Publications

Sharpton Lab Publications

A complete list of publications from the Sharpton Laboratory is found below. A bibtek file of our publications can be found here.

2019

  • Zhang, Yang, Bobe, Gerd, Revel, Johana S., Rodrigues, Richard, Sharpton, Thomas J., Fantacone, Mary L., Raslan, Kareem, Miranda, Cristobal L., Lowry, Malcolm B., Blakemore, Paul R., Morgun, Andrey, Shulzhenko, Natalia, Maier, Claudia S., Stevens, Jan F., Gombart, Adrian F. (2019) Improvements in Metabolic Syndrome by Xanthohumol Derivatives are Linked to Altered Gut Microbiota and Bile Acid Metabolism. Molecular Nutrition & Food Research. In Print. doi: 10.1002/mnfr.201900789
  • Jiang, Duo, Armour, Courtney R., Hu, Chenxiao, Mei, Meng, Tian, Chuan, Sharpton, Thomas J., Jiang, Yuan (2019) Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Frontiers in Genetics. 10(995). doi: 10.3389/fgene.2019.00995
  • Neves, A. L. A., Chen, Y., Lê Cao, K.-A., Mandal, S., Sharpton, T. J., McAllister, T., Guan, L. L. (2019) 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). doi: 10.1017/S1751731119002453
  • Kent, Michael L., Watral, Virginia, Gaulke, Christopher A., Sharpton, Thomas J. (2019) Further evaluation of the efficacy of emamectin benzoate for treating Pseudocapillaria tomentosa (Dujardin 1843) in zebrafish Danio rerio (Hamilton 1822). Journal of Fish Diseases. 42(10). doi: 10.1111/jfd.13057
  • Armour, Courtney R., Nayfach, Stephen, Pollard, Katherine S., Sharpton, Thomas J. (2019) A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. mSystems. 4(4). doi: 10.1128/mSystems.00332-18
  • Flannery, Jessica, Callaghan, Bridget, Sharpton, Thomas, Fisher, Philip, Pfeifer, Jennifer (2019) Is adolescence the missing developmental link in Microbiome-Gut-Brain axis communication?. Developmental Psychobiology. 61(5). doi: 10.1002/dev.21821
  • Li, Yuanfei, Li, Yuqi, Jin, Wei, Sharpton, Thomas J., Mackie, Roderick I., Cann, Isaac, Cheng, Yanfen, Zhu, Weiyun (2019) Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen. Frontiers in Microbiology. 10(435). doi: 10.3389/fmicb.2019.00435
  • Raber, Jacob, Yamazaki, Joy, Torres, Eileen Ruth S., Kirchoff, Nicole, Stagaman, Keaton, Sharpton, Thomas, Turker, Mitchell S., Kronenberg, Amy (2019) Combined Effects of Three High-Energy Charged Particle Beams Important for Space Flight on Brain, Behavioral and Cognitive Endpoints in B6D2F1 Female and Male Mice. Frontiers in Physiology. 10(179). doi: 10.3389/fphys.2019.00179
  • Morelan, Ian A., Gaulke, Christopher A., Sharpton, Thomas J., Vega Thurber, Rebecca, Denver, Dee R. (2019) Microbiome Variation in an Intertidal Sea Anemone Across Latitudes and Symbiotic States. Frontiers in Marine Science. 6(7). doi: 10.3389/fmars.2019.00007
  • Gaulke, Christopher A., Martins, Mauricio L., Watral, Virginia G., Humphreys, Ian R., Spagnoli, Sean T., Kent, Michael L., Sharpton, Thomas J. (2019) A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome's link to Pseudocapillaria tomentosa infection and pathology. Microbiome. 7(1). doi: 10.1186/s40168-019-0622-9
  • Kirchoff, Nicole S., Udell, Monique A. R., Sharpton, Thomas J. (2019) The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris). PeerJ. 7(e6103). doi: 10.7717/peerj.6103

