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  • 🦠 Hi, I’m a professor in the Division of Infectious Diseases at the Johns Hopkins University School of Medicine
  • 🧬 I’m interested in leveraging bioinformatics and machine learning to improve public health outcomes
  • 🔬 My research group is looking for students and postdocs interested in network science, phylogenetics, or graph neural networks

Steven Clipman's Projects

anelloflow icon anelloflow

Bioinformatics pipeline for detecting anelloviruses present in samples using our metagenomic RCA ONT protocol

augur icon augur

Pipeline components for real-time virus analysis

barabasialbert icon barabasialbert

Simulation of a scale-free network using the Barabási-Albert model.

epi-clust icon epi-clust

User-friendly distance-free method for defining clusters from phylogenetic trees

gephi-plugins icon gephi-plugins

Switch to the sigmaexporter-plugin branch (https://github.com/oxfordinternetinstitute/gephi-plugins/tree/sigmaexporter-plugin/modules/sigmaExporter) or jsonexporter-plugin branch (https://github.com/oxfordinternetinstitute/gephi-plugins/tree/jsonexporter-plugin/modules/JsonExporter) for the relevant code.

hyphy icon hyphy

HyPhy: Hypothesis testing using Phylogenies

markdown icon markdown

Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.

ngstools icon ngstools

Next-Generation Sequencing(NGS) toolkits.

pandemicpulse icon pandemicpulse

Rapid, real-time monitoring of the SARS-CoV-2 pandemic and its impacts

pgeocode icon pgeocode

Postal code geocoding and distance calculation

phydelity icon phydelity

Inference of putative transmission phylogenetic clusters

phylogeography icon phylogeography

This repository hosts code for an animated phylogeographic plot of HCV spread among PWID in India

shiver icon shiver

Sequences from HIV Easily Reconstructed

sociospatial-baseline icon sociospatial-baseline

This repository hosts data and code for an interactive sociospatial network visualization of baseline HIV/HCV prevalence among a cohort of people who inject drugs in New Delhi, India. Visit the link below to view the interactive figure.

sociospatialnet-incidence icon sociospatialnet-incidence

This repository hosts code for an interactive sociospatial network visualization of HIV incidence among a cohort of PWID in New Delhi, India

vg icon vg

tools for working with genome variation graphs

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