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Showing 1–20 of 20 results
Advanced filters: Author: Sumit Chanda Clear advanced filters

  • Using a multi-OMICS approach, Haas et al identify 54 human genes and 16 host-targeting chemical compounds that regulate influenza A virus infection in lung epithelial cells, including AHNAK and COBP1 which are also essential for SARS-CoV-2 infection.

    • Kelsey M. Haas
    • Michael J. McGregor
    • Nevan J. Krogan
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-27

  • Affinity tagging, mass spectroscopy and a tailor-made scoring system are used to identify 497 high-confidence interactions between human proteins and human immunodeficiency virus proteins.

    • Stefanie Jäger
    • Peter Cimermancic
    • Nevan J. Krogan
    Research
    Nature
    Volume: 481, P: 365-370

  • Becker et al. use live imaging of SARS-CoV-2 infected airway epithelium cultures to demonstrate a dual role for mucociliary clearance in viral spread. Initially, virus goes with the mucus flow, facilitating local spread; later, increased mucus secretion and ciliary motion defects limit spread.

    • Mark E. Becker
    • Laura Martin-Sancho
    • Thomas J. Hope
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-17

  • This study identifies regulators of the RNA sensor RIG-I. Diverse processes, including the unfolded protein response, Wnt signalling and RNA metabolism, modulate this pathway. The splicing regulator KHSRP is identified as a negative regulator of RIG-I that affects influenza replication in vivo.

    • Stephen Soonthornvacharin
    • Ariel Rodriguez-Frandsen
    • Sumit K. Chanda
    Research
    Nature Microbiology
    Volume: 2, P: 1-13

  • Here, the authors discover small molecules that inhibit glycosylation processes that occur in the Golgi apparatus of cells. The molecules reversibly inhibit formation of elaborate glycan structures without affecting secretion of glycoproteins.

    • Daniel Madriz Sørensen
    • Christian Büll
    • Yoshiki Narimatsu
    ResearchOpen Access
    Nature Communications
    Volume: 14, P: 1-19

  • Large-scale OMICs investigations of biological systems can be used to predict functional relationships between compounds, genes and proteins. Here, the authors develop a deep learning-based approach that significantly increases the number of high-quality compound-target predictions relative to existing methods.

    • Hao Chen
    • Frederick J. King
    • Yingyao Zhou
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-15

  • Identification of low abundance proteins interacting with viral proteins can be challenging. Here, Du et al. develop an mRNA display approach with a library of even distribution, identify host proteins interacting with NS1 protein of influenza A virus, and show that one interactor provides a means to regulate cellular fatty acids synthesis.

    • Yushen Du
    • Judd F. Hultquist
    • Ren Sun
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-13

  • The anti-leprosy drug clofazimine inhibits coronavirus replication in several cell models and shows potent antiviral activity against SARS-CoV-2 infection in a hamster model, particularly when used in combination with remdesivir.

    • Shuofeng Yuan
    • Xin Yin
    • Kwok-Yung Yuen
    Research
    Nature
    Volume: 593, P: 418-423

  • With the increasing obtainability of multi-OMICs data comes the need for easy to use data analysis tools. Here, the authors introduce Metascape, a biologist-oriented portal that provides a gene list annotation, enrichment and interactome resource and enables integrated analysis of multi-OMICs datasets.

    • Yingyao Zhou
    • Bin Zhou
    • Sumit K. Chanda
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-10

  • A screen of the ReFRAME library of approximately 12,000 known drugs for antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identified several candidate compounds with suitable activities and pharmacological profiles, which could potentially expedite the deployment of therapies for coronavirus disease 2019 (COVID-19).

    • Laura Riva
    • Shuofeng Yuan
    • Sumit K. Chanda
    Research
    Nature
    Volume: 586, P: 113-119

  • The small coding capacity of the influenza A virus demands that the virus use the host cellular machinery for many aspects of its life cycle. An integrated systems approach, based on genome-wide RNA interference screening, is now used to identify 295 cellular cofactors required for early-stage influenza virus replication. Knowledge of these host cell requirements provides further targets that could be pursued for antiviral drug development.

    • Renate König
    • Silke Stertz
    • Sumit K. Chanda
    Research
    Nature
    Volume: 463, P: 813-817

  • Large-scale RNA interference (RNAi)-based analyses, very much as other 'omic' approaches, have inherent rates of false positives and negatives. The variability in the standards of care applied to validate results from these studies, if left unchecked, could eventually begin to undermine the credibility of RNAi as a powerful functional approach. This Commentary is an invitation to an open discussion started among various users of RNAi to set forth accepted standards that would insure the quality and accuracy of information in the large datasets coming out of genome-scale screens. Please visit methagora to view and post comments on this article

    • Christophe J Echeverri
    • Philip A Beachy
    • René Bernards
    Comments & Opinion
    Nature Methods
    Volume: 3, P: 777-779

  • This resource describes a human MAP kinase interactome. Yeast two hybrid-derived protein interaction maps of MAP kinase pathway members are refined using multiple criteria, tested against reference sets, and functionally validated using knockdown with siRNA.

    • Sourav Bandyopadhyay
    • Chih-yuan Chiang
    • Trey Ideker
    Research
    Nature Methods
    Volume: 7, P: 801-805