# Dr. Michael J. Patton <br />PhD, MSTP Candidate at the University of Alabama at Birmingham
<img src="https://raw.githubusercontent.com/TriageDr/michaeljohnpatton.github.io/main/michaelpatton_professional_headshot_2in.png" width=200 height=300> 

My goal as a future physician-scientist is to perform bench-to-bedside translational science by extracting clinically actionable information from multi-omic experimental data and electronic medical records.  As an undergraduate researcher studying organic synthesis (2009-2013), I never produced enough data to warrant a deep dive into rigorous computational analysis; however, as a post-baccalaureate researcher at the NIH (2014-2017), I found that the application of high-throughput proteomic analysis to a bacterial disease models could produce a significant amount of complex data.  Under Dr. Harlan Caldwell’s guidance, I established foundational knowledge of human-microbial interactions through the study _Chlamydia trachomatis_ pathogenesis while gaining deep understanding of how to perform wet lab omic analyses using mass spectrometry.  During my three years at the NIH, I discovered a novel _C. trachomatis_ immune avoidance mechanism and performed experiments resulting in the highest proteomic coverage of the organism to date.  

After departing the NIH, I began my first year as a MD/PhD student at the University of Alabama at Birmingham (2017-Present) with a desire to learn the informatic expertise required to analyze more complex omic datasets in human disease studies.  By the end of my first year of medical school, I realized that my previous experience with high-throughput proteomics at the NIH was pulling me closer to a pursuit of computational methods and translational medical research.  As a current graduate student, I committed myself to the pursuit of a PhD in biomedical informatics.  With the mentorship of Dr. Matthew Might, I am currently developing a diverse skill-set in electronic medical record analysis, machine learning, outcome modeling, and clinical decision support software development at the University of Alabama at Birmingham Precision Medicine Institute (UAB-PMI). 

## Publications
### MD/PhD Research (2017-Present)
#### Dissertation 
- **Patton, MJ**. Biomedical Informatic Analysis of Critical Care Outcomes & Chronic Sequelae of SARS-CoV-2 Infection. Order No. 31327440 The University of Alabama at Birmingham, 2024. United States, Alabama: ProQuest. Web. (10/11/2024). DOI: [https://www.proquest.com/docview/3101965836](https://uab.idm.oclc.org/login?url=https://www.proquest.com/dissertations-theses/biomedical-informatic-analysis-critical-care/docview/3101965836/se-2?accountid=8240)
  
