Searching journal content for articles similar to Barbosa-Morais et al. 16 (1): 66.

Displaying results 1-10 of 59
For checked items
  1. Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
    • Isabela Gerdes Gyuricza,
    • Joel M. Chick,
    • Gregory R. Keele,
    • Andrew G. Deighan,
    • Steven C. Munger,
    • Ron Korstanje,
    • Steven P. Gygi,
    • and Gary A. Churchill
    Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
    ...driver of differential expression compared to age (887 genes compared to 206 genes at FDR < 0.01). For proteins, age is a stronger driver compared to sex (2084 genes compared to 408 genes at FDR < 0.01). Thus the number of proteins showing significant change with age is greater that the number...
    OPEN ACCESS ARTICLE
  2. 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
    ..., such as indels and splice-site polymorphs, and associating them with the coding potential of exonic loci. By systematically annotating exonic loci through EUIDs, ENACT allows inference of their multifaceted roles within gene isoforms and a detailed understanding of how exonic diversity impacts protein variations...
  3. Method: Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori
    • Jiasong Chang,
    • Ruolin Wang,
    • Kai Yu,
    • Tong Zhang,
    • Xiaoxu Chen,
    • Yue Liu,
    • Run Shi,
    • Xiaogang Wang,
    • Qingyou Xia,
    • and Sanyuan Ma
    Genome Res. May 2020 30: 757-767; Published in Advance May 18, 2020, doi:10.1101/gr.249045.119
    ..., “spliceosome”; 14 genes, “RNA degradation”), and protein processing (53 genes, “Ribosome”; 10 genes, “proteasome”). We also found that some signaling pathways, such as mTOR and FoxO, were significantly enriched. Inactivation of TOR in both Drosophila and mammalian cells has shown that TOR controls both cell...
  4. Method: Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity
    • Mayank Murali,
    • Jamie Saquing,
    • Senbao Lu,
    • Ziyang Gao,
    • Emily F. Watts,
    • Ben Jordan,
    • Zachary Peters Wakefield,
    • Ana Fiszbein,
    • David R. Cooper,
    • Peter J. Castaldi,
    • Dmitry Korkin,
    • and Gloria M. Sheynkman
    Genome Res. April 2025 35: 1012-1024; Published in Advance March 14, 2025, doi:10.1101/gr.279317.124
    ...application for quantifying differential isoform usage but also to functionally annotate such isoforms, using the module IsoAnnot (de la Fuente et al. 2020). IsoAnnot maps protein features (e.g., Pfam domains) across isoforms of a gene, and determines how splicing leads to partial or full removal of protein...
  5. 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
    ...conservation. CIRs are closer to the 5′-end, whereas LIRs are closer to the 3′-end of transcripts. EIciRNA-generating genes are more actively transcribed and associated with epigenetic marks of gene activation. Computational analyses and -wide CRISPR screening revealed that SRSF1 binds to CIRs and inhibits...
    OPEN ACCESS ARTICLE
  6. Research: Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays
    • Steffen Erkelenz,
    • Stephan Theiss,
    • Wolfgang Kaisers,
    • Johannes Ptok,
    • Lara Walotka,
    • Lisa Müller,
    • Frank Hillebrand,
    • Anna-Lena Brillen,
    • Michael Sladek,
    • and Heiner Schaal
    Genome Res. December 2018 28: 1826-1840; Published in Advance October 24, 2018, doi:10.1101/gr.235861.118
    ...by the splicing process, where splice sites, conserved sequence elements at the exon/intron boundaries, are recognized by the spliceosome.The vast majority (>99%) of all introns are excised by the major or U2-type spliceosome, associated with a multitude of accessory proteins (Wahl et al. 2009), and most...
  7. Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
    • Rui Yokomori,
    • Kotaro Shimai,
    • Koki Nishitsuji,
    • Yutaka Suzuki,
    • Takehiro G. Kusakabe,
    • and Kenta Nakai
    Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
    ...Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis Rui Yokomori 1 , Kotaro Shimai 2 , Koki Nishitsuji 3 , Yutaka Suzuki 1 , Takehiro G. Kusakabe 2 , 4...
  8. Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
    • Stefan Oberlin,
    • Alexis Sarazin,
    • Clément Chevalier,
    • Olivier Voinnet,
    • and Arturo Marí-Ordóñez
    Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
    ...and transcriptionally active transposons in A. thaliana is illustrated by our comprehensive analysis of the cotranscriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant s, and how such features impact their biology. Genome-wide transcript profiling revealed...
  9. Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
    • Fu-Yuan Zhu,
    • Xin Chen,
    • Yu-Chen Song,
    • Lydia Pui Ying Lam,
    • Yuki Tobimatsu,
    • Bei Gao,
    • Mo-Xian Chen,
    • and Fu-Liang Cao
    Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
    ...in Supplemental Fig. S9) in all the samples (Fig. 2A). A comparison of the identified differentially expressed genes (DEGs) (Supplemental Table S1) with the genes undergoing differential AS (DAS) (Supplemental Table S2), which were obtained with the Pacific Biosciences (PacBio) RSH platforms, revealed that more...
  10. Letter: Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    • Sergei A. Filichkin,
    • Henry D. Priest,
    • Scott A. Givan,
    • Rongkun Shen,
    • Douglas W. Bryant,
    • Samuel E. Fox,
    • Weng-Keen Wong,
    • and Todd C. Mockler
    Genome Res. January 2010 20: 45-58; Published in Advance October 26, 2009, doi:10.1101/gr.093302.109
    ...Genome-wide mapping of alternative splicing in Arabidopsis thaliana Sergei A. Filichkin 1 , Henry D. Priest 1 , Scott A. Givan 1 , Rongkun Shen 1 , 3 , Douglas W. Bryant 1 , 2 , Samuel E. Fox 1 , Weng-Keen Wong 2...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research