User:S. Saini

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Research interests

  1. Network Dynamics
  2. Statistics and Dynamics of Evolution in Microbial Populations
  3. Bacterial Pathogenesis


  • PhD Positions. Interested students are requested to write to Supreet with their CV.
  • Post-doctoral researchers interested in theoretical & computational biology are requested to contact Supreet with their CV and research proposal.

Research Group

Principal Investigator

  1. Supreet Saini (Associate Professor) | PhD & MS (University of Illinois, Urbana-Champaign) | B.Tech. (IIT Delhi) | saini AT

Post Doc

  1. Phaniendra Alugoju (2019 - date) | PhD, Pondicherry Central University | phaniendra.a AT
  2. Saniya Deshmukh (2019 - date) | PhD, Pune University

Graduate Students (for PhD)

  1. R G Brajesh (2015 - date) | MTech (Biotechnology) Anna University | brajeshrg AT
  2. Dibyendu Dutta (2016 - date) | MSc & BSc (Systems Biology) Hyderabad University | debudutta1 AT
  3. Anjali Mahilkar (2017 - date) | MSc IIT Kanpur | anjali.mahilkar AT
  4. Rajesh Kannan (2017 - date) | MTech IIT Chennai | rajeshkannan.e AT
  5. Sukhjeet Kaur (2019 - date)
  6. Sravanti Kasarlawar (2019 - date)

Graduate Students (for Masters)

  1. Rishi Yadav (2019 - date)


Project Research Fellows

Visiting Students

Past Members

Graduate Students (for PhD)

  1. Debika Choudhury (2011 - 2018) | [(to join as) Post Doc Nikhil Nair's group at Tufts] | debika217 AT
  2. Kirti Jain (2011 - 2017) | [Post Doc, Calin Guet's group at IST (Vienna) | kirtijn1 AT
  3. Manish Kumar (2011 - 2015) [Post Doc, Jens Nielsen's group at Chalmers (Sweden) | manish1.biotech AT]
  4. Mahendra Prajapat (2011 - 2016) [Post Doc, NIH (US) | AT]
  5. Chandrani Das (2012 - 2018) [Scientist, Biosciences R&D Division, TCS (Pune) | chandrani.das AT]

Graduate Students (for Masters)

  1. Nikhil Raj (2014 - 2016)
  2. Rohit Garg (2014 - 2016)
  3. Nitesh Meena (2013 - 2015)
  4. Ashish (2012 - 2014) [Co-Founder, The Zero Games Pvt. Ltd, ashish.19766 AT]
  5. Gauri Shankar Choudhury (2012 - 2014)

Project Research Staff

  1. Balaji Kumar (2016) [Graduate Student, Penn State]
  2. Divyae Prasad (2014)


  1. [2014] Piyush Lakhmani, Amit Aggarwal
  2. [2013] Chaitanya Gupta, Amit Pradhan

Visiting Students

  1. [2018] Nishant Gerald (Manipal), Aakanksha Chand (Mumbai Univ.)
  2. [2016] Isha Shroff (D Y Patil University)
  3. [2014] Sumedha Mangal (IIT BHU), Vaibhav Pathak (IIT BHU), Balaji Kumar (IIT Madras), Shriyam (Banasthali University)


