Friday, January 30, 2009

Research Profile of Somdatta Sinha

NAME (First Last) SOMDATTA SINHA



ADDRESS Centre for Cellular & Molecular Biology,
Uppal Road, Hyderabad 500 007, AP, INDIA

Telephone: +91 40 27192588 (Office);
27192786 (Lab)
+91 40 27160222-0241 (Reception)
Extension 2588 and 2786

Fax: +91 40 27160591; 27160311
Email: sinha@ccmb.res.in
somdattasinha@gmail.com
somdatta_sinha@yahoo.com


ACADEMIC QUALIFICATIONS


Ph.D.(1982) & M.Phil. Theoretical Biology,
School of Environmental Sciences,
Jawaharlal Nehru University, New Delhi, India

Ph.D. THESIS: A Study on The Effects of External Perturbations in
Some Biological Organisations.

M.Phil. THESIS: Analysis of Biochemical Oscillators


M.Sc. & B.Sc.(Hons) Physics, Mathematics & Chemistry
(I Class) Visva Bharati University, Santiniketan, India

High School Physics, Chemistry, Mathematics, Geography
(I Div. I Rank) Patha Bhavan, Visva Bharati, Santiniketan, WB



PRESENT POSITION
Scientist “G”

Group Leader, Mathematical & Computational Biology Group,
Centre for Cellular & Molecular Biology Hyderabad, AP, India

(A national laboratory of the Council of Scientific & Industrial Research (CSIR), India)

PREVIOUS EMPLOYMENT

Research Associate at the School of Environmental Sciences (6 months – 1982)
Research Associate at the Centre for Cellular & Molecular Biology (6 mo, 1983)
Joined CCMB as Scientist 'C' in 1983; Scientist E-I (1988), Scientist E-II (1993), Scientist F (1998-2003).

FELLOWSHIPS / ASSOCIATES / AWARDS/ VISITS

• Fellow of the Indian Academy of Sciences, India
• Fellow of the National Academy of Sciences, India
• Fellow at the Institute of Advanced Study (Wissenschaftskolleg) at Berlin, 2000-2001
• Long Term Participant at the Kavli Institute of Theoretical Physics (KITP), UCSB, USA, Aug-November, 2003
• Landahl (WOC) Travel Award, Society for Mathematical Biology, USA for ECMTB, Dresden, Germany, 2005
• Visitor to Max Planck Institutes for Self-Organisation & Mathematics for Sciences (Goettingen and Leipzig), 2005
• Visitor to Univ. of Hamburg, Germany, and Univ. of Utrecht, The Netherlands, 2005
• Visitor to Biozentrum, Basel, Switzerland, 2005
• Visitor to the Mathematical Research Branch, NIDDK, NIH, USA, June 2002
• Visiting Fellow to the Santa Fe Institute, Santa Fe, USA, 1999-2000
• Raman Research Fellowship (Govt. of India) 1999 at the Mathematical Research Branch, NIDDK, NIH, USA
• Senior Associate Fellow of the CSIR Centre for Mathematical Modelling & Computer Simulation, Bangalore
• The Wellcome Trust Travel Fellowship, 1998
• Visiting Fellowship from the Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, March-June, 1994
• Associated to Harvard School of Public Health, Harvard Univ, USA, 1992
• UNESCO Travel Award for Gordon Research Conference
• Landahl Travel Award, Society for Mathematical Biology, USA, 1991
• Indian National Science Academy - Royal Society, London Exchange Programme, Centre for Mathematical Biology, Univ. of Oxford, UK - 1986-87.
• CSIR Post Doctoral and Senior Research Fellowships - 1979-83
• National Science Talent Scholarship - 1969 -1979.
• Award for holding first rank in Higher School Certificate Examination

OTHER ACTIVITIES
• Council Member, Indian Academy of Sciences, Bangalore, India
• Editorial Board Member, Journal of Biosciences, Indian Academy of Sciences, India
• Editorial Board Member, Current Science, India.
• Member, Society for Mathematical Biology, USA.
• Member, World Outreach Committee of the Society for Mathematical Biology, USA.
• Member, Sectional Committee, Indian Academy of Sciences, India
• Member, Project Advisory Council (Animal Sciences), Department of Science & Technology, India


ORGANIZATION OF CONFERENCES

1. Discussion Meeting on “Mechanisms of Pattern Formation”, Coorg, India, Dec 6-9, 2007

2. IASc Teachers' Refresher Course on Advances in Biophysics, CCMB, Hyderabad, May 25 - June 8, 2007.

3. IASc Teachers' Refresher Course on Interdisciplinary Approaches in Biology, CCMB, Hyderabad May 25-June 8, 2005

4. International Workshop on Mathematical & Computational Biology, CCMB, Hyderabad Jan 8-13, 2001

5. Modelling Biological Systems: concepts & applications, CCMB, Hyderabad, Jan 8-9, 1997

6. Mathematical Modelling in Biology & Chemistry, CCMB, Hyderabad, 1991


• Science Education

Co-authored of Science Textbooks of Classes 7, 8, and 10 for the Central Board of Secondary Education published by the National Council for Educational Research & Training (NCERT), New Delhi, India.

