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    42 repositories

    • V2R_surfexp_rescue

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • domainome

      Public
      MIT License
      •0•5•1•0•Updated Dec 10, 2024Dec 10, 2024

    • DiMSum

      Public
      An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies
      R
      •
      MIT License
      •6•28•3•0•Updated Dec 2, 2024Dec 2, 2024

    • MoCHI

      Public
      Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational scanning data
      Python
      •
      MIT License
      •4•43•0•0•Updated Dec 2, 2024Dec 2, 2024

    • mochims

      Public
      Source code for analyses and to reproduce all figures in the following publication: MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis and allostery from deep mutational scanning data (Faure AJ & Lehner B, 2024)
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • amyloids_energy_modelling

      Public
      Energetic modelling of Amyloid beta nucleation
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • combinatorialcores

      Public
      Source code for analyses and figure reproduction in "Genetics, energetics and allostery during a billion years of hydrophobic protein core evolution", Escobedo et. al 2024
      Jupyter Notebook
      •0•1•0•0•Updated Aug 1, 2024Aug 1, 2024

    • archstabms

      Public
      Source code for analyses and to reproduce all figures in the following publication: The genetic architecture of protein stability (Faure AJ et al., 2024)
      R
      •
      MIT License
      •0•3•1•0•Updated Jul 28, 2024Jul 28, 2024

    • Stop_codon_readthrough

      Public
      Source code for computational analyses and to reproduce all figures in the following publication: Genome-scale quantification and prediction of drug-induced readthrough of pathogenic premature termination codons (Toledano I, Supek F & Lehner B, 2023)
      MIT License
      •0•2•0•0•Updated Jul 13, 2024Jul 13, 2024

    • canya

      Public
      A hybrid neural network to predict nucleation propensity
      Python
      •
      MIT License
      •0•1•1•0•Updated Jun 27, 2024Jun 27, 2024

    • src_allostery

      Public
      Source code for analyses and to reproduce all figures in the following publication: The allosteric landscape of Src (Beltran et al., 2023)
      MIT License
      •0•1•0•0•Updated May 9, 2024May 9, 2024

    • fuzzy_specificity

      Public
      Code for "A complete map of specificity encoding for a partially fuzzy protein interaction" by Taraneh Zarin and Ben Lehner
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

    • TECAN_analysis

      Public
      TECAN-reader based yeast growth measurements in R
      R
      •0•1•0•0•Updated Apr 23, 2024Apr 23, 2024

    • deep_indel_mutagenesis

      Public
      R
      •
      MIT License
      •0•0•1•0•Updated Mar 19, 2024Mar 19, 2024

    • fas-indel-library

      Public
      R
      •0•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • whmatrixextms

      Public
      Source code for analyses and to reproduce all figures in the following publication: An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity (Faure AJ, et al., 2023)
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 8, 2024Mar 8, 2024

    • krasddpcams

      Public
      Source code for computational analyses and to reproduce all figures in the following publication: The energetic and allosteric landscape for KRAS inhibition (Weng C, Faure AJ & Lehner B, 2022)
      R
      •
      MIT License
      •0•4•0•0•Updated Nov 17, 2023Nov 17, 2023

    • doubledeepms

      Public
      Source code for fitting thermodynamic models (MoCHI), downstream analyses and to reproduce all figures in the following publication: Mapping the energetic and allosteric landscapes of protein binding domains (Faure AJ, Domingo J & Schmiedel JM et al., 2022)
      R
      •
      MIT License
      •1•19•0•0•Updated Jul 20, 2023Jul 20, 2023

    • pdzextms

      Public
      Source code for analyses and to reproduce all figures in the following publication: The effects of PDZ domain extensions on energies, energetic couplings and allostery (Hidalgo-Carcedo C & Faure AJ et al., 2023)
      R
      •
      MIT License
      •0•0•0•0•Updated May 2, 2023May 2, 2023

    • SUNi_mutagenesis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 27, 2023Feb 27, 2023

    • RDGVassociation

      Public
      Script to (1) perform component extraction via ICA & VAE, (2) perform network analysis, and (3) replicate paper figures from manuscript. Pre-print on bioRxiv: https://www.biorxiv.org/content/10.1101/2021.11.14.468508v1.
      R
      •
      MIT License
      •0•3•0•0•Updated May 15, 2022May 15, 2022

    • soma-germline-timing

      Public
      Scripts to analyze C. elegans soma and germline timings, to measure length of L1 larvae and to quantify embryo fluorescence as described in the paper 'Neuronal perception of the social environment generates an inherited memory that controls the development and generation time of C. elegans'
      R
      •0•0•0•0•Updated Aug 3, 2021Aug 3, 2021

    • Higher-order_epistasis_tRNA

      Public
      Scripts needed to reproduce Domingo et al. 2018
      R
      •
      MIT License
      •1•3•0•0•Updated Oct 19, 2020Oct 19, 2020

    • Biophysical_Ambiguity

      Public
      Codes to reproduce the analysis and figures for the project "Biochemical ambiguities prevent accurate genetic prediction"
      R
      •
      MIT License
      •1•1•0•0•Updated Jul 13, 2020Jul 13, 2020

    • Constitutive_Exons

      Public
      Scripts needed to reproduce Baeza-Centurion et al. 2020
      R
      •0•2•0•0•Updated Jun 30, 2020Jun 30, 2020

    • dimsumms

      Public
      Analysis scripts to reproduce the figures and results from the computational analyses described in the paper Faure and Schmiedel et al. "DiMSum: An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies", 2020
      R
      •
      MIT License
      •1•1•0•0•Updated Jun 22, 2020Jun 22, 2020

    • abetadms

      Public
      Analysis scripts for processing Abeta deep mutational scanning (DMS) data
      R
      •
      MIT License
      •1•0•0•0•Updated Apr 6, 2020Apr 6, 2020

    • concentration_epistasis_GRN

      Public
      This is codes for 'Changes in gene expression alter mutational effects and genetic interactions in an underlying biochemical parameter-dependent way.'
      R
      •0•0•0•0•Updated Jan 15, 2020Jan 15, 2020

    • tardbpdms

      Public
      Analysis scripts for processing TDP-43 DMS data from Bolognesi & Faure et al. "The mutational landscape of a prion-like domain", 2019
      R
      •
      MIT License
      •1•2•0•0•Updated Jul 17, 2019Jul 17, 2019

    • DMS2structure

      Public
      Scripts for "Determining protein structures using deep mutagenesis", Schmiedel & Lehner, Nature Genetics, 2019
      R
      •
      MIT License
      •2•17•1•0•Updated Jul 5, 2019Jul 5, 2019