CAMERA, microbiome time series, and gut microbial ecology — from Woese-era microbial trees to daily stool sampling.
Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis
The CAMERA (Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis) community database for metagenomic data deposition is an important first step in developing methods for monitoring microbial communities.
mediaThe OptIPuter Gets Real – HPC Wire
January 27, 2006 – Last week, the UCSD division of the California Institute for Telecommunications and Information Technology (Calit2) and the J. Craig Venter Institute announced that they would collaborate to decipher the genetic code of the world’s marine microbiological communities.
- publication
CAMERA: A Community Resource for Metagenomics
R. Seshadri, SA Kravitz, L Smarr , Gilna P, M Frazier, PLoS Biol 5(3): e75.(2007).
publicationBuilding an OptIPlanet collaboratory to support microbial metagenomics
L. Smarr, P. Gilna, P. Papadopoulos, T. DeFanti, G. Hidley, J. Wooley, E. V. Armbrust, F. Rohwer, E. Frost, Future Generation Computer Systems, Volume 25, Issue 2, pp. 124-131. July 2008.
mediaMind Brain Genome Microbiome: Conversation with Deepak Chopra
Deepak Chopra interviews Dr. Larry Smarr. We discussed everything from the origins of life, life in the universe, consciousness, mind brain genome, environment and the science of epigenetics. 04.23.2014.
▶ Video
mediaFrom Quantified Self to Personalized Medicine – HPC Wire
November 6, 2014 – The University of Washington Computer Science and Engineering Distinguished Lecture series recently welcomed Calit2 luminary Larry Smarr to speak on a very interesting topic, bringing wellness into the digital age.
mediaThe Excrement Experiment – The New Yorker
But it was an inadvertent discovery in a stool analysis that led to Smarr’s Crohn’s diagnosis and, eventually, to a new calling: as an evangelist for an impending medical revolution, “quantified health.”
publicationUsing Pairwise Difference Features to Measure Temporal Changes in the Microbial Ecology
M. Yazdani, L. Smarr. 2015 IEEE International Conference on Big Data. IEEE. 10/29/2015.
publicationUsing Topological Data Analysis to find discrimination between microbial states in human microbiome data
Mehrdad Yazdani, Larry Smarr and Rob Knight. (2016).
publicationUsing Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease
Proceedings Of The 2016 IEEE International Conference On Big Data. (2016) M. Yazdani, B. C. Taylor, J. W Debelius, W. Li, R. Knight, and L. Smarr
publicationBringing the Dynamic Microbiome to Life with Animations
Y. Vazquez-Baeza, A. Gonzalez, L. Smarr, D. McDonald, J. T. Morton, J. A. Navas-Molina, and R. Knight. Cell Host and Microbe, vol. 21, pp 7-10. (2017).
mediaTeaching Computers to Recognize Unhealthy Guts – SDSC’s ‘Gordon’ Supercomputer Assists in New Microbiome Study
January 18, 2017 – A new proof-of-concept study by researchers from the University of California San Diego has succeeded in training computers to “learn” what a healthy versus an unhealthy gut microbiome looks like based on its genetic makeup.
publicationTracking Human Gut Microbiome Changes Resulting from a Colonoscopy
L. Smarr, E. R. Hyde, D. McDonald, W. J. Sandborn, R. Knight. Methods of Information in Medicine. 56(6):442-447 (2017).
publicationCreating a 3D microbial and chemical snapshot of a human habitat
C. A. Kapono, J. T. Morton, A. Bouslimani, A. V. Melnik, K. Orlinsky, T. Luzzatto Knaan, N. Garg, Y. Vázquez-Baeza, Iv. Protsyuk, S. Janssen, Q. Zhu, T. Alexandrov, L. Smarr, R. Knight, P. C. Dorrestein. Altmetric: Nature Scientific Reports, vol.8: 3669. (2018).
publicationAmerican Gut: an Open Platform for Citizen Science
D. McDonald, E. Hyde, J. W. Debelius, J. T. Morton, A. Gonzalez, G. Ackermann, A. A. Aksenov, B. Behsaz, C. Brennan, Y. Chen, L. DeRight Golda, P. C. Dorrestein, R. R. Dunn, A. Fahimipour, J. Gaffney, J. A. Gilbert, G. Gogul, J. L. Green, P. Hugenholtz, G. Humphrey, C. Huttenhower, M. A. Jackson, S. Janssen, D. V. Jeste, L. Jiang, S. T. Kelley, D. Knights, T. Kosciolek, J. Ladau, J. Leach, C. Marotz, D. Meleshk, A. V. Melnik, J. L. Metcalf, H. Mohimani, E. Montassier, J. Navas-Molina, T. T. Nguyen, S. Peddada, P. Pevzner, K. S. Pollard, G. Rahnavard, A. Robbins-Pianka, N. Sangwan, J. Shorenstein, L. Smarr, S. J. Song, T. Spector, A. D. Swafford, V. G. Thackray, L. R. Thompson, A. Tripathi, Y. Vázquez-Baeza, A. Vrbanac, P. Wischmeyer, E. Wolfe, Q. Zhu, The American Gut Consortium, Rob Knight. mSystems 3:e00031-18. (2018).
publicationEscherichia coli B2 Strains Prevalent in Inflammatory Bowel Disease Patients Have Distinct Metabolic Capabilities that Enable Colonization of Intestinal Mucosa
X. Fang, J. M. Monk, N. Mih, B. Du, A. Sastry, E. Kavvas, Y. Seif, L. Smarr, B. O. Palsson. BMC Systems Biology, 12, 66. (2018).
publicationAre microbiome studies ready for hypothesis-driven research?
