{"id":257,"date":"2023-09-27T12:57:13","date_gmt":"2023-09-27T19:57:13","guid":{"rendered":"https:\/\/dornsife.usc.edu\/fuhrmanlab\/?page_id=257"},"modified":"2023-11-20T15:57:46","modified_gmt":"2023-11-20T23:57:46","slug":"publications","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/fuhrmanlab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n\n \n \n\n\n\n\n\n\n\n
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For most complete and updated list, see Jed Fuhrman’s Google Scholar Publication List<\/a><\/p>\n

Select recent papers (2020- )<\/p>\n

Ignacio-Espinoza, J. Cesar, Nathan A. Ahlgren, and Jed A. Fuhrman. 2020. Long-term stability and Red Queen<\/i>-like strain dynamics in marine viruses. Nature Microbiology 5<\/strong>: 265\u2013271\u00a0 (online 2019)DOI 10.1038\/s41564-019-0628-x\u00a0\u00a0 https:\/\/www.nature.com\/articles\/s41564-019-0628-x<\/a><\/p>\n

Ren J, K, Song, C Deng, NA Ahlgren, JA Fuhrman, Y Li, XH Xie, R Poplin, FZ Sun. (2020) Identifying viruses from metagenomic data by deep learning. Quantitative Biology 8 (1): 64-67 https:\/\/doi.org\/10.1007\/s40484-019-0187-4<\/a>.\u00a0\u00a0\u00a0\u00a0 https:\/\/rdcu.be\/b5a4c<\/a><\/p>\n

Wang, Weili, Jie Ren, Kujin Tang; Emily Dart, J. Cesar Ignacio-Espinoza , Jed A. Fuhrman, Jonathan Braun, Fengzhu Sun, Nathan A. Ahlgren. 2020. A network-based integrated framework for predicting Virus-host interactions. NAR Genomics and Bioinformatics<\/em>, 2 (2), lqaa044, June 2020, https:\/\/doi.org\/10.1093\/nargab\/lqaa04<\/a><\/p>\n

Sieradzki, Ella T., Michael Morando and Jed A. Fuhrman. 2021. Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons biodegraders in chronically polluted seawater. mSystems 2021 6 (3): e00245-21. doi: 10.1128\/mSystems.00245-21.<\/p>\n

Long, A.M., Hou, S., Ignacio-Espinoza, J.C, and J.A. Fuhrman. 2021.<\/i> Benchmarking microbial growth rate predictions from metagenomes. ISME J, <\/i>15:183\u2013195 . https:\/\/doi.org\/10.1038\/s41396-020-00773-1<\/a>\u00a0\u00a0\u00a0 https:\/\/rdcu.be\/b7hNU<\/a><\/p>\n

Yeh, Yi-Chun, Jesse C McNichol, David M Needham, Erin B Fichot, Jed A Fuhrman. 2021. Comprehensive single\u2010PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S. Environmental Microbiology 23(6), 3240\u20133250 https:\/\/doi.org\/10.1111\/1462-2920.15553<\/a><\/p>\n

Weissman, Jake L, Shengwei Hou, Jed A Fuhrman. 2021. Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns. Proc. Nat. Acad. Sci., March 23, 2021 118 (12) e2016810118; https:\/\/doi.org\/10.1073\/pnas.2016810118<\/a> https:\/\/www.pnas.org\/content\/118\/12\/e2016810118<\/a>.<\/p>\n

McNichol, Jesse, Paul M. Berube, Steven J. Biller, Jed A. Fuhrman. 2021. Evaluating and Improving SSU rRNA PCR Primer Coverage via Metagenomes from Global Ocean Surveys. mSystems 6:e00565-21. https:\/\/doi.org\/10.1128\/mSystems.00565-21<\/a><\/p>\n

Weissman, Jake L, \u00a0Ellinor O Alseth, Sean Meaden, Edze R Westra, Jed A Fuhrman. 2021. Immune Lag Is a Major Cost of Prokaryotic Adaptive Immunity During Viral Outbreaks. Proc R\u00a0 Soc B. 288: 20211555.\u00a0 https:\/\/doi.org\/10.1098\/rspb.2021.1555<\/a><\/p>\n

