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:
| Project (Link) | Question | Target Conference | Target Journal #1 | Target Journal #2 |
|---|---|---|---|---|
| mgx-clostridioides-difficile | Metagenomic analysis of C. difficile | Houston C diff & Microbiome Conference | Nature Microbiology | Microbiome |
| mgx-cdi-vre | C. difficile and VRE co-colonization | Houston C diff & Microbiome Conference; TMC AMR; 9th International C. difficile Symposium (ICDS) | Nature Microbiology | Gut Microbes |
| amr-clostridioides-difficile | Antimicrobial resistance in C. difficile | Anaerobe Biennial; 9th International C. difficile Symposium (ICDS) | Nature Microbiology | npj Antimicrobials and Resistance |
| clostridioides_atlas | Atlas of C. difficile phylogeography, AMR, and host-microbe interactions | Houston C diff & Microbiome Conference; 9th International C. difficile Symposium (ICDS) | Nature Microbiology | Microbiome |
| amr-staphylococcus-aureus | MRSA resistance mechanisms | IDSA IDWeek; ESCMID Annual | Clinical Infectious Diseases | npj Antimicrobials and Resistance |
| amr-klebsiella-pneumoniae | Carbapenem-resistant K. pneumoniae | IDSA IDWeek; ESCMID Annual | Nature Microbiology | npj Antimicrobials and Resistance |
| amr-enterococcus-faecium | VRE genomics and resistance | TMC AMR | Journal of Antimicrobial Chemotherapy | mBio |
| amr-candida-auris | Antifungal resistance in C. auris | IMARI Annual; MSGERC Biennial | Clinical Infectious Diseases | BMC Immunology |
| amr-acinetobacter-baumannii | Carbapenem-resistant A. baumannii | IMARI Annual | Nature Microbiology | npj Antimicrobials and Resistance |
| amr-neisseria-gonorrhoeae | AMR in N. gonorrhoeae | IMARI Annual; CSIRO AMR Summit | The Lancet Infectious Diseases | npj Antimicrobials and Resistance |
| amr-aspergillus-fumigatus | Azole resistance in A. fumigatus | MSGERC Biennial | Clinical Infectious Diseases | Journal of Antimicrobial Chemotherapy |
| amr-lomentospora-prolificans | Antifungal resistance in L. prolificans | MSGERC Biennial | Clinical Infectious Diseases | Antimicrobial Agents and Chemotherapy |
| amr-hiv | HIV drug resistance | CROI Annual; ASV Annual; ESCV Annual | The Lancet HIV | Nature Microbiology |
| amr-mycobacterium-tuberculosis | MDR-TB genomics | Global TB Summit (Qiagen) | The Lancet Infectious Diseases | npj Antimicrobials and Resistance |
| amr-pseudomonas-aeruginosa | Multidrug-resistant P. aeruginosa | North American Cystic Fibrosis (CF) Conference | Clinical Infectious Diseases | npj Antimicrobials and Resistance |
| amr-env-food | Antimicrobial resistance in the food chain | CSIRO AMR Summit | Nature Microbiology | npj Antimicrobials and Resistance |
| amr-env-water | Antimicrobial resistance in wastewater surveillance | CSIRO AMR Summit | Environmental Science & Technology | Water Research |
| tx-cap | Treatment of community-acquired pneumonia | IDSA IDWeek | Clinical Infectious Diseases | Antimicrobial Resistance & Infection Control |
| tx-uuti | Treatment of uncomplicated urinary tract infections | IDSA IDWeek | Clinical Infectious Diseases | Journal of Antimicrobial Chemotherapy |
| tx-staph-bacteremia | Treatment of Staphylococcal bacteremia | ASHP Midyear | Clinical Infectious Diseases | Journal of Antimicrobial Chemotherapy |
| tx-cdi | Treatment of C. difficile infection | 9th International C. difficile Symposium (ICDS) | Clinical Infectious Diseases | Gut Microbes |
| mgx-virome | Gut virome characterization | ASV Annual; ESCV Annual | Nature Microbiology | Cell Host & Microbe |
| mgx-cap | Pulmonary metagenomics of community-acquired pneumonia | IDSA IDWeek | Clinical Infectious Diseases | The Lancet Infectious Diseases |
| mgx-mbx-abx-cdi | Metagenomic and metabolomic determinants of CDI | Houston C diff & Microbiome Conference | Nature Microbiology | Microbiome |
| mgx-abx-healthy | Antibiotic effects on healthy gut microbiome | BSAC and GARDP Antimicrobial Chemotherapy Conference | Nature Communications | Microbiome |
