{"id":65,"date":"2022-03-25T09:11:41","date_gmt":"2022-03-25T09:11:41","guid":{"rendered":"https:\/\/mathimmunelab.works\/?page_id=65"},"modified":"2022-11-01T13:45:00","modified_gmt":"2022-11-01T13:45:00","slug":"publications","status":"publish","type":"page","link":"https:\/\/mathimmunelab.works\/index.php\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n

52. Darren Wethington, Sayak Mukherjee, and Jayajit Das (2022)<\/p>\n\n\n\n

McSNAC:<\/em> A software to approximate first-order signaling networks from mass cytometry data.<\/em><\/p>\n\n\n\n

Accepted for publication in Quantitative Biology. Available at biorxiv: https:\/\/doi.org\/10.1101\/2021.12.02.470955<\/a><\/p>\n\n\n\n

51. Rajdeep Grewal and Jayajit Das (2022)<\/p>\n\n\n\n

Spatially resolved in silico modeling of NKG2D signaling kinetics suggests key role of NKG2D and Va1 co-clustering in generating Natural Killer cell activation.<\/em><\/p>\n\n\n\n

PLoS Computational Biology<\/em> 18, e1010114. PMID: 35584138<\/p>\n\n\n\n

50.<\/strong>  Soham Mukherjee, Darren Wethington, Tamal K Dey, and Jayajit Das (2022) <\/p>\n\n\n\n

Determining clinically relevant features in cytometry using persistent homology<\/em><\/p>\n\n\n\n

PLoS Computational Biology<\/em>, 18, e1009931. PMID: 35312683.<\/p>\n\n\n\n

49.  Zeguang Wu, Ph.D; Soo Park; Colleen M Lau; Yi Zhong; Sam Sheppard; Joseph C. Sun; Jayajit Das; Gr\u00e9goire Altan-Bonnet; Katharine C Hsu (2021)<\/p>\n\n\n\n

Dynamic variability in SHP-1 determines natural killer cell responsiveness <\/em>(Cover Article)<\/p>\n\n\n\n

Science Signaling<\/em>, 14, eabe5380.  PMID: 34752140.<\/p>\n\n\n\n

 48. <\/strong>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). <\/p>\n\n\n\n

Role of Nanoscale Antigen Organization on B cell Activation Probed using DNA Origami<\/em><\/p>\n\n\n\n

Nature Nanotechnology<\/em>, PMID:32601450.<\/p>\n\n\n\n

47. Wethington D, Harder O, Uppulury K, Stewart W, Chen P, King T, Reynolds S, Perelson AS, Peeples ME*, Niewiesk S*, Das J* (2019).<\/p>\n\n\n\n

Mathematical Modeling Identifies the Role of Adaptive Immunity as a Key Controller of Respiratory Syncytial Virus (RSV) Titer in Cotton Rats<\/em><\/p>\n\n\n\n

Journal of Royal Society Interface, <\/em>16, 20190389.<\/p>\n\n\n\n

46.<\/strong> Jayaprakash C* and Das J* <\/strong>(2019). <\/p>\n\n\n\n

Stochastic Sequestration Promotes Specificity in Decision Making in Single Cells.<\/em><\/p>\n\n\n\n

 Journal of Physical Chemistry B<\/em>, 123, 10323.<\/p>\n\n\n\n

45.<\/strong> Brown JR, Jurcisek J, Lakhani V, Snedden A, Ray WC, Mokrzan EM,Bakaletz LO*, Das J* (2019). <\/p>\n\n\n\n

In Silico Modeling of Biofilm Formation by Nontypeable Haemophilus influenzae In Vivo.<\/em><\/p>\n\n\n\n

 mSphere<\/em>, 4, e00254-19.<\/p>\n\n\n\n

44. <\/strong>Das J and Lanier LL(2019). <\/p>\n\n\n\n

Data Analysis to Modeling to Building Theory in NK Cell Biology and Beyond:  How Can Computational Modeling Contribute?<\/em><\/p>\n\n\n\n

