Difference between revisions of "User:Jayajit Das"

From OpenWetWare
Jump to: navigation, search
(Contact Info)
(Contact Info)
 
(20 intermediate revisions by the same user not shown)
Line 4: Line 4:
 
*'''Jayajit Das'''  
 
*'''Jayajit Das'''  
  
Assistant Professor<br />
+
Associate Professor<br />
 
Battelle Center for Mathematical Medicine<br />
 
Battelle Center for Mathematical Medicine<br />
 
The Research Institute at Nationwide Children's Hospital<br />
 
The Research Institute at Nationwide Children's Hospital<br />
Line 22: Line 22:
 
* 2000      Ph.D. Physics, Raman Research Institute, Bangalore, India
 
* 2000      Ph.D. Physics, Raman Research Institute, Bangalore, India
 
* 1996      M.Sc. Physics, Institute of Mathematical Sciences, Chennai (Madras) India
 
* 1996      M.Sc. Physics, Institute of Mathematical Sciences, Chennai (Madras) India
* 1994      B.Sc. Physics, Presidency College, Kolkata(Calcutta), India  
+
* 1994      B.Sc. Physics, Presidency College, Kolkata(Calcutta), India
  
My lab uses theoretical and computational approaches based on statistical physics to uncover basic mechanistic principles underlying our innate and adaptive immune response. Obtaining such mechanistic principles from experimental observations alone is often difficult because the pertinent processes include co-operative dynamic events with many participating components. A further complication that confounds intuition is stochastic fluctuations in these systems with small numbers of molecules. However, by synergistically integrating observations from experiments with transgenic animals, single molecule techniques and imaging studies probing molecular events in live animals with these theoretical and computational approaches we can provide system-level understanding into such complex systems. The mechanistic insight gained from such studies not only will help develop future experiments to unravel basic principles of our immune system, but may also help envision therapeutic strategies for infectious diseases and autoimmune disorders.
+
==Research Area==
 +
The primary focus of our research is uncovering mechanisms and physical principles that underlie host-microbe relationships. My group uses mathematical and computational techniques rooted in engineering, nonlinear dynamics, statistics and physics, in particular, statistical physics. A large number of the projects in my group are carried out in synergistic collaboration with our experimental collaborators. The rest of my research effort is invested in analyzing specific living systems with reduced models for unraveling novel physical principles. The long-term goal of our research endeavor is two-fold: (i) to uncover basic mechanisms to help envision therapeutic strategies for diseases related to our immune system, (ii) to find novel physical principles that underlie host-microbe relations. Our research projects can be broadly classified into three interlinked themes: (1) Lymphocyte signaling and activation. (2) Host-microbe relation in polymicrobial infections (Otitis Media). (3) Physics of single cell and cell populations.
  
 
== Lab members ==
 
== Lab members ==
 
Sayak Mukherjee (Ph.D Physics, V.Tech) Postdoc <br />
 
Sayak Mukherjee (Ph.D Physics, V.Tech) Postdoc <br />
Aleya Dhanji Graduate student, OSU Physics Department <br />
+
Vinal Lakhani (PhD Bioinformatics and Computational Biology, UNC Chapel Hill) Postdoc <br />
Arjun Venkataraman (High School Research Project) <br />
 
  
 
== Lab Alumni ==
 
== Lab Alumni ==
Line 39: Line 39:
  
 
Mithila Agnihotri Graduate student, OSU Biophysics Program  <br />
 
Mithila Agnihotri Graduate student, OSU Biophysics Program  <br />
 +
 +
Arjun Venkataraman (High School Research Project) <br />
  
