WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs Y Liao, J Wang, EJ Jaehnig, Z Shi, B Zhang Nucleic acids research 47 (W1), W199-W205, 2019 | 2883 | 2019 |
Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma MA Gillette, S Satpathy, S Cao, SM Dhanasekaran, SV Vasaikar, K Krug, ... Cell 182 (1), 200-225. e35, 2020 | 582 | 2020 |
Proteogenomic and metabolomic characterization of human glioblastoma LB Wang, A Karpova, MA Gritsenko, JE Kyle, S Cao, Y Li, D Rykunov, ... Cancer Cell 39 (4), 509-528. e20, 2021 | 502 | 2021 |
Proteogenomic landscape of breast cancer tumorigenesis and targeted therapy K Krug, EJ Jaehnig, S Satpathy, L Blumenberg, A Karpova, M Anurag, ... Cell 183 (5), 1436-1456. e31, 2020 | 404 | 2020 |
ECOD: an evolutionary classification of protein domains H Cheng, RD Schaeffer, Y Liao, LN Kinch, J Pei, S Shi, BH Kim, ... PLoS computational biology 10 (12), e1003926, 2014 | 384 | 2014 |
Proteogenomic Characterization of Endometrial Carcinoma Y Dou, EA Kawaler, DC Zhou, MA Gritsenko, C Huang, L Blumenberg, ... Cell 180 (4), 729-748. e26, 2020 | 383 | 2020 |
Proteogenomic characterization of pancreatic ductal adenocarcinoma L Cao, C Huang, DC Zhou, Y Hu, TM Lih, SR Savage, K Krug, DJ Clark, ... Cell 184 (19), 5031-5052. e26, 2021 | 378 | 2021 |
The WAVE regulatory complex links diverse receptors to the actin cytoskeleton B Chen, K Brinkmann, Z Chen, CW Pak, Y Liao, S Shi, L Henry, ... Cell 156 (1), 195-207, 2014 | 310 | 2014 |
Large-scale determination of previously unsolved protein structures using evolutionary information S Ovchinnikov, L Kinch, H Park, Y Liao, J Pei, DE Kim, H Kamisetty, ... Elife 4, e09248, 2015 | 282 | 2015 |
Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma C Huang, L Chen, SR Savage, RV Eguez, Y Dou, Y Li, ... Cancer cell 39 (3), 361-379. e16, 2021 | 272 | 2021 |
A proteogenomic portrait of lung squamous cell carcinoma S Satpathy, K Krug, PMJ Beltran, SR Savage, F Petralia, C Kumar-Sinha, ... Cell 184 (16), 4348-4371. e40, 2021 | 264 | 2021 |
Deep learning in proteomics B Wen, WF Zeng, Y Liao, Z Shi, SR Savage, W Jiang, B Zhang Proteomics 20 (21-22), 1900335, 2020 | 157 | 2020 |
CASP9 assessment of free modeling target predictions L Kinch, S Yong Shi, Q Cong, H Cheng, Y Liao, NV Grishin Proteins: Structure, Function, and Bioinformatics 79 (S10), 59-73, 2011 | 122 | 2011 |
ECOD: new developments in the evolutionary classification of domains RD Schaeffer, Y Liao, H Cheng, NV Grishin Nucleic acids research 45 (D1), D296-D302, 2017 | 90 | 2017 |
Proteogenomic data and resources for pan-cancer analysis Y Li, Y Dou, FDV Leprevost, Y Geffen, AP Calinawan, F Aguet, Y Akiyama, ... Cancer cell 41 (8), 1397-1406, 2023 | 78 | 2023 |
Manual classification strategies in the ECOD database H Cheng, Y Liao, RD Schaeffer, NV Grishin Proteins: Structure, Function, and Bioinformatics 83 (7), 1238-1251, 2015 | 78 | 2015 |
Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation Y Geffen, S Anand, Y Akiyama, TM Yaron, Y Song, JL Johnson, ... Cell 186 (18), 3945-3967. e26, 2023 | 66 | 2023 |
Pan-cancer proteogenomics connects oncogenic drivers to functional states Y Li, E Porta-Pardo, C Tokheim, MH Bailey, TM Yaron, V Stathias, ... Cell 186 (18), 3921-3944. e25, 2023 | 50 | 2023 |
WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics JM Elizarraras, Y Liao, Z Shi, Q Zhu, AR Pico, B Zhang Nucleic Acids Research, gkae456, 2024 | 44 | 2024 |
Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin WW Liang, RJH Lu, RG Jayasinghe, SM Foltz, E Porta-Pardo, Y Geffen, ... Cancer Cell 41 (9), 1567-1585. e7, 2023 | 38 | 2023 |