Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation G Rocap, FW Larimer, J Lamerdin, S Malfatti, P Chain, NA Ahlgren, ...
Nature 424 (6952), 1042-1047, 2003
1316 2003 VirFinder: a novel k -mer based tool for identifying viral sequences from assembled metagenomic data J Ren, NA Ahlgren, YY Lu, JA Fuhrman, F Sun
Microbiome 5, 1-20, 2017
588 2017 Identifying viruses from metagenomic data using deep learning J Ren, K Song, C Deng, NA Ahlgren, JA Fuhrman, Y Li, X Xie, R Poplin, ...
Quantitative Biology 8 (1), 64-77, 2020
481 2020 Alignment-free NA Ahlgren, J Ren, YY Lu, JA Fuhrman, F Sun
Nucleic acids research 45 (1), 39-53, 2017
300 2017 Copper toxicity and cyanobacteria ecology in the Sargasso Sea EL Mann, N Ahlgren, JW Moffett, SW Chisholm
Limnology and oceanography 47 (4), 976-988, 2002
262 2002 Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron JA Sohm, NA Ahlgren, ZJ Thomson, C Williams, JW Moffett, MA Saito, ...
The ISME Journal 10 (2), 333-345, 2016
227 2016 Culture Isolation and Culture-Independent Clone Libraries Reveal New Marine Synechococcus Ecotypes with Distinctive Light and N Physiologies NA Ahlgren, G Rocap
Applied and Environmental Microbiology 72 (11), 7193-7204, 2006
185 2006 Diversity and Distribution of Marine Synechococcus : Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive … NA Ahlgren, G Rocap
Frontiers in Microbiology 3, 213, 2012
172 2012 Aryl-homoserine lactone quorum sensing in stem-nodulating photosynthetic bradyrhizobia NA Ahlgren, CS Harwood, AL Schaefer, E Giraud, EP Greenberg
Proceedings of the National Academy of Sciences 108 (17), 7183-7188, 2011
144 2011 Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes NA Ahlgren, CA Fuchsman, G Rocap, JA Fuhrman
The ISME journal 13 (3), 618-631, 2019
122 2019 Measurement of Prochlorococcus ecotypes using real‐time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies NA Ahlgren, G Rocap, SW Chisholm
Environmental microbiology 8 (3), 441-454, 2006
122 2006 A network-based integrated framework for predicting virus–prokaryote interactions W Wang, J Ren, K Tang, E Dart, JC Ignacio-Espinoza, JA Fuhrman, ...
NAR genomics and bioinformatics 2 (2), lqaa044, 2020
117 2020 Long-term stability and Red Queen-like strain dynamics in marine viruses JC Ignacio-Espinoza, NA Ahlgren, JA Fuhrman
Nature Microbiology 5 (2), 265-271, 2020
83 2020 Unraveling the functional dark matter through global metagenomics GA Pavlopoulos, FA Baltoumas, S Liu, O Selvitopi, AP Camargo, ...
Nature 622 (7983), 594-602, 2023
80 2023 Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems NA Ahlgren, Y Chen, DM Needham, AE Parada, R Sachdeva, V Trinh, ...
Environmental Microbiology 19 (6), 2434-2452, 2017
76 2017 Multi‐year dynamics of fine‐scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom‐up factors NA Ahlgren, JN Perelman, YC Yeh, JA Fuhrman
Environmental Microbiology 21 (8), 2948-2963, 2019
58 2019 Prediction of virus-host infectious association by supervised learning methods M Zhang, L Yang, J Ren, NA Ahlgren, JA Fuhrman, F Sun
BMC bioinformatics 18, 143-154, 2017
56 2017 The unique trace metal and mixed layer conditions of the Costa Rica upwelling dome support a distinct and dense community of Synechococcus NA Ahlgren, A Noble, AP Patton, K Roache‐Johnson, L Jackson, ...
Limnology and Oceanography 59 (6), 2166-2184, 2014
54 2014 Optimizing de novo genome assembly from PCR-amplified metagenomes S Roux, G Trubl, D Goudeau, N Nath, E Couradeau, NA Ahlgren, Y Zhan, ...
PeerJ 7, e6902, 2019
40 2019 Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches NA Ahlgren, BS Belisle, MD Lee
Environmental Microbiology 22 (5), 1801-1815, 2020
39 2020 
Jed A. FuhrmanMcCulloch Crosby Chair of Marine Biology, University of Southern CaliforniaEmail verificata su usc.edu