#### Published Manuscripts
- **Patton, MJ**, Benson D, Robison, SW, Raval D, Locy ML, Patel K, Grumley S, Levitan EB, Morris P, Might M, Gaggar A, Erdmann N. Characteristics and Determinants of Pulmonary Long COVID. _Journal of Clinical Investigation Insight_. 2024. 23:e177518. DOI: [10.1172/jci.insight.177518](https://doi.org/10.1172/jci.insight.177518) PMID: [38652535](https://pubmed.ncbi.nlm.nih.gov/38652535/)
- **Patton, MJ**, Gaggar, A, Might, M, Erdmann, N, Orihuela, CJ, & Harrod, KS. Community-Acquired Bacterial Co-infections and COVID-19. _Physiological Reviews_. 2024. 104(1):1-21. DOI: [10.1152/physrev.00010.2023](https://journals.physiology.org/doi/abs/10.1152/physrev.00010.2023) PMID: [37589392](https://pubmed.ncbi.nlm.nih.gov/37589392/)
- **Patton, MJ** & Liu, VX. Predictive modeling using artificial intelligence and machine learning algorithms on electronic health record data. _Critical Care Clinics_. 2023. 39(4):647-673. DOI: [10.1016/j.ccc.2023.02.001](https://doi.org/10.1016/j.ccc.2023.02.001) PMID: [37704332](https://pubmed.ncbi.nlm.nih.gov/37704332/) 
- Fortmann, SD&dagger; & **Patton, MJ&dagger;**, Frey, BF, Tipper, JL, Reddy, SB, Vieira, CP, Hanumanthu, VS, Sterrett, S, Floyd, JL, Prasad, R, Zucker, JD, Crouse, AB, Huls, F, Chkheidze, R, Li, P, Erdmann, N, Harrod, KS, Gaggar, A, Goepfert, PA, Grant, MB, Might, M. Circulating SARS-CoV-2+ Megakaryocytes Associate with Severe Viral Infection in COVID-19. _Blood Advances_. 2023. 8;7(15):4200-4214. DOI: [10.1182/bloodadvances.2022009022](https://doi.org/10.1182/bloodadvances.2022009022)  PMID: [36920790](https://pubmed.ncbi.nlm.nih.gov/36920790/)
- **Patton, MJ**, Orihuela, CJ, Harrod, KS, Bhuiyan, MAN, Dominic, P, Kevil, CG, Fort, D, Liu, VX, Farhat, M, Koff, JL, Lal, CV, Gaggar, A, Richter, RP, Erdmann, N, Might, M, & Gaggar, A. COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation. _Critical Care_. 2023. 27(1), 34. DOI: [10.1186/s13054-023-04312-0](https://doi.org/10.1186/s13054-023-04312-0)  PMID: [36691080](https://pubmed.ncbi.nlm.nih.gov/36691080/)
- Foksinska, A, Crowder, CM, Crouse, AB, Henrikson, J, Byrd, WE, Rosenblatt, G, **Patton, MJ**, He, K, Tran-Nguyen, TK, Zheng, M, Ramsey, SA, Amin, N, Osborne, JD, UAB Precision Medicine Institute, & Might, M. The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren. _Frontiers in Artificial Intelligence_. 2022. 5, 910216. DOI: [10.3389/frai.2022.910216](https://doi.org/10.3389/frai.2022.910216)  PMID: [36248623](https://pubmed.ncbi.nlm.nih.gov/36248623/)
- Prasad, R, **Patton, MJ**, Floyd, JL, Fortmann, S, DuPont, M, Harbour, A, Wright, J, Lamendella, R, Stevens, BR, Oudit, GY, & Grant, MB. Plasma Microbiome in COVID-19 Subjects: An Indicator of Gut Barrier Defects and Dysbiosis. _International Journal of Molecular Sciences_. 2022. 23(16):9141. DOI: [10.3390/ijms23169141](https://doi.org/10.3390/ijms23169141)  PMID: [36012406](https://pubmed.ncbi.nlm.nih.gov/36012406/)

#### Published Abstracts
- Almunaifer, AI, Sasse, K, He, K, **Patton, MJ**, Vong, CDR, Nadimpalli, SR, Byrd, W, Osborne, JD. Addressing Treatment-Relevance in Biomedical Relation Extraction. International Conference on Functional Programming Series on Declarative Programming in Biology and Medicine (ICFP-DeclMed). 2023. Conference Abstract Link: [icfp23.sigplan.org/Addressing-Treatment-Relevance-in-Biomedical-Relation-Extraction](https://icfp23.sigplan.org/details/declmed-2023-papers/12/Addressing-Treatment-Relevance-in-Biomedical-Relation-Extraction)
- **Patton, MJ**, Liu, VX, Might, M. Temporal Analysis of Biomarker, Severity-of-Illness Score, and Machine Learning Model Performance for Sepsis Prediction. 42nd International Symposium on Intensive Care and Emergency Medicine (ISICEM). 2023. Critical Care, 27(S1):72, P131. DOI: [10.1186/s13054-023-04377-x](https://ccforum.biomedcentral.com/articles/10.1186/s13054-023-04377-x) PMCID: [PMC10268394](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10268394/)
- **Patton, MJ**, Erdmann, N, Harrod, KS, Gaggar, A, Orihuela, CJ, Crouse, A, Might M. Culture Status Improves Respiratory Failure Prediction in COVID-19+ Sepsis Patients. 41st  international symposium on intensive care and emergency medicine (ISICEM). 2022. Critical Care, 26(S1):26, P094. DOI: [10.1186/s13054-022-03927-z](https://ccforum.biomedcentral.com/articles/10.1186/s13054-022-03927-z) PMCID: [PMC8948467](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8948467/)
- Greer, R, Song, Y, **Patton, MJ**, Might, M, Harrod, K, Petit, CM, & Song, Y. Identification of FDA Approved Antiviral Drugs for COVID-19 Treatment using Unbiased Virtual Screening. Biophysical Journal. 2021. 120(3), 204a. DOI: [10.1016/j.bpj.2020.11.1394](https://doi.org/10.1016/j.bpj.2020.11.1394) PMCID: [PMC7879731](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7879731/)
- Byrd, W, Rosenblatt, G, **Patton, MJ**, Might, M. mediKanren: A System for Bio-medical Reasoning. International Conference on Functional Programming (ICFP) Series on miniKanren. 2020. Conference Abstract Link: [icfp20.sigplan.org/mediKanren-A-System-for-Bio-medical-Reasoning](https://icfp20.sigplan.org/details/minikanren-2020-papers/10/mediKanren-A-System-for-Bio-medical-Reasoning)

