Jayajit Das

Mixed effects modeling of the synergy between immune checkpoint and thrombin inhibitors in a preclinical mouse model of colon cancer

The paper uses nonlinear mixed-effects modeling to study synergy between immune checkpoint and thrombin inhibitors in a mouse colon cancer model, identifying mechanisms like CD8+ T cell expansion.

A framework integrating multiscale in-silico modeling and experimental data predicts CD33 CAR-NK cytotoxicity across target cell types

The paper develops a multiscale computational model to predict CD33 CAR-NK cytotoxicity against various target cells using experimental data and flow cytometry.

Neoantigens and Stochastic Fluctuations Regulate T Cell Proliferation in Primary and Metastatic Malignant Brain Tumors

The paper develops a stochastic model to predict T cell clone size distributions in brain tumors and finds faster proliferation in metastases and stronger responses to shared neoantigens.

Spatial statistics of submicron size clusters of activating and inhibitory Natural Killer cell receptors in the resting state regulate early time signal discrimination

The paper shows that spatial statistics of submicron NKR clusters in resting NK cells affect early signal discrimination between healthy and diseased targets.

An Entropy-Based Approach to Model Selection with Application to Single-Cell Time-Stamped Snapshot Data

The paper introduces an entropy-based method for model selection using time-stamped snapshot data, demonstrating its ability to identify the correct mechanistic model from simulated data.

Spleen Tyrosine Kinase (SYK) negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy

This study shows that SYK negatively regulates NK cell signaling and that its deletion enhances CD19-CAR NK cell efficacy in cancer immunotherapy.

Natural Killer Cell Receptor Signaling and Activation Depend on Cell Cycle Stages

This study shows that NK cell receptor signaling and activation vary with cell cycle stages, with some proteins showing non-monotonic abundance changes.

Immune and non-immune cell fencing of tumor cells is a widespread and functionally relevant spatial pattern in solid cancers

The paper examines spatial fencing patterns of tumor cells by immune and non-immune cells in solid cancers and links these patterns to cancer progression and treatment response.

BioNetGMMFit: Estimating Parameters of a BioNetGen Model from Time-Stamped Snapshots of Single Cells

BioNetGMMFit estimates parameters of BioNetGen models from time-stamped single-cell data and provides confidence intervals for improved accuracy.

McSNAC: A software to approximate first-order signaling networks from mass cytometry data

McSNAC approximates first-order signaling networks from mass cytometry data and shows accuracy in reconstructing models and predicting perturbation outcomes.

A Multiscale Protein Abundance Structured Population Kinetic Model Systematically Explores the Design Space of Constitutive and Inducible CAR-T cells

This paper develops a framework called PASCAR to systematically explore CAR-T cell design space using multiscale models and optimization, showing intermediate CAR affinities reduce healthy cell lysis while maintaining tumor cell killing.

Determining clinically relevant features in cytometry data using persistent homology

This paper applies persistent homology to cytometry data to identify structural differences between healthy donors and COVID-19 patients, revealing downregulation of T-bet and Eomes in patient non-naive CD8+ T cells.

Generalized Method of Moments improves parameter estimation in biochemical signaling models of time-stamped single-cell snapshot data

The paper improves parameter estimation in biochemical models using GMM and PSO on single-cell data, showing better results than traditional methods.

Spatially Resolved In Silico Modeling of NKG2D Signaling Kinetics Reveals Key role of NKG2D and Vav1 Co-clustering in Generating Natural Killer cell Activation

The paper develops an in silico model to study NKG2D signaling kinetics in NK cells, showing that co-clustering of NKG2D and Vav1 enhances phospho-Vav1 production and influences activation.

Mathematical Modeling Identifies the Role of Adaptive Immunity as a Key Controller of Respiratory Syncytial Virus (RSV) Titer in Cotton Rats

The paper uses mathematical modeling to show that adaptive immunity significantly reduces RSV titer in cotton rats, with key kinetic features observed in both in vitro and in vivo experiments.