| mgx-immunol-regulatory-t-cells | Microbiome-immune regulatory T cell interactions | AAAS Annual | Nature Immunology | Nature Communications |
| mgx-mbx-colorectal-cancer | Microbiome and metabolome in colorectal cancer | AAAS Annual | Nature Medicine | Cell Host & Microbe |
| mgx-mbx-glp-1 | GLP-1 agonists and gut microbiome interactions | AAAS Annual | Nature Medicine | npj Biofilms and Microbiomes |
| MicrobiomeHUES | Hierarchical Unified Ecological Spectrum of the human microbiome | ASM Microbe | Nature Microbiology | BMC Microbiology |
| ai-amr | AI methods for antimicrobial resistance prediction | IMARI Annual | Nature Machine Intelligence | npj Antimicrobials and Resistance |
| ai-forecast-influenza | AI forecasting of influenza dynamics | ASV Annual | The Lancet Infectious Diseases | npj Digital Medicine |
| ai-forecast-pharmacology | AI-driven pharmacological predictions | IUPHAR Annual | Nature Reviews Drug Discovery | Nature Machine Intelligence |
| ai-microbiome-transmission | AI modeling of microbiome transmission | ASM Microbe | Nature Microbiology | npj Digital Medicine |
| ai-structural-biology | Artificial intelligence methodology in structural biology | Biophysical Society Annual | Nature Methods | Nature Machine Intelligence |
| MicroSCOPE | Microbial speciation from colony observation and prediction | ASM Microbe | Nature Microbiology | BMC Microbiology |
| biophysics-proteins-as-complex-machines-of-physics | Biophysical analysis of protein machinery | Biophysical Society Annual | Nature Structural & Molecular Biology | Biophysical Journal |
| phys-hiv-lenacapavir | Structure and physical properties of HIV-1 capsid hyperstabilization by lenacapavir | CROI Annual | Nature Structural & Molecular Biology | Journal of Virology |
| structure-function-pharmacology | Structure-function relationships in pharmacology | IUPHAR Annual | Nature Reviews Drug Discovery | Molecular Pharmacology |
| SpaceTime | Spatiotemporal model of receptors, enzymes, and pharmacology | IUPHAR Annual | Nature Reviews Drug Discovery | Molecular Pharmacology |
| pcol-biofilm-rifamycins | Pharmacology of RNAP-targeting rifamycins on biofilms | IDSA IDWeek | Antimicrobial Agents and Chemotherapy | mBio |
| pcol-vcddmde-hbv | Pharmacology of DdmDE degradation of HBV cccDNA | AASLD Annual | Hepatology | Journal of Virology |
| cost-amr | Economic burden of antimicrobial resistance | Global AMR Innovators’ Conference (GAMRIC) | The Lancet Infectious Diseases | Clinical Infectious Diseases |
| roi-cdi | Return on investment analysis for CDI interventions | 9th International C. difficile Symposium (ICDS) | Clinical Infectious Diseases | Value in Health |
| roi-pipeline-antimicrobial | ROI analysis for antimicrobial drug development | ISPOR Annual | Value in Health | Pharmacoeconomics |
| EarthEpi | Environmental epidemiology and climate-health relationships | AAAS Annual | BMC Medicine | Nature Microbiology |
| StormPath | Storm and weather impacts on infectious disease dynamics | AAAS Annual | BMC Medicine | Clinical Infectious Diseases |
| epi-hbv | Requirements of HBV elimination in the United States | AASLD Annual | Hepatology | The Lancet Infectious Diseases |
| DigitalTwin-Society-Health | Digital twin of society’s health for implementation science | AAAS Annual | Nature Medicine | Implementation Science |
| DOOR-STEP | Desirability of Outcome Ranking with Stratified Treatment Effect Profiling | IDSA IDWeek | Clinical Infectious Diseases | Statistics in Medicine |
| PharmacyEducation | National trends in pharmacy education outcomes | AACP Annual | American Journal of Pharmaceutical Education | Academic Medicine |
| pharm-comm-ai | Interactive AI module for pharmacy student communication training | AACP Annual | Nature Medicine | npj Digital Medicine |
Grants
For more information about NIH funding opportunities, visit NIH Funding Opportunities.
