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

Entropy
2025-03 | Journal article | Author
DOI: 10.3390/e27030274
Contributors: William Stewart; Ciriyam Jayaprakash; Jayajit Das
Source: check_circle
Multidisciplinary Digital Publishing Institute

Dynamic variability in SHP-1 abundance determines natural killer cell responsiveness

Science signaling
2021 | Journal article
DOI: 10.1126/scisignal.abe5380
EID:

2-s2.0-85121741995

Part of ISSN: 19379145
Contributors: Wu, Z.; Park, S.; Lau, C.M.; Zhong, Y.; Sheppard, S.; Sun, J.C.; Das, J.; Altan-Bonnet, G.; Hsu, K.C.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

bioRxiv
2021 | Other
DOI: 10.1101/2021.12.02.470955
EID:

2-s2.0-85122847851

Part of ISSN: 26928205
Contributors: Wethington, D.; Mukherjee, S.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Spatially resolved in silico modeling of NKG2D signaling kinetics reveals key role of NKG2D and Vav1 co-clustering in generating natural killer cell activation

bioRxiv
2021 | Other
DOI: 10.1101/2021.08.24.457567
EID:

2-s2.0-85115244927

Part of ISSN: 26928205
Contributors: Grewal, R.K.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Role of nanoscale antigen organization on B-cell activation probed using DNA origami

Nature Nanotechnology
2020 | Journal article
DOI: 10.1038/s41565-020-0719-0
EID:

2-s2.0-85087004124

Part of ISSN: 17483395 17483387
Contributors: Veneziano, R.; Moyer, T.J.; Stone, M.B.; Wamhoff, E.-C.; Read, B.J.; Mukherjee, S.; Shepherd, T.R.; Das, J.; Schief, W.R.; Irvine, D.J. et al.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Corrigendum: Spatial Clustering of Receptors and Signaling Molecules Regulates NK Cell Response to Peptide Repertoire Changes (Frontiers in Immunology, (2019), 10, (605), 10.3389/fimmu.2019.00605)

Frontiers in Immunology
2019 | Journal article
DOI: 10.3389/fimmu.2019.02370
EID:

2-s2.0-85074239642

Part of ISSN: 16643224
Contributors: Mbiribindi, B.; Mukherjee, S.; Wellington, D.; Das, J.; Khakoo, S.I.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Data analysis to modeling to building theory in NK cell biology and beyond: How can computational modeling contribute?

Journal of Leukocyte Biology
2019 | Journal article
DOI: 10.1002/JLB.6MR1218-505R
EID:

2-s2.0-85065497722

Part of ISSN: 19383673 07415400
Contributors: Das, J.; Lanier, L.L.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

In silico modeling of biofilm formation by nontypeable Haemophilus influenzae in vivo

mSphere
2019 | Journal article
DOI: 10.1128/mSphere.00254-19
EID:

2-s2.0-85070863720

Part of ISSN: 23795042
Contributors: Brown, J.R.; Jurcisek, J.; Lakhani, V.; Snedden, A.; Ray, W.C.; Mokrzan, E.M.; Bakaletz, L.O.; Dasa, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Mathematical modelling identifies the role of adaptive immunity as a key controller of respiratory syncytial virus in cotton rats

Journal of the Royal Society Interface
2019 | Journal article
DOI: 10.1098/rsif.2019.0389
EID:

2-s2.0-85075664839

Part of ISSN: 17425662 17425689
Contributors: Wethington, D.; Harder, O.; Uppulury, K.; Stewart, W.C.L.; Chen, P.; King, T.; Reynolds, S.D.; Perelson, A.S.; Peeples, M.E.; Niewiesk, S. et al.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Spatial clustering of receptors and signaling molecules regulates NK cell response to peptide repertoire changes

Frontiers in Immunology
2019 | Journal article
DOI: 10.3389/fimmu.2019.00605
EID:

