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List of Publications
1. IGIPT - Integrated Genomic Island
Prediction Tool, Ruchi Jain, Sandeep
Ramineni, Nita Parekh, Bioinformation,
vol. 7(6) (2011).
2. Analysis of Centrality Measures of
Airport Network of India, Manasi Sapre and Nita Parekh, S.O. Kuznetsov,
D.P. Mandal, M.K. Kundu,
S.K. Pal (Eds.), Lecture Notes in Computer Science, vol. 6744, pg. 376-381
(2011).
Available at: http://www.springerlink.com/index/35249L23N0702311.pdf
3. Construction and Analysis of Enzyme
Centric Network of A. thaliana using
Graph Theory, Kasthuribai Viswanathan
and Nita Parekh, in A. N. Averkin, D. I. Ignatov, S. Mitra, J. Poelmans,V. B. Tarasov (Eds.),
proceedings of International Workshop on
Soft Computing Applications and Knowledge Discovery (SCAKD11), pg 125-134
(2011). ISSN 1613-0073.
Available
at: http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-758/
4. Construction and Analysis of Metabolic
Network of Arabidopsis thaliana
Pathways, Kasthuribai Viswanathan
and Nita Parekh, paper published online in proceedings of The 2011 International Conference on Bioinformatics & Computational
Biology (BIOCOMP11) 2011.
Availability:http://cerc.wvu.edu/download/WORLDCOMP%2711/2011%20CD%20papers/BIC.pdf
5. Computational Approaches to Protein
Domain Identification, Nita Parekh, chapter
in the book titled Recent Trends in
Computational Biology and Computational Statistics Applied in Biotechnology and
Bioinformatics, ed. A.K. Roy. (in press).
6. Identification of Genomic Islands by
Pattern Discovery, Nita Parekh, chapter in the book titled Pattern Discovery Using Sequence Data Mining: Applications and Studies,
Ed. Pradeep Kumar, P. Radha
Krishnan, and S. Bapi Raju,
Chapter 10, pg. 166 - 181, IGI Global Press, USA (2011).
Available
at: http://www.igi-global.com/book/pattern-discovery-using-sequence-data/51937
7. MS
Thesis titled: Analysis of Periodic
Repeats in Protein Sequences: Distribution, Function and Disease Association,
Rima Kumari and Nita Parekh
(Guide), published as a monograph by LAP LAMBERT Academic Publishing GmbH &
Co. KG, Germany, Oct 2010.(ISBN: 978-3-8433-6005-0)
Available
at:
http://www.amazon.com/Analysis-Periodic-Repeats-Protein-Sequences/dp/3848860057/ref=sr_1_1?ie=UTF8&s=books&qid=1
291888949&sr=1-1
8. Controlling Dynamical Networks, Raina Arora and
Nita Parekh, paper published in online published proceedings of The 3rd Chaotic Modeling and
Simulation International Conference (CHAOS2010)
(2010).
Available at: http://www.cmsim.net/sitebuildercontent/sitebuilderfiles/Arora_Parekh-Controlling_Dynamical_Networks-CHAOS2010-Paper.pd
f
9. Identifying Structural Repeats in
Proteins using Graph Centrality Measures, Ruchi
Jain, Hari Krishna Yalamanchili and Nita Parekh, in IEEE proceedings of World Congress on Nature & Biologically
Inspired Computing (NaBIC),
110 - 115 (2009).
Available at:
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5393609&isnumber=53
93 306. (ISBN: 978-1-4244-5053-4)
10. Graph Spectral Approach for Identifying Protein
Domains,
Hari Krishna Yalamanchili
and Nita Parekh, in Bioinformatics and Computational Biology, Ed. S. Rajasekaran, Lecture Notes in Bioinformatics
5462, pp. 437-448, LNCS, Springer Verlag Berling Heidelberg (2009). (ISBN: 978-3-642-00726-2).
Available
at: http://www.springerlink.com/content/2671816416j54078/.
11. Integrated Genomic Island Prediction Tool (IGIPT), Ruchi Jain,
Sandeep Ramineni and Nita
Parekh, in IEEE proceedings of International
Conference on Information Technology (ICIT2008), icit,
pp.131-132 (2008).
