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- Publications
- Influence
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
- E. Bolyen, J. Rideout, +109 authors J. Caporaso
- Engineering, Medicine
- Nature Biotechnology
- 1 August 2019
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) and… Expand
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
- E. Bolyen, J. Rideout, +106 authors J. Caporaso
- Computer Science
- 24 October 2018
TLDR
Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments
- M. Sullivan, K. Huang, +15 authors S. Chisholm
- Biology, Medicine
- Environmental microbiology
- 1 November 2010
T4-like myoviruses are ubiquitous, and their genes are among the most abundant documented in ocean systems. Here we compare 26 T4-like genomes, including 10 from non-cyanobacterial myoviruses, and 16… Expand
Species-level functional profiling of metagenomes and metatranscriptomes
- E. Franzosa, Lauren J. McIver, +8 authors C. Huttenhower
- Biology, Medicine
- Nature Methods
- 21 September 2018
Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping,… Expand
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
- A. Amir, Daniel McDonald, +8 authors R. Knight
- Medicine, Biology
- mSystems
- 7 March 2017
Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real… Expand
Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts
- M. Sullivan, D. Lindell, Jessica A. Lee, L. Thompson, J. Bielawski, S. Chisholm
- Biology, Medicine
- PLoS biology
- 4 July 2006
Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer among marine cyanobacteria, the numerically dominant photosynthetic organisms in the oceans. Some cyanophage… Expand
A communal catalogue reveals Earth’s multiscale microbial diversity
- L. Thompson, J. Sanders, +301 authors Hongxia Zhao
- Biology, Medicine
- Nature
- 1 November 2017
Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a… Expand
Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism.
- L. Thompson, Qinglu Zeng, +4 authors S. Chisholm
- Biology, Medicine
- Proceedings of the National Academy of Sciences…
- 27 September 2011
Cyanophages infecting the marine cyanobacteria Prochlorococcus and Synechococcus encode and express genes for the photosynthetic light reactions. Sequenced cyanophage genomes lack Calvin cycle genes,… Expand
American Gut: an Open Platform for Citizen Science Microbiome Research
- Daniel McDonald, Embriette R. Hyde, +55 authors R. Knight
- Biology, Medicine
- mSystems
- 15 May 2018
We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new… Expand
Choreography of the Transcriptome, Photophysiology, and Cell Cycle of a Minimal Photoautotroph, Prochlorococcus
- E. Zinser, D. Lindell, +9 authors S. Chisholm
- Biology, Medicine
- PloS one
- 8 April 2009
The marine cyanobacterium Prochlorococcus MED4 has the smallest genome and cell size of all known photosynthetic organisms. Like all phototrophs at temperate latitudes, it experiences predictable… Expand