Research Group Publications

 
  • A Mahanta, P Ganguli, P Barah, RR Sarkar, N Sarmah, S Phukan, M Bora And S Barua , Integrative Approaches to Understand the Mastery in Manipulation of Host Cytokine Networks by Protozoan Parasites with Emphasis on Plasmodium and Leishmania Species, Frontiers in Immunology., In Press, (2018), DOI:10.3389/fimmu.2018.00296.
  • Saikat Chowdhury, Noopur Sinha, Piyali Ganguli, Rupa Bhowmick, Vidhi Singh, Sutanu Nandi And Ram Rup Sarkar*, BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform, Journal of Integrative Bioinformatics., (Accepted), (2018).
  • Ram Rup Sarkar* And Chandrajit Chatterjee, Application of different Time Series Models on Epidemiological Data - Comparison and Predictions for Malaria Prevalence, SM Journal of Biometrics & Biostatistics., 2(4), 1022 (2017).
  • Swarnendu Banerjee, Abhishek Subramanian, Joydev Chattopadhyay And Ram Rup Sarkar*, Exploring the role of GS-GOGAT cycle in microcystin synthesis and regulation – a model based analysis, Molecular Biosystems., 13, 2603 (2017), DOI:10.1039/C7MB00342K.
  • Abhishek Subramanian, Ram Rup Sarkar And Prabhakar Ingle, Metabolic Adaptations of Leishmania parasite: a new insight, Chronicle Pharmabiz., October 19, 59 - 60 (2017).
  • Noopur Sinha, Saikat Chowdhury And Ram Rup Sarkar*, Deciphering Structural Stability and Binding Mechanisms of Potential Antagonists with Smoothened Protein, Journal of Biomolecular Structure and Dynamics., (Accepted), (2017), DOI:10.1080/07391102.2017.1372310.
  • Abhishek Subramanian And Ram Rup Sarkar*, Revealing the mystery of metabolic adaptations using a genome scale model of Leishmania infantum, Scientific Reports (Nature)., 7, 10262 (2017), DOI:10.1038/s41598-017-10743-x.
  • Rupa Bhowmick, Noopur Sinha And Ram Rup Sarkar*, An in-silico perspective towards target ability of available drugs in infectious disease treatment: a possible strategy, Journal of Bioinformatics and Genomics., 2(4), Aug 2017 (2017), DOI:http://dx.doi.org/10.18454/jbg.2017.2.4.1.
  • Sutanu Nandi, Abhishek Subramanian And Ram Rup Sarkar*, An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features, Molecular Biosystems., 13, 1584 - 1596 (2017), DOI:10.1039/C7MB00234C.
  • Santanu Biswas, Abhishek Subramanian, Ibrahim M. ELMojtaba, Joydev Chattopadhyay And Ram Rup Sarkar*, Optimal combinations of control strategies and cost-effective analysis for visceral leishmaniasis disease transmission, PLoS ONE., 12(2), e0172465 (2017), DOI:10.1371/journal.pone.0172465.
  • Ram Rup Sarkar*, Editorial: The Big Data Deluge in Biology: Challenges and Solutions, Journal of Informatics and Data Mining., 1(2), 14 (2016), DOI:10.4172/2472-1956.100014.
    Editorial
  • Abhishek Subramanian And Ram Rup Sarkar*, Network Structure and Enzymatic Evolution in Leishmania Metabolism: A Computational Study, Proceedings of the International Symposium on Mathematical and Computational Biology-BIOMAT 2015., World Scientific, ISBN: 978-981-3141-90-2, 1 - 20 (2016), DOI:10.1142/9789813141919_0001.
    Edited by: Rubem P Mondaini
  • Noopur Sinha, Saikat Chowdhury And Ram Rup Sarkar*, Structural Insight of NICD-MAML Interactions: Virtual screening, Docking and Molecular Dynamics Study for Identification of Potential Inhibitor, Letters in Drug Design & Discovery., 13(4), 301 - 313 (2016), DOI:10.2174/1570180812666150819003634.
  • Abhishek Subramanian And Ram Rup Sarkar*, Dynamics of GLI Regulation and Strategy to Control Cancerous Situation: Hedgehog Signaling Pathway Revisited, Journal of Biological Systems., 23(4), 681 - 719 (2015), DOI:10.1142/S0218339015500333.
  • Piyali Ganguli, Saikat Chowdhury, Shomeek Chowdhury And Ram Rup Sarkar*, Identification of Th1/Th2 regulatory switch to promote healing response during Leishmaniasis: a computational approach, EURASIP Journal on Bioinformatics and Systems Biology., 2015:13, (2015), DOI:10.1186/s13637-015-0032-7.
