Searching journal content for articles similar to Lee et al. 15 (9): 1189.

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  1. Research: Genomic environments scale the activities of diverse core promoters
    • Clarice K.Y. Hong and
    • Barak A. Cohen
    Genome Res. January 2022 32: 85-96; Published in Advance December 27, 2021, doi:10.1101/gr.276025.121
    ...that these specific interactions are small relative to the independent effects of genomic locations and core promoters (see Supplemental Fig. S6). The differences in how genomic locations scale the activities of each core promoter subclass are also largely explained by the average strength of each promoter class...
  2. Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
    • Kangli Wang,
    • Weikun Xia,
    • Yingli Gu,
    • Songpeng Zu,
    • Qian Yang,
    • Maria Luisa Amaral,
    • Yaozhi Wang,
    • Allen Wang,
    • Xiang-Dong Fu,
    • William C. Mobley,
    • and Bing Ren
    Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
    ...(Supplemental Fig. S2, Fig. 1B, Methods). This analysis identified 10 cell 102 classes and 27 cell subclasses (Fig. 1C, Supplemental Table S1), including nine subclasses 103 within four non-neurons (NN) classes, six subclasses within two GABAergic (GABA) classes, 104 eleven subclasses within three glutamatergic...
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  3. Method: Fast and accurate out-of-core PCA framework for large scale biobank data
    • Zilong Li,
    • Jonas Meisner,
    • and Anders Albrechtsen
    Genome Res. September 2023 33: 1599-1608; Published in Advance August 24, 2023, doi:10.1101/gr.277525.122
    ...a window-based optimization scheme that enables accelerated convergence while improving the accuracy. Additionally, PCAone incorporates out-of-core and multithreaded implementations for the existing Implicitly Restarted Arnoldi Method (IRAM) and RSVD. Through comprehensive evaluations using multiple large...
  4. Research: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
    • Kaia Mattioli,
    • Pieter-Jan Volders,
    • Chiara Gerhardinger,
    • James C. Lee,
    • Philipp G. Maass,
    • Marta Melé,
    • and John L. Rinn
    Genome Res. March 2019 29: 344-355; Published in Advance January 25, 2019, doi:10.1101/gr.242222.118
    ..., Colorado 80301, USA ↵12 These authors contributed equally to this work. Corresponding author: marta.mele.messeguer@gmail.comAbstractTranscription initiates at both coding and noncoding genomic elements, including mRNA and long noncoding RNA (lncRNA) core promoters and enhancer RNAs (eRNAs). However, each...
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  5. Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
    • Zhemin Zhou,
    • Jane Charlesworth,
    • and Mark Achtman
    Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
    ...Accurate reconstruction of bacterial pan- and core s with PEPPAN Zhemin Zhou, Jane Charlesworth and Mark Achtman Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom Corresponding author: Zhemin.Zhou@warwick.ac.ukAbstractBacterial s can contain traces of a complex...
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  6. Research: Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes
    • Shuai Sun,
    • Christian Rödelsperger,
    • and Ralf J. Sommer
    Genome Res. September 2021 31: 1590-1601; Published in Advance July 22, 2021, doi:10.1101/gr.275303.121
    ...across 13 gene age classes in both species.A core network of oscillating genes in both speciesThe observation that oscillatory genes are highly enriched in ancient gene classes does not necessarily indicate that the gene expression patterns are also conserved. To explicitly test this, we identified...
  7. Method: GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
    • Zhemin Zhou,
    • Nabil-Fareed Alikhan,
    • Martin J. Sergeant,
    • Nina Luhmann,
    • Cátia Vaz,
    • Alexandre P. Francisco,
    • João André Carriço,
    • and Mark Achtman
    Genome Res. September 2018 28: 1395-1404; Published in Advance July 26, 2018, doi:10.1101/gr.232397.117
    ...all 53 genes encoding ribosomal proteins (rMLST) (Jolley et al. 2012), thousands of core genes that are present in most isolates of a species or genus (core MLST, cgMLST) (Mellmann et al. 2011; Maiden et al. 2013; Moura et al. 2016), or even all the genes in the entire (whole MLST, wgMLST) (Nadon et...
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  8. Method: Models of human core transcriptional regulatory circuitries
    • Violaine Saint-André,
    • Alexander J. Federation,
    • Charles Y. Lin,
    • Brian J. Abraham,
    • Jessica Reddy,
    • Tong Ihn Lee,
    • James E. Bradner,
    • and Richard A. Young
    Genome Res. March 2016 26: 385-396; Published in Advance February 3, 2016, doi:10.1101/gr.197590.115
    ...Models of human core transcriptional regulatory circuitries Violaine Saint-André 1 , 5 , Alexander J. Federation 2 , 5 , Charles Y. Lin 2 , Brian J. Abraham 1 , Jessica Reddy 1 , 3 , Tong Ihn Lee 1 , James E. Bradner 2...
  9. Chicken Special/Letters: Evolution and functional classification of vertebrate gene deserts
    • Ivan Ovcharenko,
    • Gabriela G. Loots,
    • Marcelo A. Nobrega,
    • Ross C. Hardison,
    • Webb Miller,
    • and Lisa Stubbs
    Genome Res. January 2005 15: 137-145; Published in Advance December 8, 2004, doi:10.1101/gr.3015505
    ..., the majority of genes that are either flanked by stable gene deserts or are neighboring these highly conserved intervals are functionally related to core biochemical processes such as regulation of transcription, skeletal and muscle development, DNA binding, and regulation of metabolism. The density of h...
  10. Research: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
    • Joe R. Harman,
    • Ross Thorne,
    • Max Jamilly,
    • Marta Tapia,
    • Nicholas T. Crump,
    • Siobhan Rice,
    • Ryan Beveridge,
    • Edward Morrissey,
    • Marella F.T.R. de Bruijn,
    • Irene Roberts,
    • Anindita Roy,
    • Tudor A. Fulga,
    • and Thomas A. Milne
    Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
    ...genes downstream of KMT2A-AFF1 using feed-forward loop (FFL) and cascade motifs. A core set of nodes are present in both ALL and AML, and CRISPR screening revealed several factors that help mediate response to the drug venetoclax. Using our GRN, we then identified a KMT2A-AFF1:RUNX1 cascade...
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