 
==Selected Publications==
 
==Selected Publications==
 
<biblio>
 
<biblio>
#Paper1 pmid=23298061
+
#Paper1 pmid=26958894
#Paper2 pmid=23281368
+
#Paper2 pmid=26880557
#Paper3 pmid=22378749
+
#Paper3 pmid=26843809
#Paper4 pmid=20923636
+
#Paper4 pmid=26284480
#Paper5 pmid=20029448
+
#Paper5 pmid=25473880
#Paper6 pmid=19566183
+
#Paper6 pmid=25359276
#Paper7 pmid=19366993
+
#Paper7 pmid=24280043
#Paper8 pmid=19167334
+
#Paper8 pmid=24164951
#Paper9 pmid=19098101
+
#Paper9 pmid=24167288
#Paper10 pmid=18760640
+
#Paper10 pmid=24066087
#Paper11 pmid=18025473  
+
#Paper11 pmid=23298061
#Paper12 pmid=17360359
+
#Paper12 pmid=23281368
#Paper13 pmid=17346997
+
#Paper13 pmid=22378749
 +
#Paper14 pmid=20923636
 +
#Paper15 pmid=20029448
 +
#Paper16 pmid=19566183
 +
#Paper17 pmid=19366993
 +
#Paper18 pmid=19167334
 +
#Paper19 pmid=19098101
 +
#Paper20 pmid=18760640
 +
#Paper21 pmid=18025473  
 +
#Paper22 pmid=17360359
 +
#Paper23 pmid=17346997
 
</biblio>
 
</biblio>
  
 
==Useful links==
 
==Useful links==
[url=http://www3.clustrmaps.com/user/b259054d][img]http://www3.clustrmaps.com/stats/maps-no_clusters/--openwetware.org-wiki-User-Jayajit_Das-thumb.jpg[/img][/url]
+
[http://scholar.google.com/citations?user=iXkBO4MAAAAJ&hl=en&oi=ao  Google_Scholar_Link]
 +
 
 +
[http://www.clustrmaps.com/map/Openwetware.org Visitor_Map]
  
*More details at http://www.mathmed.org/#Jayajit_Das
+
*More details at http://www.nationwidechildrens.org/jayajit-das
  
 
==Jobs==
 
==Jobs==
 
'''Graduate Student''': Students with a background in Physics, Mathematics, Chemistry, Computer Science or Chemical Engineering are encouraged to apply.
 
'''Graduate Student''': Students with a background in Physics, Mathematics, Chemistry, Computer Science or Chemical Engineering are encouraged to apply.

Latest revision as of 05:22, 3 November 2016

Contact Info

Jayajit.jpg
  • Jayajit Das

Associate Professor
Battelle Center for Mathematical Medicine
The Research Institute at Nationwide Children's Hospital
Departments of Pediatrics, Physics, Integrated Biomedical Sciences, and Biophysics Graduate Program
The Ohio State University, Columbus, OH 43205

Email: das.70 @ osu.edu; jayajit.das @ nationwidechildrens.org ; jayajit @ gmail.com
Phone: 614-355-5632 (work)
Fax: 614-355-2928
[DasLab]

Education and Professional Experience

  • 2005-2008 Postdoctoral Fellow, Massachusetts Institute of Technology
  • 2002-2005 Postdoctoral Fellow, University of California at Berkeley
  • 2000-2002 Postdoctoral Fellow, Virginia Institute of Polytechnic and State University
  • 2000 Ph.D. Physics, Raman Research Institute, Bangalore, India
  • 1996 M.Sc. Physics, Institute of Mathematical Sciences, Chennai (Madras) India
  • 1994 B.Sc. Physics, Presidency College, Kolkata(Calcutta), India

Research Area

The primary focus of our research is uncovering mechanisms and physical principles that underlie host-microbe relationships. My group uses mathematical and computational techniques rooted in engineering, nonlinear dynamics, statistics and physics, in particular, statistical physics. A large number of the projects in my group are carried out in synergistic collaboration with our experimental collaborators. The rest of my research effort is invested in analyzing specific living systems with reduced models for unraveling novel physical principles. The long-term goal of our research endeavor is two-fold: (i) to uncover basic mechanisms to help envision therapeutic strategies for diseases related to our immune system, (ii) to find novel physical principles that underlie host-microbe relations. Our research projects can be broadly classified into three interlinked themes: (1) Lymphocyte signaling and activation. (2) Host-microbe relation in polymicrobial infections (Otitis Media). (3) Physics of single cell and cell populations.

