Python simulation for visualizing the net geochemical outcomes of microbial metabolism - referred to here as "dead-end states." Poster presentation at Univ. Oregon Undergrad Symposium 2022.

Build an interactive dashboard to explore the Belly Button Biodiversity dataset, which catalogues the microbes that colonize human navels by using Plotly and D3.js libraries.

A tool for phylogenetic comparison and analysis of microbe including gene's environmental association

Javascript and D3 are used to create an interactive dashboard to explore a microbes on human subjects dataset.

This repository contains python code used to create figures in the accompanying manuscript.

DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further in…

A theorectical investigation into mechanisms of drought legacy formation and influencing factors in soil microbiomes using DEMENTpy.

Classification of stressful microbial growth conditions using gene fitness data and support vector machines

Using Plotly, JavaScript, d3, and Bootstrap, created an interactive dashboard to explore the Belly Button Biodiversity dataset, which catalogs the microbes that colonize human navels. The dataset reveals that a small handful of microbial species (also called operational taxonomic units, or OTUs, in the study) were present in more than 70% of peo…

Significance of non-microbial processes in organic matter decompositon in ecosystems across scales

Nextflow pipeline for pathogen surveillance in wastewater

Classification model predicting the type of microbe from provided features

Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.

Neutral evolution modeling of microbes.

Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data

Omero based integrated Workflow for annotating Microbes in the Cloud

Targeted Probe Design Pipeline. Using mWGS genome bin clusters, prokka annotation predictions, and blast+ databases for generation, processing and filtering probe sequences.

Interactive dashboard to explore the Belly Button Biodiversity dataset using Plotly for Javascript.

A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism