Courtney R. Armour PhD

View a PDF version of my CV:  

Skills & Expertise

Education

Dates Degree Institution
2014-2020 PhD Molecular and Cellular Biology Oregon State University
Deptartment of Microbiology
Advisor: Thomas Sharpton
2008-2012 BS Biological Sciences Arizona State Univeristy
College of Liberal Arts and Sciences
Minor: Mathematics
No matching items

Research Experience

Dates Position Lab Projects
2020-present Postdoctoral Research Fellow (remote) Schloss Lab
Department of Microbiology and Immunology
Univeristy of Michigan
  • Optimizing machine learning models to predict colorectal cancer based on gut microbiome taxonomic abundace
  • Identifying early markers of colorectal cancer development in a large clinical cohort of individuals with genetic predisposition to cancer
  • Developing curriculum and teaching computational skills to coding beginners in virtual workshops
2014-2020 Graduate Research Assistant Sharpton Lab
Department of Microbiology
Oregon State University
  • Metagenomic analysis of gut microbiom samples to quantify associations with health
  • Assembly of metagenomic data from gut microbiome samples to build integrated gene catalogues of microbiome genomic diversity
  • Collaborate with a diverse group to develop methodology for analyzing analyzing microbiome data
2010-2013 Research/Laboratory Assistant Dr. Paul Boehmer and Dr. Jui-Cheng Hsieh
Department of Basic Medical Sciences
University of Arizona
  • Creation of HSV-1 viral mutants to quantify impact on replication
  • Mentor new members of the lab
  • Maintain tissue culture and order supplies
No matching items

Publications

Year Title Authors Journal
2022 Streamlined implementation of a machine learning model to classify screen relevant neoplasia using reference-based OTU clustering. Courtney R. Armour, Kelly L. Sovacool, William L. Close, Begüm D. Topçuoğlu, Jenna Wiens, Patrick D. Schloss. bioRxiv preprint
2022 A goldilocks principle for the gut microbiome: taxonomic resolution matters for microbiome-based classification of colorectal cancer. Courtney R. Armour, Begüm D. Topçuoğlu, Andrea Garretto, Patrick D. Schloss. mBio
2022 Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research Zena Lapp, Kelly L. Sovacool, Nick Lesniak, Dana King, Catherine Barnier, Matthew Flickinger, Jule Krüger, Courtney R. Armour, Maya M. Lapp, Jason Tallant, Rucheng Diao, Morgan Oneka, Sarah Tomkovich, Jacqueline Moltzau Anderson, Sarah K. Lucas, Patrick D. Schloss Journal of Open Source Education
2020 An integrated gene catalog of the zebrafish gut microbiome reveals significant homology with mammalian microbiomes Christopher A. Gaulke, Laura M. Beaver, Courtney R. Armour, Ian R. Humphreys, Carrie L. Barton, Robyn L. Tanguay, Emily Ho, Thomas J. Sharpton bioRxiv preprint
2020 Interspecies comparative metagenomics reveals correlated gut microbiome functional capacities among vertebrates Christopher A. Gaulke*, Courtney R. Armour*, Ian R. Humphreys, Laura M. Beaver, Carrie L. Barton, Lucia Carbone, Emily Ho, Robyn L. Tanguay, Yuan Jiang, Thomas Sharpton” bioRxiv preprint
2020 Supplementation with sea vegetables Palmaria mollis and Undaria pinnatifida exerts metabolic benefits in diet-induced obesity in mice Rufa L Mendez, Cristobal Miranda, Courtney R Armour, Thomas J Sharpton, Jan Frederik Stevens, Jung Yeon Kwon Current Developments in Nutrition
2019 Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities Duo Jiang, Courtney R. Armour, Chenxiao Hu, Meng Mei, Chuan Tian, Thomas J. Sharpton, Yuan Jiang Frontiers in Genetics
2019 A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome Courtney R. Armour, Stephen Nayfach, Katherine S. Pollard, Thomas J. Sharpton mSystems
2017 Development of Inflammatory Bowel Disease Is pathed to a Longitudinal Restructuring of the Gut Metagenome in Mice Thomas Sharpton, Svetlana Lyalina, Julie Luong, Joey Pham, Emily M. Deal, Courtney R. Armour, Christopher Gaulke, Shomyseh Sanjabi, Katherine S. Pollard mSystems
2014 Identification of two novel functional p53 responsive elements in the herpes simplex virus-1 genome Jui-Cheng Hsieh, Ryan Kuta, Courtney R. Armour, Paul E. Boehmer Virology
No matching items