### NIH Post-Baccalaureate Research (2014-2017)
#### Published Manuscripts
- Lei, L, Yang, C, **Patton, MJ**, Smelkinson, M, Dorward, D, Ma, L, Karanovic, U, Firdous, S, McClarty, G, & Caldwell, HD. A Chlamydial Plasmid-Dependent Secretion System for the Delivery of Virulence Factors to the Host Cytosol. MBio. 2021. e0117921. DOI: [10.1128/mBio.01179-21](https://doi.org/10.1128/mBio.01179-21)  PMID: [34101486](https://pubmed.ncbi.nlm.nih.gov/34101486/)
- Yang, C, Briones, M, Chiou, J, Lei, L, **Patton, MJ**, Ma, L, McClarty, G, & Caldwell, HD. Chlamydia trachomatis Lipopolysaccharide Evades the Canonical and Noncanonical Inflammatory Pathways To Subvert Innate Immunity. MBio. 2019. 10(2). DOI: [10.1128/mBio.00595-19](https://doi.org/10.1128/mBio.00595-19)  PMID: [31015326](https://pubmed.ncbi.nlm.nih.gov/31015326/)
- **Patton, MJ**, Chen, CY, Yang, C, McCorrister, S, Grant, C, Westmacott, G, Yuan, XY, Ochoa, E, Fariss, R, Whitmire, WM, Carlson, JH, Caldwell, HD, & McClarty, G. Plasmid Negative Regulation of CPAF Expression Is Pgp4 Independent and Restricted to Invasive Chlamydia trachomatis Biovars. MBio. 2018. 9(1). DOI: [10.1128/mBio.02164-17](https://doi.org/10.1128/mBio.02164-17)  PMID: [29382731](https://pubmed.ncbi.nlm.nih.gov/29382731/)
- Yang, C, Kari, L, Sturdevant, GL, Song, L, **Patton, MJ**, Couch, CE, Ilgenfritz, JM, Southern, TR, Whitmire, WM, Briones, M, Bonner, C, Grant, C, Hu, P, McClarty, G, & Caldwell, HD. Chlamydia trachomatis ChxR is a transcriptional regulator of virulence factors that function in in vivo host-pathogen interactions. Pathogens and Disease. 2017. 75(3). DOI: [10.1093/femspd/ftx035](https://doi.org/10.1093/femspd/ftx035)  PMID: [28369275](https://pubmed.ncbi.nlm.nih.gov/28369275/)
- **Patton, MJ**, McCorrister, S, Grant, C, Westmacott, G, Fariss, R, Hu, P, Zhao, K, Blake, M, Whitmire, WM, Yang, C, Caldwell, HD, & McClarty, G. Chlamydial Protease-Like Activity Factor and Type III Secreted Effectors Cooperate in Inhibition of p65 Nuclear Translocation. MBio. 2016. 7(5). DOI: [10.1128/mBio.01427-16](https://doi.org/10.1128/mBio.01427-16)  PMID: [27677792](https://pubmed.ncbi.nlm.nih.gov/27677792/)

## Presentations 
### Oral Presentations
- **Patton, MJ**, Benson, D, Dhaval, R, Patel K, Morris, P, Might M, Erdmann, N, Gaggar, A. _Determinants of Pulmonary Post-acute Sequelae of SARS-COV-2 (PASC): A Single-Center Retrospective Study_. Keystone Symposium on Long COVID and Post Acute Sequalae of SARS-CoV-2 (PASC): Pathogenesis and Treatment. August 27-30th, 2023, Santa Fe, New Mexico
- **Patton, MJ** & Might, M. _Has Machine Learning Made a Difference? A Retrospective Analysis of In-Hospital Mortality Prediction_. Symposium on Artificial Intelligence and Learning Health Systems (SAIL). May 9-12th, 2023, San Juan, Puerto Rico
- **Patton, MJ**, Orihuela, CJ, Harrod, KS, Bhuiyan, MAN, Dominic, P, Kevil, CG, Fort, D, Liu, VX, Farhat, M, Koff, JL, Lal, CV, Gaggar, A, Richter, RP, Erdmann, N, Might, M, Gaggar, A. _COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation_. American Medical Informatics Association (AMIA) Informatics Summit. March 13-16th, 2023, Seattle, Washington

