Modelling & Simulation
PhosKinTime
Python package for analyzing proteomics data, including time-course modelling and visualization.
PhosCrosstalk
Systems-level phospho-network ODE modelling framework integrating PTM crosstalk, kinase?substrate networks, and phosphosite time-series with multi?objective evolutionary optimisation.
Pharmacokinetic Modeling
Built an SBML-based ODE model of Tirzepatide to study how the drug is absorbed, distributed, and processed in the body.
GitHub
| 
Hsp90 smFRET Analysis Pipeline
Single-molecule FRET kinetic modelling with multistart optimisation, bootstrapping, and sensitivity analysis.
CasTuner (Python Port)
Reproducible modelling of CRISPR/Cas-based repression?derepression gene-tuning dynamics.
PhosphoVelocity
Bayesian phosphosite velocity modelling pipeline for LC?MS/MS time-course phosphoproteomics, reconstructing latent trajectories and phosphorylation ?velocity? to infer kinase activity dynamics.
acthermal_tumor
High-performance JAX-based simulator for the non?isothermal Allen?Cahn tumour growth model, coupling tumour cells, temperature, and nutrient dynamics with spectral or finite?difference solvers.
Pipelines & Workflows
SARS-CoV-2 lineage reconstruction
Nextflow-powered pipeline for SARS-CoV-2 genome reconstruction.
Genome Read Mapping and Annotation
Snakemake pipeline for matching sequencing reads to a reference genome and annotating genomic features.
Codon Analyzer
Snakemake workflow for codon usage analysis, GC content calculation, and protein hydropathy profiling.
CETSAx?NADPH
Snakemake-powered analysis pipeline for CETSA dose?response data, combining curve fitting, system-level analysis, and sequence-based models to study protein stability responses to NADPH.
Algorithms & Infrastructure
Sequence Aligner
Accelerated sequence alignment using SIMD and MPI for scalable, distributed analysis.
pynetphorest
Modern Python re-implementation of NetPhorest for kinase?substrate scoring and phosphorylation crosstalk analysis.
bio-sea-pearl
Hybrid Python + Perl bioinformatics toolkit for sequence alignment, Markov modeling, sequence analysis, and FM?index?based search, unified under a single Python CLI and API.
ode2sbml
Python package for converting Python-defined ODE systems into SBML Level 3 Version 2 models and PEtab bundles for parameter estimation.
SequenceMSAligner
C++17 multiple sequence alignment tool for DNA and proteins using AVX2?vectorized Needleman?Wunsch with affine gaps, OpenMP parallel refinement, and UPGMA guide trees.
Applied Bioinformatics & ML
Liver Prediction
ML-based classification of liver cancer tissues with transcriptomic & epigenomic analysis.
Prostate Cancer Biomarker Discovery
Identifying potent biomarkers for prostate cancer through pathway mining and gene-expression meta-analysis.
GitHub |
