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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
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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
.... It encodes the alpha chain of the HLA-DR molecule, a component of the major histocompatibility complex class II, which is essential for presenting extracellular antigenic peptides to CD4+ T-helper cells, thereby initiating and regulating immune responses (Palojärvi et al. 2013; Matern et al. 2020).As shown...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...(Loyfer et al. 2023) to ask whether CpG sites located within MD regulatory windows exhibit variable DNAm (1) between individuals in a single blood cell type (monocytes) and (2) between blood cell types within a single individual (comparing monocytes, granulocytes, NK cells, helper T cells, and B cells...
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Method: Time course regulatory analysis based on paired expression and chromatin accessibility data
- Zhana Duren,
- Xi Chen,
- Jingxue Xin,
- Yong Wang,
- and Wing Hung Wong
Genome Res. April 2020 30: 622-634; Published in Advance March 18, 2020, doi:10.1101/gr.257063.119
...multiple time points simultaneously, which would describe the module dynamics more clearly.MethodsGene regulatory network inference from a single time point by PECA2Our previous method PECA takes paired expression and chromatin accessibility data across diverse cellular contexts as input, models how trans...
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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
...; Chen et al. 2023). Moreover, IGFBP4 plays a pivotal signaling role in the differentiation of select T cell subtypes, maintaining a delicate balance between T helper 17 and regulatory T cells (Miyagawa et al. 2017; DiToro et al. 2020). Similarly, FABP5 and ZC3H12A genes are intriguing in breast cancer...
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Method: A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes
- Shang Gao,
- Yang Dai,
- and Jalees Rehman
Genome Res. July 2021 31: 1296-1311; Published in Advance June 30, 2021, doi:10.1101/gr.265595.120
...and mechanistic significance.Several methods have been developed to infer the transcription factor activities and build gene regulatory networks (GRN) from scRNA-seq data. The coexpression network is commonly used among these methods. The relationships of a transcription factor and its target genes...
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Research: Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
- Alexis Battle,
- Sara Mostafavi,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Courtney McCormick,
- Christian D. Haudenschild,
- Kenneth B. Beckman,
- Jianxin Shi,
- Rui Mei,
- Alexander E. Urban,
- Stephen B. Montgomery,
- Douglas F. Levinson,
- and Daphne Koller
Genome Res. January 2014 24: 14-24; Published in Advance October 3, 2013, doi:10.1101/gr.155192.113
....25). These findings support the hypothesis that a large fraction of regulatory variants affect expression through alterationof transcription factor (TF) binding and chromatin accessibility (Degner et al. 2012), improving the resolution of previous findings and extending these observations to variants associated...
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Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
- Alexander Morin,
- Eric Ching-Pan Chu,
- Aman Sharma,
- Alex Adrian-Hamazaki,
- and Paul Pavlidis
Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
...-specific transcription factors and chromatin proteins like MECP2 that bind methylated DNA, are a large class of proteins generalized by their ability to promote or repress gene activity (Lambert et al. 2018; Serebreni and Stark 2021). Learning the regulatory range of TRs is essential to understanding development...
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Method: Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data
- Van Hoan Do,
- Francisca Rojas Ringeling,
- and Stefan Canzar
Genome Res. April 2021 31: 677-688; Published in Advance February 24, 2021, doi:10.1101/gr.267906.120
...contained roughly equal proportions of CD56 NK cells, memory T cells, CD4 T helper cells, and naive T cells. Again, annotated cell types were used as reference partitioning of cells in the evaluation. We excluded a single data set from Duò et al. (2018) in which ground truth labels correspond to collection...

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