2-s2.0-85065418399

Part of ISSN: 16643224
Contributors: Mbiribindi, B.; Mukherjee, S.; Wellington, D.; Das, J.; Khakoo, S.I.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Stochastic Sequestration Promotes Specificity in Decision Making in Single Cells

Journal of Physical Chemistry B
2019 | Journal article
DOI: 10.1021/acs.jpcb.9b05722
EID:

2-s2.0-85075647450

Part of ISSN: 15205207 15206106
Contributors: Jayaprakash, C.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Defining pharyngeal contractile integral during high-resolution manometry in neonates: a neuromotor marker of pharyngeal vigor

Pediatric Research
2018 | Journal article
DOI: 10.1038/s41390-018-0097-6
EID:

2-s2.0-85049583141

Part of ISSN: 15300447 00313998
Contributors: Jadcherla, S.R.; Prabhakar, V.; Hasenstab, K.A.; Nawaz, S.; Das, J.; Kern, M.; Balasubramanian, G.; Shaker, R.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

bioRxiv
2018 | Other
DOI: 10.1101/451716
EID:

2-s2.0-85095630238

Part of ISSN: 26928205
Contributors: Wethington, D.; Harder, O.; Uppulury, K.; Stewart, W.C.L.; Chen, P.; King, T.; Reynolds, S.D.; Peeples, M.E.; Niewiesk, S.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

bioRxiv
2018 | Other
DOI: 10.1101/451302
EID:

2-s2.0-85095641586

Part of ISSN: 26928205
Contributors: Wethington, D.; Harder, O.; Uppulury, K.; Stewart, W.C.L.; Chen, P.; King, T.; Reynolds, S.D.; Peeples, M.E.; Niewiesk, S.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media

bioRxiv
2018 | Other
DOI: 10.1101/464321
EID:

2-s2.0-85095622409

Part of ISSN: 26928205
Contributors: Lakhani, V.; Tan, L.; Mukherjee, S.; Stewart, W.C.L.; Swords, W.E.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media

Royal Society Open Science
2018 | Journal article
DOI: 10.1098/rsos.180810
EID:

2-s2.0-85058363140

Part of ISSN: 20545703
Contributors: Lakhani, V.; Tan, L.; Mukherjee, S.; Stewart, W.C.L.; Edward Swords, W.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

Royal Society Open Science
2017 | Journal article
DOI: 10.1098/rsos.170811
EID:

2-s2.0-85028336956

Part of ISSN: 20545703
Contributors: Mukherjee, S.; Stewart, D.; Stewart, W.; Lanier, L.L.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Extracellular DNA and type IV pilus expression regulate the structure and kinetics of biofilm formation by nontypeable haemophilus influenzae

mBio
2017 | Journal article
DOI: 10.1128/mBio.01466-17
EID:

2-s2.0-85039903890

Part of ISSN: 21507511 21612129
Contributors: Das, J.; Mokrzan, E.; Lakhani, V.; Rosas, L.; Jurcisek, J.A.; Ray, W.C.; Bakaletz, L.O.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

In silico modeling identifies CD45 as a regulator of IL-2 synergy in the NKG2D-mediated activation of immature human NK cells

Science Signaling
2017 | Journal article
DOI: 10.1126/scisignal.aai9062
EID:

2-s2.0-85021631604

Part of ISSN: 19379145 19450877
Contributors: Mukherjee, S.; Jensen, H.; Stewart, W.; Stewart, D.; Ray, W.C.; Chen, S.-Y.; Nolan, G.P.; Lanier, L.L.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Multiscale Modeling of Complex Formation and CD80 Depletion during Immune Synapse Development

Biophysical Journal
2017 | Journal article
DOI: 10.1016/j.bpj.2016.12.052
EID:

2-s2.0-85015079542

Part of ISSN: 15420086 00063495
Contributors: Sugár, I.P.; Das, J.; Jayaprakash, C.; Sealfon, S.C.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Limiting Energy Dissipation Induces Glassy Kinetics in Single-Cell High-Precision Responses