  1. Phenomenological models as effective tools to discover cellular design principles Archives of Microbiology (2019)
  2. Mathematical modeling of movement on fitness landscapes BMC Systems Biology (2019)
  3. Estimating optimal lysogenic propensity for viruses in stressed environments bioRxiv (2018)
  4. Mathematical modelling of quorum sensing in bacteria INAE Letters (2018)
  5. Short term evolutionary dynamics of Escherichia coli in different carbon environments bioRxiv (2018)
  6. Dynamic control of arabinose and xylose utilization in E. coli Canadian J. of Chemical Engineering (2018)
  7. Dynamics and control of flagella assembly in Salmonella typhimurium Frontiers in Cellular and Infection Microbiology (2018)
  8. Mathematical Modelling of Actin treadmill in Apicomplexans bioRxiv (2018)
  9. Logic of two antagonizing intra-species quorum sensing systems in bacteria Biosystems (2018)
  10. Current status and challenges in biobutanol production. Bioenergy and Biofuels (Book Chapter) (2018)
  11. Cross-regulation among arabinose, xylose and rhamnose utilization in E. coli Letters in Applied Microbiology (2017)
  12. Robustnes vs Evolvability analysis for regulatory feed-forward loops. J. Bioinformatics and Computational Biology (2017)
  13. Rob And MarA Alter Susceptibility Of Escherichia coli To Antibiotics In Presence Of Salicylate. bioRxiv (2017)
  14. Optimal parameter values for control of gene regulation. Molecular BioSystems (2017) A non-technical description of the work is at: [1]
  15. Sugar Co-utilization in Microorganisms. Current Developments in Biotechnology and Bioengineering (Book Chapter) (2016)
  16. Building Metabolic Models From First Principles. Current Developments in Biotechnology and Bioengineering (Book Chapter) (2016)
  17. Analysis of a strategy for cooperating cells to survive the presence of cheaters Molecular BioSystems (2016)
  18. MarRA, SoxSR, and Rob encode a signal dependent regulatory network in Escherichia coli. Molecular BioSystems (2016)
  19. Progress toward isolation of strains and genetically engineered strains of microalgae for production of biofuel and other value added chemicals: A review. Energy Conversion and Management (2016)
  20. Analysis of optimality of the standard genetic code. Molecular BioSystems, Preprint: bioRxiv (2016)
  21. Revisiting Demand Rules for Gene Regulation. Molecular BioSystems, Preprint: bioRxiv (2016)
  22. Control of marRAB operon in Escherichia coli via autoactivation and autorepression. Biophysical Journal (2015)
  23. Mathematical model of flagella gene expression dynamics in Salmonella enterica serovar typhimurium. Systems and Synthetic Biology (2015)
  24. Elementary mode analysis reveals that Clostridium acetobutylicum modulates its metabolic strategy under external stress. Molecular BioSystems (2014)
  25. Acetone-butanol-ethanol fermentation analysis using only high performance liquid chromatography. Analytical Methods (2014)
  26. Characterization of Performance and Dynamics of Genetic Networks. IFAC Computer Applications in Biotechnology (2013)
  27. Role of feedback and network architecture in controlling virulence gene expression in Bordetella. Molecular BioSystems (2013)
  28. Role of extracellular cues to trigger the metabolic phase shifting from acidogenesis to solventogenesis in Clostridium acetobutylicum. Bioresource Technology (2013)
  29. Academic Ethics at the Undergraduate Level: Case Study from the Formative Years of the Institute. Journal of Academic Ethics (2013)
  30. Interplay between Fur and HNS in controlling virulence gene expression in Salmonella typhimurium. Computers in Biology and Medicine (2012)
  31. Continuous control of flagellar gene expression by the σ28-FlgM regulatory circuit in Salmonella enterica. Molecular Microbiology (2011)
  32. The interaction dynamics of a negative feedback loop regulates flagellar number in Salmonella enterica serovar Typhimurium. Molecular Microbiology (2010)
  33. FliZ induces a kinetic switch in flagellar gene expression. Journal of Bacteriology (2010)
  34. Role of cross talk in regulating the dynamic expression of the flagellar Salmonella pathogenicity island 1 and type 1 fimbrial genes. Journal of Bacteriology (2010)
  35. The role of coupled positive feedback in the expression of the SPI1 type three secretion system in Salmonella. PLoS Pathogens (2010)
  36. SprB is the molecular link between Salmonella pathogenicity island 1 (SPI1) and SPI4. Journal of Bacteriology (2010)
  37. Role of FimW, FimY, and FimZ in regulating the expression of type i fimbriae in Salmonella enterica serovar Typhimurium. Journal of Bacteriology (2009)
  38. Role of feedback loops in dictating flagellar gene regulation dynamics in Salmonella typhimurium. FOSBE Proceedings IET Systems Biology (2009)
  39. The rate of protein secretion dictates the temporal dynamics of flagellar gene expression. Molecular Microbiology (2008)
  40. FliZ Is a posttranslational activator of FlhD4C2-dependent flagellar gene expression. Journal of Bacteriology (2008)
  41. Pressure drop and heat transfer study in tube-in-tube helical heat exchanger. Chemical Engineering Science (2006)