Lab members

Sayak Mukherjee (Ph.D Physics, V.Tech) Postdoc
Vinal Lakhani (PhD Bioinformatics and Computational Biology, UNC Chapel Hill) Postdoc

Lab Alumni

Michael Dworkin (Math Major, OSU) Undergraduate student
Current Position: Merrimack Pharmaceuticals, Inc

Birra Abdurehman (Math Major, OSU) Undergraduate student
Jagadish Kumar (Postdoc) 2010-2011

Mithila Agnihotri Graduate student, OSU Biophysics Program

Arjun Venkataraman (High School Research Project)

Selected Publications

  1. Das J. Limiting Energy Dissipation Induces Glassy Kinetics in Single-Cell High-Precision Responses. Biophys J. 2016 Mar 8;110(5):1180-90. DOI:10.1016/j.bpj.2016.01.022 | PubMed ID:26958894 | HubMed [Paper1]
  2. Westernberg L, Conche C, Huang YH, Rigaud S, Deng Y, Siegemund S, Mukherjee S, Nosaka L, Das J, and Sauer K. Non-canonical antagonism of PI3K by the kinase Itpkb delays thymocyte β-selection and renders it Notch-dependent. Elife. 2016 Feb 11;5. DOI:10.7554/eLife.10786 | PubMed ID:26880557 | HubMed [Paper2]
  3. Das J, Mukherjee S, and Hodge SE. Maximum Entropy Estimation of Probability Distribution of Variables in Higher Dimensions from Lower Dimensional Data. Entropy (Basel). 2015 Jul;17(7):4986-4999. DOI:10.3390/e17074986 | PubMed ID:26843809 | HubMed [Paper3]
  4. Das J and Khakoo SI. NK cells: tuned by peptide?. Immunol Rev. 2015 Sep;267(1):214-27. DOI:10.1111/imr.12315 | PubMed ID:26284480 | HubMed [Paper4]
  5. Mukherjee S, Weimer KE, Seok SC, Ray WC, Jayaprakash C, Vieland VJ, Swords WE, and Das J. Host-to-host variation of ecological interactions in polymicrobial infections. Phys Biol. 2014 Dec 4;12(1):016003. DOI:10.1088/1478-3975/12/1/016003 | PubMed ID:25473880 | HubMed [Paper5]
  6. Cassidy S, Mukherjee S, Myint TM, Mbiribindi B, North H, Traherne J, Mulder A, Claas FH, Purbhoo MA, Das J, and Khakoo SI. Peptide selectivity discriminates NK cells from KIR2DL2- and KIR2DL3-positive individuals. Eur J Immunol. 2015 Feb;45(2):492-500. DOI:10.1002/eji.201444613 | PubMed ID:25359276 | HubMed [Paper6]
  7. Joshi RP, Schmidt AM, Das J, Pytel D, Riese MJ, Lester M, Diehl JA, Behrens EM, Kambayashi T, and Koretzky GA. The ζ isoform of diacylglycerol kinase plays a predominant role in regulatory T cell development and TCR-mediated ras signaling. Sci Signal. 2013 Nov 26;6(303):ra102. DOI:10.1126/scisignal.2004373 | PubMed ID:24280043 | HubMed [Paper7]
  8. Mukherjee S, Seok SC, Vieland VJ, and Das J. Data-driven quantification of the robustness and sensitivity of cell signaling networks. Phys Biol. 2013 Dec;10(6):066002. DOI:10.1088/1478-3975/10/6/066002 | PubMed ID:24164951 | HubMed [Paper8]
  9. Mukherjee S, Seok SC, Vieland VJ, and Das J. Cell responses only partially shape cell-to-cell variations in protein abundances in Escherichia coli chemotaxis. Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18531-6. DOI:10.1073/pnas.1311069110 | PubMed ID:24167288 | HubMed [Paper9]
  10. Mukherjee S, Rigaud S, Seok SC, Fu G, Prochenka A, Dworkin M, Gascoigne NR, Vieland VJ, Sauer K, and Das J. In silico modeling of Itk activation kinetics in thymocytes suggests competing positive and negative IP4 mediated feedbacks increase robustness. PLoS One. 2013;8(9):e73937. DOI:10.1371/journal.pone.0073937 | PubMed ID:24066087 | HubMed [Paper10]
  11. Das J. Positive feedback produces broad distributions in maximum activation attained within a narrow time window in stochastic biochemical reactions. J Chem Phys. 2013 Jan 7;138(1):015101. DOI:10.1063/1.4772583 | PubMed ID:23298061 | HubMed [Paper11]
