SHIVAM KUMAR Water Bottle

PhD Candidate

University of Amsterdam

METAHEALTH / DIGEST, Computational Science Lab, Informatics Institute. Multiscale spatiotemporal modelling of the microbiome during the first 1000 days of life.

52.3676° N
4.9041° E

Hello,
I'm Shivam!

PhD Candidate at the Computational Science Lab, Informatics Institute, University of Amsterdam. Part of the METAHEALTH project, I design multiscale spatiotemporal frameworks to model the microbiome during the first 1000 days of life, analyzing oral and gut microbial communities across micro, meso, and macro scales.

Systems Biology Network Science Python · Julia HPC ODE / PDE
↗   github.com/shivamkgw ↓   Open CV
Shivam Kumar

Research

01
Multivariate Recurrence Analysis
MS Thesis · IISER Tirupati / TVM

Recurrence Network Measures from Multivariate Dynamics

BS-MS from IISER Tirupati; thesis year conducted at IISER TVM under Prof G. Ambika and Prof Ranjeev Mishra (IUCAA). Multivariate data analysis using recurrence plots and recurrence network measures.

arXiv Preprint →
N
iGEM 2021
iGEM 2021 · Gold Medal

Team IISER-Tirupati India

Led the computational modelling sub-team. Built ODE-based gene-circuit models, ran parameter sensitivity analyses, and integrated model predictions with the wet-lab design loop, contributing to a Gold Medal finish.

View iGEM wiki →
G

Tools & Code

02

SEEDBiomed

Scientific Explorers of Emergent Dynamics in Biomedicine, an interdisciplinary research team at UvA & AmsterdamUMC. Brings together computational modellers, clinicians, and experimentalists across cancer, microbiome, mental health, and endothelial cell research. Maintains open-access tools, a Discovery Hub, and a Journal Club for computational biomedicine.

Visit SEEDBiomed.com →

Multiscale Simulation Frameworks

Custom Python/Julia environments for agent-based and ODE/PDE hybrid models. Designed for high-throughput parameter sweeps on HPC clusters.

View on GitHub →

Technical Stack

Languages

Python Julia C/C++ Fortran MATLAB Java

Libraries & Frameworks

NumPy / SciPy NetworkX Cytoscape

Infrastructure & Tools

HPC / SLURM Git LaTeX

Timeline

03  /  scroll to explore
2019 – 2024
BS-MS Physics, IISER Tirupati Complex Systems, Nonlinear Dynamics, Soft Matter. Final year at IISER TVM.
2021
iGEM Gold Medal + 7 nominations Computational lead, Team IISER-Tirupati India. OviCloak: gene-circuit ODE modelling.
2022
State Topper, NGPE Ranked state topper; awarded IASc-NASI-INSA Summer Research Fellowship.
IASc
2022
Summer Research Fellow, IIT Gandhinagar Extensional rheometry with a handheld mobile device. Dept. of Chemical Engineering.
2023 – 2024
MS Thesis, IISER Thiruvananthapuram Recurrence network measures from multivariate dynamics. Under Prof G. Ambika.
2024 – present
PhD Candidate, University of Amsterdam METAHEALTH / DIGEST. Multiscale spatiotemporal modelling of the microbiome.
2025
RPA-PMH Seed Grant, Co-PI €18k DIGEST: Diet, Gut Microbiome and Suicide Ideation. FNWI + FMG, UvA.

Publications

03

Loading from ORCID…


Posters

04
MetaHealth Poster preview
MetaHealth DuCoMS / Computational Science NL

MetaHealth: Linking Microbiome Dysbiosis to Childhood Obesity and Dental Caries

Scientific poster presented at DuCoMS and as part of the MetaHealth project, an NWO-funded research programme investigating the gut microbiome, dental health, and childhood obesity. Amsterdam UMC & University of Amsterdam.

↗  Open Poster (PDF)
MetaHealth Consortium Poster preview
MetaHealth

MetaHealth Consortium: Research Plans

Scientific poster presented at the MetaHealth Consortium meeting (April 2026), outlining research plans within the NWO-funded programme investigating the gut microbiome, dental health, and childhood obesity. Amsterdam UMC & University of Amsterdam.

↗  Open Poster (PDF)

Scrapbook

When I'm away from the terminal: guitar, street photography, and writing about places. The rest lives on a separate page.

Open the scrapbook → ShivAmsterdam → Kerala blog →
Guitar
Street Photography
Travel Writing