Ram Rup Sarkar

Ram Rup Sarkar

Chemical Engineering & Process Development

About Me

The major objective of our group is to study the complexity of biological  and biochemical systems from an interdisciplinary angle. We apply mathematical, computational and optimization methods and concepts in different areas of biological sciences across different levels / scales from gene to population. We are involved in abstract and formal system-level modelling that may have implications in biological systems and constitute a basis for system level understanding (System Biology), and may be useful for drug discovery with potential application in pharmaceutical industry.

Professional Experience

  • May 9, 20013 onwards, Scientist E-II (Principal Scientist), National Chemical Laboratory (CSIR), Dr. Homi Bhabha Road, Pune 411 008, India.
  • March 5, 2012 to May 8, 2013, Scientist E-I (Senior Scientist), National Chemical Laboratory (CSIR), Dr. Homi Bhabha Road, Pune 411 008, India.
  • May 9, 2009 to March 4, 2012, Scientist E-I (Senior Scientist), Centre for Cellular and Molecular Biology (CSIR), Uppal Road, Hyderabad 500 007, India.
  • May 9, 2005 to May 8, 2009, Scientist C, Centre for Cellular and Molecular Biology (CSIR), Uppal Road, Hyderabad 500 007, India.
  • May 1, 2004 to April 30, 2005, Post Doctoral Fellow under Humboldt Research Fellowship, Department of Mathematics and Computer Sciences, Institute for Environmental Systems Research, University of Osnabrueck, Artilleriestr. 34, 49069, Osnabrueck, Germany.

Visiting Assignments

  •  Visiting Scientists at Institute of Medical Biometry, University of Tuebingen, Germany, to work with Prof. Martin Eichner and Dr. Hans-Peter Duerr on Modelling Infectious Diseases under CSIR-DAAD Exchange of Scientists Programme, 2008, during August 31-November 27, 2008.
  •  Visited Unit of Epidemiology, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium, to work with Dr. Marleen Boelaert and Dr. Jean-Claude Dujardin under CSIR-DAAD Exchange of Scientists Programme, 2008, and EU-project on KalaDrug-R during November 12-November 14, 2008.
  •  Zoological Institute, University of Neuchatel, Switzerland, to work with Dr. Louis-Felix Bersier on Host-Parasite Modelling during November 1 - December 13, 2000.

Selected Publications

  • Anirudh Murali And Ram Rup Sarkar*, Mechano-immunology in microgravity, Life Sciences in Space Research., In Press, (2023), DOI:10.1016/j.lssr.2023.03.001.
  • Malobika Chakraborty#, Piyali Ganguli#, Manikanta Murahari, Ram Rup Sarkar*, Godefridus J. Peters And Mayur C Yergiri*, Study of combinatorial drug synergy of novel Acridone derivatives with Temozolomide using in-silico and in-vitro methods in the treatment of drug-resistant Glioma, Frontiers in Oncology., 11, 625899 (2021), DOI:10.3389/fonc.2021.625899.
    [# Equal First Author]
  • Gauri Panditrao, Piyali Ganguli And Ram Rup Sarkar*, Delineating infection strategies of Leishmania donovani secretory proteins in Human through Host-Pathogen protein Interactome prediction, Pathogens and Disease., 79(8):ftab051, (2021), DOI:10.1093/femspd/ftab051.
  • Sutanu Nandi, Piyali Ganguli And Ram Rup Sarkar*, Essential gene prediction using limited gene essentiality information–An integrative semisupervised machine learning strategy, PLoS ONE., 15(11), e0242943 (2020), DOI:10.1371/journal.pone.0242943.
  • Rupa Bhowmick And Ram Rup Sarkar*, Differential suitability of reactive oxygen species and the role of glutathione in regulating paradoxical behavior in gliomas: A mathematical perspective, PLoS ONE., 15(6), e0235204 (2020), DOI:10.1371/journal.pone.0235204.
  • Saikat Chowdhury And Ram Rup Sarkar*, Exploring Notch Pathway to Elucidate Phenotypic Plasticity and Intra-tumor Heterogeneity in Gliomas, Scientific Reports (Nature)., 9, 9488 (2019), DOI:10.1038/s41598-019-45892-8.
  • Anusree Mahanta, Piyali Ganguli, Pankaj Barah, Ram Rup Sarkar, Neelanjana Sarmah, Saurav Phukan, Mayuri Bora And Shashi Baruah*, 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., 9:296, (2018), DOI:10.3389/fimmu.2018.00296.
  • Abhishek Subramanian And Ram Rup Sarkar*, Evolutionary Perspectives of Genotype–Phenotype Factors in Leishmania Metabolism, Journal of Molecular Evolution., 86(7), 443 - 456 (2018), DOI:https://doi.org/10.1007/s00239-018-9857-5.
  • Samik Bose, Diksha Dhawan, Sutanu Nandi, Ram Rup Sarkar And Debashree Ghosh*, Machine Learning Prediction of Interaction Energy in Rigid Water Clusters, Physical Chemistry Chemical Physics., 20, 22987 - 22996 (2018), DOI:10.1039/C8CP03138J.
  • Piyali Ganguli And Ram Rup Sarkar*, Exploring Immuno-regulatory mechanisms in the Tumor microenvironment: Model and design of protocols for Cancer remission, PLoS ONE., 13(9), e0203030 (2018), DOI:10.1371/journal.pone.0203030.
  • Abhishek Subramanian And Ram Rup Sarkar*, Perspectives on Leishmania species and stage-specific adaptive mechanisms, Trends in Parasitology., 34(12), 1068 - 1081 (2018), DOI:10.1016/j.pt.2018.09.004.
  • 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.
  • 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.
  • 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.
  • 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, 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.
  • 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.
  • 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.
  • 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.
  • 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
  • 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.
  • 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.
  • 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.
  • R.R. Sarkar* And S. Banerjee, Cancer self remission and tumour stability - a stochastic approach, Mathematical Biosciences., 196, 65 - 81 (2005).

Research Interest

  • Bio-chemical AND Biological Engineering
  • Mathematical Modeling & Optimization
  • Theory AND Computational Science
  • Mathematical & computational modeling
  • Bioinformatics

Contact Details

Dr. Ram Rup Sarkar

Principal Scientist 
Office: Chemical Engineering and Process Development (CEPD)
CSIR-National Chemical Laboratory
National Chemical Laboratory
Dr. Homi Bhabha Road
Pune 411008, India
Phone +91 20 2590 3040
Fax +91-20-2590 2621
E-mail rr.sarkar@ncl.res.in