Available at:
http://doi.ieeecomputersociety.org/10.1109/ICIT.2008.42
http://www.computer.org/portal/web/csdl/doi/10.1109/ICIT.2008.42.
12. DRIPS - Database of Repeats in Protein Sequences, Rima Kumari and Nita Parekh, poster
paper in 19th International
Conference on Genome Informatics (GIW2008)
(2008).
Available at: http://mlaa.com.au/giw2008/GIW Posters.htm.
13. Controllability of Spatially Extended Systems Using the Pinning
Approach, Nita Parekh and S. Sinha, Physica A 318,
200-212 (2003).
14. Controlling
Spatiotemporal Dynamics in Excitable Systems,
Nita Parekh and Somdatta Sinha,
Santa Fe Institute Working Paper No. 00-06-031 (2000).
Available at:
http://www.santafe.edu/media/workingpapers/00-06-031.pdf
15. Controlling Dynamics in Spatially Extended Systems, Nita Parekh and S. Sinha, Phys.
Rev. E. 65, 036227-1 to 9 (2002).
16. Suppression of Spatiotemporal Chaos in Coupled Map Lattices, Nita Parekh and S. Sinha in Nonlinear
Dynamics and Brain Functioning, eds. N. Pradhan, P.E.
Rapp and R. Sreenivasan, Nova Science Publishers,
Inc. (New York, USA), ISBN 1560726482 (1999).
17. Global and Local Control of Spatiotemporal Chaos in Coupled Map
Lattices, Nita Parekh, S. Parthasarthy and S. Sinha, Phys.
Rev. Lett. 81, 1401 (1998).
18. Synchronization and Control of Spatiotemporal Chaos Using
Time-Series Data from Local Regions, Nita
Parekh, V. Ravi Kumar and B.D. Kulkarni, Chaos
8, 300 (1998).
19. Control of Spatiotemporal Chaos: A Study with an Autocatalytic
Reaction-Diffusion System, Nita Parekh,
V. Ravi Kumar and B.D. Kulkarni, Pramana
- J. Phys. 48, 303 (1997).
Available at:
http://www.springerlink.com/content/7486jh377v842g21/
20. Analysis and Characterization of Spatio-Temporal
Patterns in Nonlinear Reaction-Diffusion systems, Nita Parekh, V. Ravi Kumar, and B.D. Kulkarni,
Physica A 224, 369 (1996).
21. Control of Self-Replicating Patterns in a Model Reaction-Diffusion
System, Nita Parekh, V. Ravi Kumar and
B.D. Kulkarni, Phys. Rev. E 52, 5100
(1995).
22. Phase Ordering Dynamics in a Gravitational Field, S. Puri, Nita Parekh and S. Dattagupta, J. Stat. Phys. 75, 839 (1994).
23. Phase Ordering Dynamics in Disordered Systems, Nita Parekh, S. Puri and D. Chowdhury in Computational Aspects in Chaos and
Nonlinear Dynamics, eds. G. Ambika and V.M. Nandakumaran, pp. 263-273, Wiley Eastern Limited, New
Delhi, (1994).
24. Velocity Selection in Coupled Map Lattices, Nita Parekh and S. Puri, Phys.
Rev. E 47, 1415 (1993).
25. Non-algebraic Domain Growth for Phase Ordering Dynamics in a
Random Field, S. Puri and Nita
Parekh, J. Phys. A 26, 2777 (1993).
26. Non-algebraic Domain Growth in Binary Alloys with Quenched
Disorder, S. Puri and Nita
Parekh, J. Phys. A 25, 4127 (1992).
27. Non-algebraic Domain Growth in Random Magnets: A Cell Dynamical
Approach, S. Puri, D. Chowdhury, and Nita Parekh, J. Phys. A 24,
L1087 (1991).
28. A New Numerical Scheme for the Fisher Equation, Nita Parekh and S. Puri, J.
Phys. A 23, L1085 (1990).
Invited
Lectures/Presentations/Participations in Conferences/Symposia:
1.
