Larry Smarr

Title(s)	Emeritus Professor, Computer Science and Engineering
School	Vc-academic Affairs
Address	9500 Gilman Drive # La Jolla CA 92093
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Bibliographic

Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. Inflamm Bowel Dis. 2021 04 15; 27(5):603-616. Fang X, Vázquez-Baeza Y, Elijah E, Vargas F, Ackermann G, Humphrey G, Lau R, Weldon KC, Sanders JG, Panitchpakdi M, Carpenter C, Jarmusch AK, Neill J, Miralles A, Dulai P, Singh S, Tsai M, Swafford AD, Smarr L, Boyle DL, Palsson BO, Chang JT, Dorrestein PC, Sandborn WJ, Knight R, Boland BS. PMID: 33026068; PMCID: PMC8047854.

View in: PubMed Mentions: 10 Fields:
Gas Gastroenterology
Translation:Humans
De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Syst. 2020 01 22; 10(1):99-108.e5. Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA. PMID: 31864964.

View in: PubMed Mentions: 12 Fields:
Cel Cell Biology Com Computational Biology Mol Molecular Biology
Translation:Humans Cells
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun. 2019 12 02; 10(1):5477. Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. PMID: 31792218; PMCID: PMC6889312.

View in: PubMed Mentions: 81 Fields:
Bio Biology Sci Science
Translation:Cells
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biol. 2019 10 31; 20(1):226. Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. PMID: 31672156; PMCID: PMC6822431.

View in: PubMed Mentions: 19 Fields:
Gen Genetics
Translation:Humans Animals
Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. mSystems. 2019 Jan-Feb; 4(1). Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, Smarr L, Knight R, Gonzalez DJ. PMID: 30801026; PMCID: PMC6372841.

View in: PubMed Mentions: 23 Fields:
Mic Microbiology
Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Front Microbiol. 2018; 9:2559. Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L. PMID: 30425690; PMCID: PMC6218438.

View in: PubMed Mentions: 26
Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians. Clin Gastroenterol Hepatol. 2019 01; 17(2):218-230. Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R. PMID: 30240894; PMCID: PMC6391518.

View in: PubMed Mentions: 92 Fields:
Gas Gastroenterology
Translation:Humans
Are microbiome studies ready for hypothesis-driven research? Curr Opin Microbiol. 2018 08; 44:61-69. Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R. PMID: 30059804; PMCID: PMC6153026.

View in: PubMed Mentions: 8 Fields:
Mic Microbiology
Translation:Humans Animals
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Syst Biol. 2018 06 11; 12(1):66. Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO. PMID: 29890970; PMCID: PMC5996543.

View in: PubMed Mentions: 16 Fields:
Com Computational Biology
Translation:Humans Cells
American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3). McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, American Gut Consortium , Knight R. PMID: 29795809; PMCID: PMC5954204.

View in: PubMed Mentions: 273 Fields:
Mic Microbiology
Creating a 3D microbial and chemical snapshot of a human habitat. Sci Rep. 2018 02 27; 8(1):3669. Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC. PMID: 29487294; PMCID: PMC5829137.

View in: PubMed Mentions: 17 Fields:
Sci Science
Translation:Humans PHPublic Health
Tracking Human Gut Microbiome Changes Resulting from a Colonoscopy. Methods Inf Med. 2017; 56(6):442-447. Smarr L, Hyde ER, McDonald D, Sandborn WJ, Knight R. PMID: 29582916.

View in: PubMed Mentions: 3 Fields:
Med Medical Informatics
Translation:Humans
Bringing the Dynamic Microbiome to Life with Animations. Cell Host Microbe. 2017 Jan 11; 21(1):7-10. Vázquez-Baeza Y, Gonzalez A, Smarr L, McDonald D, Morton JT, Navas-Molina JA, Knight R. PMID: 28081445.

View in: PubMed Mentions: 36 Fields:
Mic Microbiology
Translation:Humans Cells
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS. 2014 Jan; 18(1):10-4. Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G. PMID: 24456465; PMCID: PMC3903324.

View in: PubMed Mentions: 19 Fields:
Com Computational Biology Mol Molecular Biology
Translation:Humans
Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data. 2013 Dec; 1(4):196-201. Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, MacNealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G. PMID: 27447251.

View in: PubMed Mentions: 2 Fields:
Med Medical Informatics Sta Statistics as Topic
Quantifying your body: a how-to guide from a systems biology perspective. Biotechnol J. 2012 Aug; 7(8):980-91. Smarr L. PMID: 22887886.

View in: PubMed Mentions: 23 Fields:
Bio Biotechnology
Translation:Humans