Repositories list

• viral-protein-function-plm

  Public
  Viral protein family functional prediction using protein language models

  PureBasic

  •

  GNU General Public License v3.0

  •4•23•3•0•Updated Jan 6, 2026Jan 6, 2026

• microbial-landscapes

  Public
  Code and data for 'Inferring the quasipotential landscape of microbial ecosystems with topological data analysis'

  R

  •2•4•1•0•Updated Apr 28, 2025Apr 28, 2025

• Using-the-gut-microbiome-to-predict-a-future-symptom-in-Inflammatory-Bowel-Disease

  Public
  0•0•0•0•Updated Mar 22, 2025Mar 22, 2025

• sequence_breadth_tools

  Public
  Extracting and analyzing sequence breadth from Anvi'o databases

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• plm-model-comparison

  Public
  Comparing novel Protein Language Models

  Jupyter Notebook

  •1•0•0•0•Updated Sep 15, 2024Sep 15, 2024

• Gardnerella_pangenomic_clades

  Public
  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

• SARS-CoV-2-surveillence

  Public
  Scripts and files related to the surveillance of SARS-CoV-2 for three years in the Bronx

  Jupyter Notebook

  •0•0•0•0•Updated Mar 3, 2024Mar 3, 2024

• viral-protein-function-annotation-with-protein-language-model

  Public
  Accompanying jupyter notebooks and data for figure generation for published manuscript

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Nov 26, 2023Nov 26, 2023

• Fireworks

  Public
  PyTorch with DataFrames

  Python

  •

  MIT License

  •3•14•0•0•Updated May 1, 2023May 1, 2023

• oral-microbes-are-a-signature-of-disease-in-the-gut

  Public
  Source code accompanying the paper "Oral Microbes are a Signature of Disease in the Gut"

  MIT License

  •0•0•0•0•Updated May 12, 2022May 12, 2022

• CuratedMetagenomicData-Python

  Public
  Python Interface for Accessing CuratedMetagenomicData

  MIT License

  •0•0•0•0•Updated Mar 10, 2022Mar 10, 2022

• longitudinal-prediction-of-covid-outcomes

  Public
  This is the code accompanying the paper "Longitudinally Monitored Biomarkers Predict the Timing of COVID-19 Outcomes"

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Aug 2, 2021Aug 2, 2021

• genomic-surveillance-of-the-bronx

  Public
  Source code repository for the paper "Genomic Surveillance of SARS-CoV-2 in the Bronx Enables Clinical and Epidemiological Inference"

  Python

  •1•0•0•0•Updated Jun 24, 2021Jun 24, 2021

• artic-docker

  Public
  Docker Image for Artic Coronavirus Sequencing Pipeline

  Dockerfile

  •

  MIT License

  •1•0•0•0•Updated Apr 18, 2020Apr 18, 2020

• Metagenomic-Disease-Classification-With-Deep-Learning

  Public
  This repository accompanies the paper "Multiclass Disease Classification from Microbial Whole-CommunityMetagenomes using Graph Convolutional Neural Networks."

  Python

  •

  MIT License

  •6•9•1•0•Updated Aug 6, 2019Aug 6, 2019

• microbeFDT-neo4j

  Public
  microbeFDT-neo4j

  MIT License

  •3•4•0•0•Updated Apr 9, 2019Apr 9, 2019

• nahant-genome-rearrangement

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jun 28, 2018Jun 28, 2018

• PhageGenomeAnnotation

  Public
  Phage genome annotation pipeline for Nahant Phages

  Jupyter Notebook

  •0•1•0•0•Updated Dec 10, 2017Dec 10, 2017

• infograf

  Public
  R functions

  rentropyinformation-theory+ 6

  rentropyinformation-theorygraph-theorydata-tablemdsigraphpcoaggraph

  R

  •

  MIT License

  •0•0•0•0•Updated Sep 12, 2017Sep 12, 2017

• DiversityWorkshop

  Public
  R

  •0•0•0•0•Updated Sep 2, 2017Sep 2, 2017

• Microbiome_CRCdrug_Turnover

  Public
  We report quantitative evidence of inter-individual variability in microbiome metabolism of the inactive metabolite of irinotecan to its active form.

  0•0•0•0•Updated Jun 29, 2017Jun 29, 2017