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Jeremiah Minich

Title(s)Lecturer - Academic Year - 1/9, Division of Biological Science
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    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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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. Biotechniques. 2021 Jan 29. Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. PMID: 33512248.
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    2. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome. 2021 01 22; 9(1):25. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 33482920.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    3. Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere. 2021 Jan 02; 271:129450. Petras D, Minich JJ, Cancelada LB, Torres RR, Kunselman E, Wang M, White ME, Allen EE, Prather KA, Aluwihare LI, Dorrestein PC. PMID: 33460888.
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    4. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. bioRxiv. 2020 Nov 14. Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant MB, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. PMID: 33200135.
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    5. The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment. Front Microbiol. 2020; 11:2015. Minich JJ, Power C, Melanson M, Knight R, Webber C, Rough K, Bott NJ, Nowak B, Allen EE. PMID: 32983024.
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    6. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Res Sq. 2020 Aug 18. Minich J, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32839765.
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    7. Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation. mSystems. 2020 Jul 28; 5(4). Malli Mohan GB, Parker CW, Urbaniak C, Singh NK, Hood A, Minich JJ, Knight R, Rucker M, Venkateswaran K. PMID: 32723791.
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    8. Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Appl Environ Microbiol. 2020 06 02; 86(12). Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J, Knight R, Nowak B, Allen EE. PMID: 32303543.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsPHPublic Health
    9. Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus. mSphere. 2020 05 20; 5(3). Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, Allen EE. PMID: 32434844.
      View in: PubMed   Mentions: 1     Fields:    
    10. Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs. medRxiv. 2020 May 18. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Shaffer JP, Carpenter CS, McDonald D, Gilbert JA, Allard SM, Knight R, Sweeney DA, Swafford AD. PMID: 32511552.
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    11. Visualizing 'omic feature rankings and log-ratios using Qurro. NAR Genom Bioinform. 2020 Jun; 2(2):lqaa023. Fedarko MW, Martino C, Morton JT, González A, Rahman G, Marotz CA, Minich JJ, Allen EE, Knight R. PMID: 32391521.
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    12. Atlantic Salmon (Salmo salar L., 1758) Gut Microbiota Profile Correlates with Flesh Pigmentation: Cause or Effect? Mar Biotechnol (NY). 2020 Dec; 22(6):786-804. Nguyen CDH, Amoroso G, Ventura T, Minich JJ, Elizur A. PMID: 31942646.
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    13. Home chemical and microbial transitions across urbanization. Nat Microbiol. 2020 01; 5(1):108-115. McCall LI, Callewaert C, Zhu Q, Song SJ, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG. PMID: 31686026.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    14. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    15. Quantifying and Understanding Well-to-Well Contamination in Microbiome Research. mSystems. 2019 Jun 25; 4(4). Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. PMID: 31239396.
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    16. Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. Microbiome. 2019 04 08; 7(1):50. Checinska Sielaff A, Urbaniak C, Mohan GBM, Stepanov VG, Tran Q, Wood JM, Minich J, McDonald D, Mayer T, Knight R, Karouia F, Fox GE, Venkateswaran K. PMID: 30955503.
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    17. Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol. 2019 02; 27(2):105-117. Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. PMID: 30497919.
      View in: PubMed   Mentions: 82     Fields:    Translation:Humans
    18. High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. mSystems. 2018 Nov-Dec; 3(6). Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R. PMID: 30417111.
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    19. 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.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    20. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). Microbiologyopen. 2018 12; 7(6):e00716. Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R. PMID: 30168288.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    21. KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018 May-Jun; 3(3). Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R. PMID: 29577086.
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    22. Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. PLoS One. 2018; 13(2):e0192772. Minich JJ, Morris MM, Brown M, Doane M, Edwards MS, Michael TP, Dinsdale EA. PMID: 29474389.
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    23. From Sample to Multi-Omics Conclusions in under 48 Hours. mSystems. 2016 Mar-Apr; 1(2). Quinn RA, Navas-Molina JA, Hyde ER, Song SJ, Vázquez-Baeza Y, Humphrey G, Gaffney J, Minich JJ, Melnik AV, Herschend J, DeReus J, Durant A, Dutton RJ, Khosroheidari M, Green C, da Silva R, Dorrestein PC, Knight R. PMID: 27822524.
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    24. Improved multiple displacement amplification (iMDA) and ultraclean reagents. BMC Genomics. 2014 Jun 06; 15:443. Motley ST, Picuri JM, Crowder CD, Minich JJ, Hofstadler SA, Eshoo MW. PMID: 24906487.
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