A. Tripathi, C. Marotz, A. Gonzalez, Y. Vázquez-Baeza, S. J. Song, A. Bouslimani, D. McDonald, Q. Zhu, J. G. Sanders, L. Smarr, P. C. Dorrestein, R. Knight, Current Opinion Microbiology 44, 61-69. (2018).
publicationMetagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn’s Disease Patient
X. Fang, J. M. Monk, S. Nurk, M. Akseshina, Q. Zhu, C. Gemmell, C. Gianetto-Hill, N. Leung, R. Szubin, J. Sanders, P. L. Beck, W. Li, W. J. Sandborn, S. D. Gray-Owen, R. Knight, E. Allen-Vercoe, B. O. Palsson, L. Smarr. Frontiers in Microbiology. Vol 9, article 2559. (2018).
publicationExtracting Insights On The Dynamic Health-Disease Transitions In The Human Gut Microbiome
Smarr, Larry, Marc Jaffrey, Michael Dushkoff, Brynn Taylor, Pilar Ackerman, Mehrdad Yezdani, and Weizhong Li. “Extracting Insights On The Dynamic Health-Disease Transitions In The Human Gut Microbiome” (2018).
PDF
publicationMicrobiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians
C. Allaband, D. McDonald, Y. Vázquez-Baeza, J. J. Minich, A. Tripathi, D. Brenner, R. Loomba, L. Smarr, W. J. Sandborn, B. Schnabl, P. Dorrestein, A. Zarrinpar, R. Knight. Clinical Gastroenterology and Hepatology 17, 218-230. (2019).
publicationEvaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn’s Disease
R. H. Mills, Y. Vázquez-Baeza, Q. Zhu, L. Jiang, J. Gaffney, G. Humphrey, L. Smarr, R. Knight, D. J. Gonzalez. mSystems 4:e00337-18. (2019).
publicationOptimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Z. Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D. Arthur, Feng Chen, Brigid S. Boland, Greg C. Humphrey, Caitriona Brennan, Karenina Sanders, James Gaffney, Kristen Jepsen, Mahdieh Khosroheidari, Cliff Green, Marlon Liyanage, Jason W. Dang, Vanessa V. Phelan, Robert A. Quinn, Anton Bankevich, John T. Chang, Tariq M. Rana, Douglas J. Conrad, William J. Sandborn, Larry Smarr, Pieter C. Dorrestein, Pavel A. Pevzner & Rob Knight, Genome Biology 20, Article: 226, (2019).
publicationPhylogenomics of 10,575 Genomes Reveals Evolutionary Proximity Between Domains Bacteria and Archaea
Q. Zhu, U. Mai, W. Pfeiffer, S. Janssen, F. Asnicar, J. G. Sanders, P. Belda-Ferre, G. A. Al-Ghalith, E. Kopylova, D. McDonald, T. Kosciolek, J. B. Yin, S. Huang, N. Salam, J.-Y. Jiao, Z. Wu, Z. Z. Xu, K. Cantrell, Y. Yang, Erfan Sayyari, M. Rabiee, J. T. Morton, S. Podell, D. Knights, W.-J. Li, C. Huttenhower, N. Segata, L. Smarr, S. Mirarab, R. Knight. Nature Communications 10, 5477. (2019).
publicationDe Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments
B. Behsaz, . Mohimani, A. Gurevich, A. Prjibelski, M. F. Fisher, L. Smarr, P. C. Dorrestein, J. S. Mylne, and P. A. Pevzner. Cell Systems 40. (2020).
publicationGastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity
X. Fang, Y. Vázquez-Baeza, E. Elijah, F. Vargas, G. Ackermann, G. Humphrey, R. Lau, K. C. Weldon, J. G. Sanders, M. Panitchpakdi, C. Carpenter, A. K. Jarmusch, J. Neill, A. Miralles, P. Dulai, S. Singh, M. Tsai, A. D. Swafford, L. Smarr, D. L. Boyle, B. O. Palsson, J. T. Chang, P. C. Dorrestein, W. J. Sandborn, R. Inflammatory Bowel Diseases, 27, 603–616 (2021). https://doi.org/10.1093/ibd/izaa262
publicationLongitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics
Basile, A., Heinken, A., Hertel, J., Smarr, L., Li, W., Treu, L., Valle, G., Campanaro, S. and Thiele, I., 2023. Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics. Gut microbes , 15 (1), p.2226921.
Revealing the Dynamics within an Individual Human Body and Its Gut Microbiome
Guest lecture for Professor Ben Smarr’s Bioengineering 211 course: Systems Biology and Bioengineering I: Biological Components, UC San Diego.
View slidesOpen PDF in a new tab ↗