Bioinformatic tool development

  1. 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. Preprint: Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?. DOI: 10.48550/arXiv.2306.03255.
  2. 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.
  3. 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.
  4. Schloss PD. 2023. The Riffomonas YouTube Channel: An Educational Resource to Foster Reproducible Research Practices. Microbiology Resource Announcements. 12: e01310-22. DOI: 10.1128/mra.01310-22.
  5. Schloss PD. 2023. Waste not, want not: Revisiting the analysis that called into question the practice of rarefaction. mSphere. DOI: 10.1128/msphere.00355-23.
  6. Lapp Z, Sovacool KL, Lesniak N, King D, Barnier C, Flickinger M, Krüger J, Armour CR, Lapp MM, Tallant J, Diao R, Oneka M, Tomkovich S, Moltzau Anderson J, Lucas SK, Schloss PD. 2022. Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research. The Journal of Open Source Education. DOI: 10.21105/jose.00144.
  7. Sovacool KL, Westcott SL, Mumphrey MB, Dotson GA, Schloss PD. 2022. OptiFit: an improved method for fitting amplicon sequences to existing OTUs. mSphere. 7: 00916-21. DOI: 10.1128/msphere.00916-21.
  8. Schloss PD. 2021. Amplicon sequence variants artificially split bacterial genomes into separate clusters. mSphere. 6: e0019121. DOI: 10.1128/mSphere.00191-21.
  9. Topçuoğlu BD, Lapp Z, Sovacool KL, Snitkin E, Wiens J, Schloss PD. 2021. mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. Journal of Open Source Software. 6: 3073. DOI: 10.21105/joss.03073.
  10. Puckett SP, Samples RM, Schloss PD, and Balunas MJ. 2020. Metabolomics of the microbiome: Characterizing molecular diversity in complex microbial systems, p. 1-17. In Begley TP and Liu H-W (ed.), Comprehensive Natural Products III: Chemistry and Biology. Elsevier. DOI: 10.1016/B978-0-12-409547-2.14802-4.
  11. Schloss PD. 2020. Reintroducing mothur: 10 years later. Appl Environ Microbiol. 86: e02343-19. DOI: 10.1128/AEM.02343-19.
  12. Schloss PD. 2018. The Riffomonas Reproducible Research Tutorial Series. The Journal of Open Source Education. 1: 13. DOI: 10.21105/jose.00013.
  13. Westcott SL, Schloss PD. 2017. OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units. mSphere. 2: e00073-17. DOI: 10.1128/mSphereDirect.00073-17.
  14. Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK. 2016. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ. 4: e1869. DOI: 10.7717/peerj.1869.
  15. Schloss PD. 2016. Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods. mSystems. 1: e00027-16. DOI: 10.1128/mSystems.00027-16.
  16. Westcott SL, Schloss PD. 2015. De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units. PeerJ. 3: e1487. DOI: 10.7717/peerj.1487.
  17. Schloss PD. 2013. Secondary structure improves OTU assignments of 16S rRNA gene sequences. ISME J. 7: 457-60. DOI: 10.1038/ismej.2012.102.
  18. Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. 2012. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 8: e1002358. DOI: 10.1371/journal.pcbi.1002358.
  19. Gevers D, Pop M, Schloss PD, Huttenhower C. 2012. Bioinformatics for the Human Microbiome Project. PLoS Comput Biol. 8: e1002779. DOI: 10.1371/journal.pcbi.1002779.
  20. Schloss PD, Westcott SL. 2011. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. 77: 3219-26. DOI: 10.1128/AEM.02810-10.
  21. Schloss PD. 2010. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol. 6: e1000844. DOI: 10.1371/journal.pcbi.1000844.
  22. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 75: 7537-41. DOI: 10.1128/AEM.01541-09.
  23. Schloss PD. 2009. A high-throughput DNA sequence aligner for microbial ecology studies. PLoS One. 4: e8230. DOI: 10.1371/journal.pone.0008230.
  24. Schloss PD. 2008. Evaluating different approaches that test whether microbial communities have the same structure. ISME J. 2: 265-75. DOI: 10.1038/ismej.2008.5.
  25. Schloss PD, Handelsman J. 2008. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics. 9: 34. DOI: 10.1186/1471-2105-9-34.
  26. Schloss PD, Handelsman J. 2007. The last word: books as a statistical metaphor for microbial communities. Annu Rev Microbiol. 61: 23-34. DOI: 10.1146/annurev.micro.61.011507.151712.
  27. Schloss PD, Handelsman J. 2006. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol. 72: 6773-9. DOI: 10.1128/AEM.00474-06.
  28. Schloss PD, Handelsman J. 2006. Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol. 72: 2379-84. DOI: 10.1128/AEM.72.4.2379-2384.2006.
  29. Schloss PD, Handelsman J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 71: 1501-6. DOI: 10.1128/AEM.71.3.1501-1506.2005.
  30. Schloss PD, Larget BR, Handelsman J. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol. 70: 5485-92. DOI: 10.1128/AEM.70.9.5485-5492.2004.