### Poster Presentations 
- **Patton, MJ**, Huls, F, LeBlanc, K, Cole, Sessions, Might, M. _Automating clinical coding of HPO for rare and undiagnosed diseases with large language models via ontological descent_. Symposium on Artificial Intelligence and Learning Health Systems (SAIL). May 6-9th, 2024, San Juan, Puerto Rico. DOI: [https://sail.health/wp-content/uploads/2024/05/Poster-8-Patton.pdf](https://sail.health/wp-content/uploads/2024/05/Poster-8-Patton.pdf)
- **Patton, MJ** & Might, M. _Has Machine Learning Made a Difference? A Retrospective Analysis of In-Hospital Mortality Prediction_. Symposium on Artificial Intelligence and Learning Health Systems (SAIL). May 9-12th, 2023, San Juan, Puerto Rico. DOI: [https://sail.health/wp-content/uploads/2023/11/18-SAIL_poster_Patton.pdf](https://sail.health/wp-content/uploads/2023/11/18-SAIL_poster_Patton.pdf)
- **Patton, MJ**, Liu, VX, Might, M. _Temporal Analysis of Biomarker, Severity-of-Illness Score, and Machine Learning Model Performance for Sepsis Prediction_. 42nd International Symposium on Intensive Care and Emergency Medicine (ISICEM). March 21-24th, 2023, Brussels, Belgium
- **Patton, MJ**, Erdmann, N, Harrod, KS, Gaggar, A, Orihuela, CJ, Crouse, A, Might M. _Culture Status Improves Respiratory Failure Prediction in COVID-19+ Sepsis Patients_. 41st Symposium on Intensive Care and Emergency Medicine (ISICEM). March 22-25th, 2022, Brussels, Belgium
- **Patton, MJ**, Chen, CY, Yang, C, McCorrister, S, Grant, B, Westmacott, G, Yuan, XY, Ochoa, E, Fariss, R, Whitmire, WM, Carlson, JH, Caldwell, HD, McClarty, G. _Comparative Proteomics Reveals New Plasmid Regulated Chlamydia trachomatis Virulence Factors_. University of Alabama at Birmingham (UAB) Medical Student Research Day. November 13th, 2017, Birmingham, Alabama
- **Patton, MJ**, McKinley CJ, Discolo CA, Deardorff, D. _An Enantioselective Synthesis of Cymbalta_. Amgen Undergraduate Research Scholarship Conference. May, 2013, Thousand Oaks, California

## Conferences Attended
- Symposium on Artificial Intelligence and Learning Health Systems (SAIL). May 6-9th, 2024, San Juan, Puerto Rico
- Keystone Symposium on Long COVID and Post Acute Sequalae of SARS-CoV-2 (PASC): Pathogenesis and Treatment, August 27-30th, 2023, Santa Fe, New Mexico
- Symposium on Artificial Intelligence and Learning Health Systems (SAIL). May 9-12th, 2023, San Juan, Puerto Rico
- 42nd International Symposium on Intensive Care and Emergency Medicine (ISICEM), March 21-24th, 2023, Brussels, Belgium
- American Medical Informatics Association (AMIA) Informatics Summit. March 13-16th, 2023, Seattle, Washington
- 41st Symposium on Intensive Care and Emergency Medicine (ISICEM). March 22-25th, 2022, Brussels, Belgium
- American Medical Informatics Association (AMIA) Virtual Annual Symposium. November 14-18th, 2020 (Virtual)
- International Conference on Functional Programming (ICFP) Series on miniKanren.  August 27th, 2020 (Virtual)
- Southeastern Medical Scientist Symposium (SEMSS). November 10-11th, 2018, Nashville, Tennessee 

