Ahlgren NA - Search Results

1

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.

Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. Ren J, et al. Among authors: ahlgren na. Microbiome. 2017 Jul 6;5(1):69. doi: 10.1186/s40168-017-0283-5. Microbiome. 2017. PMID: 28683828 Free PMC article.

2

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.

Ahlgren NA, Ren J, Lu YY, Fuhrman JA, Sun F. Ahlgren NA, et al. Nucleic Acids Res. 2017 Jan 9;45(1):39-53. doi: 10.1093/nar/gkw1002. Epub 2016 Nov 28. Nucleic Acids Res. 2017. PMID: 27899557 Free PMC article.

3

Prediction of virus-host infectious association by supervised learning methods.

Zhang M, Yang L, Ren J, Ahlgren NA, Fuhrman JA, Sun F. Zhang M, et al. Among authors: ahlgren na. BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):60. doi: 10.1186/s12859-017-1473-7. BMC Bioinformatics. 2017. PMID: 28361670 Free PMC article.

4

Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems.

Ahlgren NA, Chen Y, Needham DM, Parada AE, Sachdeva R, Trinh V, Chen T, Fuhrman JA. Ahlgren NA, et al. Environ Microbiol. 2017 Jun;19(6):2434-2452. doi: 10.1111/1462-2920.13768. Epub 2017 May 26. Environ Microbiol. 2017. PMID: 28418097

5

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes.

Ahlgren NA, Fuchsman CA, Rocap G, Fuhrman JA. Ahlgren NA, et al. ISME J. 2019 Mar;13(3):618-631. doi: 10.1038/s41396-018-0289-4. Epub 2018 Oct 12. ISME J. 2019. PMID: 30315316 Free PMC article.

6

Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors.

Ahlgren NA, Perelman JN, Yeh YC, Fuhrman JA. Ahlgren NA, et al. Environ Microbiol. 2019 Aug;21(8):2948-2963. doi: 10.1111/1462-2920.14687. Epub 2019 Jun 18. Environ Microbiol. 2019. PMID: 31106939

7

Optimizing de novo genome assembly from PCR-amplified metagenomes.

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. Roux S, et al. Among authors: ahlgren na. PeerJ. 2019 May 9;7:e6902. doi: 10.7717/peerj.6902. eCollection 2019. PeerJ. 2019. PMID: 31119088 Free PMC article.

8

Long-term stability and Red Queen-like strain dynamics in marine viruses.

Ignacio-Espinoza JC, Ahlgren NA, Fuhrman JA. Ignacio-Espinoza JC, et al. Among authors: ahlgren na. Nat Microbiol. 2020 Feb;5(2):265-271. doi: 10.1038/s41564-019-0628-x. Epub 2019 Dec 9. Nat Microbiol. 2020. PMID: 31819214

9

A network-based integrated framework for predicting virus-prokaryote interactions.

Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, Fuhrman JA, Braun J, Sun F, Ahlgren NA. Wang W, et al. Among authors: ahlgren na. NAR Genom Bioinform. 2020 Jun;2(2):lqaa044. doi: 10.1093/nargab/lqaa044. Epub 2020 Jun 23. NAR Genom Bioinform. 2020. PMID: 32626849 Free PMC article.

10

Identifying viruses from metagenomic data using deep learning.

Ren J, Song K, Deng C, Ahlgren NA, Fuhrman JA, Li Y, Xie X, Poplin R, Sun F. Ren J, et al. Among authors: ahlgren na. Quant Biol. 2020 Mar;8(1):64-77. doi: 10.1007/s40484-019-0187-4. Quant Biol. 2020. PMID: 34084563 Free PMC article.

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