Alfredo Blakeley-Ruiz

Comprehensive evaluation of statistical approaches for differential metaproteomics

Hinzke, T., Kunath, B. J., Blakeley-Ruiz, J. A., Korenek, A., Vintila, S., Wilmes, P., & Kleiner, M. (2025, December 10). (Vol. 12). Vol. 12.

Data‐Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome

Rajczewski, A. T., Blakeley‐Ruiz, J. A., Meyer, A., Vintila, S., McIlvin, M. R., Bossche, T. V. D., … Jagtap, P. D. (2025, April 10). PROTEOMICS, Vol. 4.

Dietary protein from different sources escapes host digestion and is differentially modified by gut microbiota

Awan, A., Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2025, January 1). Food & Function.

Dietary protein source alters gut microbiota composition and function

Blakeley-Ruiz, J. A., Bartlett, A., McMillan, A. S., Awan, A., Walsh, M. V., Meyerhoffer, A. K., … Kleiner, M. (2025, January 1). The ISME Journal, Vol. 19.

Evaluation of statistical approaches for differential metaproteomics: Reproducible code

Hinzke, T., Kunath, B. J., Blakeley-Ruiz, J. A., Korenek, A., Vintila, S., Wilmes, P., & Kleiner, M. (2025, December 10). Zenodo (CERN European Organization for Nuclear Research).

Evaluation of statistical approaches for differential metaproteomics: Reproducible code

Hinzke, T., Kunath, B. J., Blakeley-Ruiz, J. A., Korenek, A., Vintila, S., Wilmes, P., & Kleiner, M. (2025, December 10). Zenodo (CERN European Organization for Nuclear Research).

Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies

Bartlett, A., Blakeley‐Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2025, February 21). PROTEOMICS, Vol. 2.

Metaproteomics-based stable isotope fingerprinting links intestinal bacteria to their carbon source and captures diet-induced substrate switching

Mordant, A., Blakeley-Ruiz, J. A., & Kleiner, M. (2025, January 1). The ISME Journal, Vol. 19.

Source of dietary protein alters the abundance of proteases, intestinal epithelial and immune proteins both directly and via interactions with the gut microbiota

Awan, A., Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Ziegler, A., & Kleiner, M. (2025, January 9).

The Microbiologist’s Guide to Metaproteomics

Bossche, T. V. D., Armengaud, J., Benndorf, D., Blakeley-Ruiz, J. A., Brauer, M., Cheng, K., … Li, L. (2025, January 8).

The Microbiologist’s Guide to Metaproteomics

Bossche, T. V. D., Armengaud, J., Benndorf, D., Blakeley-Ruiz, J. A., Brauer, M., Cheng, K., … Li, L. (2025, April 1).

The microbiologist's guide to metaproteomics

Bossche, T. V. D., Armengaud, J., Benndorf, D., Blakeley‐Ruiz, J. A., Brauer, M., Cheng, K., … Initiative, T. M. (2025, May 6). IMeta, Vol. 5.

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome

Rajczewski, A. T., Blakeley-Ruiz, J. A., Meyer, A., Vintila, S., McIlvin, M. R., Bossche, T. V. D., … Jagtap, P. D. (2024, September 22).

Dietary protein from different sources escapes host digestion and is differentially modified by gut microbiota

Awan, A., Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2024, June 27).

Dietary protein source alters gut microbiota composition and function

Blakeley-Ruiz, J. A., Bartlett, A., McMillan, A. S., Awan, A., Walsh, M. V., Meyerhoffer, A. K., … Kleiner, M. (2024, April 5).

Stable isotope fingerprinting can directly link intestinal microorganisms with their carbon source and captures diet-induced substrate switching in vivo

Mordant, A., Blakeley-Ruiz, J. A., & Kleiner, M. (2024, December 11).

Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies

Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2023, December 7).

Considerations for constructing a protein sequence database for metaproteomics

Blakeley-Ruiz, J. A., & Kleiner, M. (2022, January 1). Computational and Structural Biotechnology Journal, Vol. 20, pp. 937–952.

Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice

Blakeley-Ruiz, J. A., McClintock, C. S., Shrestha, H. K., Poudel, S., Yang, Z. K., Giannone, R. J., … Hettich, R. L. (2022, August 5). ISME Communications, Vol. 2.

Extracting detailed metabolic information and connections from mammalian gut microbiomes via metaproteomics

(PhD diss., University of Tennessee). https://trace.tennessee.edu/utk_graddiss/6194

Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research

Blakeley-Ruiz, J. A., McClintock, C. S., Lydic, R., Baghdoyan, H. A., Choo, J. J., & Hettich, R. L. (2019, January 1). Behavioral and Brain Sciences.

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

Blakeley-Ruiz, J. A., Erickson, A. R., Cantarel, B. L., Xiong, W., Adams, R., Jansson, J. K., … Hettich, R. L. (2019, February 11). Microbiome.