Ongoing Projects

GitHub Organization Projects

This page provides a comprehensive index of ongoing research projects in the McPherson Lab. Our projects are organized through our GitHub Organization where we collaborate on research initiatives related to conferences, journal publications, and grant applications.

Quick Overview

We maintain 50+ active research projects across multiple domains including:

  • Antimicrobial Resistance (AMR): Genomic and clinical investigations of drug-resistant pathogens
  • Gut Microbiome: Metagenomic and metabolomic analyses of human gut microbiota
  • Treatment Optimization: Evidence-based approaches to infectious disease management
  • Artificial Intelligence: Machine learning applications in microbiology and medicine
  • Biophysics & Pharmacology: Molecular mechanisms and drug discovery
  • Health Economics: Cost-effectiveness and ROI analyses
  • Environmental Health: Climate change impacts on infectious diseases

All projects use standardized workflows, documentation templates, and CRediT contributor roles for transparent collaboration.

Project Repository Structure

Our research projects are categorized and tracked through GitHub repositories and project boards:

  • Template Project Repository: Starting template for new research projects
  • CRediT (Contributor Roles Taxonomy): Standard for identifying contributions to research outputs
  • Conference Abstracts: Research and abstracts for upcoming conferences
  • Manuscripts in Preparation: Manuscripts in preparation for journal submissions
  • Grant Projects: Grant proposals and collaborative research initiatives
  • Methods Development: Novel computational and analytical methods
  • Data Analysis: Ongoing data analysis and visualization projects

How to Connect Projects

Each conference and call for papers entry in our Research page can be linked to:

  1. GitHub Repository: A specific repository containing project code, data, and documentation
  2. GitHub Project Board: A project board tracking tasks and milestones
  3. GitHub Issues: Specific issues for abstract submissions, paper drafts, or collaborative work
Figure 1: Project Workflow and Integration. This diagram illustrates how research projects flow from initial concepts through GitHub repositories, conference presentations, and journal submissions. Projects are linked to specific calls for papers and conferences, with GitHub issues and project boards tracking progress at each stage.

Current Active Projects

Visit our GitHub Organization:

