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A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.
Hakimzadeh A, Abdala Asbun A, Albanese D, Bernard M, Buchner D, Callahan B, Caporaso JG, Curd E, Djemiel C, Brandström Durling M, Elbrecht V, Gold Z, Gweon HS, Hajibabaei M, Hildebrand F, Mikryukov V, Normandeau E, Özkurt E, M Palmer J, Pascal G, Porter TM, Straub D, Vasar M, Větrovský T, Zafeiropoulos H, Anslan S. Hakimzadeh A, et al. Among authors: caporaso jg. Mol Ecol Resour. 2023 Aug 7:10.1111/1755-0998.13847. doi: 10.1111/1755-0998.13847. Online ahead of print. Mol Ecol Resour. 2023. PMID: 37548515
Predicting Neurodegenerative Disease Using Prepathology Gut Microbiota Composition: a Longitudinal Study in Mice Modeling Alzheimer's Disease Pathologies.
Borsom EM, Conn K, Keefe CR, Herman C, Orsini GM, Hirsch AH, Palma Avila M, Testo G, Jaramillo SA, Bolyen E, Lee K, Caporaso JG, Cope EK. Borsom EM, et al. Among authors: caporaso jg. Microbiol Spectr. 2023 Mar 6;11(2):e0345822. doi: 10.1128/spectrum.03458-22. Online ahead of print. Microbiol Spectr. 2023. PMID: 36877047 Free PMC article.
Pan-Enterovirus Characterization Reveals Cryptic Circulation of Clinically Relevant Subtypes in Arizona Wastewater.
Erickson DE, Simmons KM, Barrand ZA, Ridenour CL, Hawkinson PB, Lemke L, Sellner SP, Brock BN, Rivas AN, Sheridan K, Lemmer D, Yaglom HD, Porter WT, Belanger M, Torrey RM, Stills AJR, McCormack K, Black M, Holmes W, Rostain D, Mikus J, Sotelo K, Haq E, Neupane R, Weiss J, Johnson J, Collins C, Avalle S, White C, Howard BJ, Maltinsky SA, Whealy RN, Gordon NB, Sahl JW, Pearson T, Fofanov VY, Furstenau T, Driebe EM, Caporaso JG, Barber J, Terriquez J, Engelthaler DM, Hepp CM. Erickson DE, et al. Among authors: caporaso jg. medRxiv [Preprint]. 2024 Mar 20:2023.11.20.23297677. doi: 10.1101/2023.11.20.23297677. medRxiv. 2024. PMID: 38562876 Free PMC article. Preprint.
Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay.
Keefe CR, Dillon MR, Gehret E, Herman C, Jewell M, Wood CV, Bolyen E, Caporaso JG. Keefe CR, et al. Among authors: caporaso jg. PLoS Comput Biol. 2023 Nov 27;19(11):e1011676. doi: 10.1371/journal.pcbi.1011676. eCollection 2023 Nov. PLoS Comput Biol. 2023. PMID: 38011287 Free PMC article.
Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?
Afiaz A, Ivanov AA, Chamberlin J, Hanauer D, Savonen CL, Goldman MJ, Morgan M, Reich M, Getka A, Holmes A, Pati S, Knight D, Boutros PC, Bakas S, Caporaso JG, Del Fiol G, Hochheiser H, Haas B, Schloss PD, Eddy JA, Albrecht J, Fedorov A, Waldron L, Hoffman AM, Bradshaw RL, Leek JT, Wright C. Afiaz A, et al. Among authors: caporaso jg. ArXiv [Preprint]. 2023 Jun 5:arXiv:2306.03255v1. ArXiv. 2023. PMID: 37332562 Free PMC article. Preprint.
Representative oral microbiome data for the US population: the National Health and Nutrition Examination Survey.
Vogtmann E, Chaturvedi AK, Blaser MJ, Bokulich NA, Caporaso JG, Gillison ML, Hua X, Hullings AG, Knight R, Purandare V, Shi J, Wan Y, Freedman ND, Abnet CC. Vogtmann E, et al. Among authors: caporaso jg. Lancet Microbe. 2023 Feb;4(2):e60-e61. doi: 10.1016/S2666-5247(22)00333-0. Epub 2022 Nov 28. Lancet Microbe. 2023. PMID: 36455567 Free article. No abstract available.
The Oral Microbiome and Lung Cancer Risk: An Analysis of 3 Prospective Cohort Studies.
Vogtmann E, Hua X, Yu G, Purandare V, Hullings AG, Shao D, Wan Y, Li S, Dagnall CL, Jones K, Hicks BD, Hutchinson A, Caporaso JG, Wheeler W, Sandler DP, Beane Freeman LE, Liao LM, Huang WY, Freedman ND, Caporaso NE, Sinha R, Gail MH, Shi J, Abnet CC. Vogtmann E, et al. Among authors: caporaso jg. J Natl Cancer Inst. 2022 Nov 14;114(11):1501-1510. doi: 10.1093/jnci/djac149. J Natl Cancer Inst. 2022. PMID: 35929779 Free PMC article.
120 results