Determining clinically relevant features in cytometry data using persistent homology

Authors: Mukherjee, Soham, Wethington, Darren, Dey, Tamal K., Das, Jayajit

Subject Terms: Quantitative Biology - Quantitative Methods, J.3

Access URL: http://arxiv.org/abs/2203.06263

Using in silico models to predict lymphocyte activation and development in a data rich era

Authors: Khakoo, Salim I, Das, Jayajit

Source: In ImmunoInformatics June 2024 14

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

Authors: Stewart, William C. L., Jayaprakash, Ciriyam, Das, Jayajit

Source: Entropy; Mar2025, Vol. 27 Issue 3, p274, 13p

Subject Terms: SINGLE cell proteins, GENERALIZED method of moments, KILLER cells, AKAIKE information criterion, NATURAL selection

Connecting the dots across time: Reconstruction of single cell signaling trajectories using time-stamped data

Authors: Mukherjee, Sayak, Stewart, David, Stewart, William, Lanier, Lewis L., Das, Jayajit

Subject Terms: Quantitative Biology - Quantitative Methods, Condensed Matter - Statistical Mechanics, Computer Science - Computational Geometry, Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/1609.08035

Limiting energy dissipation induces glassy kinetics in single cell high precision responses

Authors: Das, Jayajit

Subject Terms: Quantitative Biology - Cell Behavior, Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/1506.03290

Modeling the response to interleukin‐21 to inform natural killer cell immunotherapy.

Authors: Nayak, Indrani, Biondo, Rosalba, Stewart, William C, Fulton, Rebecca J, Möker, Nina, Zhang, Congcong, Khakoo, Salim I, Das, Jayajit

Source: Immunology & Cell Biology; Feb2025, Vol. 103 Issue 2, p192-212, 21p

Subject Terms: INTERLEUKIN-21, IMMUNOTHERAPY, CYTOKINES, HEPATOCELLULAR carcinoma, MATHEMATICAL models, KILLER cells, CANCER treatment

Maximum Entropy estimation of probability distribution of variables in higher dimensions from lower dimensional data

Authors: Das, Jayajit, Mukherjee, Sayak, Hodge, Susan E.

Source: Entropy 2015, 17(7), 4986-4999

Subject Terms: Quantitative Biology - Quantitative Methods, Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/1505.01066

Host-to-host variation of ecological interactions in polymicrobial infections

Authors: Mukherjee, Sayak, Weimer, Kristin E., Seok, Sang-Cheol, Ray, Will C., Jayaprakash, C., Vieland, Veronica J., Swords, W. Edward, Das, Jayajit

Subject Terms: Quantitative Biology - Populations and Evolution, Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/1404.6668

In silico Modeling of Itk Activation Kinetics in Thymocytes Suggests Competing Positive and Negative IP4 Mediated Feedbacks Increase Robustness

Authors: Mukherjee, Sayak, Rigaud, Stephanie, Seok, Sang-Cheol, Fu, Guo, Prochenka, Agnieszka, Dworkin, Michael, Gascoigne, Nicholas R. J., Vieland, Veronica J., Sauer, Karsten, Das, Jayajit

Source: PLOS ONE, Vol 8, Issue 9, Page e73937, September 2013

Subject Terms: Quantitative Biology - Cell Behavior, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1307.7084

Cell responses only partially shape cell-to-cell variations in protein abundances in Escherichia coli chemotaxis

Authors: Mukherjee, Sayak, Seok, Sang-Cheol, Vieland, Veronica J., Das, Jayajit

Source: PNAS epub, October 28, 2013

Subject Terms: Quantitative Biology - Cell Behavior, Condensed Matter - Statistical Mechanics, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1306.2605

Data-driven quantification of robustness and sensitivity of cell signaling networks

Authors: Mukherjee, Sayak, Seok, Sang-Cheol, Vieland, Veronica J., Das, Jayajit

Subject Terms: Quantitative Biology - Quantitative Methods, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1305.3902

Positive feedback produces broad distributions in maximum activation attained within a narrow time window in stochastic biochemical reactions

Authors: Das, Jayajit

Subject Terms: Quantitative Biology - Molecular Networks, Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/1212.1715

Dramatic reduction of dimensionality in large biochemical networks due to strong pair correlations

Authors: Dworkin, Michael, Mukherjee, Sayak, Jayaprakash, Ciriyam, Das, Jayajit

Subject Terms: Quantitative Biology - Quantitative Methods, Condensed Matter - Statistical Mechanics, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1201.5082

Positive Feedback Regulation Results in Spatial Clustering and Fast Spreading of Active Signaling Molecules on a Cell Membrane

Authors: Das, Jayajit, Kardar, Mehran, Chakraborty, Arup K.

Subject Terms: Condensed Matter - Soft Condensed Matter, Physics - Chemical Physics, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/0906.5280

Nonequilibrium steady states of the isotropic classical magnet

Authors: Das, Jayajit, Rao, Madan, Ramaswamy, Sriram

Subject Terms: Condensed Matter - Soft Condensed Matter

Access URL: http://arxiv.org/abs/cond-mat/0404071

Dynamics of magnetic flux lines in the presence of correlated disorder

Authors: Bullard, Thomas J., Das, Jayajit, Tauber, Uwe C.

Source: In: Trends in Superconductivity Research (P.S. Lewis, ed.) 2004, 63

Subject Terms: Condensed Matter - Superconductivity, Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/cond-mat/0305061

Vortex transport and voltage noise in disordered superconductors

Authors: Das, Jayajit, Bullard, Thomas J., Tauber, Uwe C.

Source: Physica A 318 (2003) 48

Subject Terms: Condensed Matter - Statistical Mechanics, Condensed Matter - Superconductivity

Access URL: http://arxiv.org/abs/cond-mat/0205023

Driven Heisenberg Magnets: Nonequilibrium Criticality, Spatiotemporal Chaos and Control

Authors: Das, Jayajit, Rao, Madan, Ramaswamy, Sriram

Source: Euro. Phys. Lett. 60 (2002) 418

Subject Terms: Condensed Matter - Statistical Mechanics, Condensed Matter - Soft Condensed Matter, Nonlinear Sciences - Chaotic Dynamics

Access URL: http://arxiv.org/abs/cond-mat/0104566

Ordering Dynamics of Heisenberg Spins with Torque: Crossover, Spinwaves and Defects

Authors: Das, Jayajit, Rao, Madan

Subject Terms: Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/cond-mat/0001340

Dynamics of Ordering of Isotropic Magnets

Authors: Das, Jayajit, Rao, Madan

Subject Terms: Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/cond-mat/9903052