Author

Y. C. Lou

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 6

Signature Assays, Organisms & Methods

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Assay:metagenomics· 5 Organism:human· 4 Research Focus:cell type annotation· 3 Approach:statistical model· 3 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Organism:bacteria (other)· 1 Research Focus:cell-cell communication· 1

Frequent Co-Authors

J. F. Banfield· 5 shared B. A. Firek· 4 shared A. L. Borges· 3 shared M. R. Olm· 3 shared M. J. Morowitz· 2 shared M. Morowitz· 2 shared R. Baker· 2 shared S. Diamond· 2 shared

Activity by Year

2021-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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5 shared papersMicrobiology

J. F. Banfield

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Author profile →

6 papers

Recent·Most cited

Infant gut bacteriophage strain persistence during the first three years of life

Y. C. Lou, L. Chen, A. L. Borges, J. A. West-Roberts, B. A. Firek, M. Morowitz, J. Banfield

The paper investigates phage succession in infants over three years, finding that 9% of early phage colonizers persist, with maternal transmission and stop codon reassignment playing key roles.

bioRxiv · Aug 7, 2023Microbiology

Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2'-fucosyllactose utilization can be facilitated by co-existing species

Y. C. Lou, B. E. Rubin, M. C. Schoelmerich, K. DiMarco, A. L. Borges, R. Rovinsky, L. Song, J. A. Doudna, J. F. Banfield

The paper shows that Bifidobacterium breve can utilize 2'-fucosyllactose with help from co-existing species like Ruminococcus gnavus in infant microbiomes.

bioRxiv · Mar 10, 2023Microbiology

Using strain-resolved analysis to identify contamination in metagenomics data

Y. C. Lou, J. Hoff, M. R. Olm, J. West-Roberts, S. Diamond, B. A. Firek, M. J. Morowitz, J. F. Banfield

This study identifies contamination in metagenomics data using strain-resolved analysis, finding that contamination is more common in low-biomass samples and adjacent extraction plate positions.

bioRxiv · Jan 16, 2022Microbiology

Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes

A. L. Borges, Y. C. Lou, R. Sachdeva, B. Al-Shayeb, A. L. Jaffe, S. Lei, J. M. Santini, J. F. Banfield

The paper surveys stop codon recoding in bacteriophages, finding it widespread and suggesting it regulates gene expression and lysis timing.

bioRxiv · Aug 26, 2021 · PreprintMicrobiology

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics

P. T. West, S. L. Peters, M. R. Olm, F. B. Yu, Y. C. Lou, B. A. Firek, R. Baker, A. D. Johnson, M. J. Morowitz, R. L. Hettich, J. F. Banfield

This study identifies genetic and behavioral adaptations of C. parapsilosis in the gut microbiome of hospitalized infants using in situ genomics, transcriptomics, and proteomics.

Microbiome · Jun 21, 2021Peer-reviewedMicrobiology

Infant gut strain persistence is associated with maternal origin, phylogeny, and functional potential including surface adhesion and iron acquisition

Y. C. Lou, M. R. Olm, S. Diamond, A. Crits-Christoph, B. A. Firek, R. Baker, M. Morowitz, J. F. Banfield

The paper investigates factors influencing gut microbiome strain persistence in infants, finding maternal origin and specific genetic functions are associated with strain survival.

bioRxiv · Jan 26, 2021Microbiology