Invited Talks Workshops/Conference/Meetings Professional Responsibilities Teaching Misc/Posters DATABASE/TOOLS Opportunity News

Major research areas:

  • Biochemical Pathways and Gene Circuits – Study of Small and Large biochemical networks; signalling and metabolic pathways; deterministic and stochastic modeling; Dynamics of genetic and metabolic regulatory circuits; study of transcription and translation processes in elementary gene circuits; Drug designing & Database Development

  • Cancer Biology – System Biology of cancer; Modeling signalling and metabolic pathways in Immune and Cancer cells; deterministic and stochastic modeling of tumor-immune interactions; control of malignant tumor cells; development of suitable treatment strategies; In silico identification of potential drug targets.

  • Big Data Analytics – Genome-scale Metabolic Network Reconstruction, Transcriptomics and Proteomics Data analysis in Cancer, Signalling Pathway Reconstruction, Drug Target Screening,Machine learning and integrated data analysis, Artificial Intellefience based approach for Clinical Predictions, Database, Algorithm and Software Tools Development

  • Epidemiology – Mathematical and Statistical Modelling of Kala-Azar (Visceral Leishmaniasis) and Malaria; Time Series Data Analysis of infectious diseases; study of spatio-temporal spreads of the diseases; development of control strategies; role of viral infection in ecological systems – deterministic and stochastic models (prey-predator, plankton population, etc.); identification of epidemiological parameters and demographic characteristics of Encephalitis in India.

  • Ecology – Deterministic and Stochastic modeling of different ecological processes; dynamics of marine plankton populations (control of harmful algal blooms) - spatio-temporal patterns, effects of nutrients and environmental stochasticity; models of host-parasitoid systems, agricultural ecology (medicago weed), fishery systems; development of new techniques to control stochastic instability; control of chaos in ecological processes.

Professional Experience:

  • May 9, 2018 onwards, Scientist F (Senior Principal Scientist), National Chemical Laboratory (CSIR), Dr. Homi Bhabha Road, Pune 411 008, India.

  • May 9, 2013 to May 8, 2018, 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 Indian Statistical Institute, Kolkata, India during August 19-26, 2017 and June 11-20, 2019.

  • Visiting Scientists at Institute for Systems Biology, Seattle, WA, USA, to work with Prof. Ilya Shmulevich, under Indo-US Science and Technology Research Fellowship Programme, 2013, during November 22, 2013 – March 21, 2014.

  • 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.

Academic Qualifications:

  • Ph.D. (Science), 2004 - Jadavpur University, Kolkata, India [Ph.D. work carried out in Indian Statistical Institute,  Kolkata,India]

    Title of the thesis: Mathematical and Stochastic Modelling of Biological System with special emphasis on Plankton Ecology

  • Master of Science (Appl. Mathematics), 1999; University of Calcutta, Kolkata, India.

  • Bachelor of Science (Mathematics), 1997; St. Xavier’s College, University of Calcutta, Kolkata, India.

Memberships:

  • Life member of Indian Science Congress Association, India.

  • Life member of Indian Biophysical Society, India

  • Life member of Calcutta Mathematical Society, Kolkata, India. 

Selected Publications:

  1. Malobika Chakraborty#, Piyali Ganguli#, Manikanta Murahari, Ram Rup Sarkar*, Godefridus J. Peters and Mayur C. Yergeri (2021): 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 (Accepted) DOI:10.3389/fonc.2021.625899

  2. Saikat Chowdhury and Ram Rup Sarkar* (2019): Exploring Notch Pathway to Elucidate Phenotypic Plasticity and Intra-tumor Heterogeneity in Gliomas. Scientific Reports (Nature) 9:9488. DOI: 10.1038/s41598-019-45892-8

  3. Abhishek Subramanian and Ram Rup Sarkar* (2018): Perspectives on Leishmania species and stage-specific adaptive mechanisms. Trends in Parasitology 34(12), 1068-1081. DOI: 10.1016/j.pt.2018.09.004.

  4. Piyali Ganguli and Ram Rup Sarkar* (2018): Exploring Immuno-regulatory mechanisms in the Tumor microenvironment: Model and design of protocols for Cancer remission. PLoS ONE 13(9), e0203030. DOI: 10.1371/journal.pone.0203030.

  5. Abhishek Subramanian and Ram Rup Sarkar* (2018): Evolutionary perspectives of genotype-phenotype factors in Leishmania metabolism. Journal of Molecular Evolution 86(7), 443-456. DOI: 10.1007/s00239-018-9857-5.

  6. Noopur Sinha, Saikat Chowdhury and Ram Rup Sarkar* (2018): Deciphering Structural Stability and Binding Mechanisms of Potential Antagonists with Smoothened Protein. Journal of Biomolecular Structure and Dynamics 36(11), 2917-2937. DOI: 10.1080/07391102.2017.1372310.

  7. Abhishek Subramanian and Ram Rup Sarkar* (2017): Revealing the mystery of metabolic adaptations using a genome scale model of Leishmania infantum. Scientific Reports (Nature) 7, 10262. DOI: 10.1038/s41598-017-10743-x

  8. Sutanu Nandi, Abhishek Subramanian and Ram Rup Sarkar* (2017): An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features. Molecular Biosystems 13: 1584-1596. DOI: 10.1039/C7MB00234C

  9. Abhishek Subramanian, Jitesh Jhawar, and Ram Rup Sarkar* (2015): Dissecting Leishmania infantum energy metabolism – A systems perspective. PLoS ONE 10(9): e0137976. doi:10.1371/journal.pone.0137976.

