Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., Massachusetts Institute of Technology 2010
• 

  Duke Appointment History

  • Core Faculty in Innovation & Entrepreneurship, Duke Innovation & Entrepreneurship, Initiatives 2018 - 2021
  • Assistant Professor of Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2013 - 2021
  • Affiliate of the Duke Initiative for Science & Society, Duke Science & Society, Initiatives 2014 - 2019
  • Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2016 - 2019
  • Instructor, Temporary in the Department of Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2013
• Recognition
• 

  In the News

  • MAY 25, 2021

    School of Medicine

    School of Medicine Researchers Honored for Study of the Pathogenesis of Infectious Disease

  • JUL 1, 2020

    Center for Genomic and Computational Biology

    Everybody's Microbiome Is Different. So How Do You Study It Usefully?

  • JAN 7, 2020

    Poop: It's a Great Thing to Study

  • OCT 29, 2018

    Our Microbes Are Starving, and That’s a Good Thing

  • MAY 7, 2018

    AI Detects Patterns Of Gut Microbes for Cholera Risk

  • MAR 20, 2017

    Microbes Evolved to Colonize Different Parts of the Human Body

  • SEP 22, 2016

    Science News

    Ten Scientists to Watch: Lawrence Davids gut check gets personal

  • JUN 17, 2016

    A Little Dirt Won't Hurt You

  • MAR 16, 2016

    New Collaborative Seed Grant Program Gives Eight Awards

  • APR 15, 2015

    Lawrence David Named Searle Scholar

  • JUL 25, 2014

    National Geographic

    Q-and-A: Scientist studied his poop for a year to learn about gut bugs

  • MAY 13, 2014

    Duke Research Blog

    Lawrence David Gets to the Gut of the Matter

  • FEB 18, 2014

    Five Science Faculty Win Sloan Fellowships

  • DEC 12, 2013

    Fox News, LiveScience

    Changes in diet can alter gut bacteria within 24 hours

  • OCT 23, 2013

    MIcrobes R Us
• 

  Awards & Honors

  • Sloan Research Fellowship-Molecular Biology. Alfred P. Sloan Foundation. 2014
  • Harvard Society Junior Fellows. Harvard Society of Fellows. 2010
• Research
• 

