Publications

* indicates equal author contributions; underline members of the David Lab.

  1. JD SilvermanRJ BloomS Jiang, HK DurandE Dallow, Sayan Mukherjee, LA David. “Measuring and mitigating PCR bias in microbiota datasets” PLoSComput Biol Jul 2021, 17(7): e1009113.[link]
  2. ZC HolmesJD SilvermanHK DressmanZ WeiEP DallowSC ArmstrongPC SeedJF RawlsLA David. “Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition.” mBio Aug 2020, 11 (4) e00914-20. [link]
  3. MM Villa*RJ Bloom*, JD Silverman, HK Durand, S Jiang, A Wu, EP Dallow, S Huang, L You, and LA David.”Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture” mSystems. 2020 Jun 30;5(3):e00864-19. [link]
  4. SN Nimmagadda, FS Midani, HK Durand, AT Reese, C Murdoch, BP Nicholson, T Veldman, TW Burke, AK Zaas, CW Woods, G Ginsburg, LA David. “Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection” medRxiv 2020.04.11.20061911. [link]
  5. JD Silverman, K Roche, S Mukherjee, LA David. “Naught all zeros in sequence count data are the same” Comput Struct Biotechnol J. 2020 Sep 28;18:2789-2798. [link]
  6. AT Reese, TR Kartzinel, BL Petrone, PJ Turnbaugh, RM Pringle, LA David. “Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept.” mSystems Oct 2019, 4 (5) e00458-19. [link]
  7. JD Silverman, HK Durand, RJ Bloom, S Mukherjee, and LA David. Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome6:202, Nov 2018. [link]
  8. AT Reese, FC Pereira, A Schintlmeister, D Berry, M Wagner, LP Hale, A Wu, S Jiang, HK Durand, X Zhou, RT Premont, AM Diehl, TM O’Connell, SC Alberts, TR Kartzinel, RM Pringle, RR Dunn, JP Wright & LA David. Microbial nitrogen limitation in the mammalian large intestine. Nature Microbiology,  Vol. 3, pages 1441–1450 (2018). [link]
  9. AT Reese, EH Cho, B Klitzman, SP Nichols, NA Wisniewski, MM Villa, HK Durand, S Jiang, FS Midani, SN Nimmagadda, TM O’Connell, JP Wright, MA Deshusses, LA David. Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. eLIFE, 10.7554/eLife.35987, Jun 2018. [link]
  10. FS Midani*, AA Weil*, F Chowdhury, YA Begum, AI Khan, MD Debela, HK Durand, AT Reese, SN Nimmagadda, JD Silverman, CN Ellis, ET Ryan, SB Calderwood, JB Harris, F Qadri, LA David, RC LaRocque; Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection, The Journal of Infectious Diseases, jiy192, [linkm_cover JID
  11. David, LA. 2018. Toward personalized control of the human gut bacterial communities. mSystems 3:e00165-17. [link]
  12. AT Reese, K Lulow, LA David, JP Wright. Plant community and soil conditions individually affect soil microbial community assembly in experimental old-field microcosms. Ecol Evol. 2017 Dec 20;8(2):1196-1205. [link]
  13. JD Silverman, A Washburne, S Mukherjee, LA David. A phylogenetic transform enhances analysis of compositional microbiota data. eLife, 10.7554/eLife.21887, Feb 2017. [link]
  14. AD Washburne, J Silverman, JW Leff, DJ Bennett, J Darcy, S Mukherjee, N Fierer, LA David. Phylogenetic factorization of microbiome data yields lineage-level associations in microbiome datasets. PeerJ, 5:e2969, Feb 2017. [link]
  15. J Boursier, O Mueller, M Barret, M Machado, L Fizanne, F Araujo-Perez, C Guy, P Seed, J Rawls, LA David, G Hunault, F Oberti, P Cales, AM Diehl. The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology, 63(3):764-775, Mar 2016. [link]
  16. S Wong, WZ Stephens, AR Burns, K Stagaman, LA David, BJM Bohannan, K Guillemin, JF Rawls. Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut. mBio, 6(5):e00687-15, Sept 2015. [link]
  17. LA Davidcover_nature, A Weil, ET Ryan, SB Calderwood, JB Harris, F Chowdhury, Y Begum, F Qadri, RC LaRocque, PJ Turnbaugh. Gut microbial succession follows acute secretory diarrhea in humans. mBio,6(3):e00381-15, Apr 2015. [link]
  18. LA David, AC Materna, J Friedman, I Baptista, MC Blackburn, A Perrotta, SE Erdman, EJ Alm. Host lifestyle affects human microbiota on daily timescales. Genome Biol, 15:R89, Jul 2014. [link]
  19. LA David, CF Maurice, RN Carmody, DB Gootenberg, JE Button, BE Wolfe, AV Ling, AS Devlin, Y Varma, MA Fischbach, SB Biddinger, RJ Dutton, PJ Turnbaugh. Diet rapidly and reproducibly alters the gut microbiome. Nature, 505(7484):559-563, Jan 2014.  [link]
  20. G Szabo, SP Preheim, KM Kauffman, LA David, J Shapiro, EJ Alm, MF Polz. Reproducibility of Vibrionaceae Population Structure in Coastal Bacterioplankton. ISME J, 7: 509-519, Mar 2013. [link]
  21. CS Smillie*, MB Smith*, J Friedman, OX Cordero, LA David, EJ Alm. Ecology drives a global network of gene exchange connecting the human microbiome. Nature, 480(7376):241-244, Dec, 2011. [link]angst_cover
  22. LA David, EJ Alm. Rapid evolutionary innovation during an Archean Genetic Expansion. Nature, 469(7328):93-96, Jan 2011. [link]
  23. SP Preheim, Y Boucher, H Wildschutte, LA David, D Veneziano, EJ Alm and MF Polz. Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environ Microbiol, 13:265-275, Jan 2011. [link]
  24. BJ Shapiro, LA David, J Friedman, EJ Alm. Looking for Darwin’s footprints in the microbial world. Trends Microbiol. 17(5):196-204, May 2009. [link]
  25. BJ Dubin-Thaler, JM Hofman, Y Cai, H Xenias, I Spielman, AV Shneidman, LA David, HG Dobereiner, CH Wiggins, MP Sheetz. Quantification of Cell Edge Velocities and Traction Forces Reveals Distinct Motility Modules during Cell Spreading. PLoS ONE, 3(11), Nov 2008. [link]
  26. DE Hunt*, LA David*, D Gevers, SP Preheim, EJ Alm, MF Polz. Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton. Science, 320(5879):1081-85, May 2008. [link]science_cover
  27. LA David, CH Wiggins. Benchmarking of dynamic Bayesian Networks from stochastic time-series data. Ann NY Acad Sci., 1115 90-101, Dec 2007. [link]
  28. CF Glenn, DK Chow, L David, C Cooke, M Gami, W Iser, K Hanselman, I Goldberg and CA Wolkow. Behavioral deficits during early states of aging in Caenorhabditis elegans result from locomotory deficits possibly linked to muscle frailty. J Gerontol A Biol Sci Med Sci., 59(12):1251-60, Dec 2004. [link]