Selected publications below. Full list of publications on Google Scholar

On the Microbiota-Gut-Brain axis

Hokanson, K.C., Hernández, C., Deitzler, G.E., Gaston, J.E., David, M.M., 2024. Sex shapes gut-microbiota-brain communication and disease. Trends Microbiol. 32, 151–161.

Morton, J.T., Jin, D.-M., Mills, R.H., Shao, Y., Rahman, G., McDonald, D., Zhu, Q., Balaban, M., Jiang, Y., Cantrell, K., Gonzalez, A., Carmel, J., Frankiensztajn, L.M., Martin-Brevet, S., Berding, K., Needham, B.D., Zurita, M.F., David, M., Averina, O.V., Kovtun, A.S., Noto, A., Mussap, M., Wang, M., Frank, D.N., Li, E., Zhou, W., Fanos, V., Danilenko, V.N., Wall, D.P., Cárdenas, P., Baldeón, M.E., Jacquemont, S., Koren, O., Elliott, E., Xavier, R.J., Mazmanian, S.K., Knight, R., Gilbert, J.A., Donovan, S.M., Lawley, T.D., Carpenter, B., Bonneau, R., Taroncher-Oldenburg, G., 2023. Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nat. Neurosci. 26, 1208–1217.

Tataru, C., Peras, M., Rutherford, E., Dunlap, K., Yin, X., Chrisman, B.S., DeSantis, T.Z., Wall, D.P., Iwai, S., David, M.M., 2023b. Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism. Sci. Rep. 13, 11353.

Tataru, C., Martin, A., Dunlap, K., Peras, M., Chrisman, B.S., Rutherford, E., Deitzler, G.E., Phillips, A., Yin, X., Sabino, K., Hannibal, R.L., Hartono, W., Lin, M., Raack, E., Wu, Y., DeSantis, T.Z., Iwai, S., Wall, D.P., David, M.M., 2021. Longitudinal study of stool-associated microbial taxa in sibling pairs with and without autism spectrum disorder. ISME Communications 1, 1–12.

David, M.M., Tataru, C., Daniels, J., Schwartz, J., Keating, J., Hampton-Marcell, J., Gottel, N., Gilbert, J., and Wall, D.P. 2021. Children with autism and their typically developing siblings differ in amplicon sequence variants and predicted functions of stool-associated microbes. mSystems 6(2): e00193-20.

David Maude M., 2021. The Role of the Microbiome in Autism: All That We Know about All That We Don’t Know. mSystems 6, 10.1128/msystems.00234–21.

David, M.M., Babineau, B.A., Wall, D.P., 2016a. Can we accelerate autism discoveries through crowdsourcing? Res. Autism Spectr. Disord. 32, 80–83.

Computational Biology and Deep Learning Work

Tataru, C., Eaton, A., David, M.M., 2022. GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data. Front Bioinform 2, 828703.

Tataru, C. and David, M.M. 2020. Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease. PLoS Comput Biol 4;16(5):e1007859. doi: 10.1371/journal.pcbi.1007859.

Prestat, E.*, David, M.M.*, Hultman, J., Tas, N., Lamendella, R., Dvornik, J., Mackelprang, R., Myrold, D.D., Jumpponen, A., Tringe, S.G., Holman, E., Mavromatis, K. and Jansson, J.K. 2014. FOAM (Functional Ontology Assignments for Metagenomes): A hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res. 42(10):e145-e145. *both authors contributed equally to this work

David, M.M., Tataru, C., Pope, Q., Baker, L.J., English, M.K., Epstein, H.E., Hammer, A., Kent, M., Sieler, M.J., Jr, Mueller, R.S., Sharpton, T.J., Tomas, F., Vega Thurber, R., Fern, X.Z., 2022. Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning. mSystems 7, e0105821.

Chrisman, B.S., Paskov, K.M., Stockham, N., Jung, J.-Y., Varma, M., Washington, P.Y., Tataru, C., Iwai, S., DeSantis, T.Z., David, M., Wall, D.P., 2021. Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers. BMC Bioinformatics 22, 509.

Prestat, E., David, M.M., Hultman, J., Taş, N., Lamendella, R., Dvornik, J., Mackelprang, R., Myrold, D.D., Jumpponen, A., Tringe, S.G., Holman, E., Mavromatis, K., Jansson, J.K., 2014. FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res. 42, e145.

Still on BioRxiv but still very interesting (we think)

Pope, Q., Varma, R., Tataru, C., David, M., Fern, X., 2023. Learning a deep language model for microbiomes: the power of large scale unlabeled microbiome data. bioRxiv. https://doi.org/10.1101/2023.07.17.549267

Chips! Something the lab is now working on

Tataru, C., Livni, M., Marean-Reardon, C., Franco, M.C., David, M., 2023a. Cytokine induced inflammatory bowel disease model using organ-on-a-chip technology. PLoS One 18, e0289314.

Other things Dr. David worked on before OSU

Hultman, J., Waldrop, M.P., Mackelprang, R., David, M., McFarland, J., Blazewicz, S.J., Harden, J., Turetsky, M.R., McGuire, A.D., Shah, M.B., VerBerkmoes, N.C., Lee, L.H., Mavrommatis, K., and Jansson, J.K. 2015. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521(7551):208-212.

Mackelprang, R., Waldrop, M.P., DeAngelis, K.M., David, M.M., Chavarria, K.L., Blazewicz, S.J., Rubin, E.M., and Jansson, J.K. 2011. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480 (7377):368-371.

More autism work on human genes only (no microbes involved)

Diaz-Beltran, L., Esteban, F.J., Varma, M., Ortuzk, A., David, M., Wall, D.P., 2017. Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes. BMC Genomics 18, 315.

David, M.M., Enard, D., Ozturk, A., Daniels, J., Jung, J.-Y., Diaz-Beltran, L., Wall, D.P., 2016b. Comorbid Analysis of Genes Associated with Autism Spectrum Disorders Reveals Differential Evolutionary Constraints. PLoS One 11, e0157937.