Sagar Khare
Principal Investigator
Email: khare@chem.rutgers.edu
Sagar Khare is an associate professor of Chemistry and Chemical Biology at Rutgers University. He received his PhD in Biochemistry and Biophysics from the University of North Carolina at Chapel Hill and his undergraduate degree in Biochemical Engineering and Biotechnology from the Indian Institute of Technology, Delhi.
Jonathan Ash
PhD Student
Email: ja961@scarletmail.rutgers.edu
Jonathan develops deep learning models to predict PPIs and screen designed candidate therapeutics. He primarily works on contrastive learning models and attention-based graph networks. The systems he studies include PDZ Domains and the SARS-CoV-2:ACE2 interface.
Amanda Liyanaarachchi
PhD Student
Email: al979@scarletmail.rutgers.edu
Amanda designs ligand binders towards fluorogenic targets—aiming to produce a smaller alternative to the GFP family with better cell penetration and signal-to-noise ratio—and to visible targets. In light of the recent focus on banning synthetic food dyes by the FDA, she aims to design and produce affordable, high precision detectors to the banned food dyes, both in bound and free form.
Abik Hameem P M
PhD Student
Email: ap2462@scarletmail.rutgers.edu
Abik is developing thermostable proteases with the goal of engineering them as 'protein-level CRISPRs' to target and cleave novel peptide substrates.
Nityananda Pal
PhD Student
Email: np652@scarletmail.rutgers.edu
Nithai engineers haloalkane dehalogenases (DhaA) to enhance their stability in harsh environments for environmental detoxification. Using site-specific cysteine mutants, he conjugates polymers to DhaA31 and thermostable DhaA231 via SPAAC, improving thermal and solvent stability for bioremediation of pollutants like 1,2,3-trichloropropane (TCP).
Austin Seamann
PhD Student
Website
Email: als515@scarletmail.rutgers.edu
Austin's research focuses on applying deep learning and generative models to redesign protein sequences and create novel protein binders and enzymes with enhanced stability and specificity. He develops computational tools for generative protein and enzyme design, enabling the engineering of new proteins, binders, and catalysts with tailored functions for biomedical and biotechnological applications.
Melinda Liu
PhD Student
Email: melinda.liu@rutgers.edu
Melinda combines physics-based modeling and deep learning-based protein design tools to engineer de novo zinc enzymes to overcome limitations faced by natural metalloenzymes, such as thermolysin. She is currently helping set up the new Hamilton liquid handling system to expedite the process of producing and testing proteins.
Mason Hooten
Postdoctoral Researcher
Email: mh1314@scarletmail.rutgers.edu
Mason is a postdoctoral researcher with the Rutgers Artificial Intelligence and Data Science (RAD) Collaboratory, developing AI-HPC architectures to investigate protein behavior. He earned his PhD in Biomedical Engineering at Rutgers where he studied the interplay between conformation and aggregation in biomolecular systems.
Priya Dutta
PhD Student
Email: pd621@scarletmail.rutgers.edu
Priya's research focuses on understanding and modulating α-synuclein aggregation, a hallmark of Parkinson’s disease. She is currently probing the interactions between synuclein and engineered HtrA protease/PDZ domain variants, with the goal of identifying stronger binders that can inhibit toxic aggregation pathways. By combining biochemical assays with rational design, she aims to uncover strategies for developing anti-aggregation binders that could serve as leads for therapeutic intervention.