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N. Ahlgren · SciRah

Researcher profile · Semantic Scholar

N. Ahlgren

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N. Ahlgren — researcher profile on SciRah

h-index: 23
Works: 48
Citations: 4,588

Most-cited papers

Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation
G. Rocap, F. Larimer, J. Lamerdin, S. Malfatti +20 more
2003Nature1,179 citations Open access
Semantic Scholar
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Jie Jessie Ren, N. Ahlgren, Yang Young Lu, J. Fuhrman +1 more
2017Microbiome600 citations Open access
Semantic Scholar
Identifying viruses from metagenomic data using deep learning
Jie Jessie Ren, Kai Song, C. Deng, N. Ahlgren +5 more
2020Quantitative Biology589 citations Open access
Semantic Scholar
Alignment-free \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$d_2^*$\end{document} oligonucleotide frequency dissi
N. Ahlgren, Jie Jessie Ren, Yang Young Lu, J. Fuhrman +1 more
2016Nucleic Acids Research260 citations Open access
Semantic Scholar
Copper toxicity and cyanobacteria ecology in the Sargasso Sea
Elizabeth L. Mann, N. Ahlgren, James W. Moffett, S. Chisholm
2002234 citations Open access
Semantic Scholar
Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron
Jill A. Sohm, N. Ahlgren, Z. Thomson, Cheryl Williams +4 more
2015The ISME Journal218 citations Open access
Semantic Scholar
Unraveling the functional dark matter through global metagenomics
Georgios A Pavlopoulos, Fotis A. Baltoumas, Si-Rui Liu, Oguz Selvitopi +128 more
2023Nature179 citations Open access
Semantic Scholar
Culture Isolation and Culture-Independent Clone Libraries Reveal New Marine Synechococcus Ecotypes with Distinctive Light and N Physiologies
N. Ahlgren, G. Rocap
2006Applied and Environmental Microbiology154 citations Open access
Semantic Scholar
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
N. Ahlgren, G. Rocap
2012Front. Microbio.149 citations Open access
Semantic Scholar
Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes
N. Ahlgren, C. Fuchsman, G. Rocap, J. Fuhrman
2018The ISME Journal130 citations Open access
Semantic Scholar
A network-based integrated framework for predicting virus–prokaryote interactions
Weili Wang, Jie Jessie Ren, Ku-Jin Tang, E. Dart +5 more
2020NAR Genomics and Bioinformatics126 citations Open access
Semantic Scholar
Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies.
N. Ahlgren, G. Rocap, S. Chisholm
2006Environmental Microbiology121 citations
Semantic Scholar
Aryl-homoserine lactone quorum sensing in stem-nodulating photosynthetic bradyrhizobia
N. Ahlgren, C. Harwood, A. Schaefer, E. Giraud +1 more
2011Proceedings of the National Academy of Sciences of the United States of America117 citations Open access
Semantic Scholar
Long-term stability and Red Queen-like strain dynamics in marine viruses
J. Ignacio-Espinoza, N. Ahlgren, J. Fuhrman
2019Nature Microbiology94 citations
Semantic Scholar
Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems
N. Ahlgren, Yang-Yang Chen, D. Needham, A. Parada +4 more
2017Environmental Microbiology63 citations Open access
Semantic Scholar
The unique trace metal and mixed layer conditions of the Costa Rica upwelling dome support a distinct and dense community of Synechococcus
N. Ahlgren, A. Noble, A. Patton, K. Roache-Johnson +6 more
201456 citations
Semantic Scholar
Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors.
N. Ahlgren, J. Perelman, Yi-Chun Yeh, J. Fuhrman
2019Environmental Microbiology51 citations Open access
Semantic Scholar
Prediction of virus-host infectious association by supervised learning methods
Meng-Zhu Zhang, Lianping Yang, J. Ren, N. Ahlgren +2 more
2017BMC Bioinformatics43 citations Open access
Semantic Scholar
Optimizing de novo genome assembly from PCR-amplified metagenomes
S. Roux, G. Trubl, D. Goudeau, N. Nath +11 more
2018PeerJ40 citations Open access
Semantic Scholar
Genomic mosaicism underlies the adaptation of marine Synechococcus ecotypes to distinct oceanic iron niches.
N. Ahlgren, B. S. Belisle, Michael D. Lee
2019Environmental Microbiology36 citations
Semantic Scholar
Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content
Michael D. Lee, N. Ahlgren, Joshua D. Kling, Nathan G. Walworth +4 more
2019Environmental Microbiology33 citations
Semantic Scholar
Identifying viruses from metagenomic data by deep learning.
Jie Ren, Kai Song, C. Deng, N. Ahlgren +4 more
201833 citations
Semantic Scholar
Dynamics of Prochlorococcus Diversity and Photoacclimation During Short-Term Shifts in Water Column Stratification at Station ALOHA
A. Thompson, G. J. van den Engh, N. Ahlgren, Kathleen Kouba +3 more
2018Frontiers in Marine Science28 citations Open access
Semantic Scholar
Niche partitioning of low‐light adapted Prochlorococcus subecotypes across oceanographic gradients of the North Pacific Subtropical Front
A. Thompson, Kathleen Kouba, N. Ahlgren
