Searching journal content for articles similar to DeMarco et al. 20 (8): 1112.

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  1. Research: Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation
    • Joanna Delimata-Raczek,
    • Natalia Koralewska,
    • Bart Krist,
    • Magdalena Rakoczy,
    • Marek Figlerowicz,
    • and Ireneusz Stolarek
    Genome Res. April 3, 2026 ; Published in Advance April 3, 2026, doi:10.1101/gr.281150.125
    ..., overlooks a crucial layer of regulatory complexity: the expression of distinct transcript isoforms. Alternative transcription and splicing generate multiple mRNA variants from a single gene, enabling the production of functionally diverse proteins that fine-tune cellular processes. During development...
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  2. Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
    • Philipp Rentzsch,
    • Aaron Kollotzek,
    • Kaushik Ram Ganapathy,
    • Pejman Mohammadi,
    • and Tuuli Lappalainen
    Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
    ...on genetic expression variance observed in the human population. The newly established metric ranks statistically differentially expressed genes, not by nominal change of expression, but by relative change in comparison to natural dosage variation for each gene. We apply our method to RNA sequencing data...
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  3. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ...are needed in order to properly capture the genetic composition of populations. Here, we explore deep learning techniques, namely, variational autoencoders (VAEs), to process genomic data from a population perspective. We show the power of VAEs for a variety of tasks relating to the interpretation...
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  4. 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
    ...in a dedicated resource.Gene architecture in eukaryotes facilitates generation of more than one mRNA per gene through a differential combination of exons. The exonic region determination is under regulation of several co- and post-transcriptional mechanisms, in which alternative splicing (AS) plays a central...
  5. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...† equal contribution 9 * Corresponding authors: S.L. (lutz0006@umn.edu); F.W.A. (falbert@umn.edu) 10 11 Running title: Mapping of genetic variation with CRI-SPA-Map 12 ABSTRACT 13 Genetic variation within species shapes phenotypes, but identifying the specific genes and 14 variants that cause phenotypic...
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  6. Method: Tree-based differential testing using inferential uncertainty for RNA-seq
    • Noor Pratap Singh,
    • Euphy Y. Wu,
    • Jason Fan,
    • Michael I. Love,
    • and Rob Patro
    Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
    ...-aware differential transcript/gene expression methods. Our method detects inner nodes that show a strong signal for differential expression, which would have been overlooked when analyzing the transcripts alone.RNA-seq has become the de facto technology for measuring the expression profiles of different genomic...
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  7. 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
    ...was below the threshold (see Methods).FIE genes showed signals of positive selection, assessed using dN/dS (Fig. 2A; Supplemental Note 4), indicating significant enrichment in missense, nonsense, splice, and truncating mutations compared with synonymous variants. Pancancer FIEs showed positive cancer effect...
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  8. 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
    ...influence their target expression variation in three ways (Schmiedel et al. 2015). First, by repressing their targets, the miRNAs allow the target genes to have higher transcription rates while retaining the same gene output, thus reducing transcriptional noise. Second, because the miRNAs themselves...
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  9. Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
    • Gabriela D.A. Guardia,
    • Carlos H. dos Anjos,
    • Aline Rangel-Pozzo,
    • Filipe F. dos Santos,
    • Alexander Birbrair,
    • Paula F. Asprino,
    • Anamaria A. Camargo,
    • and Pedro A.F. Galante
    Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
    ...to produce multiple distinct mRNA transcripts, increasing protein diversity (Nilsen and Graveley 2010). In humans, >90% of multiexon genes undergo alternative splicing, generating roughly seven mRNA isoforms per gene on average, although only a fraction of these yield functionally distinct proteins (Pan et...
  10. Resource: The SynMall resource for characterizing the functional impact of synonymous variation
    • Chen Ye,
    • Xiaoyan Li,
    • Na Cheng,
    • Yansen Su,
    • and Junfeng Xia
    Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
    ...functions, including transcriptional regulation, mRNA splicing, translation kinetics, and protein expression (Liu 2020; Bailey et al. 2021). For instance, a recent study identified an sSNV, PIBF1 c.954G > A, that induced exon skipping, leading to a downstream frameshift and premature termination...
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