mjenior
PhD. in Microbiology & Immunology | Multi-omics integration and machine learning analysis
Papin Lab, University of VirginiaSan Bruno
Pinned Repositories
Jenior_RIPTiDe_2020
Repository associated with RIPTiDe publication
analysis-scripts
Frequently used bioinformatic scripts I generate
ASF_genome_binning
ASF_genomic_binning
Baxter_FITs_Microbiome_2016
llmatic
Python package for improved LLM interactions using the OpenAI API.
riptide
Reaction Inclusion by Parsimony and Transcript Distribution
Smith_etal_Enterococcus
C. difficile metabolic modeling in co-culture with E. faecalis
Jenior_Metatranscriptomics_mSphere_2018
Repository associated with Jenior ML, et al. (2018). mSphere.
Jenior_Modeling_mSystems_2017
Repo associated with Jenior et. al. (2017). Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes. mSystems.
mjenior's Repositories
mjenior/riptide
Reaction Inclusion by Parsimony and Transcript Distribution
mjenior/llmatic
Python package for improved LLM interactions using the OpenAI API.
mjenior/analysis-scripts
Frequently used bioinformatic scripts I generate
mjenior/ASF_genome_binning
mjenior/ASF_genomic_binning
mjenior/Baxter_FITs_Microbiome_2016
mjenior/bigSMALL
BacterIal Genome-Scale Metabolic models for AppLied reverse ecoLogy
mjenior/Klebsiella_2021
mjenior/Smith_etal_Enterococcus
C. difficile metabolic modeling in co-culture with E. faecalis
mjenior/Binning
Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmons, B.C. Thomas, A.P. Yelton, and J.F. Banfield (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biology, 10: R85
mjenior/Blog_scripts
A repo to house the scripts I create and write about in my thesis project blog (http://mjenior.github.io/)
mjenior/cobrapy
COBRApy is a package for constraint-based modeling of biological networks
mjenior/Demo_repo
Demonstrating how GitHub and GitKraken work!
mjenior/evo
DNA foundation modeling from molecular to genome scale
mjenior/fluxNet
mjenior/hacker-scripts
Based on a true story
mjenior/HSSS
Implementation of a Hierarchical Mamba as described in the paper: "Hierarchical State Space Models for Continuous Sequence-to-Sequence Modeling"
mjenior/mamba
Mamba SSM architecture
mjenior/megahit
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
mjenior/mjenior.github.io
Personal Website Repo
mjenior/modeling_tools
mjenior/nanoGPT
The simplest, fastest repository for training/finetuning medium-sized GPTs.
mjenior/pschloss
Pat Schloss's repository
mjenior/reconstructor
Automated GENRE building from gene fastas
mjenior/schlosslab.github.io
The website for the Schloss Lab at the University of Michigan
mjenior/scripts
General scripts used in the lab. Almost all of them are in core perl, i.e require no modules that don't already come with a perl installation. These script are currently in use by the Lab, so expect full support. This material is based upon work supported by the National Science Foundation under Grant Number EAR-1035955. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
mjenior/stripedhyena
Repository for StripedHyena, a state-of-the-art beyond Transformer architecture
mjenior/StripedHyenaTrainer
mjenior/styles
Official repository for Citation Style Language (CSL) citation styles.
mjenior/water-use
Visualization using USGS water use data.