# Dr. Michael J. Patton  MD, PhD 
## Precision Medicine Post-Doctoral Research Fellow <br />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 chemistry major, I honed a wide variety of laboratory skills including, chromatography, mass-spectrometry, and 1D/2D NMR while working in Dr. Donald Deardorff's organic synthesis group at Occidental College (2009-2013). From 2014–2017 at the NIH, I applied high-throughput proteomics to bacterial disease models and, under Dr. Harlan Caldwell’s mentorship, developed expertise in _Chlamydia trachomatis_ pathogenesis and mass-spectrometry–based omics. Over those three years, I identified a novel _C. trachomatis_ immune-evasion mechanism and generated the highest proteomic coverage of the organism reported 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 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/)
- Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ; **Biomedical Data Translator Consortium**. Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. 2022 Aug;15(8):1848-1855. Epub 2022 Jun 6. DOI: [10.1111/cts.13302](https://doi.org/10.1111/cts.13302) PMID: [36125173](https://pubmed.ncbi.nlm.nih.gov/36125173/) 
- Bennett TD, Moffitt RA, Hajagos JG, Amor B, Anand A, Bissell MM, Bradwell KR, Bremer C, Byrd JB, Denham A, DeWitt PE, Gabriel D, Garibaldi BT, Girvin AT, Guinney J, Hill EL, Hong SS, Jimenez H, Kavuluru R, Kostka K, Lehmann HP, Levitt E, Mallipattu SK, Manna A, McMurry JA, Morris M, Muschelli J, Neumann AJ, Palchuk MB, Pfaff ER, Qian Z, Qureshi N, Russell S, Spratt H, Walden A, Williams AE, Wooldridge JT, Yoo YJ, Zhang XT, Zhu RL, Austin CP, Saltz JH, Gersing KR, Haendel MA, Chute CG; **National COVID Cohort Collaborative (N3C) Consortium**. Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort Collaborative. JAMA Netw Open. 2021 Jul 1;4(7):e2116901. DOI: [10.1001/jamanetworkopen.2021.16901](https://doi.org/10.1001/jamanetworkopen.2021.16901) PMID: [34255046](https://pubmed.ncbi.nlm.nih.gov/34255046/) 

#### 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
- [Google Scholar](https://scholar.google.com/citations?hl=en&user=NTL9aT4AAAAJ)
- [LinkedIn](https://www.linkedin.com/in/michael-patton-uab-md-phd/)
- [ResearchGate](https://www.researchgate.net/profile/Michael_Patton9)
- [ORCID](https://orcid.org/0000-0001-5056-6043)
- [PubMed](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)
- [UAB Medical Scientist Training Program](https://www.uab.edu/medicine/mstp/directories/current-students)