VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Ren, Jie, Ahlgren, Nathan A, Lu, Yang Young, Fuhrman, Jed A, Sun, Fengzhu
Published in Microbiome (06.07.2017)
Published in Microbiome (06.07.2017)
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Journal Article
Identifying viruses from metagenomic data using deep learning
Ren, Jie, Song, Kai, Deng, Chao, Ahlgren, Nathan A., Fuhrman, Jed A., Li, Yi, Xie, Xiaohui, Poplin, Ryan, Sun, Fengzhu
Published in Quantitative biology (01.03.2020)
Published in Quantitative biology (01.03.2020)
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Journal Article
Multi‐year dynamics of fine‐scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom‐up factors
Ahlgren, Nathan A., Perelman, Jessica N., Yeh, Yi‐Chun, Fuhrman, Jed A.
Published in Environmental microbiology (01.08.2019)
Published in Environmental microbiology (01.08.2019)
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Journal Article
A network-based integrated framework for predicting virus–prokaryote interactions
Wang, Weili, Ren, Jie, Tang, Kujin, Dart, Emily, Ignacio-Espinoza, Julio Cesar, Fuhrman, Jed A, Braun, Jonathan, Sun, Fengzhu, Ahlgren, Nathan A
Published in NAR genomics and bioinformatics (01.06.2020)
Published in NAR genomics and bioinformatics (01.06.2020)
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Journal Article
Optimizing de novo genome assembly from PCR-amplified metagenomes
Roux, Simon, Trubl, Gareth, Goudeau, Danielle, Nath, Nandita, Couradeau, Estelle, Ahlgren, Nathan A, Zhan, Yuanchao, Marsan, David, Chen, Feng, Fuhrman, Jed A, Northen, Trent R, Sullivan, Matthew B, Rich, Virginia I, Malmstrom, Rex R, Eloe-Fadrosh, Emiley A
Published in PeerJ (San Francisco, CA) (09.05.2019)
Published in PeerJ (San Francisco, CA) (09.05.2019)
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Journal Article
Dynamics of Prochlorococcus Diversity and Photoacclimation During Short-Term Shifts in Water Column Stratification at Station ALOHA
Thompson, Anne W., van den Engh, Ger, Ahlgren, Nathan A., Kouba, Kathleen, Ward, Samantha, Wilson, Samuel T., Karl, David M.
Published in Frontiers in Marine Science (21.12.2018)
Published in Frontiers in Marine Science (21.12.2018)
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Journal Article
Long-term stability and Red Queen-like strain dynamics in marine viruses
Ignacio-Espinoza, J. Cesar, Ahlgren, Nathan A., Fuhrman, Jed A.
Published in Nature microbiology (01.02.2020)
Published in Nature microbiology (01.02.2020)
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Journal Article
Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron
Sohm, Jill A, Ahlgren, Nathan A, Thomson, Zachary J, Williams, Cheryl, Moffett, James W, Saito, Mak A, Webb, Eric A, Rocap, Gabrielle
Published in The ISME Journal (01.02.2016)
Published in The ISME Journal (01.02.2016)
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Journal Article
Prediction of virus-host infectious association by supervised learning methods
Zhang, Mengge, Yang, Lianping, Ren, Jie, Ahlgren, Nathan A, Fuhrman, Jed A, Sun, Fengzhu
Published in BMC bioinformatics (14.03.2017)
Published in BMC bioinformatics (14.03.2017)
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Journal Article
Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems
Ahlgren, Nathan A., Chen, Yangyang, Needham, David M., Parada, Alma E., Sachdeva, Rohan, Trinh, Vickie, Chen, Ting, Fuhrman, Jed A.
Published in Environmental microbiology (01.06.2017)
Published in Environmental microbiology (01.06.2017)
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Journal Article
Long-term stability and Red Queen-like strain dynamics in marine viruses
Ignacio-Espinoza, J. Cesar, Ahlgren, Nathan A., Fuhrman, Jed A.
Published in Nature microbiology (01.02.2020)
Published in Nature microbiology (01.02.2020)
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Journal Article