Conference Presentations/Invited Talks

  1. Speciation Experiments in Yeast. IISc Bangalore , (2019).
  2. Understanding ecological diversity via evolutionary experiments in laboratory. India Biodiversity Meeting , Indian Statistical Institute, Kolkata (2019).
  3. Dynamics of intrinsic antibiotic resistance in Escherichia coli via the mar-sox-rob regulon. ASM Annual Meeting , Atlanta, US (2018).
  4. Historical developments in evolutionary biology St. Xavier's Mumbai (2018)
  5. Coordinated control of virulence in enteric pathogens. Biological Engineering Society (BES) Annual Conference , NSIT Delhi (2017).
  6. Dynamics of intrinsic antibiotic resistance in Escherichia coli via the mar-sox-rob regulon. Center for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad (2017).
  7. Dynamics and evolution of antibiotic resistance in enteric bacteria. Mathematical Models in Infection, Immunity, and Inflammation, IISc Bangalore (2017).
  8. Dynamics and control of intrinsic antibiotic resistance in enteric bacteria. India Biodiversity Meeting, ISI (Kolkata) & Government College of Textile & Technology (Berhampore) (2016)
  9. Robustness vs. evolvability in rapidly evolving bacterial populations. Seminar on Computational & Mathematical Biology , ICT, Mumbai (2016)
  10. Quorum sensing and bacterial strategies. NNMCB Meeting , IISER, Pune (2015)
  11. Control of mar-sox-rob regulon in E. coli and Salmonella. Bacterial Expressions II , NCBS, Bangalore (2015)
  12. Does genetic robstness aid adaptability in rapidly evolving microbial populations? Evolutionary Biology Meeting, Marseille, France (2015)
  13. Crosstalk between arabinose and xylose utilization systems in E. coli. ASM General Meeting, US (2015)
  14. Control of Mar, Sox, Rob regulon in E. coli. ASM General Meeting, US (2015)
  15. Evolvability vs. Robustness in rapidly evolving microbial populations. Society of Biological Chemists (India) Annual Meeting, Bhubaneswar (2014)
  16. Transcriptional interference as a mechanism to control gene expression. IMSc, Chennai (2014)
  17. Revisiting Demand Rules for Gene Regulation. Center for Excellence in Basic Sciences, Mumbai (2014)
  18. Characterizing Clostridium acetobutylicum metabolism using constraint-based modeling approach under stress. Clostridium XIII, China (2014)
  19. Revisiting Demand Rules for Gene Regulation. FEBS-EMBO Meeting, Paris (2014)
  20. Dynamic regulation of Pathogenicity Islands and Multiple Antibiotic Resistance loci in Salmonella typhimurium. FEBS-EMBO Meeting, Paris (2014)
  21. Logic of Interacting Quorum Sensing Systems in Bacteria. q-Bio, Santa Fe (2014)
  22. Introduction to Computational and Systems Biology. Workshop on Bioinformatics Applications and Interdisciplinary Technologies, Haffkine Institute, Mumbai (2014)
  23. Counting and control in bacteria via Secretion. Bacterial Expressions, NCBS (Bangalore) (2013)
  24. Impact of network map and architecture on gene expression dynamics. Foundations of Systems Biology in Engineering (FOSBE), Tsuruoka (Japan) (2012)
  25. Dynamics and Control of the Clostridium acetobutylicum metabolic network. Clostridium XII, Nottingham (United Kingdom) (2012)


  1. Supreet Saini, Associate Professor, Department of Chemical Engineering, IIT Bombay, Mumbai - 400 076 | Email: saini AT | Phone: 91 22 2576 7216
  2. Chemical Engineering Lab 01, 2nd Floor, DESE-CESE Building, IIT Bombay, Mumbai - 400 076 | Phone: 91 22 2576 4235