2018

  • Gaulke, Christopher A., Rolshoven, John, Wong, Carmen P., Hudson, Laurie G., Ho, Emily, Sharpton, Thomas J. (2018) Marginal Zinc Deficiency and Environmentally Relevant Concentrations of Arsenic Elicit Combined Effects on the Gut Microbiome. mSphere. 3(6). doi: 10.1128/mSphere.00521-18
  • Kent, Michael L., Gaulke, Christopher A., Watral, Virginia, Sharpton, Thomas J. (2018) Pseudocapillaria tomentosa in laboratory zebrafish Danio rerio: patterns of infection and dose response. Diseases of Aquatic Organisms. 131(2). doi: 10.3354/dao03286
  • Gaulke, Christopher A., Sharpton, Thomas J. (2018) The influence of ethnicity and geography on human gut microbiome composition. Nature Medicine. 24(10). doi: 10.1038/s41591-018-0210-8
  • Gaulke, Christopher A., Arnold, Holly K., Humphreys, Ian R., Kembel, Steven W., O'Dwyer, James P., Sharpton, Thomas J. (2018) Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota. mBio. 9(5). doi: 10.1128/mBio.01348-18
  • Torres, Eileen Ruth S., Akinyeke, Tunde, Stagaman, Keaton, Duvoisin, Robert M., Meshul, Charles K., Sharpton, Thomas J., Raber, Jacob (2018) Effects of Sub-Chronic MPTP Exposure on Behavioral and Cognitive Performance and the Microbiome of Wild-Type and mGlu8 Knockout Female and Male Mice. Frontiers in Behavioral Neuroscience. 12(140). doi: 10.3389/fnbeh.2018.00140
  • Allan, Euan R. O., Tennessen, Jacob A., Sharpton, Thomas J., Blouin, Michael S. (2018) Allelic Variation in a Single Genomic Region Alters the Microbiome of the Snail Biomphalaria glabrata. The Journal of Heredity. 109(5). doi: 10.1093/jhered/esy014
  • Sharpton, Thomas J. (2018) Role of the Gut Microbiome in Vertebrate Evolution. mSystems. 3(2). doi: 10.1128/mSystems.00174-17
  • Burns, A. R., Watral, V., Sichel, S., Spagnoli, S., Banse, A. V., Mittge, E., Sharpton, T. J., Guillemin, K., Kent, M. L. (2018) Transmission of a common intestinal neoplasm in zebrafish by cohabitation. Journal of Fish Diseases. 41(4). doi: 10.1111/jfd.12743
  • Wang, Lu, Shantz, Andrew A., Payet, Jérôme P., Sharpton, Thomas J., Foster, Amelia, Burkepile, Deron E., Vega Thurber, Rebecca (2018) Corals and Their Microbiomes Are Differentially Affected by Exposure to Elevated Nutrients and a Natural Thermal Anomaly. Frontiers in Marine Science. 5(7). doi: 10.3389/fmars.2018.00101

2017

  • Cheng, Yanfen, Wang, Ying, Li, Yuanfei, Zhang, Yipeng, Liu, Tianyi, Wang, Yu, Sharpton, Thomas J., Zhu, Weiyun (2017) Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing. Frontiers in Microbiology. 8(2165). doi: 10.3389/fmicb.2017.02165
  • Sharpton, Thomas, Lyalina, Svetlana, Luong, Julie, Pham, Joey, Deal, Emily M., Armour, Courtney, Gaulke, Christopher, Sanjabi, Shomyseh, Pollard, Katherine S. (2017) Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice. mSystems. 2(5). doi: 10.1128/mSystems.00036-17
  • Wilson, Alexandria K., Watral, Virginia G., Kent, Michael L., Sharpton, Thomas J., Gaulke, Christopher A. (2017) Draft Genome Sequence of Pseudomonas sp. Strain DrBHI1 (Phylum Proteobacteria). Genome Announcements. 5(39). doi: 10.1128/genomeA.01090-17
  • Conley, Melissa N., Roberts, Cooper, Sharpton, Thomas J., Iwaniec, Urszula T., Hord, Norman G. (2017) Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized rats. Molecular Nutrition & Food Research. 61(5). doi: 10.1002/mnfr.201600372
  • Foster, Zachary S. L., Sharpton, Thomas J., Grünwald, Niklaus J. (2017) Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS computational biology. 13(2). doi: 10.1371/journal.pcbi.1005404