Popular scientific writing - Contributed many articles in popular Science journals and magazines in English and vernacular language, and taken part in meetings on Science & Society and Women in Science.

Organised three symposiums on theoretical biology.

RESEARCH INTEREST

My area of study is theoretical biology, nonlinear dynamics and complex systems with a view to understand the logic & design of underlying biological processes. The primary interest is to study the evolution and maintenance of spatiotemporal organization in biological systems spanning multiple spatiotemporal scales – from ecological to genetic. I have studied mechanisms of self-organization in collective dynamics in spatially extended systems (e.g. metapopulation, excitable tissues, etc), and the adaptive role of biochemical nonlinearities present in biochemical pathways. The three areas of research are –

Biochemical Pathways & Gene Circuits – dynamics of genetic and metabolic regulatory circuits; artificial regulatory networks; deterministic and stochastic modelling; transient cellular processes; Comparative genomic study of biochemical pathway evolution in different organisms; modelling protein structures using network theory.

Pattern Formation & Collective behaviour: Pattern formation during development and inter-cellular communication; Role of space, interaction strength and local dynamics. Synchronization and controlling spatiotemporal dynamics; bursting dynamics of excitable tissues; and evolution of the collective.

Modelling Ecological systems – Single discrete population growth models, and metapopulation dynamics under ecological processes; Interacting species models (host-parasite, prey-predator, etc.); and spatiotemporal analysis of disease data.


RESEARCH PUBLICATIONS

1. Delay-Induced Transient Increase and Heterogeneity in Gene Expression in Negatively Auto-regulated Gene Circuits.
PLoS One (Accepted 2008)
R Maithreye, RamRup Sarkar, Veena K. Parnaik, and Somdatta Sinha

2. Ecological Networks: Structure, Interaction Strength, and Stability
In: Dynamics On and Of Complex Networks: Applications to Biology, Computer Science, Economics, and the Social Sciences, Eds. Niloy Ganguly, Andreas Deutsch, and Animesh Mukherjee, BIRKHÄUSER, BOSTON, (In press 2008)
S. Bhattacharyya, Somdatta Sinha.

3. Analysis of Protein Folds Using Protein Contact Networks
Pramana – journal of physics. (In press 2008)
Pankaj Barah and Somdatta Sinha

4. Synchronization in multi-cell systems exhibiting dynamic plasticity
Pramana – journal of physics. (In press 2008)
C. Suguna and Somdatta Sinha

5. Measuring Collective Behaviour of Multi-Cellular Ensembles: Role of Space-Time Scales. Journal of Biosciences (epublished March 3, 2008)
Somdatta Sinha

6. Assortative mixing in Protein Contact Networks and protein folding kinetics
Bioinformatics, doi: 10.1093/bioinformatics/btm257; (2007)
Ganesh Bagler; Somdatta Sinha

7. Propagation of extrinsic perturbation in a negatively auto-regulated pathway.
Physical Biology, 4, pp 48-59, (2007)
R Maithreye and Somdatta Sinha.

8. Synchronization in coupled cells with activator-inhibitor pathways.
Physical Review E, 75, 011906 (2007)
S. Rajesh, Sudeshna Sinha, and Somdatta Sinha

9. Multiplicity in Non-Linear Systems.
In: Understanding Change: Models, Methodologies and Metaphors, Eds: A. Wimmer and R. Kössler, Basingstoke: Palgrave Macmillan, ISBN:1403939411, pp 222-235 (2005)
Somdatta Sinha

10. Network properties of protein structures.
Physica A, 346(1-2), pp 27--33 (2005)
Ganesh Bagler and Somdatta Sinha

11. Dynamics of coupled cell-systems.
Physica A, 346(1-2), pp 154--164 (2005)
C. Suguna and Somdatta Sinha
12. The role of virus infection in a simple phytoplankton-zooplankton system.
J. Theor. Biol., 231, pp 153-166 (2004)
BK Singh, J Chattopadhyay and Somdatta Sinha

13. The role of heterogeneity on the spatiotemporal dynamics of host parasite metapopulation
Ecological Modelling 180, 435-443, (2004)
B.K.Singh, J.Subba Rao, R. Ramaswamy & Somdatta Sinha

