| Considerations for constructing a protein sequence database for metaproteomics JA Blakeley-Ruiz, M Kleiner Computational and structural biotechnology journal 20, 937-952, 2022 | 87 | 2022 |
| Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations … JA Blakeley-Ruiz, AR Erickson, BL Cantarel, W Xiong, R Adams, ... Microbiome 7 (1), 18, 2019 | 78 | 2019 |
| Dietary protein source strongly alters gut microbiota composition and function JA Blakeley-Ruiz, A Bartlett, AS McMillan, A Awan, M Vanhoy Walsh, ... The ISME Journal 19 (1), wraf048, 2025 | 26 | 2025 |
| The microbiologist's guide to metaproteomics T Van Den Bossche, J Armengaud, D Benndorf, JA Blakeley‐Ruiz, ... iMeta 4 (3), e70031, 2025 | 19 | 2025 |
| Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice JA Blakeley-Ruiz, CS McClintock, HK Shrestha, S Poudel, ZK Yang, ... ISME communications 2 (1), 66, 2022 | 17 | 2022 |
| Data‐Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome AT Rajczewski, JA Blakeley‐Ruiz, A Meyer, S Vintila, MR McIlvin, ... Proteomics 25 (9-10), e202400187, 2025 | 14 | 2025 |
| Dietary protein from different sources escapes host digestion and is differentially modified by gut microbiota A Awan, A Bartlett, JA Blakeley-Ruiz, T Richie, CM Theriot, M Kleiner Food & Function 16 (18), 7154-7168, 2025 | 7 | 2025 |
| Large quantities of bacterial DNA and protein in common dietary protein source used in microbiome studies A Bartlett, JA Blakeley‐Ruiz, T Richie, CM Theriot, M Kleiner Proteomics 25 (17-18), 43-50, 2025 | 3 | 2025 |
| Source of dietary protein alters the abundance of proteases, intestinal epithelial and immune proteins both directly and via interactions with the gut microbiota A Awan, A Bartlett, JA Blakeley-Ruiz, T Richie, A Ziegler, M Kleiner bioRxiv, 2025 | 2 | 2025 |
| Combining integrated systems-biology approaches with intervention-based experimental design provides a higher-resolution path forward for microbiome research JA Blakeley-Ruiz, CS McClintock, R Lydic, HA Baghdoyan, JJ Choo, ... Behavioral and Brain Sciences 42, 2019 | 2 | 2019 |
| Metaproteomics-based stable isotope fingerprinting links intestinal bacteria to their carbon source and captures diet-induced substrate switching A Mordant, JA Blakeley-Ruiz, M Kleiner The ISME Journal, wraf127, 2025 | 1* | 2025 |
| Evaluation of statistical approaches for differential metaproteomics T Hinzke, BJ Kunath, JA Blakeley-Ruiz, A Korenek, S Vintila, P Wilmes, ... bioRxiv, 2025.12. 10.693402, 2025 | | 2025 |
| Normothermic Machine Perfusion Mitigates Allograft Inflammation in Intestinal Transplantation LM Gonzalez, C McKinney-Aguirre, E Goya-Jorge, C Schaaf, E Ludwig, ... American Journal of Transplantation 25 (8), S102, 2025 | | 2025 |
| Normothermic Machine Perfusion Mitigates Allograft Inflammation in Intestinal Transplantation C McKinney-Aguirre, E Goya-Jorge, CR Schaaf, EK Ludwig, L Poisson, ... Physiology 40 (S1), 0571, 2025 | | 2025 |
| Allograft Inflammation is Reduced with Normothermic Machine Perfusion in Intestinal Transplantation CMK Aguirre, EG Jorge, C Schaaf, E Ludwig, L Poisson, A Stewart, ... Intestinal Failure 6, 2025 | | 2025 |
| Reduction of apoptosis and preservation of stem-cell proliferation in intestinal transplantation allografts with normothermic machine perfusion C McKinney-Aguirre, E Goya-Jorge, C Schaaf, E Ludwig, A Stewart, ... Intestinal Failure 6, 2025 | | 2025 |
| Extracting detailed metabolic information and connections from mammalian gut microbiomes via metaproteomics JA Blakeley-Ruiz | | 2020 |
