Debora Marks Lab

EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

DeepSequence

A generative latent variable model for biological sequence families.

plmc

Inference of couplings in proteins and RNAs from sequence variation

SeqDesign

Protein design and variant prediction using autoregressive generative models

EVmutation

Mutation effects predicted from sequence co-variation

EVzoom

Visually explore covariation in protein families

neural-fingerprint-theano

Visual Convolutional Neural Graph Fingerprints in Theano/Lasagne

NEMO

Learning protein structure with a differentiable simulator

variational-synthesis

Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).

MuE

A package for making MuE observation models in Edward2.

BEAR

This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"

3D_from_DMS_Extended_Data

nanobody-polyreactivity

Polyreactivity Website

variants_pharmacogenes

This repository contains the code used to analyse data and produce figures for the manuscript "Genetic variation in human drug-related genes"

EVE

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning"

persistent-vi

Variational Bayes for discrete undirected models

popEVE

detectDesign

toolkit for finding likely cas9 off-target binding and effect on gene expression, designing sgRNAs and pairs of sgRNAs with minimal off-target effect on gene-expression

GELMMnet

Generalized linear mixed model elastic net

Vax_design

EVEscape

Official repository for the paper "Learning from pre-pandemic data to forecast viral antibody escape"

EVdeimmunization

Dual optimization of de-immunization and protein function

edward2

A fork of Edward2, for use with the MuE package.

GerA-suppData-2021

ZIP_benchmark