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Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer A Färkkilä, DC Gulhan, J Casado, CA Jacobson, H Nguyen, ... Nature communications 11 (1), 1-13, 2020 | 223 | 2020 |
MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging D Schapiro, A Sokolov, C Yapp, YA Chen, JL Muhlich, J Hess, ... Nature methods 19 (3), 311-315, 2022 | 141 | 2022 |
Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer JR Lin, S Wang, S Coy, YA Chen, C Yapp, M Tyler, MK Nariya, CN Heiser, ... Cell 186 (2), 363-381. e19, 2023 | 119 | 2023 |
The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution AJ Nirmal, Z Maliga, T Vallius, B Quattrochi, AA Chen, CA Jacobson, ... Cancer discovery 12 (6), 1518, 2022 | 116 | 2022 |
A complementary palette of NanoCluster Beacons JM Obliosca, MC Babin, C Liu, YL Liu, YA Chen, RA Batson, M Ganguly, ... ACS nano 8 (10), 10150-10160, 2014 | 92 | 2014 |
Evolution of delayed resistance to immunotherapy in a melanoma responder D Liu, JR Lin, EJ Robitschek, GG Kasumova, A Heyde, A Shi, A Kraya, ... Nature medicine 27 (6), 985-992, 2021 | 81 | 2021 |
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR JL Muhlich, YA Chen, C Yapp, D Russell, S Santagata, PK Sorger Bioinformatics 38 (19), 4613-4621, 2022 | 78 | 2022 |
Assessing metastatic potential of breast cancer cells based on EGFR dynamics YL Liu, CK Chou, M Kim, R Vasisht, YA Kuo, P Ang, C Liu, EP Perillo, ... Scientific reports 9 (1), 1-13, 2019 | 64 | 2019 |
Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer R Rashid, G Gaglia, YA Chen, JR Lin, Z Du, Z Maliga, D Schapiro, C Yapp, ... Scientific Data 6 (1), 1-10, 2019 | 51 | 2019 |
NanoCluster Beacons Enable Detection of a Single N6-Methyladenine YA Chen, JM Obliosca, YL Liu, C Liu, ML Gwozdz, HC Yeh Journal of the American Chemical Society 137 (33), 10476-10479, 2015 | 51 | 2015 |
MITI minimum information guidelines for highly multiplexed tissue images D Schapiro, C Yapp, A Sokolov, SM Reynolds, YA Chen, D Sudar, Y Xie, ... Nature methods 19 (3), 262-267, 2022 | 45 | 2022 |
High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers JR Lin, YA Chen, D Campton, J Cooper, S Coy, C Yapp, JB Tefft, ... Nature Cancer, 1-17, 2023 | 41 | 2023 |
NanoCluster Beacons as reporter probes in rolling circle enhanced enzyme activity detection S Juul, JM Obliosca, C Liu, YL Liu, YA Chen, DM Imphean, BR Knudsen, ... Nanoscale 7 (18), 8332-8337, 2015 | 38 | 2015 |
3D single-molecule tracking enables direct hybridization kinetics measurement in solution C Liu, JM Obliosca, YL Liu, YA Chen, N Jiang, HC Yeh Nanoscale 9 (17), 5664-5670, 2017 | 27 | 2017 |
UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues C Yapp, E Novikov, WD Jang, T Vallius, YA Chen, M Cicconet, Z Maliga, ... Communications Biology 5 (1), 1-13, 2022 | 26 | 2022 |
Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data R Rashid, YA Chen, J Hoffer, JL Muhlich, JR Lin, R Krueger, H Pfister, ... Nature Biomedical Engineering 6 (5), 515-526, 2022 | 21* | 2022 |
Three-Dimensional Two-Color Dual-Particle Tracking Microscope for Monitoring DNA Conformational Changes and Nanoparticle Landings on Live Cells YL Liu, EP Perillo, P Ang, M Kim, DT Nguyen, K Blocher, YA Chen, C Liu, ... ACS nano 14 (7), 7927-7939, 2020 | 20 | 2020 |
Minerva: a light-weight, narrative image browser for multiplexed tissue images J Hoffer, R Rashid, JL Muhlich, YA Chen, DPW Russell, J Ruokonen, ... Journal of open source software 5 (54), 2020 | 19 | 2020 |
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