Ignacio-Espinoza, J. Cesar, Sarah M. Laperriere, Yi-Chun Yeh, Jake Weissman, Shengwei Hou, Andrew M. Long, & Jed A. Fuhrman. Ribosome-linked mRNA-rRNA chimeras reveal active novel virus host associations. Submitted to Nature Microbiology. bioRxiv: https:\/\/biorxiv.org\/cgi\/content\/short\/2020.10.30.332502v1<\/a><\/p>\n

Yeh, YC., Fuhrman, J.A. Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series. ISME COMMUN.<\/i> 2, <\/strong>36 (2022). https:\/\/doi.org\/10.1038\/s43705-022-00121-8<\/a><\/p>\n

Weissman, Jake L, Shengwei Hou and Jed A Fuhrman. 2022. Using DNA to Predict How Fast Bacteria Can Grow. New Discovery, Frontiers in Young Minds \u2013 Biodiversity. 10, 714713 \u00a0<\/strong>DOI: 10.3389\/frym.2022.714713<\/p>\n

Milke, Felix, Selene Sanchez-Garcia, Leon Dlugosch, Jesse McNichol, Jed Fuhrman, Meinhard Simon, Irene Wagner-D\u00f6bler. 2022. Composition and biogeography of pro- and eukaryotic communities in the Atlantic Ocean: primer choice matters. Front. Microbiol., vol 13, online 28 June 2022 | https:\/\/doi.org\/10.3389\/fmicb.2022.895875<\/a><\/p>\n

Tang, Tianqi, Shengwei Hou, Jed Fuhrman and Fengzhu Sun. 2022. Phage-bacterial contig association prediction with a convolutional neural network. Bioinformatics Jun 24;38 (Suppl 1):i45-i52. https:\/\/doi.org\/10.1093\/bioinformatics\/btac239<\/a><\/p>\n

Weissman, JL, Marie Peras, Tyler Barnum, and Jed Fuhrman. 2022. Benchmarking community-wide estimates of growth potential from metagenomes using codon usage statistics, mSystems 7,<\/strong> (5). https:\/\/doi.org\/10.1128\/msystems.00745-22<\/a><\/p>\n

Yeh, Yi-Chun and Jed A Fuhrman. 2022. Effects of phytoplankton, viral communities and warming on free-living and particle-associated marine prokaryotic community structure. Nature Communications 13:7905 ,\u00a0 https:\/\/doi.org\/10.1038\/s41467-022-35551-4<\/a><\/p>\n

Du, Yuxuan, Jed A. Fuhrman and Fengzhu Sun. 2023. ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data. Nature Communications\u00a0 (2023)14:502. https:\/\/doi.org\/10.1038\/s41467-023-35945-y<\/a><\/p>\n

Fletcher-Hoppe, C., Yeh, YC., Raut, Y. et al.<\/i> Symbiotic UCYN-A strains co-occurred with El Ni\u00f1o, relaxed upwelling, and varied eukaryotes over 10 years off Southern California. ISME COMMUN.<\/i> 3<\/b>, 63 (2023). https:\/\/doi.org\/10.1038\/s43705-023-00268-y<\/a><\/p>\n

Dart E, Fuhrman JA, Ahlgren NA. 2023. Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics. Viruses<\/em> <\/i>15(2):581. https:\/\/doi.org\/10.3390\/v15020581<\/a><\/p>\n<\/div>\n\n\n\n<\/div>\n\n\n <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":584,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-content-detail.php","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-257","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"\nPublications - Fuhrman Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/dornsife.usc.edu\/fuhrmanlab\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - Fuhrman Lab\" \/>\n<meta property=\"og:url\" content=\"https:\/\/dornsife.usc.edu\/fuhrmanlab\/publications\/\" \/>\n<meta property=\"og:site_name\" content=\"Fuhrman Lab\" \/>\n<meta property=\"article:modified_time\" content=\"2023-11-20T23:57:46+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/dornsife.usc.edu\/fuhrmanlab\/publications\/\",\"url\":\"https:\/\/dornsife.usc.edu\/fuhrmanlab\/publications\/\",\"name\":\"Publications - 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