Biochemistry PhD Student, Sharon Loverde’s Lab
Looking for a working position in research and development opportunities for 2024 in the field of drug development. Open to learning more about companies that work in drug research and development.
As a member of the Loverde lab, Rutika Patel is interested in exploring the effects of post-translational modifications in histone tails that affect nucleosome structure using all -atomistic Molecular Dynamic (MD) simulations. Epigenetic changes are ubiquitous in disease development, such as cancer. Recently, there are new class of drugs that play important role in the epigenetic regulations such as deacetylase inhibitors. It has been shown H2B histone tails play an essential role in cancer associated with p14ARF. H2B histone tails play a critical role in NCP stability and biological processes, yet not well understood, therefore, by using different protein and DNA forcefields, the MD simulations have been done. It will allow us to show the stability and plasticity of the nucleosome that aids into gene expression by performing histone tail analysis, such as Principal component analysis (PCA), Markov state model (MSM), secondary structure propensity and other free energy methods.
When not in the lab, Rutika enjoys painting, learning guitar, playing tennis, and traveling to beach destinations.
All-atomistic Molecular Dynamics Simulations, Data analysis with Python, data visualization, analyze principal component analysis (PCA), build Markov state model, free energy methods, working with high performance computing and supercomputers, such as Anton2. Other skills including PCR, cell culture, Flow Cytometry, HPLC, LC-MS, Mass Spectrometry.
Professional Development Skills
• i-CoMSE Enhanced Sampling Workshop, Mar. 2023
• Anton2 Training Workshop, Pittsburgh Supercomputing Center, PA, Dec. 2022
• DeRosa, M., C.; Lin, A.; Mallikaratchy, P.; McKeague, M.; Patel, R., Shigdar S., McConnell, E. In Vitro Selection of Aptamers and their Applications. Nature Reviews Methods Primers. Publishing on Jul 20, 2023.
• Williams, N.; Patel, R.; Mallikaratchy, P. Discovery of Aptamers Against Cell Surface Markers Using Ligand-Guided Selection. Methods Mol Biol 2023. 13-38.
• Williams, N. B.; Batool, S.; Zumrut, H. E.; Patel, R.; Sosa, G.; Jamal, M.; Mallikaratchy, P. An In Vitro Selection Platform to Identify Multiple Aptamers against Multiple Cell-Surface Markers Using Ligand-Guided Selection. Biochemistry 2022, 16 (5), 1600-1613.
DeRosa, M., C.; Lin, A.; Mallikaratchy, P.; McKeague, M.; Patel, R., Shigdar S., McConnell, E. In Vitro Selection of Aptamers and their Applications. Nature Reviews Methods Primers. Publishing on Jul 20, 2023.