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Siddhartha Kundu

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Dr.
Siddhartha Kundu

MD, PhD

Affiliation

Associate Professor
Department of
Biochemistry

Contact

Email :
siddhartha_kundu@aiims.edu
siddhartha_kundu@yahoo.co.in
Phone :
+91-11-26546514

Additional Responsibility

Office Address

General OPD

Special Clinic

Surgery Days

Speciality of work

Areas of teaching

Areas of teaching

Areas of Interest

Mathematical analyses of biochemical reactions & metabolic networks Mathematical modelling and simulations of complex biochemical systems Algorithms for molecular biology

Servers/Software developed

HyperlinkDescription
http://doi.org//10.1142/S0219720022500184 https://cran.r-project.org/package=TemporalGSSA[Siddhartha_kundu_img1.png]
http://doi.org//10.3389/fmolb.2023.1206502 https://cran.r-project.org/package=ReDirection[Siddhartha_kundu_img2.png]
http://doi.org//10.1177/11779322211045878 http://178.63.18.214/ProTG4.html[Siddhartha_kundu_img2.png]
http://doi.org/10.1186/s13104-021-05477-z http://178.63.18.214/Fe2OG.html[Siddhartha_kundu_img2.png]

Educational qualifications

DegreeSubjectUniversity/InstitutionYear
PhDComputational Biology & BioinformaticsSchool of Computational and Integrative Sciences (SCIS), Jawaharlal Nehru University, New Mehrauli Road, New Delhi 1100672014-2018
MDBiochemistryAll India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi 1100291999-2001
MBBSPre-&Para-/Medical/ Surgical subjectsUniversity College of Medical Sciences (UCMS), Dilshad Garden, New Delhi 1100951992-1996

Memberships

1.Society for Mathematical Biology (SMB): Life member (ID:36503496)
2.European Society for Mathematical and Theoretical Biology (ESMTB) : Life member ID: 50143836
3.Elected member Sigma Xi society ( Scientific Research Honors Society)

Positions held

PositionSubject/WorkUniversity/InstitutionYear
Associate Professor Assistant ProfessorBiochemistryAll India Institute of Medical Sciences (AIIMS),
Ansari Nagar, New Delhi 110029		2023-2019-2023
Associate ProfessorBiochemistry

Army College of Medical Sciences (ACMS),
Brar Square, Delhi Cantt., New Delhi – 110010

Dr. Baba SahebAmbedkar Medical College and Hospital (BSAMCH), Govt. of NCT of Delhi, Rohini, Delhi 110085

2015-2018

2018-2019

Assistant ProfessorBiochemistryArmy College of Medical Sciences (ACMS),
Brar Square, Delhi Cantt.,New Delhi – 110010		2009-2014
Scientist ‘D’ (Medical)Program OfficerIndian Council of Medical Research (ICMR),
V. RamalingaswamiBhawan,
Ansari Nagar, New Delhi 110029		07-10/2019
Senior Level ConsultantProgram DirectorInformation Technology Research Academy (ITRA),
Digital India Corporation (formerly Media Lab Asia),
Ministry of Electronics and Information Technology,
C-DOT campus, New Delhi 110030		2016-2017
Research ConsultantComputational BiologyIndia Research Labs (IRL) IBM2002-2003

Research Associate/Fellow/Scientist

 

PostDoctoral work

International Center for Genetic Engineering and Biotechnology (ICGEB)

National Institute of Immunology (NII)

ICMR-National Institute of Pathology (NIOP)

Indian Institute of Technology Delhi (IITD)

05-10/2014

2005-2008

2003-2004

01-05/2002

Award/recognition:

AIIMS excellence research award (Certificate of commendation)

1.2022Kundu S#*. TemporalGSSA: a numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm (SSA)-generated datasets. Jour Bioinf. Comp. Biol. 2022, 20(4):2250018. PMID: 35941839 JBCB2022 (Additional Material).
2.2021Kundu S#*. Mathematical modeling and stochastic simulations suggest that low-affinity peptides can bisect MHC1-mediated export of high-affinity peptides into “early”- and “late”-phases. Heliyon. 2021, 7(7):e07466. PMID: 34286133 [HYON2021] (Additional Material).

