Thomas J. Sharpton, PhD - Publications

Microbiology Oregon State University, Corvallis, OR 
Metagenomics, Comparative Genomics, Bioinformatics

42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Mirzayi C, Renson A, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, ... ... Sharpton T, et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nature Medicine. PMID 34789871 DOI: 10.1038/s41591-021-01552-x  0.584
2020 Couch CE, Arnold HK, Crowhurst RS, Jolles AE, Sharpton TJ, Witczak MF, Epps CW, Beechler BR. Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation. Scientific Reports. 10: 6582. PMID 32313214 DOI: 10.1038/S41598-020-63401-0  0.38
2020 Kashyap A, Rhodes A, Kronmiller B, Berger J, Champagne A, Davis EW, Finnegan MV, Geniza M, Hendrix DA, Löhr CV, Petro VM, Sharpton TJ, Wells J, Epps CW, Jaiswal P, et al. Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis. Bmc Genomics. 21: 153. PMID 32050897 DOI: 10.1186/S12864-019-6432-4  0.348
2020 Flannery JE, Stagaman K, Burns AR, Hickey RJ, Roos LE, Giuliano RJ, Fisher PA, Sharpton TJ. Gut Feelings Begin in Childhood: the Gut Metagenome Correlates with Early Environment, Caregiving, and Behavior. Mbio. 11. PMID 31964729 DOI: 10.1128/Mbio.02780-19  0.312
2020 Jiang D, Sharpton T, Jiang Y. Microbial Interaction Network Estimation via Bias-Corrected Graphical Lasso Statistics in Biosciences. 1-22. DOI: 10.1007/S12561-020-09279-Y  0.3
2019 Jiang D, Armour CR, Hu C, Mei M, Tian C, Sharpton TJ, Jiang Y. Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Frontiers in Genetics. 10: 995. PMID 31781153 DOI: 10.3389/Fgene.2019.00995  0.308
2019 Neves ALA, Chen Y, Lê Cao KA, Mandal S, Sharpton TJ, McAllister T, Guan LL. Taxonomic and functional assessment using metatranscriptomics reveals the effect of Angus cattle on rumen microbial signatures. Animal : An International Journal of Animal Bioscience. 1-14. PMID 31662129 DOI: 10.1017/S1751731119002453  0.41
2019 Armour CR, Nayfach S, Pollard KS, Sharpton TJ. A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. Msystems. 4. PMID 31120034 DOI: 10.1128/mSystems.00332-18  0.654
2019 Armour CR, Nayfach S, Pollard KS, Sharpton TJ. A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. Msystems. 4. PMID 31098399 DOI: 10.1128/mSystems.00332-18  0.654
2019 Li Y, Li Y, Jin W, Sharpton TJ, Mackie RI, Cann I, Cheng Y, Zhu W. Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen. Frontiers in Microbiology. 10: 435. PMID 30894845 DOI: 10.3389/Fmicb.2019.00435  0.328
2019 Gaulke CA, Martins ML, Watral VG, Humphreys IR, Spagnoli ST, Kent ML, Sharpton TJ. A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome's link to Pseudocapillaria tomentosa infection and pathology. Microbiome. 7: 10. PMID 30678738 DOI: 10.1186/S40168-019-0622-9  0.31
2019 Kirchoff NS, Udell MAR, Sharpton TJ. The gut microbiome correlates with conspecific aggression in a small population of rescued dogs . Peerj. 7: e6103. PMID 30643689 DOI: 10.7717/Peerj.6103  0.327
2019 Morelan IA, Gaulke CA, Sharpton TJ, Vega Thurber R, Denver DR. Microbiome Variation in an Intertidal Sea Anemone Across Latitudes and Symbiotic States Frontiers in Marine Science. 6. DOI: 10.3389/Fmars.2019.00007  0.361
2018 Gaulke CA, Sharpton TJ. The influence of ethnicity and geography on human gut microbiome composition. Nature Medicine. 24: 1495-1496. PMID 30275567 DOI: 10.1038/S41591-018-0210-8  0.313
2018 Gaulke CA, Arnold HK, Humphreys IR, Kembel SW, O'Dwyer JP, Sharpton TJ. Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota. Mbio. 9. PMID 30206171 DOI: 10.1128/Mbio.01348-18  0.431
2018 Allan ERO, Tennessen JA, Sharpton TJ, Blouin MS. Allelic variation in a single genomic region alters the microbiome of the snail Biomphalaria glabrata. The Journal of Heredity. PMID 29566237 DOI: 10.1093/Jhered/Esy014  0.406
2018 Wang L, Shantz AA, Payet JP, Sharpton TJ, Foster A, Burkepile DE, Vega Thurber R. Corals and Their Microbiomes Are Differentially Affected by Exposure to Elevated Nutrients and a Natural Thermal Anomaly Frontiers in Marine Science. 5. DOI: 10.3389/Fmars.2018.00101  0.311
2018 Neves A, Lê Cao K, Mandal S, Sharpton T, McAllister T, Guan L. PSI-36 Taxonomic and functional assessment reveals specific rumen microbial species and gene families associated with feed efficiency in Angus cattle. Journal of Animal Science. 96: 190-191. DOI: 10.1093/Jas/Sky404.413  0.335
2017 Cheng Y, Wang Y, Li Y, Zhang Y, Liu T, Wang Y, Sharpton TJ, Zhu W. Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing. Frontiers in Microbiology. 8: 2165. PMID 29163444 DOI: 10.3389/Fmicb.2017.02165  0.336
