Curriculum Vitae

Robert A. Petit III, PhD Senior Bioinformatics Scientist

I am a bioinformatician focused on bacterial pathogens and workflow development. Over the last 10+ years I have developed bioinformatic tools that have been used by thousands of users. I am an active member of the bioinformatic community and contribute my expertise regularly to open-source projects, such as Bioconda. My expertise has also allowed me to act as the lead bioinformatician for many research projects, as well as receiving funding from multiple awards.

Education

Doctor of Philosophy
Population Biology, Ecology, and Evoltion, Emory University, 2018

Master of Science
Bioinformatics, Georgia Institute of Technology, 2011

Bachelor of Science
Biology, Valdosta State University, 2010

Professional Experience

Adjunct Professor
University of Wyoming, Laramie, WY, 2022-Present

Senior Bioinformatics Scientist
Wyoming Public Health Laboratory, Cheyenne, WY, 2021-Present

Senior Data Analyst
Emory University, Atlanta, GA, 2018-2021

Information Analyst III
Emory University, Atlanta, GA, 2012-2013

Network and Systems Administrator
Total Technology Integrators, Valdosta, GA, 2005-2010

Software Developer and Technician
Charleston Credit Adjustment Bureau, Charleston, SC, 2004-2005

Certifications

AZ-900: Microsoft Azure Fundamentals
Achieved on April 8, 2022
Demonstrates foundational knowledge of cloud services and how those services are provided with Microsoft Azure.

Publications

30. Hamza A Babiker, Amina Al-Jardani, Saleh Al-Azri, Robert A Petit III, Eltaib Saad, Sarah Al-Mahrouqi, Reham A.H. Mohamed, Salama Al-Hamidhi, Abdullah A. Balkhair, Najma Al Kharusi, Laila Al Balushi, Samiya Al Zadjali, Lucía Pérez-Pardal, Albano Beja-Pereira, Ahmed Babiker Mycobacterium tuberculosis epidemiology in Oman: whole-genome sequencing uncovers transmission pathways. Microbiology Spectrum (2023)

29. Rohan S Mehta, Robert A Petit III, Timothy D Read, Daniel B Weissman Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes. BMC Bioinformatics (2023)

28. Abraham G. Moller, Robert A. Petit III, Michelle H. Davis, Timothy D. Read Development of an amplicon nanopore sequencing strategy for detection of mutations conferring intermediate resistance to vancomycin in Staphylococcus aureus strains Microbiology Spectrum (2023)

27. Brooke M. Talbot, Natasia F. Jacko, Robert A Petit III, David A. Pegues, Margot J. Shumaker, Timothy D. Read, Michael Z. David Unsuspected Clonal Spread of Methicillin-Resistant Staphylococcus aureus Causing Bloodstream Infections in Hospitalized Adults Detected Using Whole Genome Sequencing Clinical Infectious Diseases (2022)

26. Ahmed Babiker, Chris Bower, Joseph D. Lutgring, Robert A. Petit III, Jessica Howard-Anderson, Uzma Ansari, Gillian McAllister, Michelle Adamczyk, Erin Breaker, Sarah W. Satola, Jesse T. Jacob, Michael H. Woodworth Clinical and Genomic Epidemiology of mcr-9-Carrying Carbapenem-Resistant Enterobacterales Isolates in Metropolitan Atlanta, 2012 to 2017. Microbiology Spectrum (2022)

25. Jordan A Johnson, Timothy D Read, Robert A Petit III, Vincent C Marconi, Kathryn L Meagley, Maria C Rodriguez-Barradas, David O Beenhouwer, Sheldon T Brown, Mark Holodniy, Cynthia A Lucero-Obusan, Patricia Schirmer, Jessica M Ingersoll, Colleen S Kraft, Frederick H Neill, Robert L Atmar, Anita K Kambhampati, Jordan E Cates, Sara A Mirza, Aron J Hall, Cristina V Cardemil, Benjamin A Lopman Association of Secretor Status and Recent Norovirus Infection With Gut Microbiome Diversity Metrics in a Veterans Affairs Population Open Forum Infectious Diseases (2022)