2016

  • Kent, Michael L., Watral, Virginia G., Kirchoff, Nicole S., Spagnoli, Sean T., Sharpton, Thomas J. (2016) Effects of Subclinical Mycobacterium chelonae Infections on Fecundity and Embryo Survival in Zebrafish. Zebrafish. 13(Suppl 1). doi: 10.1089/zeb.2015.1204
  • Gaulke, Christopher A., Barton, Carrie L., Proffitt, Sarah, Tanguay, Robert L., Sharpton, Thomas J. (2016) Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish. PloS One. 11(5). doi: 10.1371/journal.pone.0154632
  • Conley, Melissa N., Wong, Carmen P., Duyck, Kyle M., Hord, Norman, Ho, Emily, Sharpton, Thomas J. (2016) Aging and serum MCP-1 are associated with gut microbiome composition in a murine model. PeerJ. 4(e1854). doi: 10.7717/peerj.1854

2015

  • Nayfach, Stephen, Bradley, Patrick H., Wyman, Stacia K., Laurent, Timothy J., Williams, Alex, Eisen, Jonathan A., Pollard, Katherine S., Sharpton, Thomas J. (2015) Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS computational biology. 11(11). doi: 10.1371/journal.pcbi.1004573
  • Sharpton, Thomas J., Gaulke, Christopher A. (2015) Modeling the Context-Dependent Associations between the Gut Microbiome, Its Environment, and Host Health. mBio. 6(5). doi: 10.1128/mBio.01367-15
  • Quandt, C. Alisha, Kohler, Annegret, Hesse, Cedar N., Sharpton, Thomas J., Martin, Francis, Spatafora, Joseph W. (2015) Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome. Environmental Microbiology. 17(8). doi: 10.1111/1462-2920.12840
  • O'Dwyer, James P., Kembel, Steven W., Sharpton, Thomas J. (2015) Backbones of evolutionary history test biodiversity theory for microbes. Proceedings of the National Academy of Sciences of the United States of America. 112(27). doi: 10.1073/pnas.1419341112

2014

  • Kent, M. L., Soderlund, K., Thomann, Estela, Schreck, C. B., Sharpton, T. J. (2014) Post-mortem sporulation of Ceratomyxa shasta (Myxozoa) after death in adult Chinook salmon. The Journal of Parasitology. 100(5). doi: 10.1645/13-490.1
  • Huttenhower, Curtis, Knight, Rob, Brown, C. Titus, Caporaso, J. Gregory, Clemente, Jose C., Gevers, Dirk, Franzosa, Eric A., Kelley, Scott T., Knights, Dan, Ley, Ruth E., Mahurkar, Anup, Ravel, Jacques, Scientists for Advancement of Microbiome Research, White, Owen (2014) Advancing the microbiome research community. Cell. 159(2). doi: 10.1016/j.cell.2014.09.022
  • Skewes-Cox, Peter, Sharpton, Thomas J., Pollard, Katherine S., DeRisi, Joseph L. (2014) Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PloS One. 9(8). doi: 10.1371/journal.pone.0105067
  • Sharpton, Thomas J. (2014) An introduction to the analysis of shotgun metagenomic data. Frontiers in Plant Science. 5(209). doi: 10.3389/fpls.2014.00209
  • Kidd, Jeffrey M., Sharpton, Thomas J., Bobo, Dean, Norman, Paul J., Martin, Alicia R., Carpenter, Meredith L., Sikora, Martin, Gignoux, Christopher R., Nemat-Gorgani, Neda, Adams, Alexandra, Guadalupe, Moraima, Guo, Xiaosen, Feng, Qiang, Li, Yingrui, Liu, Xiao, Parham, Peter, Hoal, Eileen G., Feldman, Marcus W., Pollard, Katherine S., Wall, Jeffrey D., Bustamante, Carlos D., Henn, Brenna M. (2014) Exome capture from saliva produces high quality genomic and metagenomic data. BMC genomics. 15(262). doi: 10.1186/1471-2164-15-262
  • Finucane, Mariel M., Sharpton, Thomas J., Laurent, Timothy J., Pollard, Katherine S. (2014) A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PloS One. 9(1). doi: 10.1371/journal.pone.0084689

