| Generalized biomolecular modeling and design with RoseTTAFold All-Atom R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh, I Kalvet, GR Lee, ... Science 384 (6693), eadl2528, 2024 | 936 | 2024 |
| Computed structures of core eukaryotic protein complexes IR Humphreys, J Pei, M Baek, A Krishnakumar, I Anishchenko, ... Science 374 (6573), eabm4805, 2021 | 560 | 2021 |
| Efficient and accurate prediction of protein structure using RoseTTAFold2 M Baek, I Anishchenko, I Humphreys, Q Cong, D Baker, F DiMaio bioRxiv, 2023.05. 24.542179, 2023 | 163 | 2023 |
| Computational design of serine hydrolases A Lauko, SJ Pellock, KH Sumida, I Anishchenko, D Juergens, W Ahern, ... Science 388 (6744), eadu2454, 2025 | 136 | 2025 |
| A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology CA Gaulke, ML Martins, VG Watral, IR Humphreys, ST Spagnoli, ML Kent, ... Microbiome 7 (1), 10, 2019 | 119 | 2019 |
| Ecophylogenetics clarifies the evolutionary association between mammals and their gut microbiota CA Gaulke, HK Arnold, IR Humphreys, SW Kembel, JP O’Dwyer, ... MBio 9 (5), 10.1128/mbio. 01348-18, 2018 | 95 | 2018 |
| Recent advances in predicting and modeling protein–protein interactions J Durham, J Zhang, IR Humphreys, J Pei, Q Cong Trends in biochemical sciences 48 (6), 527-538, 2023 | 91 | 2023 |
| Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle Y Wang, LA Gallagher, PA Andrade, A Liu, IR Humphreys, S Turkarslan, ... Cell 186 (22), 4803-4817. e13, 2023 | 88 | 2023 |
| Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14 I Anishchenko, M Baek, H Park, N Hiranuma, DE Kim, J Dauparas, ... Proteins: Structure, Function, and Bioinformatics 89 (12), 1722-1733, 2021 | 58 | 2021 |
| Predicting protein-protein interactions in the human proteome J Zhang, IR Humphreys, J Pei, J Kim, C Choi, R Yuan, J Durham, S Liu, ... Science, eadt1630, 2025 | 46* | 2025 |
| Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations L Combrink, IR Humphreys, Q Washburn, HK Arnold, K Stagaman, ... Frontiers in Microbiology 14, 1092216, 2023 | 37 | 2023 |
| Protein interactions in human pathogens revealed through deep learning IR Humphreys, J Zhang, M Baek, Y Wang, A Krishnakumar, J Pei, ... Nature Microbiology, 1-11, 2024 | 31 | 2024 |
| ATG5 Promotes Death Signaling in Response to the Cyclic Depsipeptides Coibamide A and Apratoxin A X Wan, JD Serrill, IR Humphreys, M Tan, KL McPhail, IG Ganley, ... Marine drugs 16 (3), 77, 2018 | 31 | 2018 |
| Protein oligomer modeling guided by predicted interchain contacts in CASP14 M Baek, I Anishchenko, H Park, IR Humphreys, D Baker Proteins: Structure, Function, and Bioinformatics 89 (12), 1824-1833, 2021 | 24 | 2021 |
| An integrated gene catalog of the zebrafish gut microbiome reveals significant homology with mammalian microbiomes CA Gaulke, LM Beaver, CR Armour, IR Humphreys, CL Barton, ... BioRxiv, 2020.06. 15.153924, 2020 | 21 | 2020 |
| Accelerating biomolecular modeling with atomworks and rf3 N Corley, S Mathis, R Krishna, MS Bauer, TR Thompson, W Ahern, ... BioRxiv, 2025 | 15 | 2025 |
| Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm M Kshirsagar, A Meller, IR Humphreys, S Sledzieski, Y Xu, R Dodhia, ... Nature Communications 16 (1), 2017, 2025 | 15* | 2025 |
| The Marine-Derived Macrolactone Mandelalide A Is an Indirect Activator of AMPK DR Mattos, X Wan, JD Serrill, MH Nguyen, IR Humphreys, B Viollet, ... Marine Drugs 20 (7), 418, 2022 | 10 | 2022 |
| Biased regulation of protein synthesis and hypoxic death by a conditional raptor mutation CL Sun, C Xu, O Itani, EL Christensen, H Vijay, J Ho, A Correa-Medina, ... Current Biology, 2025 | 2 | 2025 |
| Deep learning and coevolution reveal proteome-wide protein-protein interactions IR Humphreys University of Washington, 2024 | 1 | 2024 |
David BakerUniversity of WashingtonVerified email at uw.edu