| Title (Mechanism) | Agency | Funding Opportunity Number | Close Date |
|---|---|---|---|
| A Science of Science Approach to Analyzing and Innovating the Biomedical Research Enterprise (SoS:BIO) | National Science Foundation (NSF) and National Institutes of Health (NIH), National Institute of General Medical Sciences (NIGMS) | 23-569 | Feb 9, 2026 |
| Large Research Projects for Combating Antibiotic-Resistant Bacteria (CARB) (R01) | Agency for Healthcare Research and Quality (AHRQ) | PA-22-047 | Oct 30, 2026 |
| AHRQ Mentored Clinical Scientist Research Career Development Award (K08) | Agency for Healthcare Research and Quality (AHRQ) | PA-22-232 | Feb 12, 2027 |
| Medical Scientist Training Program (MSTP) (T32) | National Institutes of Health (NIH), National Institute of General Medical Sciences (NIGMS) | PAR-24-128 | Jan 25, 2027 |
| NARMS Cooperative Agreement Program to Strengthen Antibiotic Resistance Surveillance in Retail Food Specimens | Food and Drug Administration (FDA) | PAR-25-014 | Apr 1, 2027 |
| NIH Small Research Grant Program (Parent R03 Clinical Trial Not Allowed) | National Institutes of Health (NIH) | PA-25-302 | Jan 8, 2028 |
| Secondary Analysis and Integration of Existing Data to Elucidate Cancer Risk and Related Outcomes (R21 Clinical Trials Not Allowed) | National Institutes of Health (NIH), National Cancer Institute (NCI) | PAR-25-096 | Feb 16, 2026 |
| NIDCR Research Grants for Analyses of Existing Genomics Data (R01 Clinical Trial Not Allowed) | National Institutes of Health (NIH), National Institute of Dental and Craniofacial Research (NIDCR) | PAR-25-164 | Jun 5, 2025 |
| NIDCR Small Research Grants for Analyses of Existing Genomics Data (R03 Clinical Trial Not Allowed) | National Institutes of Health (NIH), National Institute of Dental and Craniofacial Research (NIDCR) | PAR-25-166 | Jun 16, 2025 |
| Investigator Initiated Innovation in Computational Genomics and Data Science (R01 Clinical Trial Not Allowed) | National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI) and National Library of Medicine (NLM) | PAR-25-228 | Sep 8, 2027 |
| NEI Research Grant for Vision-Related Secondary Data Analysis (R21 Clinical Trial Not Allowed) | National Institutes of Health (NIH), National Eye Institute (NEI) | PAR-25-357 | Oct 16, 2027 |
| Accelerating Research Translation (ART) | National Science Foundation (NSF) | 25-548 | Jan 15, 2026 |
| Enhancing Reuse of NHGRI Data Assets (R03 Clinical Trial Not Allowed) | National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI) | RFA-HG-25-005 | Feb 15, 2026 |
| BRAIN Initiative: Theories, Models and Methods for Analysis of Complex Data from the Brain (R01 Clinical Trial Not Allowed) | National Institutes of Health (NIH), National Institute on Drug Abuse (NIDA) | RFA-DA-27-004 | Oct 28, 2025 |
| Accelerating the Pace of Substance Use Research Using Existing Data (R21 Clinical Trial Not Allowed) | National Institutes of Health (NIH), National Institute on Drug Abuse (NIDA) | RFA-DA-26-056 | Dec 3, 2027 |
| NIDCR Small Research Grants for Dental, Oral, and Craniofacial Health-related Data Analyses and Statistical or Computational Methodology Development (R03 Clinical Trial Not Allowed) | National Institutes of Health (NIH), National Institute of Dental and Craniofacial Research (NIDCR) | NOT-DE-26-008 | Dec 12, 2025 |
| Using Archived Data and Specimen Collections to Advance Maternal and Pediatric HIV/AIDS Research | National Institutes of Health (NIH), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) | FOR-HD-25-023 | Jan 2, 2026 |
| Advancing Bioinformatics, Translational Bioinformatics and Computational Biology Research (R01 Clinical Trial Optional) | National Institutes of Health (NIH) | PAR-26-040 | Feb 4, 2026 |
| Economic and Modeling Analyses to Support Immunization Policy and Programs | Centers for Disease Control and Prevention (CDC) | RFA-IP-26-032 | TBD |
| Building Sustainable Software Tools for Open Science (R03 Clinical Trial Not Allowed) | National Institutes of Health (NIH) | RFA-OD-26-034 | May 23, 2025 |
| Summer Institute for Research Education in Biostatistics and Data Science | National Institutes of Health (NIH), National Heart, Lung, and Blood Institute (NHLBI) | RFA-HL-27-006 | 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
- Update the project table above with target venues
- 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