|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
|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), 1-20, 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, 64-77, 2020
|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
|Alignment-free oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences|
NA Ahlgren, J Ren, YY Lu, JA Fuhrman, F Sun
Nucleic acids research 45 (1), 39-53, 2017
|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
|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
|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
|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
|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
|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
|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
|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
|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
|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
|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
|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
|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
|Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a …|
MD Lee, NA Ahlgren, JD Kling, NG Walworth, G Rocap, MA Saito, ...
Environmental microbiology 21 (5), 1677-1686, 2019
|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