Biophysical Journal
2016 | Journal article
DOI: 10.1016/j.bpj.2016.01.022
EID:

2-s2.0-84961145205

Part of ISSN: 15420086 00063495
Contributors: Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Non-canonical antagonism of PI3K by the kinase Itpkb delays thymocyte β-selection and renders it Notch-dependent

eLife
2016 | Journal article
DOI: 10.7554/eLife.10786
EID:

2-s2.0-84961275617

Part of ISSN: 2050084X
Contributors: Westernberg, L.; Conche, C.; Huang, Y.H.; Rigaud, S.; Deng, Y.; Siegemund, S.; Mukherjee, S.; Nosaka, L.; Das, J.; Sauer, K.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

Physical Biology
2015 | Journal article
DOI: 10.1088/1478-3975/12/1/016003
EID:

2-s2.0-84923372001

Part of ISSN: 14783975 14783967
Contributors: Mukherjee, S.; Weimer, K.E.; Seok, S.-C.; Ray, W.C.; Jayaprakash, C.; Vieland, V.J.; Swords, W.E.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

Entropy
2015 | Journal article
DOI: 10.3390/e17074986
EID:

2-s2.0-84940556216

Part of ISSN: 10994300
Contributors: Das, J.; Mukherjee, S.; Hodge, S.E.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

NK cells: Tuned by peptide?

Immunological Reviews
2015 | Journal article
DOI: 10.1111/imr.12315
EID:

2-s2.0-84939515843

Part of ISSN: 1600065X 01052896
Contributors: Das, J.; Khakoo, S.I.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Peptide selectivity discriminates NK cells from KIR2DL2- and KIR2DL3-positive individuals

European Journal of Immunology
2015 | Journal article
DOI: 10.1002/eji.201444613
EID:

2-s2.0-84922981771

Part of ISSN: 15214141 00142980
Contributors: Cassidy, S.; Mukherjee, S.; Myint, T.M.; Mbiribindi, B.; North, H.; Traherne, J.; Mulder, A.; Claas, F.H.; Purbhoo, M.A.; Das, J. et al.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Erratum: In silico modeling of itk activation kinetics in thymocytes suggests competing positive and negative IP<sub>4</sub> mediated feedbacks increase robustness (PLoS ONE (2014) 9:1)

PLoS ONE
2014 | Journal article
DOI: 10.1371/annotation/285bb79f-ef1a-467e-9fd3-4e518d65acd3
EID:

2-s2.0-84896962731

Part of ISSN: 19326203
Contributors: Mukherjee, S.; Rigaud, S.; Seok, S.-C.; Fu, G.; Prochenka, A.; Dworkin, M.; Gascoigne, N.R.J.; Vieland, V.J.; Sauer, K.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

Proceedings of the National Academy of Sciences of the United States of America
2013 | Journal article
DOI: 10.1073/pnas.1311069110
EID:

2-s2.0-84887450223

Part of ISSN: 00278424 10916490
Contributors: Mukherjee, S.; Seok, S.-C.; Vieland, V.J.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

Physical Biology
2013 | Journal article
DOI: 10.1088/1478-3975/10/6/066002
EID:

2-s2.0-84891392910

Part of ISSN: 14783967 14783975
Contributors: Mukherjee, S.; Seok, S.-C.; Vieland, V.J.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

In Silico Modeling of Itk Activation Kinetics in Thymocytes Suggests Competing Positive and Negative IP<sub>4</sub> Mediated Feedbacks Increase Robustness

PLoS ONE
2013 | Journal article
DOI: 10.1371/journal.pone.0073937
EID:

2-s2.0-84884173733

Part of ISSN: 19326203
Contributors: Mukherjee, S.; Rigaud, S.; Seok, S.-C.; Fu, G.; Prochenka, A.; Dworkin, M.; Gascoigne, N.R.J.; Vieland, V.J.; Sauer, K.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Measurement of statistical evidence on an absolute scale following thermodynamic principles

