Microfluidic high-sensitivity and high-throughput bio assays AND MACHINE-LEARNING BASED ANALYTICS for deep characterization of immune responses
Microfluidics and nanofluidics enable higher bioassay sensitivity (i.e. lower limits of detection) and throughput (i.e. larger numbers of samples and/or experimental conditions) at lower sample volumes than traditional assays. This allows for both broader and deeper characterization of complex biological phenomena where it would otherwise be impossible - such as in the context of low sample volumes available from patients. We are interested in developing these devices and assays and applying them especially in the context of deep characterization of immune responses.
The large amounts of multivariate data these devices and methods can extract from small volumes of precious clinical samples often require advanced analytics to derive immunological and clinical insights. We use machine-learning methods to analyze such high-dimensional data.
Applications include: Discovery of novel functional biomarkers for some of the most widely devastating infectious diseases globally such as COVID-19, Tuberculosis (TB), Typhoid and Neglected Tropical DIseases (NTDs e.g. Schistosomiasis). Helping understand the emergence of anti-microbial resistance (AMR) and discovery of novel biomarkers for its early and inexpensive detection. Discovering novel immune correlates for guiding vaccine design. Discovering early biomarkers of rejection in transplant recipients (e.g. ABMR in kidney transplant recipients). Understanding variation in response to immunotherapy in cancer and discovery of early biomarkers of treatment failure.
PUBLICATIONS:
N. Rafat, L. Brewer, N. Das, D. Trivedi, B. Kaszala, A. Sarkar, Inexpensive High-Throughput Multiplexed Biomarker Detection Using Enzymatic Metallization with Cellphone-Based Computer Vision, ACS Sensors, 2023
S. P. Peddireddy, S. A. Rehman, A. R. Cilio, G. M. Vijay, A. Somasundram, C. J. Workman, W. Bain, B. J. McVeryry, B. Methe, J. S. Lee, P. Ray, A. Ray, T. C. Bruno, D. A. A. Vignali, G. D. Kitsios, A. Morris, H. Singh, A. Sarkar, J. Das, Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19, Cell Reports, 39, 11020, 2022
A. Saha, T. Chabraborty, J. Das, A. Sarkar, Comprehensive Antibody Profiling Predicts Rejection in Kidney Transplant Recipients, 2022 Annual Meeting of the Biomedical Engineering Society (BMES 2022), San Antonio TX, 2022
Sarkar A, Han J. Non-linear and Linear Enhancement of Enzymatic Reaction Kinetics Using a Nanofluidic Biomolecule Concentrator. Lab on a Chip [Internet]. 2011;11 (15) :2569-76.
Chen C-H, Miller MA, Sarkar A, Beste MT, Isaacson KB, Lauffenburger DA, Griffith LG, Han J. Multiplexed Protease Activity Assay for Low Volume Clinical Samples Using Droplet Based Microfluidics and Its Application to Endometriosis. J Am Chem Soc. 2013;135 (5) :1645-48