inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains
Olm, Matthew R., Crits-Christoph, Alexander, Bouma-Gregson, Keith, Firek, Brian A., Morowitz, Michael J., Banfield, Jillian F.
Published in Nature biotechnology (01.06.2021)
Published in Nature biotechnology (01.06.2021)
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Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants
Gopalakrishna, Kathyayini P., Macadangdang, Benjamin R., Rogers, Matthew B., Tometich, Justin T., Firek, Brian A., Baker, Robyn, Ji, Junyi, Burr, Ansen H. P., Ma, Congrong, Good, Misty, Morowitz, Michael J., Hand, Timothy W.
Published in Nature medicine (01.07.2019)
Published in Nature medicine (01.07.2019)
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Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome
Brooks, Brandon, Olm, Matthew R., Firek, Brian A., Baker, Robyn, Thomas, Brian C., Morowitz, Michael J., Banfield, Jillian F.
Published in Nature communications (27.11.2017)
Published in Nature communications (27.11.2017)
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Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella , and fimbriae-encoding bacteria
Olm, Matthew R, Bhattacharya, Nicholas, Crits-Christoph, Alexander, Firek, Brian A, Baker, Robyn, Song, Yun S, Morowitz, Michael J, Banfield, Jillian F
Published in Science advances (11.12.2019)
Published in Science advances (11.12.2019)
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Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data
Austin, George I., Park, Heekuk, Meydan, Yoli, Seeram, Dwayne, Sezin, Tanya, Lou, Yue Clare, Firek, Brian A., Morowitz, Michael J., Banfield, Jillian F., Christiano, Angela M., Pe’er, Itsik, Uhlemann, Anne-Catrin, Shenhav, Liat, Korem, Tal
Published in Nature biotechnology (01.12.2023)
Published in Nature biotechnology (01.12.2023)
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Journal Article
Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants
Brooks, Brandon, Firek, Brian A, Miller, Christopher S, Sharon, Itai, Thomas, Brian C, Baker, Robyn, Morowitz, Michael J, Banfield, Jillian F
Published in Microbiome (28.01.2014)
Published in Microbiome (28.01.2014)
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Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition
Lou, Yue Clare, Olm, Matthew R., Diamond, Spencer, Crits-Christoph, Alexander, Firek, Brian A., Baker, Robyn, Morowitz, Michael J., Banfield, Jillian F.
Published in Cell reports. Medicine (21.09.2021)
Published in Cell reports. Medicine (21.09.2021)
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Journal Article
Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms
Olm, Matthew R, West, Patrick T, Brooks, Brandon, Firek, Brian A, Baker, Robyn, Morowitz, Michael J, Banfield, Jillian F
Published in Microbiome (15.02.2019)
Published in Microbiome (15.02.2019)
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Journal Article
The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms
Brooks, Brandon, Olm, Matthew R, Firek, Brian A, Baker, Robyn, Geller-McGrath, David, Reimer, Sophia R, Soenjoyo, Karina R, Yip, Jennifer S, Dahan, Dylan, Thomas, Brian C, Morowitz, Michael J, Banfield, Jillian F
Published in Microbiome (20.06.2018)
Published in Microbiome (20.06.2018)
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Using strain-resolved analysis to identify contamination in metagenomics data
Lou, Yue Clare, Hoff, Jordan, Olm, Matthew R, West-Roberts, Jacob, Diamond, Spencer, Firek, Brian A, Morowitz, Michael J, Banfield, Jillian F
Published in Microbiome (02.03.2023)
Published in Microbiome (02.03.2023)
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Journal Article
Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics
West, Patrick T, Peters, Samantha L, Olm, Matthew R, Yu, Feiqiao B, Gause, Haley, Lou, Yue Clare, Firek, Brian A, Baker, Robyn, Johnson, Alexander D, Morowitz, Michael J, Hettich, Robert L, Banfield, Jillian F
Published in Microbiome (21.06.2021)
Published in Microbiome (21.06.2021)
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Journal Article
The Staphylococcus aureus lrgAB Operon Modulates Murein Hydrolase Activity and Penicillin Tolerance
Groicher, K H, Firek, B A, Fujimoto, D F, Bayles, K W
Published in Journal of Bacteriology (01.04.2000)
Published in Journal of Bacteriology (01.04.2000)
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Journal Article
The Staphylococcus aureus cidAB Operon: Evaluation of Its Role in Regulation of Murein Hydrolase Activity and Penicillin Tolerance
Rice, Kelly C, Firek, Brian A, Nelson, Jeremy B, Yang, Soo-Jin, Patton, Toni G, Bayles, Kenneth W
Published in Journal of Bacteriology (01.04.2003)
Published in Journal of Bacteriology (01.04.2003)
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Structure and Energetics of Encapsidated DNA in Bacteriophage HK97 Studied by Scanning Calorimetry and Cryo-electron Microscopy
Duda, Robert L., Ross, Philip D., Cheng, Naiqian, Firek, Brian A., Hendrix, Roger W., Conway, James F., Steven, Alasdair C.
Published in Journal of molecular biology (14.08.2009)
Published in Journal of molecular biology (14.08.2009)
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Safety, Clinical Response, and Microbiome Findings Following Fecal Microbiota Transplant in Children With Inflammatory Bowel Disease
Goyal, Alka, Yeh, Andrew, Bush, Brian R, Firek, Brian A, Siebold, Leah M, Rogers, Matthew Brian, Kufen, Adam D, Morowitz, Michael J
Published in Inflammatory bowel diseases (18.01.2018)
Published in Inflammatory bowel diseases (18.01.2018)
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Journal Article
Depletion of gut microbiota is associated with improved neurologic outcome following traumatic brain injury
Simon, Dennis W., Rogers, Matthew B., Gao, Yuan, Vincent, Garret, Firek, Brian A., Janesko-Feldman, Keri, Vagni, Vincent, Kochanek, Patrick M., Ozolek, John A., Mollen, Kevin P., Clark, Robert S.B., Morowitz, Michael J.
Published in Brain research (15.11.2020)
Published in Brain research (15.11.2020)
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Journal Article
Sustained Dysbiosis and Decreased Fecal Short-Chain Fatty Acids after Traumatic Brain Injury and Impact on Neurologic Outcome
Opeyemi, Oluwasinmisola M, Rogers, Matthew B, Firek, Brian A, Janesko-Feldman, Keri, Vagni, Vincent, Mullett, Steven J, Wendell, Stacy G, Nelson, Brittany P, New, Lee Ann, Mariño, Eliana, Kochanek, Patrick M, Bayır, Hülya, Clark, Robert S B, Morowitz, Michael J, Simon, Dennis W
Published in Journal of neurotrauma (15.09.2021)
Published in Journal of neurotrauma (15.09.2021)
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