14. Modelling Simple Biochemical Networks.
In: Function and Regulation of Cellular Systems: Experiments and Models. Eds: A. Deutsch, J Howard, M Falcke & W Zimmermann, Birkhauser, Basel, pp 251-257 (2003)
R. Maithreye and Somdatta Sinha

15. Controllability of Spatiotemporal Systems Using Constant Pinnings
Physica A 318, pp 200-212 (2003)
Nita Parekh and Somdatta Sinha

16. Dynamics of Cellular Processes: From Single Cell to Collective Behavior
In: Recent Research Developments in Biophysical Chemistry (ISBN: 81-7736-116-3), Eds: C.A. Condat and A. Baruzzi, Research Signpost, pp 91-103 (2002)
C. Suguna, R Maithreye, Silpa Suthram & Somdatta Sinha

17. Cellular Dynamics in Noisy Environment
Fluctuation and Noise Letters, 2 (4), pp L313-L326 (2002)
C. Suguna and Somdatta Sinha

18. Controlling Dynamics in Spatially Extended Systems.
Physical Review E, 65, pp 036227-1 to 9 (2002)
Nita Parekh & Somdatta Sinha

19. Role of nonlinearity in population growth models
In: Nonlinear Phenomena in Biological & Physical Sciences, Eds: S K Malik. M K Chandrashekaran, N. Pradhan, Ind. Nat.Sci. Acad., pp 195-222. (2000)
Parichay K. Das & Somdatta Sinha

20. Minimal model for complex dynamics in cellular processes
Physical Review E, 60 (5), pp 5943-5949 (1999)
C. Suguna, KK Chowdhury & Somdatta Sinha

21. Suppressing Spatiotemporal Chaos in Coupled Map Lattices Using Constant Pinnings
In "Nonlinear Dynamics and Brain Functioning", (Ed: R. Sreenivasan & Paul E.Rapp), Nova Science Publishers, Inc. (New York, USA), ISBN 1560726482 (1999)
N. Parekh & Somdatta Sinha.

22. Modelling Pattern Formation in Hydra
In "Recent Trends in Developmental Biology", (Ed. S.K. Gakhar & S.N. Mishra), Himalaya Publishing House (Delhi, India), pp 145-164 (1999)
Somdatta Sinha.
23. Global and Local Control of Spatiotemporal Chaos in Coupled Map Lattices
Physical Review Letters, 81, pp 1401-1404 (1998)
Parekh N., Parthasarathy, S. & Somdatta Sinha.

24. Are Ecological Systems Chaotic ? - An enquiry into population growth models
Current Science, 73 (11), pp 949 - 956, (1997).
Somdatta Sinha.

25. Behaviour of Simple One-dimensional Maps Under Perturbation.
Pramana- journal of physics, 48 (1), pp 87 - 98. (1997).
Somdatta Sinha, & Parichay K. Das.

26. Unusual Dynamics of Extinction in a Simple Ecological Model.
Proc. Nat. Acad. Sci. (USA), 93 (Feb), pp 1504 -1508. (1996).
Somdatta Sinha, & Parthasarathy, S.

27. Controlling Chaos in Unidimensional Maps Using Constant Feedback.
Physical Review E, 51 (6), pp 6239 - 6242. (1995)
Parthasarathy, S & Somdatta Sinha.

28. Behaviour of Simple Population Models Under Ecological Processes.
J. Biosciences, 19, pp 247 - 254. (1994).
Somdatta Sinha & Parthasarathy, S.

29. Perturbations in Morphogen Gradients Induce Budding in Hydra.
Developmental Biology, 154, pp 218 - 222. (1992).
Somdatta Sinha, and Mookerjee,S.

30. Pattern Formation in Hydra - a Theoretical Study.
In "Realm of Differentiation", Prof. Sivatosh Mookerjee Festschrift,
(M.Habibulla, Ed), Neelkanth Publishers, New Delhi, pp 197-208. (1992).
Somdatta Sinha.

31. Steady State Spatial Patterns in a Cell - Chemotaxis Problem.
IMA J. Maths. Appld. Med. Biol., 6, pp 69 - 79. ( 1989 ).
Grindrod,P., Murray,J.D. and Somdatta Sinha.

32. A Theoretical Study of the Tryptophan Operon : Application in Microbial Technology.
Biotech. & Bioengg., 31, pp 117 - 125. (1988 ).
Somdatta Sinha.

33. Complex Behaviour of the Repressible Operon.
J. Theor. Biol., 132, pp 307 - 318. ( 1988 ).
Somdatta Sinha and Ramaswamy,R.