2017 Burns AR, Watral V, Sichel S, Spagnoli S, Banse AV, Mittge E, Sharpton TJ, Guillemin K, Kent ML. Transmission of a common intestinal neoplasm in zebrafish by cohabitation. Journal of Fish Diseases. PMID 29023774 DOI: 10.1111/Jfd.12743  0.302
2017 Wilson AK, Watral VG, Kent ML, Sharpton TJ, Gaulke CA. Draft Genome Sequence of Pseudomonas sp. Strain DrBHI1 (Phylum Proteobacteria). Genome Announcements. 5. PMID 28963227 DOI: 10.1128/Genomea.01090-17  0.34
2017 Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS. Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice. Msystems. 2. PMID 28904997 DOI: 10.1128/mSystems.00036-17  0.653
2017 Foster ZS, Sharpton TJ, Grünwald NJ. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. Plos Computational Biology. 13: e1005404. PMID 28222096 DOI: 10.1371/Journal.Pcbi.1005404  0.343
2016 Gaulke CA, Barton CL, Proffitt S, Tanguay RL, Sharpton TJ. Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish. Plos One. 11: e0154632. PMID 27191725 DOI: 10.1371/Journal.Pone.0154632  0.355
2015 Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. Plos Computational Biology. 11: e1004573. PMID 26565399 DOI: 10.1371/Journal.Pcbi.1004573  0.752
2015 Sharpton TJ, Gaulke CA. Modeling the Context-Dependent Associations between the Gut Microbiome, Its Environment, and Host Health. Mbio. 6: e01367-15. PMID 26350971 DOI: 10.1128/Mbio.01367-15  0.335
2015 O'Dwyer JP, Kembel SW, Sharpton TJ. Backbones of evolutionary history test biodiversity theory for microbes. Proceedings of the National Academy of Sciences of the United States of America. PMID 26106159 DOI: 10.1073/Pnas.1419341112  0.389
2015 Quandt CA, Kohler A, Hesse CN, Sharpton TJ, Martin F, Spatafora JW. Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome. Environmental Microbiology. PMID 25753751 DOI: 10.1111/1462-2920.12840  0.444
2014 Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. Plos One. 9: e105067. PMID 25140992 DOI: 10.1371/Journal.Pone.0105067  0.686
2014 Sharpton TJ. An introduction to the analysis of shotgun metagenomic data. Frontiers in Plant Science. 5: 209. PMID 24982662 DOI: 10.3389/Fpls.2014.00209  0.458
2014 Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, et al. Exome capture from saliva produces high quality genomic and metagenomic data. Bmc Genomics. 15: 262. PMID 24708091 DOI: 10.1186/1471-2164-15-262  0.71
2014 Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. Plos One. 9: e84689. PMID 24416266 DOI: 10.1371/Journal.Pone.0084689  0.641
2014 Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. The between-study variability in the relative abundance of Bacteroidetes and Firmicutes is greater than the within-study differences between lean and obese individuals. Plos One. DOI: 10.1371/Journal.Pone.0084689.G003  0.608
2013 Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. Global marine bacterial diversity peaks at high latitudes in winter. The Isme Journal. 7: 1669-77. PMID 23514781 DOI: 10.1038/Ismej.2013.37  0.655
2013 Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. Erratum: Global marine bacterial diversity peaks at high latitudes in winter The Isme Journal. 7: 1876-1876. DOI: 10.1038/Ismej.2013.76  0.616
2012 Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. Bmc Bioinformatics. 13: 264. PMID 23061897 DOI: 10.1186/1471-2105-13-264  0.738
2012 Whiston E, Zhang Wise H, Sharpton TJ, Jui G, Cole GT, Taylor JW. Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp. Plos One. 7: e41034. PMID 22911737 DOI: 10.1371/Journal.Pone.0041034  0.731
2012 Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS. Novel bacterial taxa in the human microbiome. Plos One. 7: e35294. PMID 22719826 DOI: 10.1371/Journal.Pone.0035294  0.716
2011 Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. Plos Computational Biology. 7: e1001061. PMID 21283775 DOI: 10.1371/Journal.Pcbi.1001061  0.736
2010 Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, Whiston E, Hung CY, McMahan C, White J, Sykes S, Heiman D, Young S, Zeng Q, Abouelleil A, Aftuck L, et al. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research. 20: 938-46. PMID 20516208 DOI: 10.1101/Gr.103911.109  0.741
2009 Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung CY, McMahan C, Muszewska A, Grynberg M, Mandel MA, et al. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research. 19: 1722-31. PMID 19717792 DOI: 10.1101/Gr.087551.108  0.721
2008 Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. Mechanisms of intron gain and loss in Cryptococcus. Genome Biology. 9: R24. PMID 18234113 DOI: 10.1186/Gb-2008-9-1-R24  0.492
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