National Institutes of Health, National Institute of General Medical Sciences
People: Nathan Ahlgren, Fengzhu Sun
2017 – 2022 Continue Reading Computational Studies of Virus-host Interactions Using Metagenomics Data and Applications
Mo Y, Ahlgren N, Fuhrman JA, Sun F, Hou S. (2026). A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets. Current protocols, 6(2)
Reynolds LC, Dunn AL, Hansen WJ, Dilip M, Sharpe DMT, Ahlgren NA, Burmeister J, Dellert C, Hammond A, Humphrey S, Liming K, Maynard E, Smith-Mickunas K, Pagan N, Trudell Z. (2026). Urbanization impacts on stream and lake water quality in a small watershed in central Massachusetts, USA. Environmental monitoring and assessment, 198(5)
Laperriere SM, Minch B, Weissman JL, Hou S, Yeh YC, Ignacio-Espinoza JC, Ahlgren NA, Moniruzzaman M, Fuhrman JA. (2025). Phylogenetic proximity is a key driver of temporal succession of marine giant viruses in a five-year metagenomic time-series. ISME communications, 5(1)
Laperriere SM, Minch B, Weissman JL, Hou S, Yeh YC, Ignacio-Espinoza JC, Ahlgren NA, Moniruzzaman M, Fuhrman JA. (2024). Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series. bioRxiv : the preprint server for biology
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)
Dart E, Ahlgren NA. (2023). New tRNA-targeting transposons that hijack phage and vesicles. Trends in genetics : TIG, 39(6)
Bergmann PJ, Ahlgren NA, Torres Stone RA. (2022). County-level societal predictors of COVID-19 cases and deaths changed through time in the United States: A longitudinal ecological study. PLOS global public health, 2(11)
MacKenzie CA, Marston MF, Tabima JF, Ahlgren NA. (2022). Genome Sequence of the Estuarine Synechococcus sp. Strain NB0720_010. Microbiology resource announcements
Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, Fuhrman JA, Braun J, Sun F, Ahlgren NA. (2020). A network-based integrated framework for predicting virus-prokaryote interactions. NAR genomics and bioinformatics, 2(2)
Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, Li Y, Xie X, Poplin R, Sun F. (2020). Identifying viruses from metagenomic data using deep learning. Quantitative biology (Beijing, China), 8(1)
Belisle BS, Avila Paz AA, Carpenter AR, Cormier TC, Lewis AJ, Menin LS, Oliveira DR, Song B, Szeto A, Tchantouridze EI, Watson KA, Yohannes MT, Ahlgren NA. (2020). Genome Sequences of Synechococcus sp. Strain MIT S9220 and Cocultured Cyanophage SynMITS9220M01. Microbiology resource announcements, 9(30)
Ahlgren NA, Perelman JN, Yeh YC, Fuhrman JA. (2019). Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors. Environmental microbiology, 21(8)
Ahlgren NA, Belisle BS, Lee MD. (2019). Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches. Environmental microbiology
Ignacio-Espinoza JC, Ahlgren NA, Fuhrman JA. (2020). Long-term stability and Red Queen-like strain dynamics in marine viruses. Nature microbiology, 5(2)
Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Zhan Y, Marsan D, Chen F, Fuhrman JA, Northen TR, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA. (2019). Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ, (7)
Lee MD, Ahlgren NA, Kling JD, Walworth NG, Rocap G, Saito MA, Hutchins DA, Webb EA. (2019). Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content. Environmental microbiology, 21(5)
Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA. (2019). Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes. The ISME journal, 13(3)
Ahlgren NA, Chen Y, Needham DM, Parada AE, Sachdeva R, Trinh V, Chen T, Fuhrman JA. (2017). Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems. Environmental microbiology, 19(6)
Zhang M, Yang L, Ren J, Ahlgren NA, Fuhrman JA, Sun F. (2017). Prediction of virus-host infectious association by supervised learning methods. BMC Bioinformatics, 18(Suppl 3)
Ahlgren NA, Ren J, Lu YY, Fuhrman JA, Sun F. (2017). Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic acids research, 45(1)
Ahlgren NA, Rocap G. (2012). Diversity and Distribution of Marine Synechococcus: Multiple Gene Phylogenies for Consensus Classification and Development of qPCR Assays for Sensitive Measurement of Clades in the Ocean. Frontiers in microbiology, (3)
Ahlgren NA, Harwood CS, Schaefer AL, Giraud E, Greenberg EP. (2011). Aryl-homoserine lactone quorum sensing in stem-nodulating photosynthetic bradyrhizobia. Proceedings of the National Academy of Sciences of the United States of America, 108(17)
Ahlgren NA, Rocap G. (2006). Culture isolation and culture-independent clone libraries reveal new marine Synechococcus ecotypes with distinctive light and N physiologies. Applied and environmental microbiology, 72(11)
Ahlgren NA, Rocap G, Chisholm SW. (2006). Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies. Environmental microbiology, 8(3)
If you’d like to update your profile, please email modifications to questions@midasnetwork.us.