Alfredo Blakeley-Ruiz
Also known as: Alfredo
Microbiome, Proteomics, Genomics, Systems Biology
Works (9)
Updated: December 18th, 2024 15:10
2024 article
Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome
Rajczewski, A., Blakeley-Ruiz, J. A., Meyer, A., Vintila, S., McIlvin, M., Bossche, T. V. D., … Jagtap, P. (2024, September 22).
open access via www.ncbi.nlm.nih.gov (repository)
Source: ORCID
Added: October 1, 2024
2024 article
Dietary protein from different sources escapes host digestion and is differentially modified by the microbiota
Awan, A., Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C., & Kleiner, M. (2024, June 27).
Source: ORCID
Added: July 1, 2024
2024 article
Dietary protein source strongly alters gut microbiota composition and function
Blakeley-Ruiz, J. A., Bartlett, A., McMillan, A., Awan, A., Walsh, M. V., Meyerhoffer, A., … Kleiner, M. (2024, April 5).
Source: ORCID
Added: July 22, 2024
2023 article
Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies
Bartlett, A., Blakeley-Ruiz, A., Richie, T., Theriot, C., & Kleiner, M. (2023, December 7).
TL;DR:
Large quantities of microbial DNA and protein are found in casein-based diets, which highlight the necessity of evaluating diet samples in diet-microbiota studies to ensure that potential microbial content of the diet can be accounted for in microbiome measurements.
(via Semantic Scholar)
Source: ORCID
Added: December 8, 2023
2022 journal article
Considerations for constructing a protein sequence database for metaproteomics
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 20, 937–952.
Contributors: J. Blakeley-Ruiz n
author keywords: Metaproteome; Metagenomics; Microbiome; Microbial community; Multi-omics; Microbiota; Microbial ecology
TL;DR:
An overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies is provided, and a decision tree and best practices for choosing and implementing database construction strategies are provided.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: April 25, 2022
2022 journal article
Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice
ISME Communications, 2(1).
Contributors: J. Blakeley-Ruiz *
TL;DR:
Investigating the microbiome and host inflammatory responses to chronic opioid administration in genetically obese, diet-induced obese, and lean mice identified novel host-dependent phenotypes, differentiated the effects of genetic obesity versus diet induced obesity on gut microbiome composition and function, and showed that chronic morphine administration altered the gut microbiome.
(via Semantic Scholar)
Source: ORCID
Added: August 25, 2022
2020 thesis
Extracting detailed metabolic information and connections from mammalian gut microbiomes via metaproteomics
(PhD diss., University of Tennessee). https://trace.tennessee.edu/utk_graddiss/6194
Contributors: J. Blakeley-Ruiz
Source: ORCID
Added: August 25, 2022
2019 journal article
Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research
Behavioral and Brain Sciences.
TL;DR:
This commentary extends their review of microbiota-gut-brain literature by highlighting capabilities of advanced systems-biology “-omics” techniques for microbiome research and recommending that combining these high-resolution techniques with intervention-based experimental design may be the path forward for future MGB research.
(via Semantic Scholar)
Source: ORCID
Added: August 25, 2022
2019 journal article
Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes
Microbiome.
author keywords: Gut microbiome; Metaproteomics; Crohn's disease; Longitudinal analyses; Microbial metabolic function; Human microbiome
MeSH headings : Acetylglucosamine / analysis; Adult; Bacteria / genetics; Bacteria / metabolism; Crohn Disease / microbiology; Crohn Disease / surgery; Cytidine Monophosphate N-Acetylneuraminic Acid / analysis; Fatty Acids, Volatile / analysis; Feces / microbiology; Female; Gastrointestinal Microbiome / genetics; Gastrointestinal Microbiome / physiology; Humans; Male; Middle Aged; Proteome / metabolism; Proteomics; RNA, Ribosomal, 16S / genetics
TL;DR:
Examining metaproteomes measured in several Crohn’s disease patients’ post-resection surgery across the course of 1 year suggests that microbial membership composition may not be the best way to characterize a phenotype and suggests it seems to be more informative to examine and characterize the functional composition of a gut microbiome.
(via Semantic Scholar)
Source: ORCID
Added: August 25, 2022
Employment
Updated: August 26th, 2020 16:40
2020 - present
North Carolina State University Raleigh, NC, US
Postdoc
Plant and Microbial Biology
2011 - 2014
Infectious Disease Research Institute Seattle, WA, US
Research Assitant
TB Discovery
Education
Updated: August 26th, 2020 16:39
2014 - 2020
University of Tennessee Knoxville, TN, US
PhD
Genome Science and Technology
2007 - 2011
University of Notre Dame Notre Dame, IN, US
B.S.
Biological Sciences
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