Searching journal content for articles similar to Lu and Clark 22 (7): 1243.

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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...Corresponding authors: marcel.tarbier@scilifelab.se, marc.friedlander@scilifelab.seAbstractmicroRNAs are small RNA molecules that can repress the expression of protein-coding genes post-transcriptionally. Previous studies have shown that microRNAs can also have alternative functions, including influencing...
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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
...of microRNA expression analyses is reflected by the existence of thousands of sRNA-seq studies in which matched total RNA-seq data are often unavailable. The lack of paired sequencing experiments limits the analysis of microRNA–gene regulatory networks. Here, we explore whether protein-coding gene...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...to increase the stability of results in case of strong technical variation and batch effects. UCell is solely based on Mann–Whitney U statistics (Andreatta and Carmona 2021) and is expected to be robust against technical variation as it only uses per-cell gene rank information. JASMINE computes scores...
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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
...accessibility data, and prior GRNs, PRISM-GRN decomposes the observable expression of each gene into latent variables that capture the unobserved contributions of its regulatory factors. This is achieved through a regulation mechanism–informed variational inference process, enabling the precise reconstruction...
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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
...PCR primers designed against nonregulatory regions of the gene when enrichment is not expected, and ensuring DNA shearing with fragments that are not too long in order to prevent nonspecific GOI identification. ChIP has had a revolutionary impact on our understanding of biology and has spearheaded clinical...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
..., and cells maintain higher levels of MYH6.Lastly, we identified cardiomyopathy-associated genetic variants within R3 (Supplemental Fig. S11A). This underscores the impact of genetic variation on complex human traits. Allelic imbalance of disease-related genes has been observed in patients with hypertrophic...
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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...these processes are coordinated to successfully transition cells to the resting dormant state remains unclear. Here we show that microRNA activity, which is otherwise dispensable for preimplantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...primary analysis concerns the recapitulation of individual, direct gene-gene edges through graphical lasso, which we expected to be heavily impacted by sample size, we also performed a limited evaluation of the effects of data aggregation with weighted gene coexpression network analysis (WGCNA...
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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
...ORFs compared with high-translation isoforms (chi-squared test, P = 1.5 × 10−3) (Fig. 3E). These observations largely agree with canonical translation models (Pelletier and Sonenberg 1985; Calvo et al. 2009; Leppek et al. 2018). In the 3′ UTR, we assessed length, microRNA (miRNA) binding sites, and RNA...
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Resource: Dynamics of microRNA expression during mouse prenatal development
- Sorena Rahmanian,
- Rabi Murad,
- Alessandra Breschi,
- Weihua Zeng,
- Mark Mackiewicz,
- Brian Williams,
- Carrie A. Davis,
- Brian Roberts,
- Sarah Meadows,
- Dianna Moore,
- Diane Trout,
- Chris Zaleski,
- Alex Dobin,
- Lei-Hoon Sei,
- Jorg Drenkow,
- Alex Scavelli,
- Thomas R. Gingeras,
- Barbara J. Wold,
- Richard M. Myers,
- Roderic Guigó,
- and Ali Mortazavi
Genome Res. November 2019 29: 1900-1909; Published in Advance October 23, 2019, doi:10.1101/gr.248997.119
...for mouse embryonic development.Development is a well-orchestrated process primarily controlled by transcriptional regulators with posttranscriptional regulators such as microRNAs (miRNAs) playing an essential role in fine tuning gene expression dynamics. miRNAs are small ∼22 nucleotide (nt) endogenous...
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