 Journal of Leukocyte Biology, <\/em>105, 1305.<\/p>\n\n\n\n

43. Mbiribindi B, Mukherjee S, Wellington D, Das J*<\/sup> and Khakoo SI*<\/sup> (2019) <\/p>\n\n\n\n

Spatial clustering of receptors and signaling molecules regulates NK cell response to peptide repertoire changes.<\/em><\/p>\n\n\n\n

Frontiers Immunology<\/em>, 10, 605.<\/p>\n\n\n\n

42. Jadcherla SR, Prabhakar V, Hasenstab KA, Nawaz S, Das J, Kern M, Balasubramanian G, Shaker R. (2018) <\/p>\n\n\n\n

Defining pharyngeal contractile integral during high-resolution manometry in neonates: a neuromotor marker of pharyngeal vigor.<\/em><\/p>\n\n\n\n

 Pediatric Research<\/em>, 84, 341.<\/p>\n\n\n\n

41. Lakhani V, Tan L, Mukherjee S, Stewart WCL, Swords WE*, Das J*. (2018) <\/p>\n\n\n\n

Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media.<\/em><\/p>\n\n\n\n

 Royal Society Open Science<\/em>, <\/strong>5, 180810.<\/p>\n\n\n\n

40. Das, J.*, Mokrzan, E., Lakhani, V., Rosas, L., Jurcisek, J., Ray, W.C., and, Bakaletz, L. O.*<\/strong> (2017) Extracellular DNA and Type IV Pilus Expression Regulate the Structure and Kinetics of Biofilm Formation by Nontypeable Haemophilus influenza.<\/p>\n\n\n\n

      mBio<\/em> 8, e01466-17.<\/p>\n\n\n\n

39. <\/strong>Mukherjee, S., Stewart, D., Stewart, W., Lanier, L.L., Das, J.* (2017) <\/p>\n\n\n\n

Connecting the dots across time: reconstruction of single-cell signaling trajectories using time-stamped data.<\/em><\/p>\n\n\n\n

 Royal Society Open Science<\/em>, 4<\/strong>, 170811.<\/p>\n\n\n\n

38. Mukherjee, S., Jensen, H., Stewart, W., Stewart, D., Ray, W.C., Chen, W.Y., Nolan, G.P., Lanier, L.L*., Das, J.* (2017) <\/p>\n\n\n\n

In silico modeling identifies CD45 as a regulator of IL-2 synergy in the NKG2D-mediated activation of immature human NK cells.<\/em><\/p>\n\n\n\n

Science Signaling<\/em>, 10, eaai 9062<\/p>\n\n\n\n

37. Sugar I.P., Das, J.<\/strong>, Jayaprakash C., Sealfon S.C. (2017) <\/p>\n\n\n\n

Multiscale Modeling of Complex Formation and CD80 Depletion during Immune Synapse Development.<\/em><\/p>\n\n\n\n

Biophysical Journal<\/em>, 112, 997.<\/p>\n\n\n\n

36.   Das, J.* (2016) <\/p>\n\n\n\n

Limiting energy dissipation induces glassy kinetics in single cell high precision responses.<\/em><\/p>\n\n\n\n

Biophysical Journal<\/em>, 110, 1180.<\/p>\n\n\n\n

 35.  Westernberg, L., Conche, C., Huang, Y.H., Rigaud, S., Deng, Y., Siegemund, S, Mukherjee, S., Nosaka, L., Das, J., Sauer, K. (2016)<\/p>\n\n\n\n

Non-canonical antagonism of PI3K by the kinase Itpkb delays thymocyte B-selection and renders it Notch-dependent.<\/em><\/p>\n\n\n\n

Elife,<\/em> 11, 5.<\/p>\n\n\n\n

34.  Das, J.*, Mukherjee, S.<\/strong>, and, Hodge, S. E. (2015) <\/p>\n\n\n\n

Maximum Entropy estimation of probability distribution of variables in higher dimensions from lower dimensional data.<\/em><\/p>\n\n\n\n