24. Ahmed Babiker, Michael A Martin, Charles Marvil, Stephanie Bellman, Robert A Petit III, Heath L Bradley, Victoria D Stittleburg, Jessica Ingersoll, Colleen S Kraft, Yan Li, Jing Zhang, Clinton R Paden, Timothy D Read, Jesse J Waggoner, Katia Koelle, Anne Piantadosi Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic Virus Evolution (2022)

23. Vishnu Raghuram, Ashley M. Alexander, Hui Qi Loo, Robert A. Petit III, Joanna B. Goldberg, Timothy D. Read Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations Microbiology Spectrum (2022)

22. Abraham G. Moller, Robert A. Petit III, Timothy D. Read Species-Scale Genomic Analysis of Staphylococcus aureus Genes Influencing Phage Host Range and Their Relationships to Virulence and Antibiotic Resistance Genes mSystems (2022)

21. Emily F Wissel, Brooke M Talbot, Noriko A B Toyosato, Robert A Petit III, Vicki Hertzberg, Anne Dunlop, Timothy D Read hAMRoaster: a tool for comparing performance of AMR gene detection software bioRxiv (2022)

20. Karen L. Bell, Robert A. Petit III, Anya Cutler, Emily K. Dobbs, J. Michael Macpherson, Timothy D. Read, Kevin S. Burgess, Berry J. Brosi Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures Ecology and Evolution (2021)

19. Ann E. Rogers, Yi-Juan Hu, Ye Yue, Emily F. Wissel, Robert A. Petit III, Simone Jarrett, Jennifer Christie, Timothy D. Read Shiftwork, functional bowel symptoms, and the microbiome PeerJ (2021)

18. Robert A Petit III, Timothy D Read Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes mSystems (2020)

17. Eryn E. Bernardy, Robert A. Petit III, Vishnu Raghuram, Ashley M. Alexander, Timothy D. Read, Joanna B. Goldberg Genotypic and Phenotypic Diversity of Staphylococcus aureus Isolates from Cystic Fibrosis Patient Lung Infections and Their Interactions with Pseudomonas aeruginosa mBio (2020)

16. Michelle Su, James T. Lyles, Robert A. Petit III, Jessica Peterson, Michelle Hargita, Huaqiao Tang, Claudia Solis-Lemus, Cassandra L. Quave, Timothy D. Read Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains PeerJ (2020)

15. Lauren F. Collins, Fiona P. Havers, Amy Tunali, Stephanie Thomas, Julie A. Clennon, Zanthia Wiley, Melissa Tobin-D’Angelo, Tonia Parrott, Timothy D. Read, Sarah W Satola, Robert A. Petit III, Monica M. Farley Invasive Nontypeable Haemophilus influenzae Infection Among Adults With HIV in Metropolitan Atlanta, Georgia, 2008-2018 Journal of the American Medical Association (2019)

14. Monique R. Bennett, Robin G. Bombardi, Nurgun Kose, Erica H. Parrish, Marcus B. Nagel, Robert A. Petit III, Timothy D. Read, Kevin L. Schey, Isaac P. Thomsen, Eric P. Skaar, James E. Crowe Human mAbs to Staphylococcus aureus IsdA Provide Protection Through Both Heme-Blocking and Fc-Mediated Mechanisms Journal of Infectious Diseases (2019)

13. Eryn E. Bernardy, Robert A. Petit III, Abraham G. Moller, Jennifer A. Blumenthal, Alexander J. McAdam, Gregory P. Priebe, Aroon T. Chande, Lavanya Rishishwar, I. King Jordan, Timothy D. Read, Joanna B. Goldberg Whole-Genome Sequences of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections Microbial Resource Announcement (2019)

