52. Darren Wethington, Sayak Mukherjee, and Jayajit Das (2022)
McSNAC: A software to approximate first-order signaling networks from mass cytometry data.
Accepted for publication in Quantitative Biology. Available at biorxiv: https://doi.org/10.1101/2021.12.02.470955
51. Rajdeep Grewal and Jayajit Das (2022)
Spatially resolved in silico modeling of NKG2D signaling kinetics suggests key role of NKG2D and Va1 co-clustering in generating Natural Killer cell activation.
PLoS Computational Biology 18, e1010114. PMID: 35584138
50. Soham Mukherjee, Darren Wethington, Tamal K Dey, and Jayajit Das (2022)
Determining clinically relevant features in cytometry using persistent homology
PLoS Computational Biology, 18, e1009931. PMID: 35312683.
49. Zeguang Wu, Ph.D; Soo Park; Colleen M Lau; Yi Zhong; Sam Sheppard; Joseph C. Sun; Jayajit Das; Grégoire Altan-Bonnet; Katharine C Hsu (2021)
Dynamic variability in SHP-1 determines natural killer cell responsiveness (Cover Article)
Science Signaling, 14, eabe5380. PMID: 34752140.
48. Veneziano R, Moyer TJ, Stone MB, Wamhoff E-C, Read BJ, Mukherjee S, Shepherd TR, Das J, Schief WR, Irvine DJ, and Bathe M (2020).
Role of Nanoscale Antigen Organization on B cell Activation Probed using DNA Origami
Nature Nanotechnology, PMID:32601450.
47. Wethington D, Harder O, Uppulury K, Stewart W, Chen P, King T, Reynolds S, Perelson AS, Peeples ME*, Niewiesk S*, Das J* (2019).
Mathematical Modeling Identifies the Role of Adaptive Immunity as a Key Controller of Respiratory Syncytial Virus (RSV) Titer in Cotton Rats
Journal of Royal Society Interface, 16, 20190389.
46. Jayaprakash C* and Das J* (2019).
Stochastic Sequestration Promotes Specificity in Decision Making in Single Cells.
Journal of Physical Chemistry B, 123, 10323.
45. Brown JR, Jurcisek J, Lakhani V, Snedden A, Ray WC, Mokrzan EM,Bakaletz LO*, Das J* (2019).
In Silico Modeling of Biofilm Formation by Nontypeable Haemophilus influenzae In Vivo.
mSphere, 4, e00254-19.
44. Das J and Lanier LL(2019).
Data Analysis to Modeling to Building Theory in NK Cell Biology and Beyond: How Can Computational Modeling Contribute?
Journal of Leukocyte Biology, 105, 1305.
43. Mbiribindi B, Mukherjee S, Wellington D, Das J* and Khakoo SI* (2019)
Spatial clustering of receptors and signaling molecules regulates NK cell response to peptide repertoire changes.
Frontiers Immunology, 10, 605.
42. Jadcherla SR, Prabhakar V, Hasenstab KA, Nawaz S, Das J, Kern M, Balasubramanian G, Shaker R. (2018)
Defining pharyngeal contractile integral during high-resolution manometry in neonates: a neuromotor marker of pharyngeal vigor.
Pediatric Research, 84, 341.
41. Lakhani V, Tan L, Mukherjee S, Stewart WCL, Swords WE*, Das J*. (2018)
Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media.
Royal Society Open Science, 5, 180810.
40. Das, J.*, Mokrzan, E., Lakhani, V., Rosas, L., Jurcisek, J., Ray, W.C., and, Bakaletz, L. O.* (2017) Extracellular DNA and Type IV Pilus Expression Regulate the Structure and Kinetics of Biofilm Formation by Nontypeable Haemophilus influenza.
mBio 8, e01466-17.
39. Mukherjee, S., Stewart, D., Stewart, W., Lanier, L.L., Das, J.* (2017)
Connecting the dots across time: reconstruction of single-cell signaling trajectories using time-stamped data.
Royal Society Open Science, 4, 170811.
38. Mukherjee, S., Jensen, H., Stewart, W., Stewart, D., Ray, W.C., Chen, W.Y., Nolan, G.P., Lanier, L.L*., Das, J.* (2017)
In silico modeling identifies CD45 as a regulator of IL-2 synergy in the NKG2D-mediated activation of immature human NK cells.
Science Signaling, 10, eaai 9062
37. Sugar I.P., Das, J., Jayaprakash C., Sealfon S.C. (2017)
Multiscale Modeling of Complex Formation and CD80 Depletion during Immune Synapse Development.
Biophysical Journal, 112, 997.
36. Das, J.* (2016)
Limiting energy dissipation induces glassy kinetics in single cell high precision responses.
Biophysical Journal, 110, 1180.
35. Westernberg, L., Conche, C., Huang, Y.H., Rigaud, S., Deng, Y., Siegemund, S, Mukherjee, S., Nosaka, L., Das, J., Sauer, K. (2016)
Non-canonical antagonism of PI3K by the kinase Itpkb delays thymocyte B-selection and renders it Notch-dependent.
Elife, 11, 5.
34. Das, J.*, Mukherjee, S., and, Hodge, S. E. (2015)
Maximum Entropy estimation of probability distribution of variables in higher dimensions from lower dimensional data.
Entropy, 17, 4986.
33. Khakoo, S. I. & Das, J. (2015)
NK cells: tuned by peptide?
Immunological Reviews. 267, 214-27
32. Mukherjee, S., Weimer, K.E., Seok, S.C., Ray, W.C., Jayaprakash, C., Vieland, V.J., & Swords, W. E., Das, J.* (2015)
Host-to-host variation of ecological interactions in polymicrobial infections.
Physical Biology. 12, 16003. (highlights of 2015 selection)
31. Cassidy, S., Mukherjee, S., Myint, T.M., North, H., Traherne, J., Claas, A.M.F.HJ., Purbhoo, M.A., Das, J., Khakoo, S.I. (2015)
Peptide selectivity discriminates NK cells from KIR2DL2-and KIR2DL3-positive individuals.
European Journal of Immunology. 45, 492.
29. Mukherjee, S., Seok, S.C. Vieland, V.J., & Das, J.* (2013)
Cell responses only partially shaped cell-to-cell variations in protein abundances in Escherichia coli chemotaxis.
Proceedings of National Academy of Science USA. 110, 18531-6
28. Mukherjee, S., Seok, S.C., Vieland, V.J., & Das, J.* (2013)
Data-driven quantification of the robustness and sensitivity of cell signaling networks.
Physical Biology. 10, 66002.
27. Joshi, R.P., Schmidt, A., Das, J., Pytel, D., Riese, M.J., Lester, M., Diehl, J.A., Behrens, D.M., Kambayashi, T., & Koretzky, G.A. (2013)
A predominant role for the ζ isoform of diacylglycerol kinase in regulatory T cell development and TCR-mediated Ras signaling.
Science Signaling. 6, ral 102.
26. Mukherjee, S., Rigaud, S., Seok, S.C., Fu, G., Porchenka, A., Dworkin, M.*, Gascoigne, N., Vieland, V.J., Sauer, K*.,& Das, J.* (2013)
In Silico modeling of Itk activation kinetics in thymocytes suggests competing positive and negative IP4 mediated feedbacks increase robustness.
PLOS ONE. 8, e73937.
25. Das, J.* (2013)
Positive feedback produces broad distributions in maximum activation attained within a narrow time window in stochastic biochemical reactions.
Journal of Chemical Physics. 138, 15101.
24. Mukherjee, S., Zhu, J., Zikherman, J., Parameswaran, R., Kadlecek, T.A., Wang, Q., Au-Yeung, B., Ploegh, H., Kuriyan, H., Das, J.*, & Weiss, A*. (2013)
Monovalent and multivalent ligation of the B cell receptor exhibit differential dependence upon Syk and Src family kinases.
Science Signaling. 6. (Faculty 1000 Prime selection)
23. Vieland, V.J., Das, J., Hodge, S., & Seok, S.C. (2013)
Measurement of statistical evidence on an absolute scale following thermodynamics principles.
Theory in Biosciences. 132, 181-194.
22. Dworkin, M.*, Mukherjee, S., Jayapakash, C., & Das, J.* (2012)
Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations.
Journal of the Royal Society Interface. 9, 1824-1835.
21. Riese, M.J., Grewal, J., Das, J., Zou, T., Patil, V., Chakaborty, A.K., & Koretzky, G. (2011)
Decreased DAG metabolism enhances Erk activation and augments CD8+ T cell function responses.
Journal of Biological Chemistry. 286,5254-5265.
20. Das, J.* (2010)
Activation or tolerance on Naural Killer cells is modulated by ligand quality in a non-monotonic manner.
Biophysical Journal. 99, 2028-2037.
