Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Deep probabilistic analysis of single-cell and spatial omics data

Spatiotemporal modeling of spatial transcriptomics

Applying polygenic scores (PGS) on imputed genotypes

Reference mapping for single-cell genomics

Biological sequence analysis for the modern age.

snakemake pipeline for creating trees from sequence sets

A generative model for programmable protein design

SARS-CoV-2 RBD antibody escape calculator

tools for working with genome variation graphs

Accelerated BLAST compatible local sequence aligner.

Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests.

Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

A software to resolve the phylogeny of haploid SNPs

A project designed with algorithms to compute PD Stats

Scalable machine 🤖 learning for time series forecasting.

A high-performance, zero-overhead, extensible Python compiler using LLVM

Opinion model that simulates how individuals, influencers and media interact on social media platforms. The model is formulated as an agent-based model and by a PDE-approximation. Different strateg…

FRACTAL: framework for distributed computing to trace large accurate lineages

Single-cell analysis in Python. Scales to >1M cells.

Collections of library structure and sequence of popular single cell genomic methods

Online material for the Perspective: "Julia for Biologists" presented at JuliaCon 2021: https://www.youtube.com/watch?v=gRj7E5kYG1I

Nextstrain build for novel coronavirus SARS-CoV-2

Final Project for FUB 22Win Phylogeny Inference and Application

Read-only mirror (squashed) of the polymake project for convex geometry. For more information please visit

Listing of papers about machine learning for proteins.