12. Timothy D. Read, Robert A. Petit III, Zachary Yin, Tuyaa Montgomery, Moira C. McNulty, Michael Z. David USA300 Staphylococcus aureus persists on multiple body sites following an infection BMC Microbiology (2018)

11. Robert A. Petit III, James M. Hogan, Matthew N. Ezewudo, Sandeep J. Joseph, Timothy D. Read Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data PeerJ (2018)

10. Robert A. Petit III, Timothy D. Read Staphylococcus aureus viewed from the perspective of 40,000+ genomes PeerJ (2018)

9. M. B. Frisch, S. Castillo-Ramı́rez, Robert A. Petit III, M. M. Farley, S. M. Ray, V. S. Albrecht, B. M. Limbago, J. Hernandez, I. See, S. W. Satola, T. D. Read Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages mSphere (2018)

8. Timothy D. Read, Robert A. Petit III, Sandeep J. Joseph, Md. Tauqeer Alam, M. Ryan Weil, Maida Ahmad, Ravila Bhimani, Jocelyn S. Vuong, Chad P. Haase, D. Harry Webb, Milton Tan, Alistair D. M. Dove Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828 BMC Genomics (2017)

7. Sandeep J. Joseph, Ben Li, Robert A. Petit III, Zhaohui S. Qin, Lyndsey Darrow, Timothy D. Read The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data PeerJ (2016)

6. Md Tauqeer Alam, Timothy D. Read, Robert A. Petit III, Susan Boyle-Vavra, Loren G. Miller, Samantha J. Eells, Robert S. Daum, Michael Z. David Transmission and microevolution of USA300 MRSA in U.S. households: evidence from whole-genome sequencing mBio (2015)

5. Md Tauqeer Alam, Robert A. Petit III, Emily K. Crispell, Timothy A. Thornton, Karen N. Conneely, Yunxuan Jiang, Sarah W. Satola, Timothy D. Read Dissecting vancomycin-intermediate resistance in Staphylococcus aureus using genome-wide association Genome Biology and Evolution (2014)

4. Md Tauqeer Alam, Robert A. Petit III, Timothy D. Read, Alistair D. M. Dove The complete mitochondrial genome sequence of the world’s largest fish, the whale shark (Rhincodon typus), and its comparison with those of related shark species Gene (2014)

3. Lavanya Rishishwar, Robert A. Petit III, Colleen S. Kraft, I. King Jordan Genome sequence-based discriminator for vancomycin-intermediate Staphylococcus aureus Journal of Bacteriology (2014)

2. James M. Hogan, Peter Holland, Alexander P. Holloway, Robert A. Petit III, Timothy D. Read Read classification for next generation sequencing European Symposium on Artificial Neural Networks (2013)

1. I. King Jordan, Andrew B. Conley, Ivan V. Antonov, Robert A. Arthur, Erin D. Cook, Guy P. Cooper, Bernard L. Jones, Kristen M. Knipe, Kevin J. Lee, Xing Liu, Gabriel J. Mitchell, Pushkar R. Pande, Robert A. Petit III, Shaopu Qin, Vani N. Rajan, Shruti Sarda, Aswathy Sebastian, Shiyuyun Tang, Racchit Thapliyal, Neha J. Varghese, Tianjun Ye, Lee S. Katz, Xin Wang, Lori Rowe, Michael Frace, Leonard W Mayer Genome sequences for five strains of the emerging pathogen Haemophilus haemolyticus Journal of Bacteriology (2011)

Software

Software tools which I developed or maintain, have been downloaded 347,360 times using Conda and have 908 total Stargazers.