Entropy, <\/em>17, 4986.<\/p>\n\n\n\n

33. Khakoo, S. I. & <\/strong>Das, J. <\/strong>(2015) <\/p>\n\n\n\n

NK cells: tuned by peptide?<\/em><\/p>\n\n\n\n

Immunological Reviews<\/em>. 267, 214-27<\/p>\n\n\n\n

32. Mukherjee, S., Weimer, K.E., Seok, S.C., Ray, W.C., Jayaprakash, C., Vieland, V.J., & Swords, W. E., Das, J.* <\/strong>(2015) <\/p>\n\n\n\n

Host-to-host variation of ecological interactions in polymicrobial infections.<\/em><\/p>\n\n\n\n

Physical Biology. <\/em>12, 16003. (highlights of 2015 selection)<\/p>\n\n\n\n

31. Cassidy, S., Mukherjee, S., Myint, T.M., North, H., Traherne, J., Claas, A.M.F.HJ., Purbhoo, M.A., Das, J., <\/strong>Khakoo, S.I. (2015) <\/p>\n\n\n\n

Peptide selectivity discriminates NK cells from KIR2DL2-and KIR2DL3-positive individuals.<\/em><\/p>\n\n\n\n

European Journal of Immunology. <\/em>45, 492.<\/p>\n\n\n\n

29. Mukherjee, S., Seok, S.C. Vieland, V.J., & Das, J.* <\/strong>(2013) <\/p>\n\n\n\n

Cell responses only partially shaped cell-to-cell variations in protein abundances in Escherichia coli chemotaxis.<\/em><\/p>\n\n\n\n

Proceedings of National Academy of Science USA.<\/em> 110, 18531-6<\/p>\n\n\n\n

28. Mukherjee, S., Seok, S.C., Vieland, V.J., & Das, J.* (2013) <\/p>\n\n\n\n


Data-driven quantification of the robustness and sensitivity of cell signaling networks.<\/em><\/p>\n\n\n\n

Physical Biology. <\/em>10, 66002.<\/p>\n\n\n\n

27. Joshi, R.P., Schmidt, A., Das, J., <\/strong>Pytel, D., Riese, M.J., Lester, M., Diehl, J.A., Behrens, D.M., Kambayashi, T., & Koretzky, G.A. (2013) <\/p>\n\n\n\n

A predominant role for the \u03b6 isoform of diacylglycerol kinase in regulatory T cell development and TCR-mediated Ras signaling.<\/em><\/p>\n\n\n\n

Science Signaling.<\/em> 6, ral 102.<\/p>\n\n\n\n

26. Mukherjee, S., Rigaud, S., Seok, S.C., Fu, G., Porchenka, A., Dworkin, M.*<\/strong>, Gascoigne, N., Vieland, V.J., Sauer, K*.,&  Das, J.* <\/strong>(2013) <\/p>\n\n\n\n

In Silico modeling of Itk activation kinetics in thymocytes suggests competing positive and negative IP4 mediated feedbacks increase robustness.<\/em><\/p>\n\n\n\n

PLOS ONE.<\/em> 8, e73937.<\/p>\n\n\n\n

25. Das, J.* (2013) <\/p>\n\n\n\n

Positive feedback produces broad distributions in maximum activation attained within a narrow time window in stochastic biochemical reactions.<\/em><\/p>\n\n\n\n

Journal of Chemical Physics. <\/em>138, 15101.<\/p>\n\n\n\n

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) <\/p>\n\n\n\n

Monovalent and multivalent ligation of the B cell receptor exhibit differential dependence upon Syk and Src family kinases.<\/em><\/p>\n\n\n\n

Science Signaling. <\/em>6.   (Faculty 1000 Prime selection)<\/p>\n\n\n\n

23. Vieland, V.J., Das, J., Hodge, S., & Seok, S.C. (2013)<\/p>\n\n\n\n

Measurement of statistical evidence on an absolute scale following thermodynamics principles.<\/em><\/p>\n\n\n\n