Research publications (complete citations)

2024
  • (Preprint) Kundu S#*. Construction, analysis and assessment of relevance of an algebraic model for a class of biochemical networks. (https://doi.org/10.1101/2024.03.07.583960)
  • Kundu S#*. A mathematically rigorous algorithm to define, compute and assess relevance of the probable dissociation constants in characterizing a biochemical network. Scientific Reports2024, 14. PMID: 38347039 [SCIR2024] (Additional Material).
2023
  • Kundu S#*. ReDirection: an R-package to compute the probability dissociation constant for every reaction of a user-defined biochemical network. Front Mol Biosci. 2023, 10. PMID: 37942290 [FMBI2023]. (Additional Material)
2022
  • Kundu S#*. Modeling ligand-macromolecular interactions as eigenvalue-based transition-state dissociation constants may offer insights into biochemical function of the resulting complexes. Math Biosci Eng. 2022, 19(12): 13252-275. [MBE2022] (Additional Material).
  • Kundu S#*. TemporalGSSA: a numerically robust R-wrapper to facilitate computation of a metabolite-specific and simulation time-dependent trajectory from stochastic simulation algorithm (SSA)-generated datasets. Jour Bioinf. Comp. Biol. 2022, 20(4):2250018. PMID: 35941839JBCB2022 (Additional Material).
2021
  • Kundu S#*. ProTG4: A Web Server to Approximate the Sequence of a Generic Protein From an in Silico Library of Translatable G-Quadruplex (TG4)-Mapped Peptides. Bioinform Biol Insights. 2021, Sep 28;15:11779322211045878. PMID: 34602814. [BBI2021](Additional Material).
  • Kundu S#*. Mathematical modeling and stochastic simulations suggest that low-affinity peptides can bisect MHC1-mediated export of high-affinity peptides into “early”- and “late”-phases. Heliyon. 2021, 7(7):e07466. PMID: 34286133 [HYON2021](Additional Material).
  • Kundu S#*. Fe(2)OG: An integrated HMM profile-based web server to predict and analyze putative non-haemiron(II)- and 2-oxoglutarate- dependent dioxygenase function in protein sequences. BMC Res Notes. 2021, 14(1):80. PMID: 33648553. [BMRN2021] (Additional Material).
2020
  • Kundu S#*. Mathematical model of a short translatable G-quadruplex and an assessment of its relevance to misfolding-induced proteostasis. Math Biosci Eng. 2020, 17(3): 2470-2493. PMID: 32233549. [MBE2020] (Additional Material).
2019
  • Kundu S#*. Insights into the mechanism(s) of digestion of crystalline cellulose by plant class C GH9 endoglucanases. J Mol Model. 2019 Jul 23;25(8):240. PMID: 31338614 [JMM-2019] (Additional Material).
2018
  • Kundu S#*. Mathematical basis of predicting dominant function in protein sequences by a generic HMM-ANN algorithm. Acta Biotheor. 2018 Jun;66(2):135-148. PMID: 29700659,32385619 [ACBI2018] (Additional Material).
  • Kundu S*, Sharma R*. Origin, evolution, and divergence of plant class C GH9 endoglucanases. BMC Evol. Biol. 2018 May 30;18(1):79. PMID: 29848310 [BMEB2018] (Additional Material).
2017
  • Kundu S#*. Mathematical basis of improved protein subfamily classification by a HMM-based sequence filter. Math Biosci. 2017 Nov;293:75-80. doi:10.1016/j.mbs.2017.09.001. Epub 2017 Sep 13. PubMed PMID: 28916136. (Additional Material).
2016
  • Kundu S*, Sharma R*. In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases. Front Plant Sci. 2016 Aug 12;7:1185. PMID: 27570528 [FPS2016] (Additional Material).
  • Kundu S#*. Stochastic modelling suggests that an elevated superoxide anion-hydrogen peroxide ratio can drive extravascular phagocyte transmigration by lamellipodium formation. J Theor Biol. 2016 Oct 21;407:143-54. PMID: 27380944. (Additional Material).
2015
  • Kundu S#*. Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology. Front Plant Sci. 2015 Jul 15;6:489. PMID: 26236316 [FPS2015a] (Additional Material).
  • Kundu S#*. Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases. Front Plant Sci. 2015 Mar 11;6:98. PMID: 25814993 [FPS2015b] (Additional Material).
2012
  • Kundu S#*. Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases. BMC Res Notes. 2012 Aug 4;5:410. PMID: 22862831 [BMRN2012] (Additional Material).
2011
  • Kundu S*, Subodh S. Gradient sensing in vectorial chemotaxis – a novel role for Reactive Oxygen Species. International Journal of Trends in Medicine. 2011 1; 54-59. [IJTM2011]
2002
  • Singh N, Khanna N, Sharma H, Kundu S, Azmi S. Insights into the molecular mechanism of apoptosis induced by TNF-alpha in mouse epidermal JB6-derived RT-101cells. Biochem Biophys Res Commun. 2002 Jul 5;295(1):24-30. PMID:12083761. [BBRC2002]
 (#) Single author; (*)Corresponding author

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