Recent & Preprints

Minot S.S. (2019). De novo Assembly Vastly Expands the Known Microbial Universe. Trends in Microbiology. doi: 10.1016/j.tim.2019.02.007.

Minot S.S. & Willis A.D. (2019). Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease. bioRxiv. doi: 10.1101/567818

Golob J.L. & Minot S.S. (2018). Functional Analysis of Metagenomes by Likelihood Inference (FAMLI) Successfully Compensates for Multi-Mapping Short Reads from Metagenomic Samples. bioRxiv. doi: 10.1101/295352.


McIntyre, A., Ounit, R., Afshinnekoo, E., Prill, R., Henaff, E., Alexander, N., … Mason, C. E. (2017). Comprehensive Benchmarking and Ensemble Approaches for Metagenomic Classifiers. Genome Biol. Sep 21;18(1):182. doi: 10.1186/s13059-017-1299-7.

Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE (2017). Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications. J Biomol Tech. 2017 Apr;28(1):46-55. doi: 10.7171/jbt.17-2801-008.

Brown, B. L., Watson, M., Minot, S. S., Rivera, M. C., & Franklin, R. B. (2017). MinION nanopore sequencing of environmental metagenomes: A synthetic approach. GigaScience, 6(3).

Sim, J. H. C., Truong, C., Minot, S. S., Greenfield, N., Budvytiene, I., Lohith, A., … Banaei, N. (2017). Determining the cause of recurrent Clostridium difficile infection using whole genome sequencing. Diagnostic Microbiology and Infectious Disease, 87(1)., S., Afshinnekoo, E., Gandara, J., Hakyemezoğlu, M., Bezdan, D., Minot, S., … Mason, C. E. (2017). Assessment of REPLI-g multiple displacement whole genome amplification (WGA) techniques for metagenomic applications. Journal of Biomolecular Techniques, 28(1).

Hannigan, G. D., Zheng, Q., Meisel, J. S., Minot, S. S., Bushman, F. D., & Grice, E. A. (2017). Evolutionary and functional implications of hypervariable loci within the skin virome. PeerJ, 2017(2).


Minot, S. S., Krumm, N., & Greenfield, N. B. (2015). One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification. bioRxiv. Retrieved from

Palopoli, M. F., Fergus, D. J., Minot, S., Pei, D. T., Simison, W. B., Fernandez-Silva, I., … Trautwein, M. (2015). Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages. Proceedings of the National Academy of Sciences of the United States of America, 112(52).

Hannigan, G. D., Meisel, J. S., Tyldsley, A. S., Zheng, Q., Hodkinson, B. P., Sanmiguel, A. J., … Grice, E. A. (2015). The human skin double-stranded DNA virome: Topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. mBio, 6(5).

Kilianski, A., Haas, J. L., Corriveau, E. J., Liem, A. T., Willis, K. L., Kadavy, D. R., … Minot, S. S. (2015). Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. GigaScience, 4(1).

Budowle, B., Connell, N. D., Bielecka-Oder, A., Colwell, R. R., Corbett, C. R., Fletcher, J., … Minot, S. (2014). Validation of high throughput sequencing and microbial forensics applications. Investigative Genetics, 5(1).

Palopoli, M. F., Minot, S., Pei, D., Satterly, A., & Endrizzi, J. (2014). Complete mitochondrial genomes of the human follicle mites Demodex brevis and D. folliculorum: Novel gene arrangement, truncated tRNA genes, and ancient divergence between species. BMC Genomics, 15(1).


Minot, S., Bryson, A., Chehoud, C., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013). Rapid evolution of the human gut virome. Proceedings of the National Academy of Sciences of the United States of America, 110(30).

Minot, S., Melo, M. B., Li, F., Lu, D., Niedelman, W., Levine, S. S., & Saeij, J. P. J. (2012). Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity. Proceedings of the National Academy of Sciences of the United States of America, 109(33).

Stoltzfus, J. D., Minot, S., Berriman, M., Nolan, T. J., & Lok, J. B. (2012). RNAseq Analysis of the Parasitic Nematode Strongyloides stercoralis Reveals Divergent Regulation of Canonical Dauer Pathways. PLoS Neglected Tropical Diseases, 6(10).

Minot, S., Grunberg, S., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2012). Hypervariable loci in the human gut virome. Proceedings of the National Academy of Sciences of the United States of America, 109(10)., S., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2012). Conservation of gene cassettes among diverse viruses of the human gut. PLoS ONE, 7(8).

Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., … Bushman, F. D. (2011). The human gut virome: Inter-individual variation and dynamic response to diet. Genome Research, 21(10).