Computational Biology & Data Science

Anurag
Passi, PhD.

Developing AI-driven metabolic modeling frameworks that transform high-dimensional biological data into actionable insights for therapeutic discovery — integrating multi-omics, genome-scale models, and deep learning to simulate disease dynamics and precision intervention.

Anurag Passi
Get in Touch India
376Total Citations
12Publications
5h-index
3i10-index
20122026
15+
Years of ResearchSystems Biology | Computational Biology | Drug Repurposing
01 — About

Profile

A skilled computational biologist and systems biologist with deep expertise in multi-omics data analysis, drug discovery, genome-scale metabolic modelling, and artificial intelligence. Adept at deciphering biological complexities, identifying therapeutic targets, and optimizing drug development through predictive modelling. A collaborative team player with a passion for improving healthcare through data-driven innovation, committed to making a meaningful impact in global health.

Research Interests

Artificial IntelligenceBig Data AnalyticsCheminformaticsDrug Discovery & RepurposingMetabolic ModelingMicrobial InteractionsMultilevel Data IntegrationOmics Data ScienceSystems Biology
EnglishFluent
HindiNative
FrenchBasic
02 — Career

Research Experience

Over 15 years advancing computational biology from TB drug discovery to plant metabolic modeling.

2024 — 2025
UC San Diego, La Jolla, CA

Asst. Project Scientist

Supervisor: Karsten Zengler, Ph.D.
  • Developed the largest multi-tissue and multi-compartment metabolic model of Brachypodium distachyon — 2,278 genes, 7,613 metabolites, 9,842 reactions.
  • Model enables assessment of nitrogen use efficiency (NUE) across diverse environments.
2019 — 2024
UC San Diego, La Jolla, CA

Postdoctoral Researcher

Supervisor: Karsten Zengler, Ph.D.
  • Built the largest multi-tissue metabolic model of Citrus clementina — 2,616 genes, 8,653 metabolites, 10,654 reactions.
  • Reconstructed metabolic model for Brachypodium distachyon to study plant–microbiome interactions.
  • Central role in adding complex lipid metabolism across multiple organism models.
2012 — 2019
CSIR-IMTECH, Chandigarh, India

Doctoral Research

Supervisors: Anshu Bhardwaj, Ph.D. & David Wild, Ph.D.
  • Created a predictive algorithm using Network Based Inference (NBI) to predict repurposed drugs against Mycobacterium tuberculosis.
  • Identified regulatory mechanisms as potential drug targets against TB.
2015 — 2016
Indiana University, Bloomington, IN

Fulbright Research Fellow

Supervisor: David J. Wild, Ph.D.
  • Large-scale data science, networks, and data mining for drug discovery and biomedicine with focus on tuberculosis.
2010 — 2012
CSIR-IMTECH, Chandigarh, India

Project Assistant

Supervisors: Anshu Bhardwaj, Ph.D. & David J. Wild, Ph.D.
  • Classification & regression models using Random Forest and Naive Bayes to identify active anti-TB compounds.
  • Cheminformatics & pharmacology methods to screen compound space for anti-TB molecules.
03 — Education

Academic Background

2019
Ph.D. in Biological Sciences
CSIR-Institute of Microbial Technology, Chandigarh, India
2010
M.Tech in Bioinformatics
Hamdard University, New Delhi, India
2008
B.Tech in Biotechnology
Amity University, Uttar Pradesh, India
04 — Toolkit

Skills & Expertise

Programming & OS

PythonRMATLABLinuxWindows

Bioinformatics

Multi-omics Data Analysis and IntegrationNGS Processing

Metabolic Modeling

COBRA ToolboxCOBRApyOmics Data IntegrationAI/ML Layering

AI / Machine Learning

PyTorchTensorFlow
05 — Research Output

Publications

Selected peer-reviewed journal articles and book chapters.

