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    12 repositories

    • Trias

      Public
      Trias: an encoder-decoder model for generating synthetic eukaryotic mRNA sequences
      language-modelcodon-optimizationencoder-decoder-modelsmrna-design
      Jupyter Notebook
      •
      MIT License
      •3•13•1•0•Updated Jan 20, 2026Jan 20, 2026

    • synonymous-citrines

      Public
      data, analysis, and plotting for citrine codons project
      R
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • codon_constraints

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Aug 19, 2025Aug 19, 2025

    • psix

      Public
      Python
      •7•17•0•0•Updated Feb 16, 2024Feb 16, 2024

    • analysis_psix

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Aug 12, 2023Aug 12, 2023

    • choros

      Public
      bias correction on ribosome profiling data
      R
      •
      MIT License
      •1•3•0•0•Updated Mar 9, 2023Mar 9, 2023

    • choros_paper

      Public
      Analyses and scripts for choros paper
      R
      •0•0•0•0•Updated Feb 21, 2023Feb 21, 2023

    • cas13a_guide_design

      Public
      HTML
      •2•0•0•0•Updated Nov 7, 2022Nov 7, 2022

    • simRiboSeq

      Public
      R
      •1•0•0•0•Updated Mar 29, 2022Mar 29, 2022

    • bioe_190_290_2021

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 16, 2021Sep 16, 2021

    • sc_binary_splicing

      Public
      Dataset analysis, simulations and figures from single cell splicing paper
      Jupyter Notebook
      •
      MIT License
      •2•4•0•0•Updated Sep 3, 2020Sep 3, 2020

    • iXnos

      Public
      Neural network regression model of translation elongation rate, with DP algorithm to optimize fast coding sequences under model
      Python
      •8•9•1•0•Updated May 3, 2018May 3, 2018