Papers

Our research lab has many ways of outputting our discoveries. One of our primary approaches and the one our peers judge us by are our publications. Here are all of the papers generated by the lab along with PDF copies of the papers. Of course, a paper is just a way station along the scientific method. With this in mind, in 2014 we started to generate papers as reproducible documents that contain the code used to go from raw data to the final version of the manuscript that we submitted to the journal for review. We'd love it if you were able to take our data or code and build upon it to help your scientific story. Feel free to holler if you have questions about this process or about how we analyzed the data in our other publications.

Legend

  • PDF version of published paper
  • Preprint version of manuscript
  • GitHub repository for paper
  • Raw data used in manuscript
  • Google Scholar page
  1. 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.
  2. 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.
  3. 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.
  4. 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.