Searching journal content for articles similar to Herrgård et al. 16 (5): 627.

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  1. Method: Bayesian inference of sample-specific coexpression networks
    • Enakshi Saha,
    • Viola Fanfani,
    • Panagiotis Mandros,
    • Marouen Ben Guebila,
    • Jonas Fischer,
    • Katherine H. Shutta,
    • Dawn L. DeMeo,
    • Camila M. Lopes-Ramos,
    • and John Quackenbush
    Genome Res. September 2024 34: 1397-1410; Published in Advance August 12, 2024, doi:10.1101/gr.279117.124
    ..., we then explored its performance in analyzing correlation networks in real-world data. Saccharomyces cerevisiae (brewer's yeast) has been extensively used to explore gene function and to explore various network models (Reimand et al. 2010; Hahn and Young 2011; Costanzo et al. 2016, 2021; Teixeira et...
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  2. Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
    • Alexis Morrissey,
    • Jeffrey Shi,
    • Daniela Q. James,
    • and Shaun Mahony
    Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
    ...sizes of paired-end reads to make allocation predictions (Shah and Ruthenburg 2021).Finally, all probabilistic MMR mapping methods to date have outputs that are not easily integrated into most regulatory genomic pipelines as they output custom file types (Hashimoto et al. 2009) or file types...
  3. Method: Dissecting and improving gene regulatory network inference using single-cell transcriptome data
    • Lingfeng Xue,
    • Yan Wu,
    • and Yihan Lin
    Genome Res. September 2023 33: 1609-1621; Published in Advance August 14, 2023, doi:10.1101/gr.277488.122
    ..., 100871; 3Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China, 100871 Corresponding author: yihan.lin@pku.edu.cnAbstractSingle-cell transcriptome data has been widely used to reconstruct gene regulatory networks (GRNs) controlling...
  4. 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
    ...of regulatory binding. (3) Indirect interactions were integrated with the R package GeneNetworkBuilder (v1.26.1) using TF interaction data from the FANTOM consortium (The FANTOM Consortium and the Riken Omics Science Center 2009). TF interactions that do not explain connectivity between the central node...
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  5. Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
    • Monica R. Sanchez,
    • Celia Payen,
    • Frances Cheong,
    • Blake T. Hovde,
    • Sarah Bissonnette,
    • Adam P. Arkin,
    • Jeffrey M. Skerker,
    • Rachel B. Brem,
    • Amy A. Caudy,
    • and Maitreya J. Dunham
    Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
    ...-throughput experimental testing of gene dispensability in Saccharomyces uvarum, a sister species of Saccharomyces cerevisiae. We created haploid and heterozygous diploid Tn7 insertional mutagenesis libraries in S. uvarum to identify species-dependent essential genes, with the goal of detecting genes with divergent...
  6. Research: Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae
    • Orla M. Keane,
    • Christina Toft,
    • Lorenzo Carretero-Paulet,
    • Gary W. Jones,
    • and Mario A. Fares
    Genome Res. November 2014 24: 1830-1841; Published in Advance August 22, 2014, doi:10.1101/gr.176792.114
    ...Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae Orla M. Keane 1 , 2 , 8 , Christina Toft 3 , 4 , 8 , Lorenzo Carretero-Paulet 5 , Gary W. Jones 6 and Mario A...
  7. Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
    • Juan Carlos Rivera-Mulia,
    • Sebo Kim,
    • Haitham Gabr,
    • Abhijit Chakraborty,
    • Ferhat Ay,
    • Tamer Kahveci,
    • and David M. Gilbert
    Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
    ...and mesenchymal differentiation, whereas EtoLtoE networks included communities linked to neurogenesis and axon development (Supplemental Fig. S2). Overall, our results revealed that dynamic changes in RT can be exploited to characterize the complex regulatory interactions established during cell fate commitment...
  8. Research: Fitness benefits of loss of heterozygosity in Saccharomyces hybrids
    • Samuel M. Lancaster,
    • Celia Payen,
    • Caiti Smukowski Heil,
    • and Maitreya J. Dunham
    Genome Res. October 2019 29: 1685-1692; Published in Advance September 23, 2019, doi:10.1101/gr.245605.118
    ..., Marck C, Cruz JA, et al. 2012. Pichia sorbitophila, an interspecies yeast hybrid, reveals early steps of resolution after polyploidization. G3 (Bethesda) 2: 299–311. doi:10.1534/g3.111.000745 ↵Maclean CJ, Greig D. 2008. Prezygotic reproductive isolation between Saccharomyces cerevisiae and Saccharomyces...
  9. Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
    • Jennifer Hammelman,
    • Konstantin Krismer,
    • Budhaditya Banerjee,
    • David K. Gifford,
    • and Richard I. Sherwood
    Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
    ...for measuring the local DNA accessibility of genomically integrated large-scale reporter libraries, and probe the regulatory sequence determinants driving differential chromatin accessibility between stem cells and definitive endoderm.ResultsMultiplexed integrated accessibility assay measures local...
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  10. Research: Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit
    • Yulong Song,
    • Lishi Li,
    • Wenbing Yang,
    • Qiang Fu,
    • Wanying Chen,
    • Zeng Fang,
    • Wen Li,
    • Nannan Gu,
    • and Rui Zhang
    Genome Res. May 2020 30: 661-672; Published in Advance May 18, 2020, doi:10.1101/gr.257121.119
    ...–antisense pairs suggest that the antisense miRNAs might interact with sense miRNAs to form an elaborate regulatory network. First, a unique characteristic of sense–antisense miRNA pair is that the antisense transcript could be directly down-regulated by the coexpressed sense miRNA via complementary base pairing...
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