  12. Mukherjee S, Zhu J, Zikherman J, Parameswaran R, Kadlecek TA, Wang Q, Au-Yeung B, Ploegh H, Kuriyan J, Das J, and Weiss A. Monovalent and multivalent ligation of the B cell receptor exhibit differential dependence upon Syk and Src family kinases. Sci Signal. 2013 Jan 1;6(256):ra1. DOI:10.1126/scisignal.2003220 | PubMed ID:23281368 | HubMed [Paper12]
  13. Dworkin M, Mukherjee S, Jayaprakash C, and Das J. Dramatic reduction of dimensionality in large biochemical networks owing to strong pair correlations. J R Soc Interface. 2012 Aug 7;9(73):1824-35. DOI:10.1098/rsif.2011.0896 | PubMed ID:22378749 | HubMed [Paper13]
  14. Das J. Activation or tolerance of natural killer cells is modulated by ligand quality in a nonmonotonic manner. Biophys J. 2010 Oct 6;99(7):2028-37. DOI:10.1016/j.bpj.2010.07.061 | PubMed ID:20923636 | HubMed [Paper14]
  15. Chakraborty AK and Das J. Pairing computation with experimentation: a powerful coupling for understanding T cell signalling. Nat Rev Immunol. 2010 Jan;10(1):59-71. DOI:10.1038/nri2688 | PubMed ID:20029448 | HubMed [Paper15]
  16. Das J, Kardar M, and Chakraborty AK. Positive feedback regulation results in spatial clustering and fast spreading of active signaling molecules on a cell membrane. J Chem Phys. 2009 Jun 28;130(24):245102. DOI:10.1063/1.3149861 | PubMed ID:19566183 | HubMed [Paper16]
  17. Chakraborty AK, Das J, Zikherman J, Yang M, Govern CC, Ho M, Weiss A, and Roose J. Molecular origin and functional consequences of digital signaling and hysteresis during Ras activation in lymphocytes. Sci Signal. 2009 Apr 14;2(66):pt2. DOI:10.1126/scisignal.266pt2 | PubMed ID:19366993 | HubMed [Paper17]
  18. Das J, Ho M, Zikherman J, Govern C, Yang M, Weiss A, Chakraborty AK, and Roose JP. Digital signaling and hysteresis characterize ras activation in lymphoid cells. Cell. 2009 Jan 23;136(2):337-51. DOI:10.1016/j.cell.2008.11.051 | PubMed ID:19167334 | HubMed [Paper18]
  19. Prasad A, Zikherman J, Das J, Roose JP, Weiss A, and Chakraborty AK. Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):528-33. DOI:10.1073/pnas.0805981105 | PubMed ID:19098101 | HubMed [Paper19]
  20. Cemerski S, Das J, Giurisato E, Markiewicz MA, Allen PM, Chakraborty AK, and Shaw AS. The balance between T cell receptor signaling and degradation at the center of the immunological synapse is determined by antigen quality. Immunity. 2008 Sep 19;29(3):414-22. DOI:10.1016/j.immuni.2008.06.014 | PubMed ID:18760640 | HubMed [Paper20]
  21. Artyomov MN, Das J, Kardar M, and Chakraborty AK. Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities. Proc Natl Acad Sci U S A. 2007 Nov 27;104(48):18958-63. DOI:10.1073/pnas.0706110104 | PubMed ID:18025473 | HubMed [Paper21]
  22. Wylie DC, Das J, and Chakraborty AK. Sensitivity of T cells to antigen and antagonism emerges from differential regulation of the same molecular signaling module. Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5533-8. DOI:10.1073/pnas.0611482104 | PubMed ID:17360359 | HubMed [Paper22]
  23. Cemerski S, Das J, Locasale J, Arnold P, Giurisato E, Markiewicz MA, Fremont D, Allen PM, Chakraborty AK, and Shaw AS. The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse. Immunity. 2007 Mar;26(3):345-55. DOI:10.1016/j.immuni.2007.01.013 | PubMed ID:17346997 | HubMed [Paper23]
All Medline abstracts: PubMed | HubMed

Useful links

Google_Scholar_Link

Visitor_Map

Jobs

Graduate Student: Students with a background in Physics, Mathematics, Chemistry, Computer Science or Chemical Engineering are encouraged to apply.