  • Rupa Bhowmick, Abhishek Subramanian And Ram Rup Sarkar*, Exploring the differences in metabolic behavior of astrocyte and glioblastoma: A flux balance analysis approach, Systems and Synthetic Biology., 9, 159 - 177 (2015), DOI:10.1007/s11693-015-9183-9.
  • Piyali Ganguli, Saikat Chowdhury, Rupa Bhowmick And Ram Rup Sarkar*, Temporal Protein Expression Pattern in Intracellular Signaling Cascade during T-cell Activation: A Computational Study, Journal of Bioscience., 40(4), 769 - 789 (2015), DOI:10.1007/s12038-015-9561-1.
  • Abhishek Subramanian, Vidhi Singh And Ram Rup Sarkar*, Understanding Visceral Leishmaniasis Disease Transmission and its Control - A study based on Mathematical Modelling, Mathematics., 3, 913 - 944 (2015), DOI:10.3390/math3030913.
    This article belongs to the Special Issue Optimal Control and Management of Infectious Diseases
  • Abhishek Subramanian, Jitesh Jhawar And Ram Rup Sarkar*, Dissecting Leishmania infantum energy metabolism – A systems perspective, PLoS ONE., 10(9), e0137976 (2015), DOI:10.1371/journal.pone.0137976.
  • Abhishek Subramanian And Ram Rup Sarkar*, Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions, Genomics., 106, 232 - 241 (2015), DOI:10.1016/j.ygeno.2015.05.009.
  • Abhishek Subramanian And Ram Rup Sarkar*, Data in support of large scale comparative codon usage analysis in Leishmania and Trypanosomatids, Data in Brief., 4, 269 - 272 (2015), DOI:10.1016/j.dib.2015.06.003.
  • Saikat Chowdhury And Ram Rup Sarkar*, Comparison of Human Cell Signaling Pathway Databases - Evolution, Drawbacks and Challenges, DATABASE The Journal of Biological Databases and Curation (Oxford University Press)., 2015: bau126, (2015), DOI:10.1093/database/bau126.
  • Saikat Chowdhury And Ram Rup Sarkar* , Drug Targets and Biomarker Identification from Computational Study of Human Notch Signaling Pathway, Journal of Clinical and Experimental Pharmacology., 3:4, 137 (2013), DOI:10.4172/2161-1459.1000137.
  • Sandip Mandal, Somdatta Sinha And Ram Rup Sarkar*, A Realistic Host-Vector Transmission Model for Describing Malaria Prevalence Pattern, Bulletin of Mathematical Biology., 75, 2499 - 2528 (2013), DOI:10.1007/s11538-013-9905-7.
  • Saikat Chowdhury, Rachana N. Pradhan And Ram Rup Sarkar*, Structural and Logical Analysis of a comprehensive Hedgehog Signaling Pathway to identify alternative drug targets for Glioma, Colon and Pancreatic Cancer, PLoS ONE., 8(7), e69132 (2013), DOI:10.1371/journal.pone.0069132.
  • Ram Rup Sarkar, R. Maithreye And Somdatta Sinha, Design of regulation and dynamics in simple biochemical pathways, Journal of Mathematical Biology., 63, 283 - 307 (2011), DOI:10.1007/s00285-010-0375-3.
  • Sandip Mandal, Ram Rup Sarkar And Somdatta Sinha, Mathematical models of malaria - a review, Malaria Journal., 10, 202 (2011), DOI:10.1186/1475-2875-10-202.
    Highly accessed
  • Sayantani Basu Roy, Ram Rup Sarkar* And Somdatta Sinha, Theoretical Investigation of Malaria Prevalence in two Indian Cities using the Response Surface Method, Malaria Journal., , (2011), DOI:10:301.
  • Anette Stauch, Ram Rup Sarkar, Albert Picado, Bart Ostyn, Shyam Sundar, Suman Rijal, Marleen Boelaert, Jean-Claude Dujardin And Hans-Peter Duerr , Visceral Leishmaniasis in the Indian Subcontinent: Modelling Epidemiology and Control, PLoS Neglected Tropical Diseases., 55, 11 - 11 (2011), DOI:10.1371/journal.pntd.0001405.
  • S. Bhattacharyya And R. R. Sarkar*, Effect of migration on Malaria Incidence under environmental variability-a model based approach, Nonlinear Phenomena in Medical and Biological Sciences: Proceedings of the Fifth National Conference on Nonlinear Systems and Dynamics., , (2009).