Theory in Biosciences
2013 | Journal article
DOI: 10.1007/s12064-013-0180-9
EID:

2-s2.0-84890314196

Part of ISSN: 14317613 16117530
Contributors: Vieland, V.J.; Das, J.; Hodge, S.E.; Seok, S.-C.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Monovalent and multivalent ligation of the B cell receptor exhibit differential dependence upon Syk and Src family kinases

Science Signaling
2013 | Journal article
DOI: 10.1126/scisignal.2003220
EID:

2-s2.0-84872585135

Part of ISSN: 19450877 19379145
Contributors: Mukherjee, S.; Zhu, J.; Zikherman, J.; Parameswaran, R.; Kadlecek, T.A.; Wang, Q.; Au-Yeung, B.; Ploegh, H.; Kuriyan, J.; Das, J. et al.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

Journal of Chemical Physics
2013 | Journal article
DOI: 10.1063/1.4772583
EID:

2-s2.0-84872060072

Part of ISSN: 00219606
Contributors: Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Science Signaling podcast: 1 January 2013

Science Signaling
2013 | Journal article
DOI: 10.1126/scisignal.2003867
EID:

2-s2.0-84872555496

Part of ISSN: 19450877 19379145
Contributors: Weiss, A.; Das, J.; VanHook, A.M.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

The ζ isoform of diacylglycerol kinase plays a predominant role in regulatory T cell development and TCR-mediated Ras signaling

Science Signaling
2013 | Journal article
DOI: 10.1126/scisignal.2004373
EID:

2-s2.0-84889254459

Part of ISSN: 19450877 19379145
Contributors: Joshi, R.P.; Schmidt, A.M.; Das, J.; Pytel, D.; Riese, M.J.; Lester, M.; Diehl, J.A.; Behrens, E.M.; Kambayashi, T.; Koretzky, G.A.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

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

Journal of the Royal Society Interface
2012 | Journal article
DOI: 10.1098/rsif.2011.0896
EID:

2-s2.0-84865094962

Part of ISSN: 17425662 17425689
Contributors: Dworkin, M.; Mukherjee, S.; Jayaprakash, C.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Decreased diacylglycerol metabolism enhances ERK activation and augments CD8<sup>+</sup> T cell functional responses

Journal of Biological Chemistry
2011 | Journal article
DOI: 10.1074/jbc.M110.171884
EID:

2-s2.0-79953141058

Part of ISSN: 00219258 1083351X
Contributors: Riese, M.J.; Grewal, J.; Das, J.; Zou, T.; Patil, V.; Chakraborty, A.K.; Koretzky, G.A.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Activation or tolerance of natural killer cells is modulated by ligand quality in a nonmonotonic manner

Biophysical Journal
2010 | Journal article
DOI: 10.1016/j.bpj.2010.07.061
EID:

2-s2.0-77958488363

Part of ISSN: 15420086 00063495
Contributors: Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Pairing computation with experimentation: A powerful coupling for understanding T cell signalling

Nature Reviews Immunology
2010 | Journal article
DOI: 10.1038/nri2688
EID:

2-s2.0-72949108077

Part of ISSN: 14741733
Contributors: Chakraborty, A.K.; Das, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Digital Signaling and Hysteresis Characterize Ras Activation in Lymphoid Cells

Cell
2009 | Journal article
DOI: 10.1016/j.cell.2008.11.051
EID:

2-s2.0-58249092059

Part of ISSN: 00928674
Contributors: Das, J.; Ho, M.; Zikherman, J.; Govern, C.; Yang, M.; Weiss, A.; Chakraborty, A.K.; Roose, J.P.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Molecular origin and functional consequences of digital signaling and hysteresis during ras activation in lymphocytes