Theory in Biosciences. <\/em>132, 181-194.<\/p>\n\n\n\n

22. Dworkin, M.*<\/strong>, Mukherjee, S., Jayapakash, C., & Das, J.* (2012) <\/p>\n\n\n\n

Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations.<\/em><\/p>\n\n\n\n

Journal of the Royal Society Interface.<\/em> 9, 1824-1835.<\/p>\n\n\n\n

21. Riese, M.J., Grewal, J., Das, J., <\/strong>Zou, T., Patil, V., Chakaborty, A.K., & Koretzky, G. (2011) <\/p>\n\n\n\n

Decreased DAG metabolism enhances Erk activation and augments CD8+ T cell function responses.<\/em><\/p>\n\n\n\n

Journal of Biological Chemistry. <\/em>286,5254-5265.<\/p>\n\n\n\n

20. Das, J.* <\/strong>(2010) <\/p>\n\n\n\n

Activation or tolerance on Naural Killer cells is modulated by ligand quality in a non-monotonic manner.<\/em><\/p>\n\n\n\n

Biophysical Journal.<\/em> 99, 2028-2037.<\/p>\n\n\n\n

19. Chakraborty, A.K. & Das, J. <\/strong>(2010) <\/p>\n\n\n\n

Pairing computation with experimentation: A powerful coupling for studying T cell signaling.<\/em><\/p>\n\n\n\n

Nature Reviews Immunology. <\/em>10, 59-71<\/p>\n\n\n\n

18. Das, J.*, <\/strong>Frechet, J.M.J., & Chakraborty, A.K. (2009) <\/p>\n\n\n\n

Self-Assembly of dendronized polymers.<\/em><\/p>\n\n\n\n

Journal of Physical Chemistry. <\/em>130, 13768-13775.<\/p>\n\n\n\n

17. Das, J., <\/strong>Kardar, M., & Chakraborty, A.K. (2009) <\/p>\n\n\n\n

Positive feedback regulation results in spatial clustering and fast spreading of active signaling molecules on a cell membrane.<\/em><\/p>\n\n\n\n

Journal of Chemical Physics. <\/em>130, 245102.<\/p>\n\n\n\n

16. Chakraborty, A.K., Das, J., Zikerman, J., Ming, Y., Govern, C., Ho, M., Weiss, A., Chakraborty, A.K., & Roose, J. (2009) <\/p>\n\n\n\n

Molecular origin and functional consequences of digital signaling and hysteresis during Ras activation in lymphocytes.<\/em><\/p>\n\n\n\n

Science Signaling. <\/em>2, pt2.<\/p>\n\n\n\n

15. Das, J., <\/strong>Ho, M., Zikherman, J., Govern, C., Ming, Y., Weiss, A., Chakraborty, A.K., & Roose, J. (2009) <\/p>\n\n\n\n

Digital signaling and hysteresis characterize Ras activation in lymphocytes.<\/em><\/p>\n\n\n\n

Cell. <\/em>136, 337-351.<\/p>\n\n\n\n

14. Prasad, A., Zikherman, J., Das, J., Roose, J., Weiss, A.,&  Chakraborty, A.K., (2009)<\/p>\n\n\n\n

Origin of the sharp boundary that discriminates positive and negative selection of thymocytes.<\/em><\/p>\n\n\n\n

Proceedings of National Academy of Sciences USA. 106, 528-533.<\/em><\/p>\n\n\n\n

13. Cemerski, S., Das, J., Giurisato, E., Markiewicz, M.A., Allen, P.M., Chakraborty, A.K., & Shaw, A.S. (2008) <\/p>\n\n\n\n

The balance between T cell receptor signaling and degradation at the center of the immunological synapse is determined by antigen quality.<\/em><\/p>\n\n\n\n

Immunity. <\/em>29, 414-422.<\/p>\n\n\n\n

12. Bullard, T.J., Das, J., <\/strong>Daquila, G.L.,  & Tauber, U.C., (2008)<\/p>\n\n\n\n

Vortex washboard voltage noise in type II superconductors.<\/em><\/p>\n\n\n\n

European Physical Jornal B.<\/em> 65, 464.<\/p>\n\n\n\n

11. Artyomov, M., Das, J., <\/strong>Kardar, M., & Chakraborty, A., K. (2007) <\/p>\n\n\n\n

Purely stochastic binary decision in cell signaling models without underlying deterministic bistabilities.<\/em><\/p>\n\n\n\n

