Pipeline for exploring protein families using homology based or vector representation based methods to generate clusters in sequence space.

An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.

Deep learning framework for proteomics

Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations

Nature Computational Science: Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model

A Python package designed for analyzing the internal degrees of freedom within molecular structures, focusing particularly on membrane proteins. It conducts statistical analyses, providing deep ins…

Genome modeling and design across all domains of life

Flexible analysis of high-content CRISPR screening

A tool to optimize real world problems

ChatGPT plugin wrapper to simulate Construction Files using pydna

Literate, reproducible computing

Protein language model trained on coding DNA

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

DeepT2 utilizes deep learning techniques to identify type II polyketide (T2PK) synthases KSβ and their corresponding T2PK product within bacterial genomes. The method leverages ESM2 to transform KS…

Flexible and accessible design of experiments in Python. Provides industry with an easy package to create designs based with limited expert knowledge. Provides researchers with the ability to easil…

Source code for "Computational design of CRISPR guide RNAs to enable strain-specific control of microbial consortia"

BioNeMo Framework: For building and adapting AI models in drug discovery at scale

Super-fast and accurate demultiplexing of direct RNA-seq runs.

Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction (CASP16)

AutoML system for building trustworthy peptide bioactivity predictors

Code for the paper "Learning to engineer protein flexibility".

PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.

Extension of ThermoMPNN for double mutant predictions

Plugin for folding sequences directly in PyMOL

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

ActinoMation: Automated Medium-Throughput Conjugation for Streptomyces spp. My PhD project revolving laboratory automation of actinomycetes (mostly streptomyces) via literate programming.

Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval