Publications

Recent & Preprints

Minot S.S., Barry K.C., Kasman C., Golob J.L., Willis A.D. (2020). Gene-level metagenomics identifies genome islands associated with immunotherapy response. bioRxiv. doi: 10.1101/2020.10.09.333971

Golob J.L. & Minot S.S. (2020). In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision. BMC Bioinformatics 21, 459. doi: 10.1186/s12859-020-03802-0.

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. Microbiome 7, 110. doi: 10.1186/s40168-019-0722-6.

2017

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). https://doi.org/10.1093/gigascience/gix007

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). http://doi.org/10.1016/j.diagmicrobio.2016.09.023Ahsanuddin, 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). http://doi.org/10.7171/jbt.17-2801-008

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). http://doi.org/10.7717/peerj.2959

2014-2015

Minot, S. S., Krumm, N., & Greenfield, N. B. (2015). One Codex: A Sensitive and Accurate Data Platform for Genomic Microbial Identification. bioRxiv. Retrieved from http://biorxiv.org/content/early/2015/09/28/027607.abstract

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). http://doi.org/10.1073/pnas.1512609112

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). http://doi.org/10.1128/mBio.01578-15

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). http://doi.org/10.1186/s13742-015-0051-z

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). http://doi.org/10.1186/2041-2223-5-9

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). http://doi.org/10.1186/1471-2164-15-1124

2011-2013

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). http://doi.org/10.1073/pnas.1300833110

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). http://doi.org/10.1073/pnas.1117047109

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). http://doi.org/10.1371/journal.pntd.0001854

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). http://doi.org/10.1073/pnas.1119061109Minot, 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). http://doi.org/10.1371/journal.pone.0042342

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). http://doi.org/10.1101/gr.122705.111