    NCNSD-2009
  • R.R. Sarkar* And M Rahuman Sheriff, Mathematical modeling of T-cell Signalling network and cancer, Proceedings of the Symposium “Integrating Physics, Chemistry, Mathematics and Biology to Understand Living Systems”., , 99 - 116 (2009).
    Eds. J. Basu, M Kundu and I. Bose, Bose Institute, Kolkata.
  • Ram Rup Sarkar* And M. Rahuman Sheriff, Signalling Networks of T-Cell – a study based on Logical Steady State Analysis, Proceedings of the International Workshop on “Physics in Biology: A Synergy”., , 57 - 71 (2009).
    Eds. P Anantha Lakshmi and V. Srivastava), Department of Physics, University of Hyderabad (Allied Publishers, ISBN 978-81-8424-576-9)
  • C. Chatterjee And R.R. Sarkar*, Multi-step Polynomial Regression Method to Model and Forecast Malaria Incidence, PLoS ONE., 4(3), e4726 (2009), DOI:10.1371/journal.pone.0004726.
  • S. Banerjee And R. R. Sarkar*, Delay induced model for tumor-immune interaction and control of malignant tumor growth, BioSystems., 91, 268 - 288 (2008), DOI:Elsevier Science.
  • R. Maithreye, R.R. Sarkar, V.K. Parnaik And S. Sinha, Delay-Induced Transient Increase and Heterogeneity in Gene Expression in Negatively Auto-regulated Gene Circuits, PLoS ONE., 3, 8 - 8 (2008), DOI:e2972.
  • N. Bairagi, R.R. Sarkar And J. Chattopadhyay, Impacts of incubation delay on the dynamics of an eco-epidemiological system – a theoretical study, Bulletin of Mathematical Biology., 70, 2017 - 2038 (2008).
  • M Rahuman Sheriff And R. R. Sarkar*, Computational Approaches and Modelling of Signaling Processes in Immune System, Proceedings of the Indian National Science Academy., 74, 4 - 4 (2008), DOI:187-200.
  • R.R. Sarkar, J. Pal, K.P. Das And J. Chattopadhyay, Control of Harmful Algal Blooms through input of Competitive Phytoplankton and the Effect of Environmental Variability, Journal of the Calcutta Mathematical Society., 1&2, 1 - 8 (2008).
  • P. Banik, P. Pramanik, R. R. Sarkar, S. Bhattacharya And J. Chattopadhayay, A mathematical model on the effect of Medicago denticulata weed on different winter crops, BioSystems., 90, 818 - 829 (2007), DOI:Elsevier Science.
  • R. R. Sarkar*, R. Bhattacharyya, B. Mukhopadhyay And S. Banerjee, Time lags can control algal blooms in two harmful phytoplankton-zooplankton system, Applied Mathematics and Computation., 186, 445 - 459 (2007).
  • R.R. Sarkar* And S. Banerjee , A time delay model for control of malignant tumor growth, Nonlinear Phenomena in Medical and Biological Sciences: Proceedings of the Third National Conference on Nonlinear Systems and Dynamics., , (2006).
    M. Lakshmanan and R. Sahadevan (eds.) Proceedings of the Third National Conference on Nonlinear Systems and Dynamics, pp.223-226, NCNSD-2006 (ISBN: 81-7764-993-0), Allied Publishers Pvt. Ltd.
  • R.R. Sarkar, S.V. Petrovskii, M. Biswas, A. Gupta And J. Chattopadhyay, An Ecological Study of a Marine Plankton Community based on the field data collected from Bay of Bengal, Ecological Modelling., 193, 589 - 601 (2006).
  • R.R. Sarkar*, The occurrence of Malignant Malaria – a Model Based Study, The SPSS Analyst., 1, 11 - 15 (2005).
  • N. Bairagi, P.K. Roy,  R.R. Sarkar And J. Chattopadhyay, Virus replication factor may be a controlling agent for obtaining disease -free system in a multi-species eco-epidemiological system, Journal of Biological Systems., 13(3), 245 - 259 (2005).
  • H. Malchow, F.M. Hilker,  R.R. Sarkar And K. Brauer, Spatiotemporal Patterns in an excitable Plankton System with Lysogenic Viral infection, Mathematical and Computer Modelling., 42, 1035 - 1048 (2005).
  • R.R. Sarkar* And H. Malchow, Nutrient and Toxin Producing Phytoplankton Control Algal Blooms - a Spatiotemporal Study in a Noisy Environment, Journal of Bioscience., 30, 749 - 760 (2005).
