Blar i forfatter "Hsieh, Yin-Chen"

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    • Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson–Boltzmann Theories 

      Hsieh, Yin-Chen; Delarue, Marc; Orland, Henri; Koehl, Patrice (Journal article; Tidsskriftartikkel; Peer reviewed, 2023-06-13)
      The current SARS-CoV-2 pandemic highlights our fragility when we are exposed to emergent viruses either directly or through zoonotic diseases. Fortunately, our knowledge of the biology of those viruses is improving. In particular, we have more and more structural information on virions, i.e., the infective form of a virus that includes its genomic material and surrounding protective capsid, and ...

    • COSNeti: ComplexOme-Structural Network Interpreter used to study spatial enrichment in metazoan ribosomes 

      Martinez-Seidel, Federico; Hsieh, Yin-Chen; Walther, Dirk; Kopka, Joachim; Pereira Firmino, Alexandre Augusto (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-12-20)
      Background: Upon environmental stimuli, ribosomes are surmised to undergo com‑ positional rearrangements due to abundance changes among proteins assembled into the complex, leading to modulated structural and functional characteristics. Here, we present the ComplexOme-Structural Network Interpreter (COSNeti), a computational method to allow testing whether ribosomal proteins (rProteins) that exhibit ...

    • Early Evolutionary Selection of NAD Biosynthesis Pathway in Bacteria 

      Sharma, Suraj; Hsieh, Yin-Chen; Dietze, Jørn; Bockwoldt, Mathias; Strømland, Øyvind; Ziegler, Mathias; Heiland, Ines (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-06-21)
      Bacteria use two alternative pathways to synthesize nicotinamide adenine dinucleotide (NAD) from nicotinamide (Nam). A short, two-step route proceeds through nicotinamide mononucleotide (NMN) formation, whereas the other pathway, a four-step route, includes the deamidation of Nam and the reamidation of nicotinic acid adenine dinucleotide (NAAD) to NAD. In addition to having twice as many enzymatic ...

    • Spatially enriched paralog rearrangements argue functionally diverse ribosomes arise during cold acclimation in arabidopsis 

      Martinez-Seidel, Federico; Beine‐golovchuk, Olga; Hsieh, Yin-Chen; El Eshraky, Kheloud; Gorka, Michal; Cheong, Bo-Eng; Jimenez‐posada, Erika V.; Walther, Dirk; Skirycz, Aleksandra; Roessner, Ute; Kopka, Joachim; Pereira Firmino, Alexandre Augusto (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-06-07)
      Ribosome biogenesis is essential for plants to successfully acclimate to low temperature. Without dedicated steps supervising the 60S large subunits (LSUs) maturation in the cytosol, e.g., Rei-like (REIL) factors, plants fail to accumulate dry weight and fail to grow at suboptimal low temperatures. Around REIL, the final 60S cytosolic maturation steps include proofreading and assembly of functional ...