1. assembly-scan
Generate basic stats for an assembly
18,470 total downloads and 9 Stargazers

2. bactopia
A flexible pipeline for complete analysis of bacterial genomes
103,271 total downloads and 414 Stargazers

3. call_variants
A ruffus pipeline to call variants following GATK best practices. (archived)
2 Stargazers

4. dragonflye
Assemble bacterial isolate genomes from Nanopore reads
37,724 total downloads and 116 Stargazers

5. ena-dl
Download FASTQ files from ENA (archived)
2,927 total downloads

6. fastq-dl
Download FASTQ files from SRA or ENA repositories.
31,640 total downloads and 277 Stargazers

7. fastq-scan
Output FASTQ summary statistics in JSON format
34,799 total downloads and 29 Stargazers

8. goblin
GOBLIN - Generate trusted prOteins to supplement BacteriaL annotatIoN
1,302 total downloads and 2 Stargazers

9. illumina-cleanup
A Nextflow pipeline for pre-processing Illumina FASTQ files
4,713 total downloads and 3 Stargazers

10. illumina-simulation
Dockerized Illumina sequencing simulation and 31-mer counting using ART and Jellyfish

11. pasty
A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates
6,984 total downloads and 11 Stargazers

12. pbptyper
In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies
8,434 total downloads and 9 Stargazers

13. pmga
A fork of PMGA (PubMLST Genome Annotator) for all Neisseria species and Haemophilus influenzae
4,021 total downloads and 1 Stargazers

14. shovill-se
A fork of Shovill that includes support for single end reads
5,902 total downloads

15. staphopia
A workflow and database focused on the genomes of the bacterial pathogen Staphylococcus aureus
7 Stargazers

16. staphopia-sccmec
A standalone version of Staphopia’s SCCmec typing method.
3,097 total downloads

17. tbl2asn-forever
A fork of tbl2asn-forever available from Bioconda
70,994 total downloads and 2 Stargazers

18. vcf-annotator
Add biological annotations to variants in a given VCF file.
13,082 total downloads and 26 Stargazers

Presentations

Talks

12. Robert A Petit III, Bactopia v3 enhancements for on-going genomic surveillance, Nextflow Summit - Boston 2023 (November 2023) (Recording)

11. Robert A Petit III, Designing mechanisms into Bactopia to support its users and contribute back to the community, Nextflow Summit 2022 (October 2022) (Recording)

10. Robert A Petit III, Bactopia & it’s usage of nf-core components, nf-core Bytesize Talks (July 2022) (Recording)

9. Robert A Petit III, Microreact and Data.flo for more than genomic epidemiology, SPHERES Meeting (May 2022)

8. Robert A Petit III, Using Bactopia for the complete analysis of bacterial genomes, African Bioinformatics Network (May 2022) (Recording)

7. Robert A Petit III, Deeper dives, workflows and Bactopia, CLIMB Big Data - Bioinformatics Skills for Microbial Genomics Workshop (February 2022) (Recording)

6. Robert A Petit III, Bactopia and using workflow managers in bioinformatics part 2, Micro Binfie Podcast (January 2022)

5. Robert A Petit III, Bactopia and using workflow managers in bioinformatics part 1, Micro Binfie Podcast (January 2022)

4. Robert A Petit III, Integrating Staphopia into S. aureus genomic investigations, Virtual S. aureus Seminar Series Early Career Symposium (February 2021) (Recording)

3. Robert A Petit III, Bacterial Genome Analysis Using Bactopia, State Public Health Bioinformatics (StaPH-B) Monthly Webinar (May 2020) (Recording)

2. Robert A Petit III, Bioinformatics behind Staphopia and the Read Lab, State Public Health Bioinformatics (StaPH-B) Monthly Seminar (November 2018)

1. Robert A Petit III, Staphopia, a web application for rapid analysis of Staphylococcus aureus whole genome sequencing projects, Emory DSAC Student Research Symposium (January 2016)

Posters

21. Daniel J.R. Hintz, Robert A Petit III, Taylor Fearing, Chayse Rowley, Jim Mildenberger, Rob Christensen, Timothy J. Robinson, Joseph M. Reed, Production pipeline for wastewater surveillance, a new tool for Wyoming public health, Wyoming Association of Rural Water Systems 32nd Annual Training Conference (April 2023)