Science Signaling
2009 | Journal article
DOI: 10.1126/scisignal.266pt2
EID:

2-s2.0-70349235821

Part of ISSN: 19450877 19379145
Contributors: Chakraborty, A.K.; Das, J.; Zikherman, J.; Yang, M.; Govern, C.C.; Ho, M.; Weiss, A.; Roose, J.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Origin of the sharp boundary that discriminates positive and negative selection of thymocytes

Proceedings of the National Academy of Sciences of the United States of America
2009 | Journal article
DOI: 10.1073/pnas.0805981105
EID:

2-s2.0-58249087468

Part of ISSN: 00278424 10916490
Contributors: Prasad, A.; Zikherman, J.; Das, J.; Roose, J.P.; Weiss, A.; Chakraborty, A.K.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Positive feedback regulation results in spatial clustering and fast spreading of active signaling molecules on a cell membrane

Journal of Chemical Physics
2009 | Journal article
DOI: 10.1063/1.3149861
EID:

2-s2.0-67650541578

Part of ISSN: 00219606
Contributors: Das, J.; Kardar, M.; Chakraborty, A.K.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Self-assembly of dendronized polymers

Journal of Physical Chemistry B
2009 | Journal article
DOI: 10.1021/jp902927p
EID:

2-s2.0-70350101424

Part of ISSN: 15206106
Contributors: Das, J.; Fréenet, J.M.J.; Chakraborty, A.K.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

The Balance between T Cell Receptor Signaling and Degradation at the Center of the Immunological Synapse Is Determined by Antigen Quality

Immunity
2008 | Journal article
DOI: 10.1016/j.immuni.2008.06.014
EID:

2-s2.0-51349131307

Part of ISSN: 10747613
Contributors: Čemerski, S.; Das, J.; Giurisato, E.; Markiewicz, M.A.; Allen, P.M.; Chakraborty, A.K.; Shaw, A.S.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Vortex washboard voltage noise in type-II superconductors

European Physical Journal B
2008 | Journal article
DOI: 10.1140/epjb/e2008-00358-7
EID:

2-s2.0-55849122279

Part of ISSN: 14346028 14346036
Contributors: Bullard, T.J.; Das, J.; Daquila, G.L.; Täuber, U.C.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities

Proceedings of the National Academy of Sciences of the United States of America
2007 | Journal article
DOI: 10.1073/pnas.0706110104
EID:

2-s2.0-37649018636

Part of ISSN: 00278424 10916490
Contributors: Artyomov, M.N.; Das, J.; Kardar, M.; Chakraborty, A.K.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Sensitivity of T cells to antigen and antagonism emerges from differential regulation of the same molecular signaling module

Proceedings of the National Academy of Sciences of the United States of America
2007 | Journal article
DOI: 10.1073/pnas.0611482104
EID:

2-s2.0-34248399201

Part of ISSN: 00278424
Contributors: Wylie, D.C.; Das, J.; Chakraborty, A.K.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

The Stimulatory Potency of T Cell Antigens Is Influenced by the Formation of the Immunological Synapse

Immunity
2007 | Journal article
DOI: 10.1016/j.immuni.2007.01.013
EID:

2-s2.0-33947189706

Part of ISSN: 10747613
Contributors: Čemerski, S.; Das, J.; Locasale, J.; Arnold, P.; Giurisato, E.; Markiewicz, MaryA.; Fremont, D.; Allen, P.M.; Chakraborty, A.K.; Shaw, A.S.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier

Effect of cross-linking on the structure and thermodynamics of lamellar block copolymers

Macromolecules
2006 | Journal article
DOI: 10.1021/ma052323r
EID:

2-s2.0-33746304757

Part of ISSN: 00249297
Contributors: Gomez, E.D.; Das, J.; Chakraborty, A.K.; Pople, J.A.; Balsara, N.P.
Source: Self-asserted source
Jayajit Das via Scopus - Elsevier
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