  Selected Grants

  • Dietary strategies for enhancing bacterial pathogen resistance in the gut awarded by Burroughs Wellcome Fund 2021 - 2026
  • A Randomized Phase 2 Trial to Evaluate Prebiotic Intervention in Allogeneic Hematopoietic Stem Cell Transplantation awarded by National Institutes of Health 2020 - 2025
  • Genetic and Genomics Training Grant awarded by National Institutes of Health 2020 - 2025
  • Genetic analysis of mucin utilization by Akkermansia muciniphila and its impact on host physiology awarded by National Institutes of Health 2018 - 2023
  • Duke KURe Program awarded by National Institutes of Health 2013 - 2023
  • Duke CTSA (TL1) awarded by National Institutes of Health 2018 - 2023
  • Testing the need to personalize prebiotic therapies targeting human gut microbiota awarded by National Institutes of Health 2017 - 2022
  • Accurate and automated tracking of patient urine and stool awarded by North Carolina Biotechnology Center 2019 - 2022
  • Medical Scientist Training Program awarded by National Institutes of Health 1997 - 2022
  • Personalized Prebiotics to Optimize Microbiota Metabolism and Improve Transplant Outcomes awarded by Damon Runyon Cancer Research Foundation 2018 - 2021
  • A comprehensive research resource to define mechanisms underlying microbial regulation of host metabolism in pediatric obesity and obesity-targeted therapeutics awarded by National Institutes of Health 2016 - 2021
  • Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
  • Predicting prebiotic effects on human microbiota, behavior, and cognition. awarded by Office of Naval Research 2018 - 2021
  • Using natural bacterial interactions to control host-associated microbial communities awarded by Arnold and Mabel Beckman Foundation 2015 - 2020
  • Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
  • AZD9668 and Neutrophil Elastase Inhibition to Prevent Graft-versus-Host Disease awarded by National Institutes of Health 2018 - 2019
  • Personalizing prebiotic therapies for astronauts' gut microbiota awarded by Baylor College of Medicine 2017 - 2019
  • A high througput platform for screening microbial interactions awarded by Burroughs Wellcome Fund 2016 - 2019
  • Personalizing prebiotic treatments that manipulate human gut microbiota awarded by University of North Carolina - Chapel Hill 2017 - 2018
  • Genetic Analysis in an intractable gut microbe awarded by National Institutes of Health 2016 - 2018
  • Linking oxygen and bacterial ecology in necrotizing enterocolitis awarded by Hartwell Foundation 2015 - 2018
  • Quantifying Nitrogen Limitation in the Gut Microbiota awarded by  National Science Foundation 2015 - 2017
  • HARDAC+:Reproducible HPC for next-generation genomics awarded by North Carolina Biotechnology Center 2016 - 2017
  • Alfred P. Sloan Research Fellowship for Dr. Lawrence David in Computational & Evolutionary Molecular Biology awarded by Alfred P. Sloan Foundation 2014 - 2016
  • Automated Library Preparation System for Next-Generation Sequencing awarded by North Carolina Biotechnology Center 2014 - 2015
  • Discovering natural bacterial interactions within the human gut microbiota awarded by The Global Probiotic Council 2014 - 2015
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Silverman, Justin D., Rachael J. Bloom, Sharon Jiang, Heather K. Durand, Eric Dallow, Sayan Mukherjee, and Lawrence A. David. “Measuring and mitigating PCR bias in microbiota datasets.” Plos Comput Biol 17, no. 7 (July 2021): e1009113. https://doi.org/10.1371/journal.pcbi.1009113.
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    • Becken, Bradford, Lauren Davey, Dustin R. Middleton, Katherine D. Mueller, Agastya Sharma, Zachary C. Holmes, Eric Dallow, et al. “Genotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila.” Mbio 12, no. 3 (May 18, 2021). https://doi.org/10.1128/mBio.00478-21.
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    • McCann, Jessica R., Nathan A. Bihlmeyer, Kimberly Roche, Cameron Catherine, Jayanth Jawahar, Lydia Coulter Kwee, Noelle E. Younge, et al. “The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights.” Obesity (Silver Spring) 29, no. 3 (March 2021): 569–78. https://doi.org/10.1002/oby.23081.
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    • Levade, Inès, Morteza M. Saber, Firas S. Midani, Fahima Chowdhury, Ashraful I. Khan, Yasmin A. Begum, Edward T. Ryan, et al. “Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study.” J Infect Dis 223, no. 2 (February 3, 2021): 342–51. https://doi.org/10.1093/infdis/jiaa358.
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    • Cholan, Pradeep Manuneedhi, Alvin Han, Brad R. Woodie, Maxinne Watchon, Angela Rm Kurz, Angela S. Laird, Warwick J. Britton, et al. “Conserved anti-inflammatory effects and sensing of butyrate in zebrafish.” Gut Microbes 12, no. 1 (November 9, 2020): 1–11. https://doi.org/10.1080/19490976.2020.1824563.
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    • Holmes, Zachary C., Justin D. Silverman, Holly K. Dressman, Zhengzheng Wei, Eric P. Dallow, Sarah C. Armstrong, Patrick C. Seed, John F. Rawls, and Lawrence A. David. “Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition.” Mbio 11, no. 4 (August 11, 2020). https://doi.org/10.1128/mBio.00914-20.
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    • Villa, Max M., Rachael J. Bloom, Justin D. Silverman, Heather K. Durand, Sharon Jiang, Anchi Wu, Eric P. Dallow, Shuqiang Huang, Lingchong You, and Lawrence A. David. “Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture.” Msystems 5, no. 3 (June 30, 2020). https://doi.org/10.1128/mSystems.00864-19.