Construction
and Analysis of Enzyme Centric Network of A.
thaliana using Graph Theory, Kasthuribai
Viswanathan and Nita Parekh, oral presentation
in the International
Workshop on Soft Computing Applications and Knowledge Discovery
(SCAKD-2011), Moscow, Russia, 25th June (2011).
2.
Analysis
of Centrality Measures of Airport Network of India, Manasi Sapre and Nita Parekh, oral presentation in 4th International Conference on
Pattern Recognition and Machine Intelligence (PReMI11),
Moscow, Russia, June 27 - July 1 (2011).
3.
Construction
and Analysis of Metabolic Network of Arabidopsis
thaliana Pathways, Kasthuribai Viswanathan
and Nita Parekh, poster presentation in The
2011 International Conference on Bioinformatics & Computational Biology
(BIOCOMP11), USA, July 18 - 21, (2011).
4.
Analysis
of Airport Network of India (ANI), Manasi
Sapre and Nita Parekh, poster presentation at Grace Hopper Celebration of Women in
Computing, Bangalore, 7 - 9 Dec, (2010).
5.
Invited lecture titled Graph
Spectral Analysis of Protein Structures at the National Workshop on
Bioinformatics, Vijaywada, 30th
Sept. (2010).
6.
Controlling
Dynamical Networks, Raina
Arora and Nita Parekh, oral presentation at CHAOS2010, The 3rd Chaotic Modeling and Simulation
International Conference, Chania, Crete, Greece
June 1 - 4 (2010). Report no: IIIT/TR/2010/81
7.
Controlling
Spatiotemporal Dynamics on Small World Topology,
Raina Arora and Nita Parekh, oral presentation at ICARUS (Indian Conference for Academic Research by Undergraduate
Students) at IIT, Kanpur, 26 - 28 March (2010).
8.
Graph
Spectral Analysis of Protein Structures - Domain Identification,
Institute of Life Sciences, Hyderabad, 17th Feb. (2010).
9.
Graph
Spectral Analysis of Protein Structures - Domain Identification,
ICRISAT, Hyderabad, 11th Feb. (2010).
10.
Controlling
Dynamics in Different Topological Networks, Raina Arora and
Nita Parekh, poster presentation at International
Conference on Frontiers of Interface between Statistics and Sciences, CR Rao AIMSCS, Hyderabad, 30 Dec 2009
- 2 Jan 2010. Report no: IIIT/TR/2009/248
11.
Comparative
Analysis of Metabolic Networks, Shubhi Gupta and Nita
Parekh, poster presentation at International
Conference on Frontiers of Interface between Statistics and Sciences, CR Rao AIMSCS, Hyderabad, 30 Dec 2009 - 2 Jan 2010. Report no:
IIIT/TR/2009/251
12.
Identifying
Structural Repeats in Proteins using Graph Centrality Measures, Ruchi Jain, Hari Krishna Yalamanchili and Nita Parekh, poster presentation at World Congress on Nature & Biologically
Inspired Computing (NaBIC), Coimbatore, 9 - 11
Dec. (2009). Report no: IIIT/TR/2009/174
13.
Dynamical
Networks,
Raina Arora and Nita Parekh, poster presentation at Symposium on Theoretical and Mathematical Biology, IISER, Pune, 10 - 11, October (2009). Report no: IIIT/TR/2009/249
14.
Graph Spectral
Approach for Identifying Protein Domains, Hari Krishna Yalamanchili and Nita Parekh, poster presentation at Symposium on Theoretical and Mathematical
Biology, IISER, Pune, 10 - 11, October (2009).
15.
Graph Spectral
Approach for Identifying Protein Domains, Hari Krishna Yalamanchili and Nita Parekh, poster presentation at the 1st International Conference on
Bioinformatics and Computational Biology (BICoB),
New Orleans, Louisiana, USA, 8 - 10 April (2009).
16.
Gene Identification
in silico, Nita Parekh, in
proceedings of the National Workshop on
Bioinformatics Computing, Sri Sathya Sai University, Prasanthinilayam,
Puttaparthy, 6 - 7 March (2009).
