of Life...
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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
..., making it possible to search for a similar function. The richest source of potentially unexpected perturbation-based data comes from correlating genetic variability in candidate regulatory regions with known phenotypes. The GTEx Consortium et al. (2020) has analyzed variations in potential regulatory...
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Method: A gene regulatory network–aware graph learning method for cell identity annotation in single-cell RNA-seq data
- Mengyuan Zhao,
- Jiawei Li,
- Xiaoyi Liu,
- Ke Ma,
- Jijun Tang,
- and Fei Guo
Genome Res. July 2024 34: 1036-1051; Published in Advance August 12, 2024, doi:10.1101/gr.278439.123
....In single-cell transcriptome sequencing, high-resolution quantification of gene expression profiles provides insights into cellular heterogeneity and the molecular underpinnings of tissue phenotype variations (Kalucka et al. 2020; Argelaguet et al. 2021). Analyzing cell type composition using sc...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
.... Nonetheless, bacteria offer several unique avenues for research into the process and mechanics of gene birth at a resolution not feasible in other organisms. Both their amenability to experimental evolutionary analysis and their strain-level variation in gene content foster investigations of how noncoding...
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Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
- Yingxin Lin,
- Tung-Yu Wu,
- Xi Chen,
- Sheng Wan,
- Brian Chao,
- Jingxue Xin,
- Jean Y.H. Yang,
- Wing H. Wong,
- and Y.X. Rachel Wang
Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
...the functions of gene regulatory networks (GRNs) in shaping cell identity and cell fate is one of the central quests in understanding the mapping from genomic blueprints to phenotypes. Over the past decades, much effort has been devoted to developing statistical and computational methods for inferring GRNs from...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...to be a promising approach toward modeling the role of genomic variants in cis regulatory logic. In particular, CNNs have already shown great promise in modeling the contribution of promoter genetic variation on mean gene expression levels. Agarwal and Shendure (2020) first introduced their algorithm, Xpresso...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...gene expression knockdown phenotype observed.DiscussionMoving from computational predictions to functional evidence of gene regulatory activity remains an important and challenging area of modern genomics. Because there is substantial evidence for tissue-specific gene regulation and evidence...
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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...dynamics were revealed for many 30 orthologous Hox genes, notable cross-species differences were identified from 31 pre-ZGA leading up to hatching. This multi-omics investigation provides a novel 32 atlas of non-coding regulatory elements controlling turbot development, with key 33 applications...
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