34. On the Dynamics of Controlled Metabolic Network and Cellular Behaviour.
Biosystems, 20, pp 341 - 354. ( 1987 ).
Somdatta Sinha and Ramaswamy,R.

35. Dynamics of Controlled Metabolic Network and Cellular Behaviour.
In "Chaos in Biological Systems", (H.Degn, A.V.Holden, & L.F.Olsen,Eds).
Plenum Press, New York, pp 59 - 66. ( 1987 ).
Somdatta Sinha and Ramaswamy,R.

36. Pattern Forming Mechanisms in Hydra as Revealed by Host - Graft Interactions.
Indian J. Exp. Biol., 23, pp 535 - 540. (1985 ).
Somdatta Sinha, Rao,J.S., and Mookerjee,S.

37. A Four Variable Model for the Pattern Forming Mechanisms in Hydra.
Biosystems, 17, pp 15 - 22. ( 1984 ).
Somdatta Sinha, Joshi,N.V., Rao,J.S., and Mookerjee,S.

38. Hydra Pattern is Controlled by two Distinct but Interacting Morphogen Sets.
Wilhelm Roux's Archiv. Dev. Biol., 194, pp 56 - 60. ( 1984 ).
Somdatta Sinha and Mookerjee,S.

39. Are Circadian Oscillators Structurally Unstable ?
J. Theor. Biol., 101, pp 401 - 414. ( 1983 ).
Somdatta Sinha.

40. A Linear Oscillator Model for Circadian Rhythms : Implications for Phase Response Curves.
Chronobiologia, VII, No.4, pp 377 - 391. ( 1981 ).
Somdatta Sinha.

41. Regenerative Capacity of Isolated Mid-gastric Annulus of Hydra by Varying its Cell Quanta.
Indian J. Exp. Biol., 17, pp 1001 - 1006. ( 1979 ).
Mookerjee,S., Chakraborty,D., and Somdatta Sinha.


OTHER PUBLICATIONS

• Controlling Spatiotemporal Dynamics in Excitable Systems. Nita Parekh and Somdatta Sinha. Santa Fe Institute Working Paper No. 00-06-031 (2000)

• Guest-edited a Special Section in “Modelling in Biology” of 8 papers for the Current Science vol 73, N0. 11, 1997 (published by the Indian Academy of Science)

• Co-author of Science Textbooks of Classes 7, 8, and 10 for the Central Board of Secondary Education published by the National Council for Educational Research & Training (NCERT), New Delhi, India.

• Reviewed several scientific and technical articles and books for journals and grant agencies.

(Publications (abstracts and short papers) in Proceedings of Conferences are not included here)


Teaching Experience:

1) Biostatistics to I year Ph.D. students (12 lectures) at CCMB,
2) Biochemical pathway Modelling to M.Sc. Bioinformatics students (4 lectures) at the Bioinformatics Centre, Pune University, Pune, Maharshtra, India
3) Biochemical pathway Modelling to B.Tech. Bioinformatics students (4 lectures) at the International Institute of Information Technology (IIIT), Hyderabad, India
4) Systems Biology - an introduction to B.Tech. Bioinformatics students (2 lectures) at the International Institute of Information Technology (IIIT), Hyderabad, India
5) Modelling biological systems to M.Tech. students (2 lectures) at the Centre for Modelling & Simulation, Pune University, Pune, Maharshtra, India
6) Numerous lectures on the above topics in teaching workshops and training courses in India.

Grants received (2002 onwards):

1) "Development of a comprehensive web resource on biochemical pathways useful for interdisciplinary research in Bioinformatics",
Department of Biotechnology (BT/PR5446/BID/07/106/2004)

2) "Towards a realistic model of insect population growth at the single and metapopulation level: Drosophila as a model system",
Department of Science & Technology (SR/SO/AS-09/2002)

3) "Comparative genomic analysis of the Tryptophan biosynthetic pathway", Department of Biotechnology (BT/PR3098/MED/12/136/2002). Completed


Research personnel in the Group:

a) Dr. C. Suguna, Sci.E1 (1997-)
b) Dr. Ramrup Sarkar, Sci.C (2005-)
c) Dr. Samit Bhattacharyya PDF (2007-)
d) Mr. Pankaj Barah Proj. Asst. (2007-)
e) Ms. Susmita Sarkar Proj. Asst. (2007-)
f) Mr. Ankur Malhotra Proj. Asst. (2008-)
g) Mr. Aridaman Pandit Research Student (2007-)


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Personal Details:

Date of Birth: October 14, 1951

Gender: Female

Nationality: Indian

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