Passi, A., Campos D.T., Kumar, M., et al. Unveiling organ-specific metabolism of Citrus clementina. Proc. Natl. Acad. Sci. 2025; 122 (29).
Campos, D.T., Tibocha-Bonilla J.D., ..., Passi A, et al. Genome-scale metabolic model for Thauera sp. MZ1T. PLOS Computational Biology. 2025; 21(1).
Kumar, M., ..., Passi, A. et al. Mixotrophic growth of a ubiquitous marine diatom. Sci. Adv. 2024; 10, eado2623.
J.J. Yang, et al. Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of M. tuberculosis. Tuberculosis. 2024; p. 146.
Passi, A., Tibocha-Bonilla, J.D., et al. Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data. Metabolites 2022, 12, 14.
Campos, D.T., Zuñiga, C., Passi, A., et al. Modeling nitrogen fixation in Azotobacter vinelandii DJ. Metabolic Eng. Comm. 2020; Vol 11.
Passi, A., Rajput, N.K., Wild, D.J., Bhardwaj, A. RepTB: a gene ontology-based drug repurposing approach for tuberculosis. J Cheminform. 2018;10(1):24.
Gaur et al. Assessing therapeutic potential of molecules: MPDSTB. J. Chemical Sciences. 2017;129(5).
Seal, A., Passi, A., et al. In-silico predictive mutagenicity model generation using supervised learning. J Cheminform. 2012;4(1):10.
Vashisht et al. Crowdsourcing interactome-driven drug target identification in M. tuberculosis. PLoS One. 2012;7(7).
Passi, A., Bani, J., et al. Data-Driven Systems Level Approaches for Drug Repurposing. Academic Press. 2019 (Book Chapter).
Ghosh et al. Software Platform for Metabolic Network Reconstruction of M. tuberculosis. Springer. 2013 (Book Chapter).
06 — Recognition

Honors & Awards

🏅
Fulbright–Nehru Doctoral Research FellowshipAwarded by the United States–India Educational Foundation (USIEF)
2015 – 2016
🎓
CSIR-Senior Research FellowshipAwarded by the Council of Scientific & Industrial Research
2014 – 2017
07 — Certifications

Professional Certificates

🏫
Machine Learning SpecializationDeepLearning.AI & Stanford Online · 3 Courses — Supervised ML, Advanced Learning Algorithms, Unsupervised Learning & RL
Mar 2026
🧠
Deep Learning SpecializationDeepLearning.AI · 5 Courses — Neural Networks, Hyperparameter Tuning, ML Projects, CNNs, Sequence Models
Mar 2026
💻
AI Python for BeginnersDeepLearning.AI · Coursera
Feb 2026
🤖
Neural Networks and Deep LearningDeepLearning.AI · Coursera
Jul 2019
📊
Introduction to Big DataUC San Diego · Coursera
Oct 2016
🔧
The Data Scientist's ToolboxJohns Hopkins University · Coursera
Jun 2016
08 — Training

Research Training

Indiana University, USA
Fulbright-Nehru Doctoral ResearchSchool of Informatics, Computing and Engineering, with Dr. David J. Wild
Oct 2015 — Jul 2016
JNU, New Delhi
Molecular Modeling of Drug Target Proteins of P. falciparumSchool of Information Technology, under Dr. Naidu Subbarao
Jan 2010 — May 2010
Amity University
Docking Studies on HIV Protease InhibitorsAmity Institute of Biotechnology, under Mr. Amitava Bhattacharya
Mar 2008 — May 2008
IARI, New Delhi
Amplification and Cloning of Plant Viral GenesIndian Agricultural Research Institute, under Dr. Shelly Praveen
Jun 2007 — Jul 2007
TCGA, New Delhi
High Throughput DNA Analysis Using ABI 3730XL Genetic AnalyzerThe Center for Genomic Application, under Dr. Bhaswar Maity
Jun 2006 — Jul 2006
09 — Conferences

Workshops & Conferences

Poster
Unveiling Organ-Specific Metabolism of Citrus clementina9th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2024), San Diego, CA
Oct 2024
Poster
UK-India Workshop on Antimicrobial ResistanceCSIR-IMTECH, India
Nov 2016
Workshop
2nd BD2K / 4th Network of BioThings Hackathon 2015Stanford University, USA
2015
Poster
Gordon Research Conference on TB Drug DevelopmentIL Ciocco Hotel and Resort, Lucca (Barga), Italy
Jun 2011
Speaker
C2D Cheminformatics: Methods, Tools and ResultsOSDD-CDAC Science Conference, Malabar Christian College, Calicut, India
Dec 2010
Workshop
High Performance Computing and Applications (HPCA 2009)Banaras Hindu University, Varanasi
Feb 2009
Workshop
Bioinformatics Applications in Research and DevelopmentJamia Millia Islamia, New Delhi
Feb 2009