Proceedings of National Academy of Sciences.<\/em> 104, 18958-18963.<\/p>\n\n\n\n

10. Wylie, D., Das, J., & Chakrabory, A.K. (2007) <\/p>\n\n\n\n

Sensitivity of T cells to antigen and antagonism emerges from differential regulation of the same signaling module.<\/em><\/p>\n\n\n\n

Proceedings of National Academy of Sciences USA. <\/em>104. 5533-5538<\/p>\n\n\n\n

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) <\/p>\n\n\n\n

The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse.<\/em><\/p>\n\n\n\n

Immunity. <\/em>26, 345-355.<\/p>\n\n\n\n

8. Gomez, E.D., Das, J.,  Chakraborty, A. K., Pople, J.A., & Balsara, N.P. (2006) <\/p>\n\n\n\n

Effect of crosslinking on the structure and thermodynamics of lamellar block copolymers.<\/em><\/p>\n\n\n\n

Macromolecules.<\/em> 39, 4848-4859.<\/p>\n\n\n\n

7. Das, J., <\/strong>Yoshida, M., Fresco, Z., Choi, T.L., Frechet, J.M.J., & Chakraborty. (2005) <\/p>\n\n\n\n

A Dendronized polymer is a single molecule glass.<\/em><\/p>\n\n\n\n

Journal of Physical Chemistry B.<\/em> 109, 6535-6543.<\/p>\n\n\n\n

6. Hahn, H., Chakraborty, A.K., Das, J.,<\/strong> Pople, J., & Balsara. N.P. (2005) <\/p>\n\n\n\n

Order-Disorder transitions in cross-linked block copolymer solids.<\/em><\/p>\n\n\n\n

Macromolecules. <\/em>38, 1277-1285.<\/p>\n\n\n\n

5. Bullard, T.J., Das, J., <\/strong>& Tauber, U.C. (2004) <\/p>\n\n\n\n

Dynamics of magnetic flux lines in the presence of correlated disorder.<\/em><\/p>\n\n\n\n

Trends in Superconductivity Research.<\/em> 67-76.<\/p>\n\n\n\n

4. Das, J., <\/strong>Bullard, T.J., & Tauber, U.C. (2003) <\/p>\n\n\n\n

Vortex transport and voltage noise in disordered superconductors.<\/em><\/p>\n\n\n\n

Physica A. <\/em>318, 48<\/p>\n\n\n\n

3. Das, J., <\/strong>Rao, M., & Ramaswamy, S. (2002) <\/p>\n\n\n\n

Nonequilibrium criticality, spatiotemporal chaos and control.<\/em><\/p>\n\n\n\n

Europhysics Letters.<\/em> 60, 418.<\/p>\n\n\n\n

2. Das, J. <\/strong>& Rao, M. (2000). <\/p>\n\n\n\n

Ordering dynamics of Heisenberg spins with torque: Crossover, spin waves and defects.<\/em><\/p>\n\n\n\n

Physical Review E. <\/em>62, 1601.Das, J. <\/strong>& Rao, M. (1999). <\/p>\n\n\n\n

Dynamics of ordering of isotropic magnets.<\/em><\/p>\n\n\n\n

Physica A.<\/em> 270, 253.<\/p>\n\n\n\n

  1. Das, J. <\/strong>& Rao, M. (1998). Dynamics of ordering of Heisenberg spins with torque \u2013 nonconserved case.<\/em> Physical Review E. <\/li><\/ol>\n\n\n\n

    <\/h1>\n\n\n\n

    <\/p>\n\n\n\n

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    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 … <\/p>\n

    Continue reading “Publications”<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":""},"yoast_head":"\nPublications - Laboratory of Computational immunology<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/mathimmunelab.works\/index.php\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications\" \/>\n<meta property=\"og:description\" content=\"52. Darren Wethington, Sayak Mukherjee, and Jayajit Das (2022) McSNAC: A software to approximate first-order signaling networks from mass cytometry data. 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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. 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