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:
- GitHub Repository: A specific repository containing project code, data, and documentation
- GitHub Project Board: A project board tracking tasks and milestones
- GitHub Issues: Specific issues for abstract submissions, paper drafts, or collaborative work
Current Active Projects
Visit our GitHub Organization:
Grants
For more information about NIH funding opportunities, visit NIH Funding Opportunities.
- Large Research Projects for Combating Antibiotic-Resistant Bacteria (CARB) (R01) — AHRQ | Close: Oct 30, 2026
- AHRQ Mentored Clinical Scientist Research Career Development Award (K08) — AHRQ | Close: Feb 12, 2027
- Medical Scientist Training Program (MSTP) (T32) — NIH/NIGMS | Close: Jan 25, 2027
- NARMS Cooperative Agreement Program to Strengthen Antibiotic Resistance Surveillance in Retail Food Specimens — FDA | Close: Apr 1, 2027
- NIH Small Research Grant Program (Parent R03 Clinical Trial Not Allowed) — NIH | Close: Jan 8, 2028
- Investigator Initiated Innovation in Computational Genomics and Data Science (R01 Clinical Trial Not Allowed) — NIH/NHGRI & NLM | Close: Sep 8, 2027
- NEI Research Grant for Vision-Related Secondary Data Analysis (R21 Clinical Trial Not Allowed) — NIH/NEI | Close: Oct 16, 2027
- Accelerating the Pace of Substance Use Research Using Existing Data (R21 Clinical Trial Not Allowed) — NIH/NIDA | Close: Dec 3, 2027
- Economic and Modeling Analyses to Support Immunization Policy and Programs — CDC | Close: TBD
- Summer Institute for Research Education in Biostatistics and Data Science — NIH/NHLBI | Close: Jul 1, 2026
Contributing to Projects
Lab members and collaborators can contribute to projects by following these steps:
- Start a New Project:
- Fork or use the Template Project Repository
- Set up project structure with README, data directories, and analysis scripts
- Define contributor roles using CRediT taxonomy
- 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
- 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
- Collaborate Effectively:
- Submit pull requests for code review
- Participate in discussions on issues and PRs
- Follow lab coding standards and documentation guidelines
- Prepare for Submission:
- Ensure all analyses are reproducible
- Complete documentation and data availability statements
- Prepare manuscripts using lab templates
Project Resources
- GitHub Organization: McPherson Lab on GitHub
- CRediT Roles: Contributor Roles Taxonomy
- Template Repository: Project Template
Project Categories and Prefixes
Our projects use standardized naming conventions:
amr-*: Antimicrobial resistance studiesmgx-*: Metagenomics and microbiome researchtx-*: Treatment and therapeutic interventionsai-*: Artificial intelligence and machine learningcost-*orroi-*: Health economics and cost-effectivenessbiophysics-*: Structural biology and biophysicsstructure-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