20. Daniel J.R. Hintz, Robert A Petit III, Taylor Fearing, Chayse Rowley, Jim Mildenberger, Rob Christensen, Timothy J. Robinson, Joseph M. Reed, Production pipeline for wastewater surveillance, a new tool for Wyoming public health, 60th International Biomedical Sciences Instrumentation Symposium (April 2023)

19. Robert A Petit III, Taylor Fearing, Chayse Rowley, Ashley Norberg, Jim Mildenberger, Rob Christensen, Joseph M. Reed, Automated genomic surveillance in Wyoming with Microsoft Azure and Nextflow, APHL ID Lab Con 2023 (March 2023)

18. Robert A Petit III, Taylor Fearing, Chayse Rowley, Jim Mildenberger, Timothy D Read, Supporting the bioinformatics community by supporting Bactopia users, ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (ASMNGS) (October 2022)

17. Robert A Petit III, Taylor Fearing, Chayse Rowley, Jim Mildenberger, Timothy D Read, Using Bactopia for highly scalable, portable and customizable bacterial genome analyses, 11th International Conference on Emerging Infectious Diseases (ICEID) (August 2022)

16. Robert A Petit III, Davi J. Marcon, Abhinav Sharma, Timothy D Read, Using Bactopia for highly scalable, portable and customizable bacterial genome analyses, Sequencing to Function Analysis and Applications for the Future (June 2022)

15. Robert A Petit III, Davi J. Marcon, Abhinav Sharma, Timothy D Read, Bactopia v2 Highly scalable, portable and customizable bacterial genome analyses, APHL Annual Conference (May 2022)

14. Robert A Petit III, Davi J. Marcon, Abhinav Sharma, Timothy D Read, Bactopia v2 Highly scalable, portable and customizable bacterial genome analyses, Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (April 2022) (Recording)

13. Robert A Petit III, Davi J. Marcon, Abhinav Sharma, Timothy D Read, Bactopia v2 Highly scalable, portable and customizable bacterial genome analyses, Sequencing to Function, Analysis, and Applications for the Future 2021 (September 2021) (Recording)

12. Robert A Petit III, Timothy D Read, Using Bactopia to process 67,000 Staphylococcus aureus genomes with AWS Batch, Applied Bioinformatics & Public Health Microbiology 2021 (May 2021) (Recording)

11. Robert A Petit III, Timothy D Read, Bactopia, A Flexible Pipeline for Complete Analysis of Bacterial Genomes, 4th ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (December 2020)

10. Robert A Petit III, Timothy D Read, Lauren F Collins, Sarah W Satola, Monica M Farley, Genomic investigation of invasive nontypeable Haemophilus influenzae in adults in Atlanta, 17th Annual Georgia Emerging Infections Program Meeting (Cancelled due to SARS-CoV-2) (March 2020)

9. Robert A Petit III, Timothy D Read, Staphylococcus aureus viewed from the perspective of 40,000+ Genomes, ASM Southeastern Branch Meeting (November 2018)

8. Robert A Petit III, Timothy D Read, Staphylococcus aureus viewed from the perspective of 40,000+ Genomes, 2018 Emory Department of Medicine Research Day (October 2018)

7. Robert A Petit III, Timothy D Read, Staphylococcus aureus viewed from the perspective of 40,000+ Genomes, 3rd ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (September 2018)

6. Robert A Petit III, Timothy D Read, Staphopia, an analysis pipeline and Application Programming Interface focused on Staphylococcus aureus, 11th International Conference on Bioinformatics (November 2017)

5. Robert A Petit III, Timothy D Read, Staphopia, an analysis pipeline and Application Programming Interface focused on Staphylococcus aureus, 2nd ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (October 2017)

4. Robert A Petit III, Timothy D Read, Staphopia, an analysis pipeline and Application Programming Interface focused on Staphylococcus aureus, Emory-LGS STEM Symposium (October 2017)

3. Robert A Petit III, Timothy D Read, Staphopia, a web application for S. aureus whole genome shotgun sequencing data, Emory Antibiotic Resistance Symposium (January 2016)

