brca1

Python-based bioinformatics toolkit for DNA sequence analysis using the BRCA1 reference sequence.

Zero-shot SNV effect prediction with DNA language models (HyenaDNA, Nucleotide Transformer) benchmarked on BRCA1 saturation genome editing and ClinVar

Bioinformatics project analyzing the BRCA1 gene using NCBI, FASTA, and BLAST sequence alignment tools

Lab profile

A computational framework utilizing Boolean implication networks to decipher asymmetric regulatory logic in 17q-amplified breast cancer, integrating transcriptomic and epigenomic data under BRCA1 stratification.

R code to compute weighted literature-keyword co-occurrence scores and construct gene-set networks (Fig. 1c), from Mateo, He, Mei, et al. "Modification of BRCA1-associated breast cancer risk by HMMR overexpression." Nature Communications, 2022.

This repository contains an end-to-end tumour-only somatic variant-calling pipeline (GATK Mutect2 + snpEff) for triple-negative breast cancer whole-exome data, focused on BRCA1/BRCA2/TP53, built on Google Colab via Visual Studio Code.

Visualization and structural interpretation of the human BRCA1 protein using PyMOL, including secondary structure analysis, surface topology visualization, and three-dimensional structural exploration.

Domain-driven C++20 agent-based simulator of BRCA1-mutant tumor initiation, calibrated against clinical penetrance data via ABC-SMC Bayesian inference.

Integrating MAGMA gene-level genetic association scores with single-cell transcriptional perturbation profiles to identify cell-type- and state-specific genetic–transcriptomic convergence.

Reproducible pipeline for cross-GWAS identification of recurrent moderate-effect BRCA1/2 breast cancer modifier loci

Gillespie stochastic-simulation model of BRCA1-mutant tumor clone dynamics, tracking wild-type, mutant, immune, and exhausted-immune populations under logistic crowding and immune interaction.