19. Chakraborty, A.K. & Das, J. (2010)
Pairing computation with experimentation: A powerful coupling for studying T cell signaling.
Nature Reviews Immunology. 10, 59-71
18. Das, J.*, Frechet, J.M.J., & Chakraborty, A.K. (2009)
Self-Assembly of dendronized polymers.
Journal of Physical Chemistry. 130, 13768-13775.
17. Das, J., Kardar, M., & Chakraborty, A.K. (2009)
Positive feedback regulation results in spatial clustering and fast spreading of active signaling molecules on a cell membrane.
Journal of Chemical Physics. 130, 245102.
16. Chakraborty, A.K., Das, J., Zikerman, J., Ming, Y., Govern, C., Ho, M., Weiss, A., Chakraborty, A.K., & Roose, J. (2009)
Molecular origin and functional consequences of digital signaling and hysteresis during Ras activation in lymphocytes.
Science Signaling. 2, pt2.
15. Das, J., Ho, M., Zikherman, J., Govern, C., Ming, Y., Weiss, A., Chakraborty, A.K., & Roose, J. (2009)
Digital signaling and hysteresis characterize Ras activation in lymphocytes.
Cell. 136, 337-351.
14. Prasad, A., Zikherman, J., Das, J., Roose, J., Weiss, A.,& Chakraborty, A.K., (2009)
Origin of the sharp boundary that discriminates positive and negative selection of thymocytes.
Proceedings of National Academy of Sciences USA. 106, 528-533.
13. Cemerski, S., Das, J., Giurisato, E., Markiewicz, M.A., Allen, P.M., Chakraborty, A.K., & Shaw, A.S. (2008)
The balance between T cell receptor signaling and degradation at the center of the immunological synapse is determined by antigen quality.
Immunity. 29, 414-422.
12. Bullard, T.J., Das, J., Daquila, G.L., & Tauber, U.C., (2008)
Vortex washboard voltage noise in type II superconductors.
European Physical Jornal B. 65, 464.
11. Artyomov, M., Das, J., Kardar, M., & Chakraborty, A., K. (2007)
Purely stochastic binary decision in cell signaling models without underlying deterministic bistabilities.
Proceedings of National Academy of Sciences. 104, 18958-18963.
10. Wylie, D., Das, J., & Chakrabory, A.K. (2007)
Sensitivity of T cells to antigen and antagonism emerges from differential regulation of the same signaling module.
Proceedings of National Academy of Sciences USA. 104. 5533-5538
9. Cemerski, S., Das, J., Locasale, J., Arnold, P., Giurisato, E., Markiewicz, M.A., Fremont, D., Allen, P.M., Chakraborty, A.K., & Shaw, A.S. (2007)
The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse.
Immunity. 26, 345-355.
8. Gomez, E.D., Das, J., Chakraborty, A. K., Pople, J.A., & Balsara, N.P. (2006)
Effect of crosslinking on the structure and thermodynamics of lamellar block copolymers.
Macromolecules. 39, 4848-4859.
7. Das, J., Yoshida, M., Fresco, Z., Choi, T.L., Frechet, J.M.J., & Chakraborty. (2005)
A Dendronized polymer is a single molecule glass.
Journal of Physical Chemistry B. 109, 6535-6543.
6. Hahn, H., Chakraborty, A.K., Das, J., Pople, J., & Balsara. N.P. (2005)
Order-Disorder transitions in cross-linked block copolymer solids.
Macromolecules. 38, 1277-1285.
5. Bullard, T.J., Das, J., & Tauber, U.C. (2004)
Dynamics of magnetic flux lines in the presence of correlated disorder.
Trends in Superconductivity Research. 67-76.
4. Das, J., Bullard, T.J., & Tauber, U.C. (2003)
Vortex transport and voltage noise in disordered superconductors.
Physica A. 318, 48
3. Das, J., Rao, M., & Ramaswamy, S. (2002)
Nonequilibrium criticality, spatiotemporal chaos and control.
Europhysics Letters. 60, 418.
2. Das, J. & Rao, M. (2000).
Ordering dynamics of Heisenberg spins with torque: Crossover, spin waves and defects.
Physical Review E. 62, 1601.Das, J. & Rao, M. (1999).
Dynamics of ordering of isotropic magnets.
Physica A. 270, 253.
- Das, J. & Rao, M. (1998). Dynamics of ordering of Heisenberg spins with torque – nonconserved case. Physical Review E.