17.
Graph Spectral
Analysis of Protein Structures, delivered invited lecture in the DST
sponsored Bioinformatics Training Program for Senior Scientists/Technologists
(working with Government of India) on Perspectives
and Current Trends in Bioinformatics, CCMB, Hyderabad, 12 - 18 February
(2009). Report no: IIIT/TR/2009/72
18.
Graph Spectral
Approach for Identifying Protein Domains, Hari Krishna Yalamanchili and Nita Parekh, poster presentation at National Symposium on Cellular and Molecular
Biophysics, CCMB, Hyderabad 22 - 24 January (2009). Report no: IIIT/TR/2009/72.
19.
CompreSNPdb: Comprehensive
Data-mining Workflow for SNPs, Genes,Diseases and
Pathways, Anshu Bhardwaj, Ajeet Pandey, P Krishna Manjari, V Kiran Kumar, Nita Parekh, Shrish Tiwari, poster presentation at HGM2008, HUGOs 13th Human Genome Meeting, Hyderabad, 27 - 30 Sept
(2008).
http://hgm2008.hugointernational.org/Abstracts/Publish/WorkshopPosters/WorkshopPosters10/
hgm381.html.
20.
Graph Spectral Analysis of Protein Repeat Families, Nita Parekh, delivered invited lecture and published in the proceedings
of the AICTE sponsored National
Conference on Recent Developments and Applications of Probability Theory,
Random Process and Random Variables in Computer Science, MACFAST, Tiruvalla, 27 - 29 August (2008). Report no:
IIIT/TR/2008/186
21.
Identifying
Genomic Islands in Prokaryotic Genomes, Ruchi Jain
and Nita Parekh, poster presentation at the International
Conference on Bioinformatics & Drug Discovery, held at Hyderabad
Central University, 20 - 22, Dec(2007). (Awarded 2nd best poster
prize)
Report no: IIIT/TR/2008/28.
22.
Protein Tandem
Repeat DataBase, Krishna Manjari,
V. Kiran Kumar, Rima Kumari and Nita Parekh, poster presentation at the International Conference on Bioinformatics
& Drug Discovery, Hyderabad Central University, 20 - 22, Dec(2007).
(Awarded 5th best poster prize). Report no: IIIT/TR/2008/69.
23.
Participated
in the Workshop on Structural Biology organized
by Indian National Science Academy & Chinese Academy of Sciences, IISc Bangalore, 21 - 23 Dec. (2007).
24.
Delivered
two invited lectures in the DST sponsored Bioinformatics Training Program for
Senior Scientists/Technologists (working with Government of India) on Perspectives and Current Trends in
Bioinformatics, titled: (i) Genomic Variations and its applications, (ii) Identifying Tandem Repeats in Protein Sequences, CCMB, Hyderabad,
12 - 18 Sept. (2007).
25.
PEPPER - A Tool
for Identifying Peptide Periodic Repeats, Kasturi K. Kiran, Radhika B. and Nita Parekh accepted for poster presentation
at the International Conference on
Bioinformatics (INCOB), New Delhi, 18 - 20 Dec. (2006). Report no:
IIIT/TR/2008/38.
26.
Invited
lecture on Gene Prediction in silico at National
Workshop on Bioinformatics, organized by R&D Unit, J.N.T.U. Hyderabad,
8 - 9 July (2006).
27.
Invited
lecture on Gene Prediction in silico at National
Seminar on Bioinformatics and Functional Genomics, organized by
Bioinformatics Centre, Pondicherry University, 15 - 17 Feb. (2006). Report no:
IIIT/TR/2006/31
28.
Invited
Bioinformatics Tutorial on Computational
Issues in Gene Prediction, at 40th
National Convention of Computer Society India, hosted by CSI Hyderabad
Chapter, 9 - 12 Nov. (2005).
29.
Invited
lecture in a Refresher Course on Recent Trends in Biotechnology, Centre for Biotechnology, J.N.T.U.,
Hyderabad, 13th June - 6th July (2005).
30.