  10. Abhishek Subramanian and Ram Rup Sarkar* (2015): Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions. Genomics 106: 232–241.  DOI: 10.1016/j.ygeno.2015.05.009.
     
  11. Saikat Chowdhury and Ram Rup Sarkar* (2015): Comparison of Human Cell Signaling Pathway Databases - Evolution, Drawbacks and Challenges. DATABASE-The Journal of Biological Databases and Curation bau126. DOI:10.1093/database/bau126.

  12. Saikat Chowdhury, Rachana N. Pradhan and Ram Rup Sarkar* (2013): 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. doi:10.1371/journal.pone.0069132.

  13. Anette Stauch, Ram Rup Sarkar, Albert Picado, Bart Ostyn, Shyam Sundar, Suman Rijal, Marleen Boelaert, Jean-Claude Dujardin and Hans-Peter Duerr (2011): Visceral Leishmaniasis in the Indian Subcontinent: Modelling Epidemiology and Control. PLoS Neglected Tropical Diseases 5(11): e1405.doi:10.1371/journal.pntd.0001405

  14. Sayantani Basu Roy, Ram Rup Sarkar* and Somdatta Sinha (2011): Theoretical Investigation of Malaria Prevalence in two Indian Cities using the Response Surface Method. Malaria Journal, 10:301.

  15. Ram Rup Sarkar, R. Maithreye and Somdatta Sinha (2011): Design of regulation and dynamics in simple biochemical pathways. Journal of Mathematical Biology, 63:283–307, DOI 10.1007/s00285-010-0375-3, Springer.

 

Organization of Conferences/Symposiums/Workshops:

  • Local Organising Committee Member for the Platinum Jubilee Meeting of Indian Academy of Sciences, Bangalore, held at Indian Institute of Chemical Technology (IICT) and Centre for Cellular and Molecular Biology (CCMB), Hyderabad during July 1-5, 2009.

  • Co-organizer of DST Workshop on Quantitative Analysis and Modelling in Animal Sciences and “CCMB - IISER Pune - NCL National Symposium on Theoretical and Mathematical Biology” held at the Yashwantrao Chavan Academy of Development Administration (YASHADA, a Govt. of Maharashtra Institute), Pune during October 6-11, 2009.

  • Co-organizer of the Satellite Meeting of ICM 2010 on “Application of Control Theory and Optimization Techniques in Biochemical Pathways” at the Hyderabad International Convention Centre, Hyderabad, from August 16-18, 2010.

  • Organising Committee Member for the International Conference & Humboldt-Kolleg on “Interface between Chemistry and Biology - A Perspective” held at Indian Institute of Chemical Technology (IICT), Hyderabad during September 21-24, 2010.

  • Co-organizer of the Workshop and Symposium on “Mathematical Ecology” at IISER-Kolkata, Mohanpur, Nadia, West Bengal, from December 7-14, 2010.

  • Co-organizer of the International Conference on Mathematical and Theoretical Biology at Pune, India, from January 23-27, 2012.

  • Co-organizer of NNMCB Symposium on Mathematical and Computational Biiology, held at IIT-Gandhinagar, India during March 21-22, 2015.

  • Co-organizer of 9th Biophysics Paschim Meeting, held at CSIR-National Chemical Laboratory, Pune, India on October 3, 2015.

  • Co-organizer of the NNMCB National Meeting (National Network for Mathematical and Computational Biology), held at CSIR-National Chemical Laboratory and IISER, Pune, India during December 27-30, 2015.

  • Joint Organizer of the National Seminar on Computational and Mathematical Biology, held at Department of Mathematics, Institute of Chemical Technology, Mumbai, India during September 10-11, 2016.

  • Co-organizer of the NNMCB 2017 Meeting (National Network for Mathematical and Computational Biology) on Mathematical Modeling of Natural and Synthetic Genetic Networks, held at Karla MTDC, Pune, India during March 18-19, 2017.

  • Scientific Advisory Committee Member for the International Conference on Mathematical Analysis and Application in Modeling (ICMAAM 2018) held at Department of Mathematics, Jadavpur University, Kolkata during January 9-12, 2018.

  • Co-organizer of the Humboldt Kolleg on Innovation & Entrepreneurship: Role of Science & Technology by Humboldt Academy, Pune Chapter, held at Prakruti Resorts, Kashid, Maharashtra, India during January 31 - February 2, 2019.

  • Co-organizer of the Humboldt Fourth Minisymposium by Humboldt Academy, Pune Chapter, held virtual on September 10, 2020.

  • Co-organizer of the Humboldt Fifth Minisymposium by Humboldt Academy, Pune Chapter, held virtual on September 25, 2020.

  • Co-organizer of the Humboldt Sixth Minisymposium by Humboldt Academy, Pune Chapter, held virtual on August 23, 2021.

  • Co-organizer of the Humboldt Seventh Minisymposium by Humboldt Academy, Pune Chapter, held virtual on March 25, 2022.

  • Organizer of a one-day workshop on “Biomodelling using R” by DBT Bioinformatics Center at CSIR-National Chemical Laboratory, Pune, held on February 21, 2023.