2. Robert A Petit III, Timothy D Read, Staphopia, a web application for S. aureus whole genome shotgun sequencing data, 10th International Conference on Bioinformatics (November 2015)

1. Robert A Petit III, Timothy D Read, Staphopia, a web application for S. aureus whole genome shotgun sequencing data, Emory Microbiome Symposium (November 2015)

Grants

Amazon Web Services Cloud Credits for Research, $10,000, 2022

Amazon Web Services Cloud Credits for Research, $12,500, 2019

Seven Bridges Cancer Genomics Cloud Collaborative Grant, $15,000, 2017

Amazon Web Services Education Grant, $15,000, 2015

Amazon Web Services Education Grant, $10,000, 2013

Awards

ASMNGS Student Travel Award, American Society of Microbiology, August 2017
Provided $500 towards travel to ASMNGS 2017

Graduate Research Assistantship, School of Biology, Georgia Institute of Technology, August 2011
Provided a tuition waiver for the semester

Graduate Research Assistantship, School of Biology, Georgia Institute of Technology, May 2011
Provided a tuition waiver for the semester

Graduate Research Assistantship, School of Biology, Georgia Institute of Technology, January 2011
Provided a tuition waiver for the semester

Professional Development Training

Specialization - Microsoft Azure Fundamentals AZ-900 Exam Prep
A Coursera specialization which includes 4 courses to prepare the learned for the Microsoft Azure AZ-900 certification. Completed on April 4, 2022.

Preparing for the AZ-900 Microsoft Azure Fundamentals Exam
A Coursera course with an overview of AZ-900 and practice exams Completed on April 4, 2022.

Microsoft Azure Services and Lifecycles
A Coursera course introducing Microsoft Azure service level agreements and service lifecycles. Completed on March 30, 2022.

Microsoft Azure Management Tools and Security Solutions
A Coursera course introducing Microsoft Azure portal and security related services. Completed on March 22, 2022.

Introduction to Microsoft Azure Cloud Services
A Coursera course for a basic introductions into the Microsoft Azure ecosystem. Completed on March 7, 2022.

Machine Learning Foundations: A Case Study Approach
A Coursera course covering machine learning with a series of practical case-studies. Completed on May 15, 2016.

Teaching Experience

Instructor
Building NGS Data Analysis Workflows, Professional Level, Wyoming Public Health Laboratory, 2023
A workshop on workflow managers and their usage in genomics delivered at ASM Microbe 2023

Instructor
Bacterial or Fungal WGS Bioinformatics, Professional Level, Wyoming Public Health Laboratory, 2023
An introductory course on bacterial and fungal WGS delivered at ASM Microbe 2023

Instructor
Nextflow on ARCC, Professional Level, Wyoming Public Health Laboratory, 2023
A workshop for using Nextflow on the University of Wyoming's Advanced Research Compute Cluster

Instructor
Workshop for using Bactopia, Professional Level, Wyoming Public Health Laboratory, 2023
A workshop conducted with the CDC Enteric Diseases Laboratory Branch (EDLB), introducing Bactopia and Bactopia Tools.

Instructor
Advance Python Programming in Bioinformatics, Graduate Level, Emory University, 2016
Supervised by Dr. Tim Read
Developed and taught an advanced Python programming course to a group of graduate students.

Teaching Assistant
Introduction to Microbiology, Undergraduate Level, Emory University, 2016
Supervised by Dr. Bruce Levin
Facilitated weekly discussions with a group of 11 undergraduate and graduate students covering broad topics in the field of microbiology.

Teaching Assistant
Computational Biology and Bioinformatics, Graduate Level, Emory University, 2015
Supervised by Dr. Carlos Moreno, Dr. Tim Read, Dr. Hao Wu, and Dr. Michael Zwick
Taught a group of ~30 graduate students the basics of programming. Developed a ‘manual’ of tips using GitHub pages for future classes to use.