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    • Martiny, Jennifer B. H., Katrine L. Whiteson, Brendan J. M. Bohannan, Lawrence A. David, Nicole A. Hynson, Margaret McFall-Ngai, John F. Rawls, et al. “The emergence of microbiome centres.” Nat Microbiol 5, no. 1 (January 2020): 2–3. https://doi.org/10.1038/s41564-019-0644-x.
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    • Silverman, Justin D., Kimberly Roche, Sayan Mukherjee, and Lawrence A. David. “Naught all zeros in sequence count data are the same.” Comput Struct Biotechnol J 18 (2020): 2789–98. https://doi.org/10.1016/j.csbj.2020.09.014.
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    • Reese, Aspen T., Tyler R. Kartzinel, Brianna L. Petrone, Peter J. Turnbaugh, Robert M. Pringle, and Lawrence A. David. “Using DNA Metabarcoding To Evaluate the Plant Component of Human Diets: a Proof of Concept.” Msystems 4, no. 5 (October 8, 2019). https://doi.org/10.1128/mSystems.00458-19.
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    • Washburne, A. D., J. D. Silverman, J. T. Morton, D. J. Becker, D. Crowley, S. Mukherjee, L. A. David, and R. K. Plowright. “Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data.” Ecological Monographs 89, no. 2 (May 1, 2019). https://doi.org/10.1002/ecm.1353.
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    • Reese, Aspen T., Fátima C. Pereira, Arno Schintlmeister, David Berry, Michael Wagner, Laura P. Hale, Anchi Wu, et al. “Microbial nitrogen limitation in the mammalian large intestine.” Nat Microbiol 3, no. 12 (December 2018): 1441–50. https://doi.org/10.1038/s41564-018-0267-7.
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    • Silverman, Justin D., Heather K. Durand, Rachael J. Bloom, Sayan Mukherjee, and Lawrence A. David. “Correction to: Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.” Microbiome 6, no. 1 (November 27, 2018): 212. https://doi.org/10.1186/s40168-018-0601-6.
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    • Silverman, Justin D., Heather K. Durand, Rachael J. Bloom, Sayan Mukherjee, and Lawrence A. David. “Dynamic linear models guide design and analysis of microbiota studies within artificial human guts.” Microbiome 6, no. 1 (November 12, 2018): 202. https://doi.org/10.1186/s40168-018-0584-3.
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    • Midani, Firas S., Ana A. Weil, Fahima Chowdhury, Yasmin A. Begum, Ashraful I. Khan, Meti D. Debela, Heather K. Durand, et al. “Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection.” J Infect Dis 218, no. 4 (July 13, 2018): 645–53. https://doi.org/10.1093/infdis/jiy192.
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    • Reese, Aspen T., Eugenia H. Cho, Bruce Klitzman, Scott P. Nichols, Natalie A. Wisniewski, Max M. Villa, Heather K. Durand, et al. “Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut.” Elife 7 (June 19, 2018). https://doi.org/10.7554/eLife.35987.
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    • Silverman, Justin, Heather Durand, Rachael Bloom, Sayan Mukherjee, and Lawrence David. “Dynamic linear models guide design and analysis of microbiota studies within artificial human guts,” April 24, 2018. https://doi.org/10.1101/306597.
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    • David, Lawrence A. “Toward Personalized Control of Human Gut Bacterial Communities.” Msystems 3, no. 2 (March 2018). https://doi.org/10.1128/mSystems.00165-17.
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    • Reese, Aspen T., Kyrstin Lulow, Lawrence A. David, and Justin P. Wright. “Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms.” Ecol Evol 8, no. 2 (January 2018): 1196–1205. https://doi.org/10.1002/ece3.3734.
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    • Silverman, Justin D., Alex D. Washburne, Sayan Mukherjee, and Lawrence A. David. “A phylogenetic transform enhances analysis of compositional microbiota data.” Elife 6 (February 15, 2017). https://doi.org/10.7554/eLife.21887.
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    • Washburne, Alex D., Justin D. Silverman, Jonathan W. Leff, Dominic J. Bennett, John L. Darcy, Sayan Mukherjee, Noah Fierer, and Lawrence A. David. “Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.” Peerj 5 (2017): e2969. https://doi.org/10.7717/peerj.2969.
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    • Washburne, Alex, Justin Silverman, Jonathan Leff, Dominic Bennett, John Darcy, Sayan Mukherjee, Noah Fierer, and Lawrence David. “Phylogenetic factorization of compositional data,” September 8, 2016. https://doi.org/10.1101/074112.
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    • Silverman, Justin, Alex Washburne, Sayan Mukherjee, and Lawrence David. “A phylogenetic transform enhances analysis of compositional microbiota data,” August 31, 2016. https://doi.org/10.1101/072413.
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    • David, Lawrence A., Arne C. Materna, Jonathan Friedman, Maria I. C. Baptista, Matthew C. Blackburn, Allison Perrotta, Susan E. Erdman, and Eric J. Alm. “Erratum to: Host lifestyle affects human microbiota on daily timescales.” Genome Biol 17, no. 1 (May 31, 2016): 117. https://doi.org/10.1186/s13059-016-0988-y.
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    • Boursier, Jérôme, Olaf Mueller, Matthieu Barret, Mariana Machado, Lionel Fizanne, Felix Araujo-Perez, Cynthia D. Guy, et al. “The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota.” Hepatology 63, no. 3 (March 2016): 764–75. https://doi.org/10.1002/hep.28356.
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    • Wong, Sandi, W Zac Stephens, Adam R. Burns, Keaton Stagaman, Lawrence A. David, Brendan J. M. Bohannan, Karen Guillemin, and John F. Rawls. “Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut.” Mbio 6, no. 5 (September 29, 2015): e00687–e00615. https://doi.org/10.1128/mBio.00687-15.