2021Limnology and Oceanography23 citations Open access
Semantic Scholar
Characterization of IS1676 from Rhodococcus erythropolis SQ1
P. Lessard, X. O’Brien, N. Ahlgren, S. Ribich +1 more
1999Applied Microbiology and Biotechnology17 citations
Semantic Scholar
Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics
E. Dart, J. Fuhrman, N. Ahlgren
2023Viruses15 citations Open access
Semantic Scholar
County-level societal predictors of COVID-19 cases and deaths changed through time in the United States: A longitudinal ecological study
P. Bergmann, N. Ahlgren, Rosalie A. Torres Stone
2022PLOS Global Public Health4 citations Open access
Semantic Scholar
A network-based integrated framework for predicting virus-host interactions
Weili Wang, J. Ren, Ku-Jin Tang, E. Dart +5 more
2018bioRxiv4 citations Open access
Semantic Scholar
Genome Sequences of Synechococcus sp. Strain MIT S9220 and Cocultured Cyanophage SynMITS9220M01
B. S. Belisle, Andres A. Avila Paz, Angelina R. Carpenter, Tayla C. Cormier +9 more
2020Microbiology Resource Announcements3 citations Open access
Semantic Scholar
Genomic catalogue of giant viruses reveals expanded diversity and functional potential
Yumary M. Vasquez, Tiago Nardi, G. M. Terasaki, P. Byl +26 more
2026Nature Microbiology2 citations Open access
Semantic Scholar
Phylogenetic proximity is a key driver of temporal succession of marine giant viruses in a five-year metagenomic time-series
Sarah M. Laperriere, Benjamin Minch, J. L. Weissman, Shengwei Hou +5 more
2025ISME Communications2 citations
Semantic Scholar
New tRNA-targeting transposons that hijack phage and vesicles.
E. Dart, N. Ahlgren
2023Trends in Genetics2 citations
Semantic Scholar
Expansive Diversity and Temporal Dynamics of Emerging Polinton-like Viruses in a Marine Ecosystem
Ethan Mimick, C. Bellas, N. Ahlgren, J. Fuhrman +1 more
2026bioRxiv1 citations Open access
Semantic Scholar
Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series
S. Laperriere, Benjamin Minch, J. Weissman, Shengwei Hou +5 more
2024bioRxiv1 citations Open access
Semantic Scholar
Multiple measures of structural racism as predictors of U.S. county-level COVID-19 cases and deaths
Rosalie A. Torres Stone, N. Ahlgren, P. Bergmann
2022Ethnic and Racial Studies1 citations
Semantic Scholar
Urbanization impacts on stream and lake water quality in a small watershed in central Massachusetts, USA
L. Reynolds, A. Dunn, William J. Hansen, Meghna Dilip +11 more
2026Environmental Monitoring & Assessment0 citations
Semantic Scholar
A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets
Yuqian Mo, N. Ahlgren, J. Fuhrman, Feng-Zhu Sun +1 more
2026Current Protocols0 citations
Semantic Scholar
Effects of urbanization on the microbial fungal communities from water, sediment, and amphibian hosts across a rural-to-urban waterway in Worcester, Massachusetts
Sara J. Wheeler, Manning DelCogliano, Brennan Hare, A. Bradshaw +5 more
2025bioRxiv0 citations Open access
Semantic Scholar
Host species and body site equally impact microbiome structure between sympatric Atlantic sea cucumber species
Catherine A. Crowley, B. S. Belisle, E. Dart, N. Ahlgren
2025bioRxiv0 citations Open access
Semantic Scholar
Genome Sequence of the Estuarine Synechococcus sp. Strain NB0720_010
Campbell A. MacKenzie, M. Marston, J. Tabima, N. Ahlgren
2022Microbiology Resource Announcements0 citations Open access
Semantic Scholar
Peer Review #1 of "Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils (v0.2)"
G. Trubl, S. Roux, N. Solonenko, Yueh-Fen Li +356 more
20190 citations Open access
Semantic Scholar
A NETWORK-BASED INTEGRATED FRAMEWORK FOR PREDICTING VIRUS-HOST INTERACTIONS WITH APPLICATIONS
Weili Wang, Jie Ren, N. Ahlgren, J. Fuhrman +3 more
20180 citations
Semantic Scholar
Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.
N. Ahlgren, A. Parada, J. Fuhrman
20160 citations
Semantic Scholar
The complete genome of a new marine Thaumarchaea strain contains evidence of previous virus infection and a possible defense mechanism from infection
N. Ahlgren, A. Parada, J. Fuhrman
20160 citations
Semantic Scholar
Changes in picocyanobacterial community structure across transitions from oligotrophic to upwelling regions off of Costa Rica
N. Ahlgren, L. Moore, K. Noble, M. Saito +1 more
20080 citations
Semantic Scholar
Optimizing de novo genome assembly from PCR-amplified Optimizing de novo genome assembly from PCR-amplified metagenomes metagenomes
A. M. Eren, Simon Roux, G. Trubl, D. Goudeau +15 more
0 citations
Semantic Scholar
Dynamics of Prochlorococcus Diversity and Photoacclimation Dynamics of Prochlorococcus Diversity and Photoacclimation During Short-Term Shifts in Water Column Stratification at Station During Short-Term Shifts in Water Column Stratification at Station ALOHA ALOHA
Anne W. Thompson, G. J. van den Engh, N. Ahlgren, Kathleen Kouba +3 more
0 citations
Semantic Scholar

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