Bioinformatics Core 2 - Zeldovich, UMASS Medical School Core 2 will provide bioinformatics support to the Program Project, developing a laboratory information management system (LIMS) integrated with deep sequencing data analysis pipeline, identification of mutations critical for drug resistance, and HIV genome browsing and visualization tools. Core 2 will develop a LIMS with web front end and MySQL database engine, which will capture the experimental conditions for multiple samples of HIV grown in the presence and absence of protease inhibitors. The database will be integrated with data analysis pipeline, which will identify statistically significant resistance mutations. We will use population genetics simulations to build null models of HIV sequence evolution, and compare the results with deep sequencing data to identify sites undergoing statistically significant selection. For those sites, we will determine selection coefficients, and provide this information to Projects 1-3 for experimental follow up and integration into the I-READSS model of interaction of HIV protease with inhibitors.
Bioinformatics Core 2 - Zeldovich, UMASS Medical School Core 2 will provide bioinformatics support to the Program Project, developing a laboratory information management system (LIMS) integrated with deep sequencing data analysis pipeline, identification of mutations critical for drug resistance, and HIV genome browsing and visualization tools. The LIMS will be integrated with data analysis pipeline, which will identify statistically significant resistance mutations, and determine their selection coefficients. Using the tools developed, Core 2 will be also responsible for public dissemination of the data generated by the Program Project.
|Leidner, Florian; Kurt Yilmaz, Nese; Paulsen, Janet et al. (2018) Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput 14:2784-2796|
|Nemmara, Venkatesh V; Subramanian, Venkataraman; Muth, Aaron et al. (2018) The Development of Benzimidazole-Based Clickable Probes for the Efficient Labeling of Cellular Protein Arginine Deiminases (PADs). ACS Chem Biol 13:712-722|
|Ilina, Tatiana V; Slack, Ryan L; Elder, John H et al. (2018) Effect of tRNA on the Maturation of HIV-1 Reverse Transcriptase. J Mol Biol 430:1891-1900|
|Khan, Shahid N; Persons, John D; Paulsen, Janet L et al. (2018) Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance. Biochemistry 57:1652-1662|
|Persons, John D; Khan, Shahid N; Ishima, Rieko (2018) An NMR strategy to detect conformational differences in a protein complexed with highly analogous inhibitors in solution. Methods 148:9-18|
|Potempa, Marc; Lee, Sook-Kyung; Kurt Yilmaz, Nese et al. (2018) HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites. J Mol Biol 430:5182-5195|
|Tilvawala, Ronak; Nguyen, Son Hong; Maurais, Aaron J et al. (2018) The Rheumatoid Arthritis-Associated Citrullinome. Cell Chem Biol 25:691-704.e6|
|Venev, Sergey V; Zeldovich, Konstantin B (2018) Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis. Mol Biol Evol 35:211-224|
|Wong, Alicia; Bryzek, Danuta; Dobosz, Ewelina et al. (2018) A Novel Biological Role for Peptidyl-Arginine Deiminases: Citrullination of Cathelicidin LL-37 Controls the Immunostimulatory Potential of Cell-Free DNA. J Immunol 200:2327-2340|
|Sun, Bo; Dwivedi, Nishant; Bechtel, Tyler J et al. (2017) Citrullination of NF-?B p65 promotes its nuclear localization and TLR-induced expression of IL-1? and TNF?. Sci Immunol 2:|
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