Presentations

Talks

Date Event Title Location
Mar 2020 Dissertation Defense Comparative metagenomic investigations link the functional capacity of the gut microbiome to vertebrate physiology Oregon State University
Feb 2020 Microbiology and Immunology Seminar The functional diversity of the gut microbiome in association with host physiology University of Michigan
Apr 2019 Center for Genome Research and Biocomputing Spring Conference The power of poop: diagnostic potential of the gut microbiome in human disease Oregon State University
Nov 2018 Microbiology Seminar Series A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome Oregon State University
Jul 2018 International Symbiosis Society. A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome Oregon State University
Jun 2013 Basic Medical Sciences Research Retreat Interaction between herpes simplex virus-1 DNA polymerase and uracil-DNA glycosylase
awarded best undergraduate presentation 		University of Arizona
Mar 2013 Basic Medical Sciences Intra-Departmental Seminar Series Interaction between herpes simplex virus-1 DNA polymerase and uracil- DNA glycosylase University of Arizona
No matching items

Posters

Date Event Title Location
Jun 2019 ASM Microbe Modeling the functional variation of the gut microbiome across vertebrates San Francisco CA
Sep 2018 Lake Arrowhead Microbial Genomics Conference A metagenomic meta-analysis reveals functional signatures of health and disease in the human gut microbiome Lake Arrowhead CA
Oct 2018 Fall Center for Genome Research and Biocomputing Conferences A Metagenomic Meta-Analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome
awarded best graduate student poster 		Oregon State University
Aug 2017 EMSL/PNNL Multi-Omics for Microbiomes Conference Large-scale analysis of human gut metagenomes reveals functional indicators of disease in the gut microbiome Pasco WA
May 2017 OSU Microbiome Initiative Forum Integrating clinical data reveals functional indicators of disease in the gut microbiome Oregon State University
Aug 2016 META Center Symposium Integrating clinical metagenomic data reveals microbiome signatures of dysbiosis University of Oregon
Aug 2015 META Center Symposium An automated workflow for the quality control and functional analysis of host-associated metagenomes University of Oregon
No matching items

Fellowships

Year Award Amount
2018 - 2019 Larry W. Martin and Joyce B. O’Neill Fellowship $25,000
Winter 2018 Nicholas R. Tartar Graduate Student Fellowship $6,671
AUG 2017 Pacific Northwest National Lab Travel Grant Cost of conference registration
2016 - 2020 ASM SIGHPC and Intel Data and Computational Science Fellowship $15,000 per year - $60,000 total
2008 - 2012 President’s Scholarship $9,000 per year - $36,000 total
No matching items

Specialized Training

Year Course University
2019 Deep Learning for Life scientists
6-week workshop on neural networks 		Center for Genome Research and Biocomputing
Oregon State University
2014 - 2019 Specialized workshop courses:
- RNAseq I & II
- Computing in Life Sciences (Perl)
- Python I & II
- Command-line Data Analysis
- Introduction to Unix/Linux 		Center for Genome Research and Biocomputing
Oregon State University
2014 Certificate in Applied Biostatistics Department of Biostatistics
University of Washington
No matching items

Teaching and Mentorship

Teaching

Year Course University
Fall 2016 Teaching Assistant (ST599)
Introduction to Quantitative Genomics 		Department of Statistics
Oregon State University
Fall 2016 Teaching Assistant (BI211)
Principles of Biology for Life Science Majors 		Department of Statistics
Oregon State University
No matching items

Mentorship

Year Student University
2019 - 2020 Austin Hammer
PhD Student 		Department of Microbiology
Oregon State University
2017 - 2019 Ian Humphreys
Accelerated Masters Student 		Department of Microbiology
Oregon State University
2012 - 2013 Ryan Kuta
Undergraduate Student 		Department of Basic Medical Sciences
University of Arizona
No matching items