Assoc. Prof. Dr. Siddhartha Kundu | Mathematics |  Best Researcher Award

Associate Professor at All India Institute Of Medical Sciences Delhi, India

Dr. Siddhartha Kundu is an Associate Professor in the Department of Biochemistry at the All India Institute of Medical Sciences (AIIMS), New Delhi. He holds an MBBS, MD, and PhD, and brings extensive expertise in clinical biochemistry and molecular diagnostics. With a strong background in academic research and teaching, Dr. Kundu has contributed to several national and international scientific publications. He is actively engaged in advancing biochemical research and medical education in India.

Profile:

• Google Scholar

Professional Experience:

With over 20 years of post-MD experience, Dr. Siddhartha Kundu is a medical doctor and biochemical scientist with recognized contributions in teaching, research, and academic leadership.

• Teaching/Research: 18+ years

• Advisory Roles: 2+ years

• Leadership Positions: 2+ years

Research Interests:

• Mathematical Modeling of macromolecules and complex biochemical systems (both physiological and pathological)

• Bioinformatics & Algorithm Development for molecular biology applications

Technical Skills:

• Programming Languages: PERL, C, Python

• Data Analysis Platforms: R, Cygwin

• Bioinformatics: Algorithm design, modeling, and simulation

Editorial Contributions:

• Invited Reviewer for peer-reviewed journals such as:

  • Scientific Reports

  • Bioinformatics

  • PLOS ONE

  • Indian Journal of Medical Research (IJMR)

Research Output:

(A) Software and Servers Developed

1. TemporalGSSA
   R package for time-step parameterization in biochemical networks.

2. ReDirection
   R package for calculating dissociation constants and dominant reaction direction.

3. ProTG4
   Web server predicting protein sequences from TG4-mapped peptide libraries.

4. Fe2OG
   Web server predicting Fe(II)/2-oxoglutarate-dependent dioxygenase functions.

(B) Selected Peer-Reviewed Publications

(Author is sole and corresponding author in most; # = single author, * = corresponding)

1. Kundu S#*. Scientific Reports (2024) – Dissociation constants in biochemical networks.

2. Kundu S#*. Front Mol Biosci (2023) – ReDirection R-package.

3. Kundu S#*. Math Biosci Eng (2022) – Ligand interactions as eigenvalue functions.

4. Kundu S#*. J Bioinf Comp Biol (2022) – TemporalGSSA.

5. Kundu S#*. Bioinform Biol Insights (2021) – ProTG4 server.

(Full publication list available upon request or via PubMed search)

(C) Conferences, Abstracts & Chapters

• Conference Abstract: “Role of mathematical models in elucidating biochemical rules”, WGC Singapore (2018).

• Book Reviews: National Medical Journal of India (2005), Indian Journal of History of Science (2006)

(D) Posters

Presented at:

• BIOSPARKS 2018, JNU, New Delhi

• 3rd International Plant Physiology Congress, JNU

• 3rd International Conference on Integrative Biology, Valencia, Spain

Honors and Awards:

• AIIMS Excellence in Research Award – 2021, 2022

Additional Information:

• Dr. Kundu is a passionate educator and innovator in the application of mathematical and computational models to unravel biological complexity. His work bridges medical biochemistry, theoretical biology, and systems modeling.

Citation Metrics:

• Total Citations: 133

• Citations since 2020: 78

• h-index: 7

• h-index since 2020: 6

• i10-index: 5

• i10-index since 2020: 1

Publication Top Notes:

• Insights into the molecular mechanism of apoptosis induced by TNF-α in mouse epidermal JB6-derived RT-101 cells
  N. Singh, N. Khanna, H. Sharma, S. Kundu, S. Azmi
  Biochemical and Biophysical Research Communications, 2002

• Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases
  S. Kundu
  BMC Research Notes, 2012

• Origin, evolution, and divergence of plant class C GH9 endoglucanases
  S. Kundu, R. Sharma
  BMC Evolutionary Biology, 2018

• In silico identification and taxonomic distribution of plant class C GH9 endoglucanases
  S. Kundu, R. Sharma
  Frontiers in Plant Science, 2016

• Unity in diversity: A systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases
  S. Kundu
  Frontiers in Plant Science, 2015

• Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology
  S. Kundu
  Frontiers in Plant Science, 2015

• Insights into the mechanism(s) of digestion of crystalline cellulose by plant class C GH9 endoglucanases
  S. Kundu
  Journal of Molecular Modeling, 2019

• Stochastic modelling suggests that an elevated superoxide anion-hydrogen peroxide ratio can drive extravascular phagocyte transmigration by lamellipodium formation
  S. Kundu
  Journal of Theoretical Biology, 2016

• Mathematical modeling and stochastic simulations suggest that low-affinity peptides can bisect MHC-I mediated export of high-affinity peptides into “early”- and “late”-phases
  S. Kundu
  Heliyon, 2021

• Modeling ligand-macromolecular interactions as eigenvalue-based transition-state dissociation constants may offer insights into biochemical function of the resulting complexes
  S. Kundu
  Mathematical Biosciences and Engineering, 2022

• ReDirection: An R-package to compute the probable dissociation constant for every reaction of a user-defined biochemical network
  S. Kundu
  Frontiers in Molecular Biosciences, 2023

• Fe(II)OG: An integrated HMM profile-based web server to predict and analyze putative non-haem iron (II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences
  S. Kundu
  BMC Research Notes, 2021

• Mathematical basis of improved protein subfamily classification by a HMM-based sequence filter
  S. Kundu
  Mathematical Biosciences, 2017

• A mathematically rigorous algorithm to define, compute and assess relevance of the probable dissociation constants in characterizing a biochemical network
  S. Kundu
  Scientific Reports, 2024

• TemporalGSSA: A numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm output
  S. Kundu
  Journal of Bioinformatics and Computational Biology, 2022