Dr. Swathi Alagesan

Dr. Swathi Alagesan

Assistant Professor, Synthetic Biology

Research Focus Keywords

Synthetic biology, Flux Analysis, Metabolic Engineering


Dr. Swathi Alagesan completed Bachelors in Engineering from Delhi College of Engineering. Subsequently, she joined the Department of Chemical Engineering at IIT Bombay for a PhD. Under the guidance of Prof. Pramod Wangikar, she worked on studying the circadian rhythms in cyanobacteria. For her postdoctoral work, she joined Dr. Nigel Minton’s group at the Synthetic Biology Research Centre, University of Nottingham. During this time she was involved in generating synthetic biology parts and using them for metabolic engineering of autotrophic bacteria. In 2017, she joined Anna University as a DST-INSPIRE Faculty. She moved to IBAB in 2020 and her current research is focussed on generating various synthetic biology tools, and using the insights obtained from flux analysis to engineer microorganisms for optimizing behaviour.


  1. B.E. (Biotechnology) – Delhi College of Engineering, Delhi, India (2006-2010)
  2. Ph.D – IIT Bombay, Mumbai, India (2010-2015)
  3. Post-doctoral research – University of Nottingham, Nottingham, UK (2015-2017)

Professional Experience

  1. DST-INSPIRE Faculty – Anna University, Chennai, India (2017-2020)
  2. DST-INSPIRE Faculty Scientist – IBAB, Bengaluru, India (2020- present)

Research Interest

In-depth understanding of the underlying metabolism of an organism is critical for rationalized metabolic engineering. Hence, in our lab, we focus on

  1. Understanding the underlying metabolism of micro-organisms through flux analysis – We mainly carry out 13C-based metabolic flux analysis where a 13C labelled carbon substrate is fed to the micro-organism and based on the labelling profile of metabolites within the cell, the flux through different pathways is studied. This gives key insights into the organism’s preferential metabolism under different growth conditions and also aids in rationalizing engineering strategies.
  1. Developing synthetic biology tools for metabolic engineering of autotrophic micro-organisms – Well characterized libraries of genetic elements are essential for building robust controllable synthetic circuits. We, at IBAB, are involved in developing such synthetic biology parts and tools for controlling gene expression in a predictable manner.

Looking for students having a research aptitude, who wish to work in the field of synthetic biology. If interested, please contact me at a_swathi@ibab.ac.in

Group Members

Anantika Banerjee, PhD student
I completed my M.Sc in Biochemistry and Molecular biology from GITAM University and my bachelors in Microbiology and Biotechnology from Andhra University. I joined the Synthetic Biology Lab under Dr. Swathi in 2022 as a Ph.D. student. I am currently working on RNA targeting CRISPR-Cas proteins with the aim of expanding the CRISPR-CAS toolbox for cyanobacteria. Apart from research, music is my escape from the chaotic world. Motto in life: “The important thing is to never stop questioning. Everything is theoretically impossible until it is done”
Sugandhi G – Research Assistant
I have a triple major Bachelor’s degree in Biotechnology, Chemistry and Botany and a Master’s degree in Biotechnology, both from CHRIST (Deemed to be University). I joined IBAB as an intern for my M.Sc. Dissertation, and am now working as Project Assistant for the application of synthetic biology tools for metabolic engineering and development of synthetic circuits in cyanobacteria, for the production of bioproducts. I am a voracious reader, a digital creator and painter, while I wait for my cyano to grow.
Aishwarya S, Research Assistant
I have done my Masters in Technology from SASTRA Deemed to be University. During my internship at IBAB, I worked on creating knockout mutants of Synechocystis sp. PCC 6803 and analyzing the fluctuations in carbon metabolism through MFA.  I joined IBAB as a Research Assistant in July 2023. I love to invest my time in Mandala art, listening to the strings and getting the fine curves in a piece of paper is a satisfaction. Would like to shine like the autofluorescence of cyano, without contamination.


  1. Jubin Thomas – Project Assistant
  2. Shrilaxmi Bhat – Project Assistant –pursuing masters in North Eastern Univ -Boston Campus
  3. Akhila R- Project Assistant, now working in BBRC, Syngene
  4. Kean Francis – MSc Dissertation Intern (IBAB), currently employed with Novartis
  5. Nidhish P – MSc Dissertation Intern (Dayananda Sagar Univ)
  6. Yasha Nirati – MSc Dissertation Intern (IBAB), now working in Biocon
  7. Elvis Christie – MSc Dissertation Intern (IBAB)
  8. Jeet Nanshi – B.tech Dissertation Intern (SRM)


  1. Shrilaxmi Bhat, Anantika Banerjee, and Swathi Alagesan*
    AraC-Based Biosensor for the Detection of Isoprene in E. coli. ACS Omega (2023).
  2. Nirati, Y., Purushotham, N. & Alagesan, S.
    Quantitative insight into the metabolism of isoprene-producing Synechocystis sp. PCC 6803 using steady state 13C-MFA. 
    Photosynth Res, https://doi.org/10.1007/s11120-022-00957-0 (2022).
  3. Swathi Alagesan*, Erik KR Hanko*, Naglis Malys*, Muhammad Ehsaan, Klaus Winzer, Nigel P Minton
    Functional genetic elements for controlling gene expression in Cupriavidus necator H16.
    Appl. Environ. Microbiol., 84 (19), e00878-18, (2018) (*equal contribution)
  4. Swathi Alagesan, Nigel P Minton, Naglis Malys
    13C-assisted metabolic flux analysis to investigate heterotrophic and mixotrophic metabolism in Cupriavidus necator H16. 
    Metabolomics, 14(1), 9, (2018)
  5. Swathi Alagesan, Sandeep B. Gaudana, Pramod P. Wangikar
    Rhythmic oscillations in KaiC1 phosphorylation and ATP charge in nitrogen-fixing cyanobacterium Cyanothece sp. ATCC 51142 under continuous light.
    Biological Rhythm Research, 47(2): 285-301, (2016)
  6. Swathi Alagesan, Sandeep B. Gaudana, Avinash Sinha, Pramod P. Wangikar
    Metabolic Flux analysis of Cyanothece sp. ATCC 51142 under mixotrophic conditions.
    Photosynthesis Research, 118(1-2): 191-8, (2013)
  7. Swathi Alagesan, Sandeep B. Gaudana, Krishnakumar S., Pramod P. Wangikar
    Model based optimization of high cell density cultivation of nitrogen fixing cyanobacteria.
    Bioresource Technology, 148:228-233, (2013)
  8. Sandeep B. Gaudana, Swathi Alagesan, Madhu Chetty, Pramod P. Wangikar
    Diurnal rhythm of a unicellular diazotrophic cyanobacterium under mixotrophic conditions and elevated carbon dioxide.
    Photosynthesis Research, 118: 51-7, (2013)
  9. Sandeep B. Gaudana, Krishnakumar S., Swathi Alagesan, Madhuri G Digmurti, Ganesh A. Viswanathan, Madhu Chetty, Pramod P. Wangikar
    Rhythmic and sustained oscillations in metabolism and gene expression of Cyanothece sp. ATCC 51142 under constant light.
    Frontiers in Microbiology, 4:374, (2013)


Institute of Bioinformatics and Applied Biotechnology
Biotech Park, Electronic City Phase I,
Bengaluru 560100,


080 28528901/02, extension 209