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    • David, Lawrence A., Ana Weil, Edward T. Ryan, Stephen B. Calderwood, Jason B. Harris, Fahima Chowdhury, Yasmin Begum, Firdausi Qadri, Regina C. LaRocque, and Peter J. Turnbaugh. “Gut microbial succession follows acute secretory diarrhea in humans.” Mbio 6, no. 3 (May 19, 2015): e00381–e00315. https://doi.org/10.1128/mBio.00381-15.
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    • David, Lawrence A., Corinne F. Maurice, Rachel N. Carmody, David B. Gootenberg, Julie E. Button, Benjamin E. Wolfe, Alisha V. Ling, et al. “Diet rapidly and reproducibly alters the human gut microbiome.” Nature 505, no. 7484 (January 23, 2014): 559–63. https://doi.org/10.1038/nature12820.
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    • David, Lawrence A., Arne C. Materna, Jonathan Friedman, Maria I. Campos-Baptista, Matthew C. Blackburn, Allison Perrotta, Susan E. Erdman, and Eric J. Alm. “Host lifestyle affects human microbiota on daily timescales.” Genome Biol 15, no. 7 (2014): R89. https://doi.org/10.1186/gb-2014-15-7-r89.
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    • Szabo, Gitta, Sarah P. Preheim, Kathryn M. Kauffman, Lawrence A. David, Jesse Shapiro, Eric J. Alm, and Martin F. Polz. “Reproducibility of Vibrionaceae population structure in coastal bacterioplankton.” Isme J 7, no. 3 (March 2013): 509–19. https://doi.org/10.1038/ismej.2012.134.
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    • Smillie, Chris S., Mark B. Smith, Jonathan Friedman, Otto X. Cordero, Lawrence A. David, and Eric J. Alm. “Ecology drives a global network of gene exchange connecting the human microbiome.” Nature 480, no. 7376 (October 30, 2011): 241–44. https://doi.org/10.1038/nature10571.
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    • David, Lawrence A., and Eric J. Alm. “Rapid evolutionary innovation during an Archaean genetic expansion.” Nature 469, no. 7328 (January 6, 2011): 93–96. https://doi.org/10.1038/nature09649.
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    • Preheim, Sarah P., Yan Boucher, Hans Wildschutte, Lawrence A. David, Daniele Veneziano, Eric J. Alm, and Martin F. Polz. “Metapopulation structure of Vibrionaceae among coastal marine invertebrates.” Environ Microbiol 13, no. 1 (January 2011): 265–75. https://doi.org/10.1111/j.1462-2920.2010.02328.x.
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    • Shapiro, B Jesse, Lawrence A. David, Jonathan Friedman, and Eric J. Alm. “Looking for Darwin's footprints in the microbial world.” Trends Microbiol 17, no. 5 (May 2009): 196–204. https://doi.org/10.1016/j.tim.2009.02.002.
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    • Hunt, Dana E., Lawrence A. David, Dirk Gevers, Sarah P. Preheim, Eric J. Alm, and Martin F. Polz. “Resource partitioning and sympatric differentiation among closely related bacterioplankton.” Science 320, no. 5879 (May 23, 2008): 1081–85. https://doi.org/10.1126/science.1157890.
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    • Dubin-Thaler, Benjamin J., Jake M. Hofman, Yunfei Cai, Harry Xenias, Ingrid Spielman, Anna V. Shneidman, Lawrence A. David, Hans-Günther Döbereiner, Chris H. Wiggins, and Michael P. Sheetz. “Quantification of cell edge velocities and traction forces reveals distinct motility modules during cell spreading.” Plos One 3, no. 11 (2008): e3735. https://doi.org/10.1371/journal.pone.0003735.
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    • David, Lawrence A., and Chris H. Wiggins. “Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data.” Ann N Y Acad Sci 1115 (December 2007): 90–101. https://doi.org/10.1196/annals.1407.009.
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    • Glenn, Charles F., David K. Chow, Lawrence David, Carol A. Cooke, Minaxi S. Gami, Wendy B. Iser, Keaton B. Hanselman, Ilya G. Goldberg, and Catherine A. Wolkow. “Behavioral deficits during early stages of aging in Caenorhabditis elegans result from locomotory deficits possibly linked to muscle frailty.” J Gerontol a Biol Sci Med Sci 59, no. 12 (December 2004): 1251–60. https://doi.org/10.1093/gerona/59.12.1251.
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    • Holmes, Zachary C., Max M. Villa, Heather K. Durand, Sharon Jiang, Eric P. Dallow, Brianna L. Petrone, Justin D. Silverman, Pao-Hwa Lin, and Lawrence A. David. “Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake,” n.d. https://doi.org/10.1101/2021.06.26.450023.
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    • Letourneau, Jeffrey, Zachary C. Holmes, Eric P. Dallow, Heather K. Durand, Sharon Jiang, Savita K. Gupta, Adam C. Mincey, Michael J. Muehlbauer, James R. Bain, and Lawrence A. David. “Ecological memory of prior nutrient exposure in the human gut microbiome,” n.d. https://doi.org/10.1101/2021.06.21.448853.
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    • Levade, Inès, Morteza M. Saber, Firas Midani, Fahima Chowdhury, Ashraful I. Khan, Yasmin A. Begum, Edward T. Ryan, et al. “Predicting Vibrio cholerae infection and disease severity using metagenomics in a prospective cohort study,” n.d. https://doi.org/10.1101/2020.02.25.960930.
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    • Nimmagadda, Sai N., Firas S. Midani, Heather Durand, Aspen T. Reese, Caitlin C. Murdoch, Bradley P. Nicholson, Timothy Veldman, et al. “Nasal microbiota exhibit neither reproducible nor orderly dynamics following rhinoviral infection,” n.d. https://doi.org/10.1101/2020.04.11.20061911.
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  • Conference Papers

