Dohoon Lee's Projects
Implementation of Abyssal, a deep neural network trained with a new "mega" dataset to predict the impact of an amino acid variant on protein stability.
💻 Analysis codes and bioinformatic pipelines for paper "Targeted erasure of DNA methylation by TET3 drives adipogenic reprogramming and differentiation" (Park et al., Nature Metabolism. 2022)
An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.
:memo: Useful bioinformatics one-line commands.
Implementation of BPNet, a base-resolution convolutional neural network for transcription-factor binding prediction, in PyTorch.
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
:white_check_mark: Solve one rosalind problem per day.
An unofficial re-implementation of DeepAb, an interpretable deep learning model for antibody structure prediction.
A minimal python class implementation for early stopping during deep learning model training.
An unofficial re-implementation of DiffAb, a diffusion-based generative model for antigen-specific antibody design and optimization.
Python implementation for nonparametric bayesian clustering with dirichlet process.
💻 Analysis codes and bioinformatics pipelines for paper "Increased local DNA methylation disorder in AMLs with DNMT3A-destabilizing variants and its clinical implication"
A beautiful, simple, clean, and responsive Jekyll theme for academics
Implementation of evolutionary model of variant effect (EVE), a deep generative model of evolutionary data, in PyTorch.
An unofficial re-implementation of FoldingDiff, a diffusion-based generative model for protein backbone structure generation.
Download genomes the easy way.
Implementation of GeoDiff, a geometric diffusion model for molecular conformation generation, in PyTorch.
💻 Analysis codes and bioinformatic pipelines for paper "HIV-1-induced host genomic R-loops dictate HIV-1 integration site selection"
Small minfi wrapper to convert IDAT files to beta values.
Unofficial re-implementation of IgFold, a fast antibody structure prediction method, in PyTorch.
Machine learning in julia.
:pencil2: SED tutorial
Fitting 5-parameter 1D Ising models for regionwise information-theoretic properties of DNA methylation states. Implemented in Rust.
Python tool for visualizing methylation status as lollipop diagram.
:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
Tutorials for DNA methylome analysis tools