Debora Marks Lab

All

27 repositories

ML_affinity_maturation
Public
Repository containing the code performing ML assisted affinity maturation
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Apr 7, 2025Apr 7, 2025
EVcouplings
Public
Evolutionary couplings from protein and RNA sequence alignments
protein structure-prediction 3d-structure protein-complexes
Jupyter Notebook
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Other
•78•262•55•6•Updated Mar 2, 2025Mar 2, 2025
sequenceMDS
Public
Jupyter Notebook
•0•0•0•0•Updated Oct 22, 2024Oct 22, 2024
popEVE
Public
Python
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GNU General Public License v3.0
•3•11•0•0•Updated Jul 2, 2024Jul 2, 2024
EVEscape
Public
Official repository for the paper "Learning from pre-pandemic data to forecast viral antibody escape"
Python
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MIT License
•9•1•0•1•Updated Mar 5, 2024Mar 5, 2024
Vax_design
Public
Jupyter Notebook
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MIT License
•0•4•0•0•Updated Mar 5, 2024Mar 5, 2024
SeqDesign
Public
Protein design and variant prediction using autoregressive generative models
Python
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MIT License
•21•99•2•0•Updated Jan 23, 2024Jan 23, 2024
nanobody-polyreactivity
Public
Polyreactivity Website
Python
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MIT License
•4•12•1•0•Updated Jun 26, 2023Jun 26, 2023
BEAR
Public
This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"
tensorflow probabilistic-programming biological-data-analysis genomes
Python
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MIT License
•3•13•1•0•Updated Jun 7, 2023Jun 7, 2023
ZIP_benchmark
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Jun 1, 2023Jun 1, 2023
plmc
Public
Inference of couplings in proteins and RNAs from sequence variation
protein-structure protein-interaction protein-sequences undirected-graphs sequence-alignments
C
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MIT License
•36•108•7•2•Updated Jan 21, 2023Jan 21, 2023
detectDesign
Public
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
Jupyter Notebook
•2•7•0•1•Updated Jun 22, 2022Jun 22, 2022
DeepSequence
Public
A generative latent variable model for biological sequence families.
Python
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MIT License
•46•214•5•5•Updated Mar 15, 2022Mar 15, 2022
variational-synthesis
Public
Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
generative-model protein-sequences dna-sequences experimental-design
Python
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MIT License
•8•34•1•0•Updated Feb 17, 2022Feb 17, 2022
GerA-suppData-2021
Public
HTML
•1•0•0•0•Updated Oct 27, 2021Oct 27, 2021
MuE
Public
A package for making MuE observation models in Edward2.
machine-learning proteins tensorflow probabilistic-programming biological-sequences
Python
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MIT License
•2•13•0•0•Updated Jun 10, 2021Jun 10, 2021
EVE
Public
Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning"
Python
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MIT License
•55•8•0•0•Updated Apr 29, 2021Apr 29, 2021
edward2
Public
A fork of Edward2, for use with the MuE package.
Jupyter Notebook
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Apache License 2.0
•0•0•0•0•Updated Oct 3, 2020Oct 3, 2020
EVdeimmunization
Public
Dual optimization of de-immunization and protein function
Python
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MIT License
•0•0•0•0•Updated Apr 27, 2020Apr 27, 2020
EVzoom
Public
Visually explore covariation in protein families
evolution protein-interaction protein-sequences undirected-graphs d3js amino-acids
JavaScript
•6•37•0•0•Updated Dec 8, 2019Dec 8, 2019
NEMO
Public
Learning protein structure with a differentiable simulator
Python
•7•27•2•0•Updated Jul 8, 2019Jul 8, 2019
3D_from_DMS_Extended_Data
Public
Jupyter Notebook
•5•10•0•0•Updated Apr 28, 2019Apr 28, 2019
variants_pharmacogenes
Public
This repository contains the code used to analyse data and produce figures for the manuscript "Genetic variation in human drug-related genes"
Jupyter Notebook
•4•10•0•0•Updated Dec 19, 2017Dec 19, 2017
EVmutation
Public
Mutation effects predicted from sequence co-variation
HTML
•13•64•0•0•Updated Sep 3, 2017Sep 3, 2017
GELMMnet
Public
Generalized linear mixed model elastic net
gwas p-value elastic-net lasso
Jupyter Notebook
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Other
•1•7•1•0•Updated Aug 9, 2017Aug 9, 2017
persistent-vi
Public
Variational Bayes for discrete undirected models
C
•6•10•0•0•Updated Aug 7, 2017Aug 7, 2017
neural-fingerprint-theano
Public
Visual Convolutional Neural Graph Fingerprints in Theano/Lasagne
HTML
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MIT License
•19•34•0•0•Updated Sep 23, 2016Sep 23, 2016