    • Zhang, Y., Y. Zhao, L. David, R. Henao, and L. Carin. “Dynamic poisson factor analysis.” In Proceedings  Ieee International Conference on Data Mining, Icdm, 1359–64, 2017. https://doi.org/10.1109/ICDM.2016.111.
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• Teaching & Mentoring
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  Recent Courses

  • MGM 293: Research Independent Study I 2021
  • MGM 593: Research Independent Study 2021
  • UPGEN 778E: University Program in Genetics and Genomics Biological Solutions Module V 2021
  • EGR 393: Research Projects in Engineering 2020
  • MGM 293: Research Independent Study I 2020
  • MGM 593: Research Independent Study 2020
  • STA 693: Research Independent Study 2020
  • UPGEN 778A: University Program in Genetics and Genomics Biological Solutions Module I 2020
  • BIOLOGY 728F: University Program in Genetics and Genomics Biological Solutions Module VI 2019
  • CMB 778F: University Program in Genetics and Genomics Biological Solutions Module VI 2019
  • EGR 393: Research Projects in Engineering 2019
  • MGM 293: Research Independent Study I 2019
  • MGM 593: Research Independent Study 2019
  • MGM 778F: University Program in Genetics and Genomics Biological Solutions Module VI 2019
  • UPGEN 778F: University Program in Genetics and Genomics Biological Solutions Module VI 2019

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