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@MolEvolEpid LANL Molecular Evolution & Epidemiology Team

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    18 repositories

    • sweden-incidence

      Public
      Code from "Sweden surpasses the UNAIDS 95-95-95 Target: Estimating HIV-1 incidence between 2003-2022"
      R
      •
      Other
      •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • ContactTracingForPhylogenies

      Public
      Code from Kupperman et al_ "Predicting Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data" (2023).
      Jupyter Notebook
      •
      Other
      •0•2•0•0•Updated Feb 19, 2025Feb 19, 2025

    • SIV_divergence_dynamics

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 18, 2025Feb 18, 2025

    • hypermut3

      Public
      Find hypermutations or other patterns in nucleotide sequences
      Python
      •
      Other
      •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

    • biophybreak

      Public
      Code from Lundgren et al "Combining biomarker and virus phylogenetic models improves epidemiological source identification" in PLOS Computational Biology 2022 Aug 26;18(8):e1009741
      R
      •
      Other
      •10•1•1•0•Updated Feb 10, 2025Feb 10, 2025

    • SEEPS

      Public
      SEEPS: Sequence Evolution and Epidemiological Process Simulator
      evolutionsimulation-frameworkepidemiologyr-packagehivbiological-sequences
      R
      •
      Other
      •0•3•0•0•Updated Jan 22, 2025Jan 22, 2025

    • MolEvolEpid.r-universe.dev

      Public
      Build and deployment toolchain for r-universe
      0•0•0•0•Updated Sep 25, 2024Sep 25, 2024

    • novel_hcv_subtypes

      Public
      Code and data from Mbisa et al. "Identification of two novel subtypes of hepatitis C virus genotype 8 and a potential new genotype in the UK successfully treated with direct acting antivirals."
      HTML
      •0•0•0•0•Updated May 20, 2024May 20, 2024

    • SimReassort

      Public
      Code from Lin et al., "The number and pattern of viral genomic reassortments are not necessarily identifiable from segment trees", 2024; msae078.
      R
      •
      Other
      •0•3•0•0•Updated May 16, 2024May 16, 2024

    • HIV_pipeline

      Public
      End-to-End computational pipeline for nationwide HIV outbreak monitoring.
      HTML
      •1•0•0•0•Updated May 10, 2024May 10, 2024

    • infectionAgeHIV

      Public
      A lightweight version of the Multiple Biomarker Model for predicting HIV-1 infection times found in the R package biophybreak
      R
      •
      Other
      •0•0•0•0•Updated Dec 12, 2023Dec 12, 2023

    • coinfection_cotransmission_cofeeding_in_ticks

      Public
      Code from Belluccini et al. "A story of viral co-infection, co-transmission and co-feeding in ticks: how to compute an invasion reproduction number"
      Mathematica
      •
      MIT License
      •0•0•0•0•Updated Nov 13, 2023Nov 13, 2023

    • timeslice

      Public
      Time-slice Markov model for phylogenetic inference of transmission time
      Python
      •
      Other
      •1•0•0•0•Updated Jun 27, 2023Jun 27, 2023

    • MachineLearningModelforHIVOutbreaks

      Public
      Code from Kupperman et al "A deep learning approach to real-time HIV outbreak detection using genetic data" in PLOS Comp Biol 2022 18(10):e1010598
      PureBasic
      •
      Other
      •2•3•0•0•Updated Nov 28, 2022Nov 28, 2022

    • General_Info

      Public
      Information about this collection of work.
      0•0•0•0•Updated Aug 9, 2022Aug 9, 2022

    • git_practice

      Public
      Practice collaborating with git
      0•0•0•0•Updated Jun 28, 2022Jun 28, 2022

    • ARG_simul-decomp

      Public
      Code from Castro et al "Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies"
      R
      •
      Other
      •0•0•0•0•Updated Feb 15, 2022Feb 15, 2022

    • prev_project_1

      Public
      This could be the code for an already-published paper, now public.
      grant1grant2
      Other
      •0•0•0•0•Updated Oct 5, 2021Oct 5, 2021