Project (Link) Question Target Conference Call for Paper Big Name Journal
ai-forecast-pharmacology AI-driven pharmacological predictions IUPHAR Annual
Abstract: TBD		 British Journal of Pharmacology
Deadline: May 01, 2026		 Nature Reviews Drug Discovery
EarthEpi Environmental epidemiology and climate-health relationships AAAS Annual
Abstract: TBD		 Nature Microbiology/Nature Health
Deadline: June 01, 2026		 BMC Medicine
StormPath Storm and weather impacts on infectious disease dynamics AAAS Annual
Abstract: TBD		 Nature Microbiology/Nature Health
Deadline: June 01, 2026		 BMC Medicine
mgx-abx-healthy Antibiotic effects on healthy gut microbiome BSAC and GARDP Antimicrobial Chemotherapy Conference
Abstract: TBD		 Nature Communications
Deadline: May 31, 2026		 Nature Communications
mgx-clostridioides-difficile Metagenomic analysis of C. difficile Houston C diff & Microbiome Conference
Abstract: TBD		 npj Genomic Medicine
Deadline: March 28, 2026		 Nature Microbiology
mgx-mbx-abx-cdi Metagenomic and metabolomic determinants of CDI Houston C diff & Microbiome Conference
Abstract: TBD		 BMC Personalized Medicine
Deadline: August 05, 2026		 Nature Microbiology
amr-acinetobacter-baumannii Carbapenem-resistant A. baumannii IMARI Annual
Abstract: TBD		 npj Antimicrobials and Resistance
Deadline: June 24, 2026		 Nature Microbiology
amr-enterococcus-faecium VRE genomics and resistance TMC AMR
Abstract: TBD		 npj Antimicrobials and Resistance
Deadline: June 24, 2026		 Journal of Antimicrobial Chemotherapy
amr-klebsiella-pneumoniae Carbapenem-resistant K. pneumoniae IDSA IDWeek; ESCMID Annual
Abstract: TBD		 npj Antimicrobials and Resistance
Deadline: June 24, 2026		 Nature Microbiology
ai-amr AI methods for antimicrobial resistance prediction IMARI Annual
Abstract: TBD		 ACS Infectious Diseases
Deadline: April 01, 2026		 Nature Machine Intelligence
MicroSCOPE Microbial speciation from colony observation and prediction ASM Microbe
Abstract: TBD		 npj Antimicrobials and Resistance
Deadline: April 07, 2026		 Nature Microbiology
ai-forecast-influenza AI forecasting of influenza dynamics ASV Annual
Abstract: TBD		 npj Digital Medicine/npj Digital Public Health
Deadline: May 15, 2026		 The Lancet Infectious Diseases
ai-microbiome-transmission AI modeling of microbiome transmission ASM Microbe
Abstract: TBD		 npj Digital Medicine/npj Digital Public Health
Deadline: May 15, 2026		 Nature Microbiology
MicrobiomeHUES Hierarchical Unified Ecological Spectrum of the human microbiome ASM Microbe
Abstract: TBD		 BMC Microbiology
Deadline: May 20, 2026		 Nature Microbiology
mgx-mbx-glp-1 GLP-1 agonists and gut microbiome interactions AAAS Annual
Abstract: TBD		 npj Biofilms and Microbiomes
Deadline: May 20, 2026		 Nature Medicine
ai-structural-biology Artificial intelligence methodology in structural biology Biophysical Society Annual
Abstract: TBD		 Nature Communications/Nature Structural & Molecular Biology
Deadline: May 31, 2026		 Nature Methods
amr-pseudomonas-aeruginosa Multidrug-resistant P. aeruginosa North American Cystic Fibrosis (CF) Conference
Abstract: TBD		 Nature Communications
Deadline: May 31, 2026		 Clinical Infectious Diseases
mgx-immunol-regulatory-t-cells Microbiome-immune regulatory T cell interactions AAAS Annual
Abstract: TBD		 Nature Communications
Deadline: May 31, 2026		 Nature Immunology
tx-cap Treatment of community-acquired pneumonia IDSA IDWeek
Abstract: TBD		 Antimicrobial Resistance & Infection Control
Deadline: June 25, 2026		 Clinical Infectious Diseases
amr-aspergillus-fumigatus Azole resistance in A. fumigatus MSGERC Biennial
Abstract: TBD		 BMC Immunology
Deadline: June 26, 2026		 Clinical Infectious Diseases
amr-candida-auris Antifungal resistance in C. auris IMARI Annual; MSGERC Biennial
Abstract: TBD		 BMC Immunology
Deadline: June 26, 2026		 Clinical Infectious Diseases
amr-lomentospora-prolificans Antifungal resistance in L. prolificans MSGERC Biennial
Abstract: TBD		 BMC Immunology
Deadline: June 26, 2026		 Clinical Infectious Diseases
amr-env-food Antimicrobial resistance in the food chain CSIRO AMR Summit
Abstract: TBD		 npj Antimicrobials and Resistance
Deadline: July 08, 2026		 Nature Microbiology
mgx-virome Gut virome characterization ASV Annual; ESCV Annual
Abstract: TBD		 npj Biofilms and Microbiomes
Deadline: July 15, 2026		 Nature Microbiology
amr-mycobacterium-tuberculosis MDR-TB genomics TBD
Abstract: TBD		 BMC Microbiology
Deadline: July 16, 2026		 The Lancet Infectious Diseases
amr-clostridioides-difficile Antimicrobial resistance in C. difficile Anaerobe Biennial; 9th International C. difficile Symposium (ICDS)
Abstract: TBD		 BMC Infectious Diseases
Deadline: July 20, 2026		 Nature Microbiology
amr-staphylococcus-aureus MRSA resistance mechanisms IDSA IDWeek; ESCMID Annual
Abstract: TBD		 BMC Infectious Diseases
Deadline: July 20, 2026		 Clinical Infectious Diseases
tx-staph-bacteremia Treatment of Staphylococcal bacteremia ASHP Midyear
Abstract: TBD		 BMC Infectious Diseases
Deadline: July 20, 2026		 Clinical Infectious Diseases
tx-uuti Treatment of uncomplicated urinary tract infections IDSA IDWeek
Abstract: TBD		 BMC Infectious Diseases
Deadline: July 20, 2026		 Clinical Infectious Diseases
amr-env-water Antimicrobial resistance in wastewater surveillance CSIRO AMR Summit
Abstract: TBD		 npj Antimicrobials and Resistance
Deadline: July 28, 2026		 Environmental Science & Technology
DOOR-STEP Desirability of Outcome Ranking with Stratified Treatment Effect Profiling IDSA IDWeek
Abstract: TBD		 BMC Medical Research Methodology
Deadline: July 30, 2026		 Clinical Infectious Diseases
DigitalTwin-Society-Health Digital twin of society’s health for implementation science AAAS Annual
Abstract: TBD		 Implementation Science
Deadline: TBD		 Nature Medicine
PharmacyEducation National trends in pharmacy education outcomes AACP Annual
Abstract: TBD		 Academic Medicine
Deadline: TBD		 American Journal of Pharmaceutical Education
SpaceTime Spatiotemporal model of receptors, enzymes, and pharmacology IUPHAR Annual
Abstract: TBD		 Molecular Pharmacology
Deadline: TBD		 Nature Reviews Drug Discovery
amr-hiv HIV drug resistance CROI Annual; ASV Annual; ESCV Annual
Abstract: TBD		 Nature Microbiology
Deadline: TBD		 The Lancet HIV
amr-neisseria-gonorrhoeae AMR in N. gonorrhoeae IMARI Annual; CSIRO AMR Summit
Abstract: TBD		 npj Antimicrobials and Resistance
Deadline: TBD		 The Lancet Infectious Diseases
biophysics-proteins-as-complex-machines-of-physics Biophysical analysis of protein machinery Biophysical Society Annual
Abstract: TBD		 Biophysical Journal
Deadline: TBD		 Nature Structural & Molecular Biology
clostridioides_atlas Atlas of C. difficile phylogeography, AMR, and host-microbe interactions Houston C diff & Microbiome Conference; 9th International C. difficile Symposium (ICDS)
Abstract: TBD		 Microbiome
Deadline: TBD		 Nature Microbiology
cost-amr Economic burden of antimicrobial resistance Global AMR Innovators’ Conference (GAMRIC)
Abstract: TBD		 Clinical Infectious Diseases
Deadline: Ongoing		 The Lancet Infectious Diseases
epi-hbv Requirements of HBV elimination in the United States AASLD Annual
Abstract: TBD		 The Lancet Infectious Diseases
Deadline: TBD		 Hepatology
mgx-cap Pulmonary metagenomics of community-acquired pneumonia IDSA IDWeek
Abstract: TBD		 The Lancet Infectious Diseases
Deadline: TBD		 Clinical Infectious Diseases
mgx-cdi-vre C. difficile and VRE co-colonization Houston C diff & Microbiome Conference; TMC AMR; 9th International C. difficile Symposium (ICDS)
Abstract: TBD		 Gut Microbes
Deadline: TBD		 Nature Microbiology
mgx-mbx-colorectal-cancer Microbiome and metabolome in colorectal cancer AAAS Annual
Abstract: TBD		 Cell Host & Microbe
Deadline: TBD		 Nature Medicine
pcol-biofilm-rifamycins Pharmacology of RNAP-targeting rifamycins on biofilms IDSA IDWeek
Abstract: TBD		 mBio
Deadline: Ongoing		 Antimicrobial Agents and Chemotherapy
pcol-vcddmde-hbv Pharmacology of DdmDE degradation of HBV cccDNA AASLD Annual
Abstract: TBD		 Journal of Virology
Deadline: TBD		 Hepatology
pharm-comm-ai Interactive AI module for pharmacy student communication training AACP Annual
Abstract: TBD		 npj Digital Medicine
Deadline: June 03, 2026		 Nature Medicine
phys-hiv-lenacapavir Structure and physical properties of HIV-1 capsid hyperstabilization by lenacapavir CROI Annual
Abstract: TBD		 Journal of Virology
Deadline: TBD		 Nature Structural & Molecular Biology
roi-cdi Return on investment analysis for CDI interventions 9th International C. difficile Symposium (ICDS)
Abstract: TBD		 Value in Health
Deadline: TBD		 Clinical Infectious Diseases
roi-pipeline-antimicrobial ROI analysis for antimicrobial drug development ISPOR Annual
Abstract: TBD		 Pharmacoeconomics
Deadline: TBD		 Value in Health
structure-function-pharmacology Structure-function relationships in pharmacology IUPHAR Annual
Abstract: TBD		 Molecular Pharmacology
Deadline: TBD		 Nature Reviews Drug Discovery
tx-cdi Treatment of C. difficile infection 9th International C. difficile Symposium (ICDS)
Abstract: TBD		 Gut Microbes
Deadline: TBD		 Clinical Infectious Diseases

