Searching journal content for articles similar to McKinnon et al. 6 (11): 1077.

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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...diversity. Our findings and case studies unveil systemic exon inclusion roles in regulating diversity in coding region. Correspondingly, annotation of protein-coding genes and associated transcripts from C. elegans, D. melanogaster, D. rerio, M. musculus, and H. sapiens are publicly accessible...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...aberrations in cell-cycle control. In non-small-cell lung cancer (NSCLC), instability occurs early in tumor growth, resulting in pronounced intratumor heterogeneity, including changes in gene copy number, and whole- doubling (WGD) in ∼75% of tumors. Gene duplication, genetic drift, and selection mediate...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...of the transcripts (Supplemental Fig. S9E). This finding was consistent with the reported localization pattern of start and end exons for circRNAs (Guo et al. 2014; Westholm et al. 2014; Rybak-Wolf et al. 2015). LIRs tend to locate to the 3′ region of genes, and a position closer to the 3′-end might be associated...
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Method: Parallel analysis of replication timing, gene expression and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 gr.281532.125; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...Sadu Murari et al., Page 1 Parallel analysis of replication timing, gene expression and copy number 1 with PARTAGE 2 Lakshana Sruthi Sadu Murari 1,† , Quinn Dickinson 1,† , Silvia Meyer-Nava , Juan Carlos Rivera-3 Mulia 1,2,3,4* 4 Department of Biochemistry, Molecular Biology and Biophysics...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...−19), with its corresponding CRE mapped to an exonic region, whereas BIN1 was linked to the rs6733839 locus (AD GWAS P-value 6.48 × 10−90), with its CRE located in a distal regulatory region (Fig. 4F). Additionally, AD-associated genes such as ACE, DGKQ, GRN, and MIR8085 were enriched in excitatory neurons...
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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
...of Mariculture Breeding, Xiamen University, Xiamen, Fujian 361000, China; 4Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision, Xiamen, Fujian 361005, China Corresponding author: wangying@xmu.edu.cnAbstractUnderstanding gene regulatory networks (GRNs) is crucial for deciphering cellular...
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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
...rates with gene length, exon density, and first intron length (Jonkers et al. 2014; Veloso et al. 2014), we found no dependence of RNAPII elongation rates on gene length (Fig. 4C). Moreover, it is common to observe genes of varying lengths exhibiting similar RNAPII elongation rates (Supplemental Fig. S6...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...Revisiting models of enhancer–promoter communication in gene regulation Gilad Barshad1,2 and Charles G. Danko1,2 1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA; 2Department of Biomedical Sciences, College of Veterinary Medicine...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
.... To demonstrate the importance of visualizing the data within the gene context, we also plot the isoform ENST00000329819, which is expressed and translated at low levels relative to ENST00000310999, as shown by the small number of periodic reads in exon 5 of ENST00000329819 (Fig. 3E).Next, we examine the human...
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