  • R.R. Sarkar*, S. Pal And J. Chattopadhyay, Role of toxin producing plankton and their effect on phytoplankton-zooplankton system - a mathematical study supported by experimental findings, BioSystems., 80, 11 - 23 (2005).
  • R.R. Sarkar* And S. Banerjee, Cancer self remission and tumour stability - a stochastic approach, Mathematical Biosciences., 196, 65 - 81 (2005).
  • R.R. Sarkar*, Mathematical modelling of harmful algal blooms, Complexity and Integrated Resources Management: Transactions of the 2nd Biennial Meeting of the International Environmental Modelling and Software Society., 2, 876 - 882 (2004).
    Pahl-Wostl, C., Schmidt, S., Rizzoli, A.E. and Jakeman, A.J. (eds), Complexity and Integrated Resources Management, Transactions of the 2nd Biennial Meeting of the International Environmental Modelling and Software Society, iEMSs, 2004, (ISBN: 88-900787-1-5; http://www.iemss.org).
  • J. Chattopadhyay,  R.R. Sarkar, S, Chaki, S And Bhattacharya, Effects of Environmental Fluctuations on the Occurrence of Malignant Malaria - A Model Based Study, Ecological Modelling., 177, 179 - 192 (2004).
  • R. R. Sarkar*, A stochastic model for autotroph - herbivore system with nutrient recycling, Ecological Modelling., 178, 429 - 440 (2004).
  • J. Chattopadhyay,  R.R. Sarkar And S.Pal, Mathematical modelling of harmful algal blooms supported by experimental findings, Ecological Complexity., 1, 225 - 235 (2004).
  • J. Chattopadhyay And R.R. Sarkar, Chaos to order: preliminary experiments with a population dynamics models of three trophic levels, Ecological Modelling., 163, 45 - 50 (2003).
  • J. Chattopadhyay,  R.R. Sarkar And S. Pal, Dynamics of nutrient-phytoplankton interaction in the presence of viral infection, BioSystems., 68, 5 - 17 (2003).
  • R. R. Sarkar And J. Chattopadhyay, A technique for maximum harvesting effort in a noise induced bioeconomic fishery model, Journal of Bioscience ., 28, 497 - 506 (2003).
  • Ram Rup Sarkar And J. Chattopadhyay, Occurrence of planktonic blooms under environmental fluctuations and its possible control mechanism - mathematical models and experimental observations, Journal of Theoretical Biology., 224, 501 - 516 (2003).
  • R.R. Sarkar And J. Chattopadhyay, The role of environmental stochasticity in a toxic phytoplankton - non-toxic phytoplankton - zooplankton system, Environmetrics., 14, 775 - 792 (2003).
  • J. Chattopadhyay,  R.R. Sarkar And S. Mandal, Toxin producing plankton may act as a biological control for planktonic blooms- field study and mathematical modeling, Journal of Theoretical Biology., 215(3), 333 - 344 (2002).
  • J. Chattopadhyay,  R.R. Sarkar And G. Ghosal, Removal of infected prey prevent limit cycle oscillations in an infected prey-predator system - a mathematical study, Ecological Modelling., 156, 113 - 121 (2002).
  • J. Chattopadhyay,  R.R. Sarkar And A. El abdllaoui, A delay differential equation model on harmful algal blooms in the presence of toxic substances,  IMA Journal of Mathematics Applied in Medicine and Biology., 19, 137 - 161 (2002).
  • Ram Rup Sarkar, J. Chattopadhyay And N. Bairagi, Effect of environmental fluctuation on an eco-epidemiological model of Salton Sea, Environmetrics., 12, 289 - 300 (2001).
  • J. Chattopadhyay,  Ram Rup Sarkar, G. Ghoshal And S. Ghosh, Uniqueness of limit cycle of a harvested prey-predator system with Holling type III functional response, Nonlinear Studies., 8, 261 - 281 (2001).
  • J. Chattopadhyay,  Ram Rup Sarkar, Maria Elena Fritzsche- Hoballah, Ted C. J. Turlings And Louis-Felix Bersier, Parasitoids may determine plant fitness - a mathematical model based on experimental data, Journal of Theoretical Biology., 212, 295 - 302 (2001).
  • J. Chattopadhyay, N. Bairagi And  Ram Rup Sarkar, A predator-prey model with some cover on prey species, Nonlinear Phenomena in Complex Systems., 3:4, 407 - 420 (2000).