Author

B. A. Firek

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· 7

Signature Assays, Organisms & Methods

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Assay:metagenomics· 7 Organism:human· 6 Research Focus:cell type annotation· 5 Approach:statistical model· 4 Research Focus:differential expression· 2 Research Focus:clustering· 1 Research Focus:deconvolution· 1 Approach:deep learning· 1

Frequent Co-Authors

J. F. Banfield· 6 shared M. R. Olm· 6 shared M. J. Morowitz· 5 shared R. Baker· 5 shared Y. C. Lou· 4 shared A. Crits-Christoph· 2 shared B. Brooks· 2 shared M. Morowitz· 2 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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6 shared papersMicrobiology

J. F. Banfield

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7 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

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

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

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors

M. R. Olm, N. Bhattacharya, A. Crits-Christoph, B. A. Firek, R. Baker, Y. S. Song, M. J. Morowitz, J. F. Banfield

The paper identifies microbial features predictive of necrotizing enterocolitis (NEC) in premature infants using metagenomic analysis and machine learning.

bioRxiv · Feb 22, 2019Microbiology

Strain-level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes

M. R. Olm, P. T. West, B. Brooks, B. A. Firek, R. Baker, M. J. Morowitz, J. F. Banfield

The paper analyzes metagenomic data from premature infants and NICUs to identify fungal strains and their genetic diversity, revealing high similarity between infant and hospital-associated fungi.

bioRxiv · May 17, 2018Microbiology

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms

B. Brooks, M. R. Olm, B. A. Firek, R. Baker, D. Geller-McGrath, S. R. Reimer, K. R. Soenjoyo, J. S. Yip, D. Dahan, B. C. Thomas, M. J. Morowitz, J. F. Banfield

The paper investigates how the gut microbiome of premature infants shapes the microbial composition of NICU rooms over time.

bioRxiv · May 7, 2018Microbiology