Sudeepti Kulshrestha

About

An enthusiastic research scholar currently pursuing her PhD in Bioinformatics. My work involves deep analysis of 16s rRNA sequences from microbiome studies to understand the implications of various microbes, genes and pathways on various diseases.

Skills: NGS Data Analysis, Phylogenetic studies, Whole Genome Sequencing (Bioinformatics), Functional Divergence studies, Metagenomic Data Analysis including taxonomic classification and functional profiling of 16s rRNA sequences and subsequent visualization and statistical analysis, Drug discovery, Molecular Docking, MM-GBSA analysis, Molecular Dynamics, Network Analysis based on interactions amongst genes/proteins using Cytoscape, Metabolic Engineering, Kinetic Modeling using COPASI, Genome-scale metabolic modeling, Flux Balance Analysis, and more! Proficient in working in Linux, R, Python, MATLAB. Some experience in Variant calling, Perl, C/C++, Machine Learning using Python.

Always looking to learn more!

Employment

• Indian Council of Medical Research Project Research Scientist - II
  2025 - Present

Education

• Amity University Ph.D. Bioinformatics
  2020 - 2024
• Amity University B.Tech. + M.Tech (Dual) Biotechnology
  2015 - 2020

Projects & Funding

Projects & funding information is unavailable.

Publications (10)

• Systems biology-driven analysis of obesity-associated genes with transcript mapping and post-translational modification annotations
  Biochemical and Biophysical Research Communications 2026 DOI: 10.1016/j.bbrc.2026.153942
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• A concept-enhanced, knowledge graph-guided framework for interpretable PCOS prediction: a case study in explainable biomedical artificial intelligence
  Reproduction, Fertility and Development 2026 DOI: 10.1071/RD25145
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• Systems biology approach reveals succinyl-CoA and hydroxycitrate as potential therapeutics for the treatment of vulvovaginal candidiasis
  Next Research 2025 DOI: 10.1016/j.nexres.2025.100190
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• Genomics and Transcriptomics in Reproductive Health
  2024 DOI: 10.1201/9781003487548-3
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• Proteomics and Metabolomics in Reproductive Health
  2024 DOI: 10.1201/9781003487548-4
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• Metagenomic investigation of 16S rRNA marker gene samples to analyze the role of race, ethnicity, and location in preterm birth: A comprehensive vaginal microbiome meta-analysis
  Human Gene 2024 DOI: 10.1016/j.humgen.2024.201260
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• Identification of Distinct Vaginal Microbiota Signatures Contributing Toward Preterm Birth Using an Integrative Computational Approach
  Microbiology and Biotechnology Letters 2023 DOI: 10.48022/mbl.2210.10008
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• Mucormycosis Metabolic Network Modeling: A Constraint-Based Approach
  2023 6th International Conference on Information Systems and Computer Networks (ISCON) 2023 DOI: 10.1109/iscon57294.2023.10111947
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• Systems-wide analysis of A. fumigatus using kinetic modeling of metabolic pathways to identify putative drug targets
  Journal of Biomolecular Structure and Dynamics 2023 DOI: 10.1080/07391102.2023.2223726
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• Integrating artificial intelligence techniques for analysis of next-generation sequencing data
  Artificial Intelligence and Computational Dynamics for Biomedical Research 2022 DOI: 10.1515/9783110762044-005
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