Research portfolio
I translate biological questions into quantitative representations, solve and interrogate those models, and package the resulting methods as reproducible research software.
Biological question → mathematical representation → mechanistic model → inference → biological interpretation → reproducible output
Filter by method or data context
Research theme
Dynamic Signalling & Regulatory Systems
PhosKinTime
Flagship ResearchMechanistic framework for reconstructing phosphorylation dynamics from time-resolved molecular measurements and kinase–substrate networks using ODE models, constrained optimization and sensitivity analysis.
Methods ODE modelling · constrained optimization · sensitivity analysis
PhosCrosstalk
Active ResearchSystems-level phospho-network modelling that integrates post-translational crosstalk, kinase–substrate networks and phosphosite time series with multi-objective evolutionary optimization.
Methods ODE networks · PTM crosstalk · multi-objective optimization
PhosphoVelocity
Research PrototypeBayesian phosphosite-velocity pipeline for reconstructing latent trajectories and kinase-activity dynamics from time-course LC–MS/MS phosphoproteomics.
Methods Bayesian inference · latent trajectories · phosphoproteomics
Research theme
Mechanistic Cancer & Drug-Response Modelling
Tirzepatide PBPK model
Research ModelSBML-based ordinary differential equation model of tirzepatide absorption, distribution and elimination, developed as a reproducible pharmacokinetic modelling study.
Methods PBPK · ODEs · SBML · parameter estimation
Hsp90 smFRET analysis pipeline
Research SoftwareSingle-molecule FRET kinetic modelling workflow using multistart optimization, bootstrap analysis and sensitivity analysis.
Methods kinetic modelling · multistart optimization · bootstrapping
Allen–Cahn tumour growth model
Research SoftwareJAX-based simulation of a non-isothermal Allen–Cahn tumour-growth model coupling cell, temperature and nutrient dynamics with spectral or finite-difference solvers.
Methods PDEs · JAX · spectral methods · finite differences
Cancer robustness–load trade-off model
Research PrototypePython framework adapting the robustness–load trade-off model described by Choi et al. to questions in cancer systems biology.
Methods quantitative modelling · parameter exploration
CNA-ResistDynamics
Research PrototypeDynamical modelling of chemotherapy-resistance trajectories from longitudinal liquidCNA measurements.
Methods dynamical systems · liquid biopsy · treatment response
Research theme
Proteomics & Multi-Omics Inference
CETSAxNADPH
Research SoftwareCETSA-MS modelling toolkit for dose–response analysis, binder classification, Bayesian inference, curve typing and proteome-wide stability networks.
Methods CETSA-MS · Bayesian inference · dose–response modelling
Research theme
Scientific Computing & Research Infrastructure
nf-illumina2lineage
Research SoftwareNextflow workflow for reproducible SARS-CoV-2 genome reconstruction and lineage analysis from Illumina reads.
Methods Nextflow · containers · genome reconstruction
nf-grmap
Research SoftwareNextflow workflow for mapping sequencing reads to a reference genome and annotating matches with gene, TSS, CpG and repeat metadata.
Methods Nextflow · read mapping · genomic annotation
nf-codonanalyzer
Research SoftwareNextflow DSL2 workflow for multi-FASTA sequence analysis with per-record fan-out to modular processing steps.
Methods Nextflow DSL2 · sequence analysis · Perl
ode2sbml
ReleasedPython package that converts Python-defined ODE systems into SBML Level 3 models and PEtab bundles for parameter estimation.
Methods SBML · PEtab · model interoperability
SequenceAligner
Research SoftwareParallel implementation of global and local alignment and longest-common-subsequence algorithms for nucleotide and protein sequences.
Methods C++ · MPI · OpenMP · SIMD
SequenceMSAligner
Research PrototypeMultiple-sequence alignment implementation combining AVX2 acceleration with affine-gap scoring.
Methods C++ · AVX2 · sequence alignment
PyNetPhorest
ReleasedPython reimplementation of NetPhorest for kinase–substrate scoring and phosphorylation-crosstalk analysis.
Methods kinase prediction · network biology · Python
PyNetworKIN
ReleasedPython 3 port of NetworKIN 3.0, with support for contemporary STRING protein-interaction data.
Methods kinase prediction · protein networks · Python
bio-sea-pearl
Research SoftwareHybrid Python and Perl toolkit for sequence alignment, Markov modelling, sequence analysis and FM-index search through a unified CLI and API.
Methods sequence algorithms · FM-index · Python · Perl
Fast DP Plotter
Research SoftwareRust-accelerated dot-plot renderer for bioinformatics data, provided as a Python library, command-line tool and desktop interface.
Methods Rust · Python · scientific visualization
Research theme
Earlier Work
Liver Prediction
Archived / Earlier WorkCoursework project exploring liver-cancer tissue classification with transcriptomic and epigenomic data.
Methods machine learning · transcriptomics · epigenomics
Prostate Cancer Biomarker Discovery
Thesis / Earlier WorkBachelor’s thesis on candidate biomarker identification through pathway mining and gene-expression meta-analysis across AR, MAPK and mTOR signalling.
Methods gene-expression meta-analysis · pathway analysis
Perl bioinformatics snippets
Educational / Earlier WorkEarly scripts for sequence analysis, string manipulation, alignment, motif search and algorithmic practice.
Methods Perl · bioinformatics algorithms