## Press & News Releases 
- University of Alabama at Birmingham Featured Scientific Discovery (July, 2023): [COVID-19: Bacterial co-infection is a major risk factor for death, ICU admission and mechanical ventilation](https://www.uab.edu/medicine/news/component/k2/item/2816-covid-19-bacteremic-co-infection-is-a-major-risk-factor)
- New England Journal of Medicine Scholarship for Presentation at the Symposium on Artifical Intelligence and Learning Health Systems (May, 2023): [Patton receives NEJM scholarship for SAIL](https://www.uab.edu/medicine/news/latest/item/2900-nejm-sail-scholarship)

## Employment, Education, & Awards
### MD/PhD Candidate in the University of Alabama Medical Scientist Training Program (2017-Present)
#### University of Alabama at Birmingham (UAB)
- Analyzed electronic health record data from multiple institutions (Cerner, EPIC systems) 
- Performed risk factor and outcome modeling analyses for acute COVID-19 outcomes and chronic post-COVID symptoms
- Programming Skills
    - R
    - Python
    - SparkR and PySpark
    - SQL
    - Racket
    - Scheme

### NIH Intramural Research Training Award Research (IRTA) Scholar (2014-2017)
#### National Institute of Allergy and Infectious Diseases (NIAID)
- Performed experiments analyzing host-bacterial interactions of the human pathogen _Chlamydia trachomatis_. Focal points of my two publications were the chlamydial plasmid and the putative virulence factor CPAF, the chlamydial protease-like activity factor, and their respective functions in host immune avoidance and the chlamydial life cycle. 
- Laboratory Skills
    - High-throughput Proteomic Mass Spectrometry (Q Exactive™ Hybrid Quadrupole-Orbitrap)
    - Confocal Microscopy (Zeiss LSM 700 & 880 Confocal Airyscan Detection™)
    - Bacterial Cloning
    - Cell/Viral/Bacterial Culture & Sterile Technique
    - Flow Cytometry (BD LSRII - Quad/IRF)
    - DNA/RNA purification, PCR, qRT-PCR 
    - ELISA Assays 
    - 1D/2D Western Blotting 
    - Flow Cytometry (8-channel)

### Fulbright Scholar (2013-2014)
#### United States-India Educational Foundation (USIEF), Chennai India
- Primary and Secondary School Teacher for English at the Hindu Senior Secondary School
- Tamil language training for the duration of the grant
- Presented English, Public Health, and American History and Culture seminars for after school youth programs in both urban and rural Tamil Nadu

### Occidental College (2009-2013)
#### Bachelor of Arts (B.A.), Chemistry
- Undergraduate laboratory researcher for Dr. Donald Deardorff 
- Performed a novel organic synthesis of the commercially sold pharmaceutical product Duloxetine, (marketed as Cymbalta®)
- Laboratory Skills
    - Nuclear Magnetic Resonance Imaging (Carbon & Proton 1-D/2-D Bruker 300™)
    - High Performance, Column, Radial, & Thin-layer Chromatography
    - Gas Chromatography Mass Spectrometry (GC-MS)
    - Infrared, Fluorescent & Raman Spectroscopy 
    - Liquid-Phase Polarimetry
- Organic Chemistry Tutor
    - Led two-hour tutor sessions for undergraduate organic chemistry students twice a week
    - Collaborated with other facilitators in a team environment to create original practice exams for students


## Contact Me
You can reach me at:

- Email: mjpatton@uab.edu
- LinkedIn: [https://www.linkedin.com/in/michael-patton-uab-md-phd/](https://www.linkedin.com/in/michael-patton-uab-md-phd/)
- ResearchGate: [https://www.researchgate.net/profile/Michael_Patton9](https://www.researchgate.net/profile/Michael_Patton9)
- ORCID: [https://orcid.org/0000-0001-5056-6043](https://orcid.org/0000-0001-5056-6043)
- PubMed: [https://pubmed.ncbi.nlm.nih.gov/?size=200&term=Patton+MJ&cauthor_id=36012406](https://pubmed.ncbi.nlm.nih.gov/?size=200&term=Patton+MJ&cauthor_id=36012406)
- UAB Precision Medicine Institute: [https://www.uab.edu/medicine/pmi/our-team](https://www.uab.edu/medicine/pmi/our-team)
- UAB Medical Scientist Training Program: [https://www.uab.edu/medicine/mstp/directories/current-students](https://www.uab.edu/medicine/mstp/directories/current-students)