Publications

For most complete and updated list, see Jed Fuhrman's Google Scholar Publication List

Select recent papers (2020- )

Ignacio-Espinoza, J. Cesar, Nathan A. Ahlgren, and Jed A. Fuhrman. 2020. Long-term stability and Red Queen-like strain dynamics in marine viruses. Nature Microbiology 5: 265–271  (online 2019)DOI 10.1038/s41564-019-0628-x   https://www.nature.com/articles/s41564-019-0628-x

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.     https://rdcu.be/b5a4c

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, 2 (2), lqaa044, June 2020, https://doi.org/10.1093/nargab/lqaa04

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. Also bioRxiv http://biorxiv.org/cgi/content/short/777730v1

Long, A.M., Hou, S., Ignacio-Espinoza, J.C, and J.A. Fuhrman. 2021. Benchmarking microbial growth rate predictions from metagenomes. ISME J, 15:183–195 . https://doi.org/10.1038/s41396-020-00773-1    https://rdcu.be/b7hNU     bioRxiv https://www.biorxiv.org/content/10.1101/786939v1

Yeh, Yi-Chun, Jesse C McNichol, David M Needham, Erin B Fichot, Jed A Fuhrman. 2021. Comprehensive single‚ÄźPCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S. Environmental Microbiology 23(6), 3240–3250 https://doi.org/10.1111/1462-2920.15553  bioRxiv : https://biorxiv.org/cgi/content/short/866731v1

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 https://www.pnas.org/content/118/12/e2016810118.  bioRxiv  https://biorxiv.org/cgi/content/short/2020.07.25.221176v1\

 

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 Also bioRxiv https://www.biorxiv.org/content/10.1101/2020.11.09.375543v1

 

Weissman, Jake L,  Ellinor 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  Soc B. 288: 20211555.  https://doi.org/10.1098/rspb.2021.1555      

bioRxiv https://www.biorxiv.org/content/10.1101/2020.09.30.321075v1

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

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. 2, 36 (2022). https://doi.org/10.1038/s43705-022-00121-8

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 – Biodiversity. 10, 714713  DOI: 10.3389/frym.2022.714713

 Milke, Felix, Selene Sanchez-Garcia, Leon Dlugosch, Jesse McNichol, Jed Fuhrman, Meinhard Simon, Irene Wagner-Döbler. 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

 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

 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, (5). https://doi.org/10.1128/msystems.00745-22

 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 ,  https://doi.org/10.1038/s41467-022-35551-4

 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  (2023)14:502. https://doi.org/10.1038/s41467-023-35945-y

Fletcher-Hoppe, Colette ,Yi-Chun Yeh, Yubin Raut, J.L. Weissman, Jed A. Fuhrman. 2023. Symbiotic diazotrophic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California Bight. ISME Comm. In press, and BioRxiv doi: https://doi.org/10.1101/2022.11.07.514914

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 15(2):581. https://doi.org/10.3390/v15020581