Participated - Refresher
Course on Interdisciplinary Approaches in Biology, organized by
Indian Academy of Sciences, Bangalore and CCMB, Hyderabad, 25 May - 8 June
(2005).
31.
GUI for
Stand-alone BLAST on Unix/Linux Platform, Nandan Kumar,
Nita Parekh and Shrish Tiwari,
developed and installed on Alpha ES45 server at CCMB. Report no:
IIIT/TR/2005/13
32.
Delivered
three invited lectures in the Lecture Programme on Biostatistics and Mathematical Modeling,
titled: (1) Cluster Analysis - Applications in Bioinformatics, (2) Regression,
Correlation and ANOVA, and (3) Control of Spatiotemporal Population Dynamics,
Dept. of Zoology, Kakatiya University, Warangal, 6 -
8 Nov. (2004).
33.
Tool for
Identifying Absolute Location of Genes on Human Chromosome, presented at National Seminar on Systems Approach to
Bioinformatics, Bioinformatics Centre, Pondicherry University, 18 - 20,
Feb. (2004). Report no: IIIT/TR/2004/31
34.
Participated - Lecture
Course on Proteomics and DNA Microarrays, 7th ADNAT Convention,
CCMB, Hyderabad, February 25 - March 10 (2003).
35.
Invited
lecture on Targeting Spatiotemporal
Dynamical States Using Constant Pinnings, at
Center for Nonlinear and Complex Systems, Duke University, USA, 8 Feb. (2000).
36.
Invited
lecture on Control of Spatiotemporal Chaos in Coupled Map lattices Using
Constant Pinnings,
Colloquium Lecture at the Department of Physics, The Catholic University of
America, Sept. (2000).
37.
Global and Local
Control of Spatiotemporal Chaos in Coupled Map Lattices, poster presentation in The 5th Experimental Chaos
Conference, Orlando, Florida, USA, 28 June - 1 July (1999).
38.
Lecture
at JNCAR, Bangalore, titled Targetting
Spatiotemporal Dynamical States Using Constant Pinnings,
24 June (1998).
39.
Suppressing
Spatiotemporal Chaos in Coupled Map Lattices Using Constant Pinnings, oral presentation in the Nonlinear
Dynamics and Brain Functioning, I.I.Sc. Bangalore, 5 - 11 Feb. (1998).
40.
Suppression of
Spatiotemporal Chaos in Coupled Map Lattices, oral presentation in Nonlinear Dynamics: Integrability
and Chaos,
Dept. of Physics, Bharathidasan University, Tiruchirapalli, 12 - 16, February (1998).
41.
Controlling Chaos
in Logistic Coupled Map Lattices, lecture at JNCAR, Bangalore, 12 Dec
(1997).
42.
Characterization
and Control of Spatio-Temporal Dynamics in Chemical
Reaction Diffusion Systems, invited lecture at CMMACS Bangalore, 9 Dec. (1997).
43.
International
Conference on Dynamical Systems, participated, I.I.Sc.,
Bangalore, Jan. 10 - 15 (1997).
44.
Participated - Second
SERC Winter School on Chemical Applications
of Statistical Mechanics, Department of Science and Technology and Department
of Chemistry and RSIC, I.I.T. Bombay, Nov 28 - Dec 15, 1994.
45.
Pattern Formation in
Spatially Extended Systems,
Ph.d. thesis
presentation in the DAE
Solid State Physics Symposium, University of Rajasthan, Jaipur, 27 - 31, Dec. (1994).
46.
Phase Ordering Dynamics in
a Gravitational Field, poster
presentation in the XIth
International Congress of Mathematical Physics, Unesco-Sourborne-Paris, France, 18 - 23, July (1994).
47.
Phase Ordering Dynamics in
Disordered Systems, oral presentation in the National Seminar on Computational Aspects in
Chaos and Nonlinear Dynamics, Maharajas College, Cochin, 21 - 25,
March (1994).
48.
Domain Growth in Disordered and Fractal Systems, oral presentation in the DAE Solid State
Physics Symposium,
S.V. University, Tirupati, Dec 28 1992 - Jan 1
(1993).