Searching journal content for articles similar to Keren et al. 25 (12): 1893.

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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
...sample when performing sRNA-seq for dual profiling. In contrast, degradation bias (half-life analysis) and noise from housekeeping genes do not appear to have a significant effect upon or bias our approach. For the latter, Gene Ontology analysis identified tissue-specific pathways, reinforcing...
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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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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...sacrificing signal from genuine nascent transcripts.The second stage of the analysis involved quantifying RNAPII elongation rates from noise-corrected read coverage profiles. For each individual gene, read coverage was quantified at every single base pair position from the transcription start site...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...using edgeR (v4.2.1) and ranked using the Signal2Noise metric with the local version of the GSEA tool (v4.3.3; http://www.broadinstitute.org/gsea/index.jsp). GSEA was performed using the Hallmark, C2, and C5 gene sets from MSigDB, with clusterProfiler (v4.12.6) (Xu et al. 2024). Statistical testing...
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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
...as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.Master transcription factors (TFs), which...
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Research: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters
- Sachin Pundhir,
- Jinyu Su,
- Marta Tapia,
- Anne Meldgaard Hansen,
- James Seymour Haile,
- Klaus Hansen,
- and Bo Torben Porse
Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
....porse@finsenlab.dk, sachin.pundhir@finsenlab.dkAbstractSWI/SNF and NuRD are protein complexes that antagonistically regulate DNA accessibility. However, repression of their activities often leads to unanticipated changes in target gene expression (paradoxical), highlighting our incomplete understanding of their activities...
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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
...–dependent gene regulatory interactions, which cannot be represented as static networks (Huang et al. 2018). Because of the specificity and dynamics of tissue microenvironments, technical noise, and impacts from other sources at single-cell resolution, the transcriptomic gene expression levels may be partially...
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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
...genes (HVGs) as input through a pair of coupled batchnorm layers to account for large variations in gene expression levels, making it more robust and generalizable. Third, scTIE provides the means to extract interpretable features from the common embedding space by linking the developmental trajectories...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins...
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Method: Dissecting and improving gene regulatory network inference using single-cell transcriptome data
- Lingfeng Xue,
- Yan Wu,
- and Yihan Lin
Genome Res. September 2023 33: 1609-1621; Published in Advance August 14, 2023, doi:10.1101/gr.277488.122
..., 100871; 3Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China, 100871 Corresponding author: yihan.lin@pku.edu.cnAbstractSingle-cell transcriptome data has been widely used to reconstruct gene regulatory networks (GRNs) controlling...

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