Grants

For more information about NIH funding opportunities, visit NIH Funding Opportunities.

Contributing to Projects

Lab members and collaborators can contribute to projects by following these steps:

  1. Start a New Project:
  2. Link to Opportunities:
    • Add the project to relevant conference entries
    • Associate with calls for papers that match the research topic
    • The project table above will sync its target venues from the Research page data
  3. Track Progress:
    • Use GitHub Issues for tasks, bugs, and feature requests
    • Maintain a GitHub Project Board for milestone tracking
    • Document progress in regular commits with meaningful messages
  4. Collaborate Effectively:
    • Submit pull requests for code review
    • Participate in discussions on issues and PRs
    • Follow lab coding standards and documentation guidelines
  5. Prepare for Submission:
    • Ensure all analyses are reproducible
    • Complete documentation and data availability statements
    • Prepare manuscripts using lab templates

Project Resources

Project Categories and Prefixes

Our projects use standardized naming conventions:

  • amr-*: Antimicrobial resistance studies
  • mgx-*: Metagenomics and microbiome research
  • tx-*: Treatment and therapeutic interventions
  • ai-*: Artificial intelligence and machine learning
  • cost-* or roi-*: Health economics and cost-effectiveness
  • biophysics-*: Structural biology and biophysics
  • structure-function-*: Pharmacology and drug design

Questions or want to join a project? Contact jacobmcpherson@utexas.edu

Browse all repositories: https://github.com/McPhersonLab _BEGIN_COMMAND_DONE_MARKER___0