2013

  • Ladau, Joshua, Sharpton, Thomas J., Finucane, Mariel M., Jospin, Guillaume, Kembel, Steven W., O'Dwyer, James, Koeppel, Alexander F., Green, Jessica L., Pollard, Katherine S. (2013) Global marine bacterial diversity peaks at high latitudes in winter. The ISME journal. 7(9). doi: 10.1038/ismej.2013.37

Before 2013

  • Sharpton, Thomas J., Jospin, Guillaume, Wu, Dongying, Langille, Morgan G. I., Pollard, Katherine S., Eisen, Jonathan A. (2012) Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC bioinformatics. 13(264). doi: 10.1186/1471-2105-13-264
  • Whiston, Emily, Zhang Wise, Hua, Sharpton, Thomas J., Jui, Ginger, Cole, Garry T., Taylor, John W. (2012) Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp. PloS One. 7(7). doi: 10.1371/journal.pone.0041034
  • Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature. 486(7402). doi: 10.1038/nature11234
  • Human Microbiome Project Consortium (2012) A framework for human microbiome research. Nature. 486(7402). doi: 10.1038/nature11209
  • Wylie, Kristine M., Truty, Rebecca M., Sharpton, Thomas J., Mihindukulasuriya, Kathie A., Zhou, Yanjiao, Gao, Hongyu, Sodergren, Erica, Weinstock, George M., Pollard, Katherine S. (2012) Novel bacterial taxa in the human microbiome. PloS One. 7(6). doi: 10.1371/journal.pone.0035294
  • Sharpton, Thomas J., Riesenfeld, Samantha J., Kembel, Steven W., Ladau, Joshua, O'Dwyer, James P., Green, Jessica L., Eisen, Jonathan A., Pollard, Katherine S. (2011) PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS computational biology. 7(1). doi: 10.1371/journal.pcbi.1001061
  • Neafsey, Daniel E., Barker, Bridget M., Sharpton, Thomas J., Stajich, Jason E., Park, Daniel J., Whiston, Emily, Hung, Chiung-Yu, McMahan, Cody, White, Jared, Sykes, Sean, Heiman, David, Young, Sarah, Zeng, Qiandong, Abouelleil, Amr, Aftuck, Lynne, Bessette, Daniel, Brown, Adam, FitzGerald, Michael, Lui, Annie, Macdonald, J. Pendexter, Priest, Margaret, Orbach, Marc J., Galgiani, John N., Kirkland, Theo N., Cole, Garry T., Birren, Bruce W., Henn, Matthew R., Taylor, John W., Rounsley, Steven D. (2010) Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research. 20(7). doi: 10.1101/gr.103911.109
  • Sharpton, Thomas J., Stajich, Jason E., Rounsley, Steven D., Gardner, Malcolm J., Wortman, Jennifer R., Jordar, Vinita S., Maiti, Rama, Kodira, Chinnappa D., Neafsey, Daniel E., Zeng, Qiandong, Hung, Chiung-Yu, McMahan, Cody, Muszewska, Anna, Grynberg, Marcin, Mandel, M. Alejandra, Kellner, Ellen M., Barker, Bridget M., Galgiani, John N., Orbach, Marc J., Kirkland, Theo N., Cole, Garry T., Henn, Matthew R., Birren, Bruce W., Taylor, John W. (2009) Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research. 19(10). doi: 10.1101/gr.087551.108
  • Sharpton, Thomas J., Neafsey, Daniel E., Galagan, James E., Taylor, John W. (2008) Mechanisms of intron gain and loss in Cryptococcus. Genome Biology. 9(1). doi: 10.1186/gb-2008-9-1-r24
  • Sharpton, Thomas J., Jhaveri, Arpan A. (2006) Leveraging the knowledge of our peers: online communities hold the promise to enhance scientific research. PLoS biology. 4(6). doi: 10.1371/journal.pbio.0040199