Pat Schloss
Professor, Frederick G. Novy Collegiate Professor of Microbiome Research
PI since 2006
Research areas
- Colorectal cancer
- C. difficile
- Crohn's disease
- microbial ecology
- mothur
Education
- BS: Cornell University (1997)
- PhD: Cornell University (2002)
- Postdoc: University of Wisconsin (2006)
Background
My interests span the breadth of microbiome research. My work in this field can be divided into “wet” and “dry” components that are each a result of my interdisciplinary training and drive to look at microbial research questions differently. My interdisciplinary training motivates me to investigate bacteria as members of communities. This community-based approach has yielded recent publications from my laboratory where, instead of trying to link individual bacteria with pathogenesis, we seek to understand how entire microbial communities and subsets of those communities could be used to classify people by their health status or risk of disease. When I started pursuing these questions as a postdoc, we didn’t have the necessary computational tools to find the answers. So we made them ourselves. Trained as a biological engineer, I acquired the skills needed to develop several prominent computer programs for analyzing the DNA sequence data generated from microbial ecology experiments. Together, my papers describing these tools have been cited thousands of times. The ability to bridge biology and computational sciences has allowed me to leave a positive impact on a diverse array of important research questions spanning from colon cancer and Clostridium difficile infections to the soil and deep sea.
Here are a few links to interviews Pat has done that discuss his scientific journey and a few blog posts that encapsulate some of his thoughts on mentoring scientists
- What Are You Going to do With Your Tool?
- People Behind the Science Podcast
- TWiM Podcast
- Your Personal Effort Report
- Labbies Having Babies
- Deliberate Practice as an Academic
- Suck Until You Don’t
Papers from time in Schloss lab
- Schloss PD. 2024. Preprint: Removal of rare amplicon sequence variants from 16S rRNA gene sequence surveys biases the interpretation of community structure data. DOI: 10.1101/2020.12.11.422279.
- Schloss PD. 2024. Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses. mSphere. DOI: 10.1128/msphere.00354-23.
- Rifkin SB, Sze MA, Tuck K, Koeppe E, Stoffel EM, Schloss PD. 2024. Gut microbiome composition in Lynch Syndrome with and without history of colorectal neoplasia and non-Lynch controls. J Gastrointest Cancer. 55: 207-218. DOI: 10.1007/s12029-023-00925-4.
- Afiaz A, Ivanov A, Chamberlin J, Hanauer D, Savonen C, Goldman MJ, Morgan M, Reich M, Getka A, Holmes A, Pati S, Knight D, Boutros PC, Bakas S, Caporaso JG, Del Fiol G, Hochheiser H, Haas B, Schloss PD, Eddy JA, Albrecht J, Fedorov A, Waldron L, Hoffman AM, Bradshaw RL, Leek JT, Wright C. 2024. Best practices to evaluate the impact of biomedical research software-metric collection beyond citations. Bioinformatics. 40: btae469. DOI: 10.1093/bioinformatics/btae469.