Searching journal content for articles similar to Sharma et al. 28 (9): 1372.

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  1. Resource: Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library
    • Jianjie He,
    • Kai Zhang,
    • Shuxiang Yan,
    • Mi Tang,
    • Weixian Zhou,
    • Yongtai Yin,
    • Kang Chen,
    • Chunyu Zhang,
    • and Maoteng Li
    Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123
    ...), consistent with the correct efficiency of the pooled CRISPR library.View larger version: In this window In a new window Figure 2. Identification of the 20-nt target recognition sequences and editing efficiency evaluation of the constructed transgenic collection in the T0 generation. (A) The ratio...
  2. Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
    • Borislav Hrisimirov Hristov,
    • William Stafford Noble,
    • and Alessandro Bertero
    Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
    ...and Duan 2019; Zheng and Xie 2019).Most of our current understanding of 3D architecture centers around chromatin folding within individual chromosomes, that is, on intrachromosomal or cis contacts. These contacts give rise to a variety of hierarchical features at different genomic scales, including...
  3. Research: Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
    • Christelle Cayrou,
    • Philippe Coulombe,
    • Alice Vigneron,
    • Slavica Stanojcic,
    • Olivier Ganier,
    • Isabelle Peiffer,
    • Eric Rivals,
    • Aurore Puy,
    • Sabine Laurent-Chabalier,
    • Romain Desprat,
    • and Marcel Méchali
    Genome Res. September 2011 21: 1438-1449; Published in Advance July 12, 2011, doi:10.1101/gr.121830.111
    ...results demonstrate thatmetazoanOris are in large excess relative to their standard use, and computational simulations suggest that flexible Oris are clustered in groups that define the replicons, where activation of one Ori silences the others in the same group. Results Genome-scale mapping of DNA...
  4. Method: SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
    • Zhengqing Ouyang,
    • Michael P. Snyder,
    • and Howard Y. Chang
    Genome Res. February 2013 23: 377-387; Published in Advance October 11, 2012, doi:10.1101/gr.138545.112
    ...SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data Zhengqing Ouyang 1 , 2 , 3 , Michael P. Snyder 2 and Howard Y. Chang 1 , 3 1 Howard Hughes Medical Institute and Program...
    OPEN ACCESS ARTICLE
  5. Methods: Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis
    • Josephine N. Harada,
    • Kristen E. Bower,
    • Anthony P. Orth,
    • Scott Callaway,
    • Christian G. Nelson,
    • Casey Laris,
    • John B. Hogenesch,
    • Peter K. Vogt,
    • and Sumit K. Chanda
    Genome Res. August 2005 15: 1136-1144; Published in Advance July 15, 2005, doi:10.1101/gr.3889305
    ...Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis Josephine N. Harada 1 , 5 , Kristen E. Bower 2 , 5 , Anthony P. Orth 1 , 5 , Scott Callaway 3 , Christian G. Nelson 1 , Casey...
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  6. Methods: Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing
    • Ken J. Kalafus,
    • Andrew R. Jackson,
    • and Aleksandar Milosavljevic
    Genome Res. April 2004 14: 672-678; doi:10.1101/gr.1963804
    ...Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing Ken J. Kalafus 1 , 2 , Andrew R. Jackson 2 , and Aleksandar Milosavljevic 1 , 2 , 3 , 4 1 Program in Structural and Computational Biology and Molecular Biophysics...
  7. RESOURCE: Construction of a genome-scale structural map at single-nucleotide resolution
    • Jason A. Greenbaum,
    • Bo Pang,
    • and Thomas D. Tullius
    Genome Res. June 2007 17: 947-953; doi:10.1101/gr.6073107
    ...Construction of a genome-scale structural map at single-nucleotide resolution Jason A. Greenbaum 1 , Bo Pang 2 , and Thomas D. Tullius 1 , 2 , 3 1 Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA; 2...
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  8. Research: The identification and functional annotation of RNA structures conserved in vertebrates
    • Stefan E. Seemann,
    • Aashiq H. Mirza,
    • Claus Hansen,
    • Claus H. Bang-Berthelsen,
    • Christian Garde,
    • Mikkel Christensen-Dalsgaard,
    • Elfar Torarinsson,
    • Zizhen Yao,
    • Christopher T. Workman,
    • Flemming Pociot,
    • Henrik Nielsen,
    • Niels Tommerup,
    • Walter L. Ruzzo,
    • and Jan Gorodkin
    Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
    ...and sequencebased alignments (Managadze et al. 2011) have indicated that RNA secondary structures are depleted in lncRNAs (Ulitsky and Bartel 2013). The low sequence conservation of most lncRNAs, while complicating identification of CRSs, does not preclude their existence, such as in telomerase RNA (structurally...
    OPEN ACCESS ARTICLE
  9. Method: Iterative improvement of deep learning models using synthetic regulatory genomics
    • André M. Ribeiro-dos-Santos and
    • Matthew T. Maurano
    Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
    ...and ultimately enable functional classification of regulatory variants identified by population studies.Most genetic associations with human diseases and traits lie within noncoding regulatory DNA (Maurano et al. 2012). Genome-scale methods to analyze the function of noncoding regulatory elements within...
  10. Method: Identification of microRNA-regulated gene networks by expression analysis of target genes
    • Vincenzo Alessandro Gennarino,
    • Giovanni D'Angelo,
    • Gopuraja Dharmalingam,
    • Serena Fernandez,
    • Giorgio Russolillo,
    • Remo Sanges,
    • Margherita Mutarelli,
    • Vincenzo Belcastro,
    • Andrea Ballabio,
    • Pasquale Verde,
    • Marco Sardiello,
    • and Sandro Banfi
    Genome Res. June 2012 22: 1163-1172; Published in Advance February 15, 2012, doi:10.1101/gr.130435.111
    ...-resolution biological functions to miRNAs and provides a comprehensive, genome-scale analysis of human miRNA regulatory networks. Moreover, gene cotargeting analyses show that miRNAs synergistically regulate cohorts of genes that participate in similar processes. We experimentally validate the CoMeTa procedure through...
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