Searching journal content for articles similar to Li et al. 34 (7): 1027.

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Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...spRefine denoises and imputes spatial1 transcriptomics with a reference-free framework2 powered by genomic language model3 Tianyu Liu1,2, Tinglin Huang3, Wengong Jin4,5, Tinyi Chu2, Rex4 Ying3, Hongyu Zhao1,2*5 1Interdepartmental Program in Computational Biology &6 Bioinformatics, Yale University...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...Corresponding author: jmurr@pennmedicine.upenn.eduAbstractDuring embryonic development, cells undergo dynamic changes in gene expression that are required for appropriate cell fate specification. Although both transcription and mRNA degradation contribute to gene expression dynamics, patterns of mRNA decay...
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Method: Leveraging protein language models for accurate multiple sequence alignments
- Claire D. McWhite,
- Isabel Armour-Garb,
- and Mona Singh
Genome Res. July 2023 33: 1145-1153; Published in Advance July 6, 2023, doi:10.1101/gr.277675.123
...:10.1007/s00439-021-02411-y ↵Mirarab S, Nguyen N, Guo S, Wang L-S, Kim J, Warnow T. 2015. PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. J Comput Biol 22: 377–386. doi:10.1089/cmb.2014.0156 ↵Miyata T, Yasunaga T. 1980. Molecular evolution of mRNA: a method...
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Research: Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation
- Blandine C. Mercier,
- Emmanuel Labaronne,
- David Cluet,
- Laura Guiguettaz,
- Nicolas Fontrodona,
- Alicia Bicknell,
- Antoine Corbin,
- Mélanie Wencker,
- Fabien Aube,
- Laurent Modolo,
- Karina Jouravleva,
- Didier Auboeuf,
- Melissa J. Moore,
- and Emiliano P. Ricci
Genome Res. March 2024 34: 394-409; Published in Advance March 20, 2024, doi:10.1101/gr.277863.123
....ricci@ens-lyon.org, melissa.moore@umassmed.eduAbstractmRNA translation and decay are tightly interconnected processes both in the context of mRNA quality-control pathways and for the degradation of functional mRNAs. Cotranslational mRNA degradation through codon usage, ribosome collisions, and the recruitment of specific...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...Genomics Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA ↵4 Present address: Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA Corresponding author: jarriber@ucsc.eduAbstractPremature stop codon–containing mRNAs can produce...
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Method: Designing realistic regulatory DNA with autoregressive language models
- Avantika Lal,
- David Garfield,
- Tommaso Biancalani,
- and Gokcen Eraslan
Genome Res. September 2024 34: 1411-1420; Published in Advance September 25, 2024, doi:10.1101/gr.279142.124
..., low, or cell type–specific activity, using autoregressive language models in conjunction with supervised sequence-to-function models. We used our framework to design synthetic yeast promoters and cell type–specific human enhancers. We demonstrate that the synthetic CREs generated by our approach...
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Method: Parameter-efficient fine-tuning on large protein language models improves signal peptide prediction
- Shuai Zeng,
- Duolin Wang,
- Lei Jiang,
- and Dong Xu
Genome Res. September 2024 34: 1445-1454; Published in Advance July 26, 2024, doi:10.1101/gr.279132.124
...in protein translocation in cells. The development of large protein language models (PLMs) and prompt-based learning provide a new opportunity for SP prediction, especially for the categories with limited annotated data. We present a parameter-efficient fine-tuning (PEFT) framework for SP prediction, PEFT...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...to revolutionize scientific discoveries in RNA biology through the comprehensive identification and quantification of full-length mRNA isoforms. Despite great promise, challenges remain in the widespread implementation of LRS technologies for RNA-based applications, including concerns about low coverage, high...
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Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
- Juncheng Lin,
- Fu-Yu Hung,
- Congting Ye,
- Liwei Hong,
- Yuan-Hsin Shih,
- Keqiang Wu,
- and Qingshun Q. Li
Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
...361102, China Corresponding authors: liqq@xmu.edu.cn, kewu@ntu.edu.twAbstractEukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). Although nucleosomes have been reported to regulate mRNA...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA ↵3 These authors contributed equally to this work. Corresponding author: jsanfor2@ucsc.eduAbstractAlternative splicing (AS) alters the cis-regulatory landscape of mRNA isoforms, leading to transcripts with distinct...
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