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Addressing persistent challenges in digital image analysis of cancer tissue: resources developed from a hackathon Prabhakaran, Sandhya; Yapp, Clarence; Baker, Gregory J.; Beyer, Johanna; Chang, Young Hwan; Creason, Allison L.; Krueger, Robert; Muhlich, Jeremy; Patterson, Nathan Heath; Sidak, Kevin; Sudar, Damir; Taylor, Adam J.; Ternes, Luke; Troidl, Jakob; Yubin, Xie; Sokolov, Artem; Tyson, Darren R. Share Save
Multimodal spatial profiling reveals the emergence of an immune suppressive microenvironment at the initial stages of high-grade serous ovarian cancer development Kader, Tanjina; Lin, Jia-Ren; Coy, Shannon; Hug, Clemens; Chen, Yu-An; Pelletier, Roxanne J.; Leon, Mariana; Lee, John; Xu, Yi-Lin; Yapp, Clarence; Shih, Natalie; Mingo, Gabriel; Jung, Euihye; Rathore, Srishti; Agudo, Judith; Drescher, Charles; Sorger, Peter K.; Drapkin, Ronny; Santagata, Sandro Share Save
Spatial multi-omics profiling of tumor cell phenotypes in primary cutaneous melanoma at single-cell resolution Vallius, Tuulia; Novikov, Edward; Johnson, Ajit Nirmal; Shi Yingxiao; Pelletier, Roxanne; Pant, Shishir; Maliga, Zoltan; Chen, Alyce; Yapp, Clarence; Chan, Sabrina; Lian, Christine; Murphy, George F.; Santagata, Sandro; Sorger, Peter Share Save
High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers Lin, Jia-Ren; Chen, Yu-An; Campton, Daniel; Cooper, Jeremy; Coy, Shannon; Yapp, Clarence; Tefft, Juliann B.; McCarty, Erin; Ligon, Keith L.; Rodig, Scott J.; Reese, Steven; George, Tad; Santagata, Sandro; Sorger, Peter K. Share Save
UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues Yapp, Clarence; Novikov, Edward; Jang, Won-Dong; Vallius, Tuulia; Chen, Yu-An; Cicconet, Marcelo; Maliga, Zoltan; Jacobson, Connor A.; Wei, Donglai; Santagata, Sandro; Pfister, Hanspeter; Sorger, Peter K. Share Save
Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop Mills, Caitlin E.; Subramanian, Kartik; Hafner, Marc; Niepel, Mario; Gerosa, Luca; Chung, Mirra; Victor, Chiara; Gaudio, Benjamin; Yapp, Clarence; Nirmal, Ajit J.; Clark, Nicholas; Sorger, Peter K. Share Save
A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses Gross, Sean M.; Dane, Mark A.; Smith, Rebecca L.; Devlin, Kaylyn L.; McLean, Ian C.; Derrick, Daniel S.; Mills, Caitlin E.; Subramanian, Kartik; London, Alexandra B.; Torre, Denis; Evangelista, John Erol; Clarke, Daniel J. B.; Xie, Zhuorui; Erdem, Cemal; Lyons, Nicholas; Natoli, Ted; Pessa, Sarah; Lu, Xiaodong; Mullahoo, James; Li, Jonathan; Adam, Miriam; Wassie, Brook; Liu, Moqing; Kilburn, David F.; Liby, Tiera A.; Bucher, Elmar; Sanchez-Aguila, Crystal; Daily, Kenneth; Omberg, Larsson; Wang, Yunguan; Jacobson, Connor; Yapp, Clarence; Chung, Mirra; Vidovic, Dusica; Lu, Yiling; Schurer, Stephan; Lee, Albert; Pillai, Ajay; Subramanian, Aravind; Papanastasiou, Malvina; Fraenkel, Ernest; Feiler, Heidi S.; Mills, Gordon B.; Jaffe, Jake D.; Ma'ayan, Avi; Birtwistle, Marc R.; Sorger, Peter K.; Korkola, James E.; Gray, Joe W.; Heiser, Laura M. Share Save
Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma Coy, Shannon; Wang, Shu; Stopka, Sylwia A.; Lin, Jia-Ren; Yapp, Clarence; Ritch, Cecily C.; Salhi, Lisa; Baker, Gregory J.; Rashid, Rumana; Baquer, Gerard; Regan, Michael; Khadka, Prasidda; Cole, Kristina A.; Hwang, Jaeho; Wen, Patrick Y.; Bandopadhayay, Pratiti; Santi, Mariarita; De Raedt, Thomas; Ligon, Keith L.; Agar, Nathalie Y. R.; Sorger, Peter K.; Touat, Mehdi; Santagata, Sandro Share Save
Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients Wu, Hua-Jun; Temko, Daniel; Maliga, Zoltan; Moreira, Andre L.; Sei, Emi; Minussi, Darlan Conterno; Dean, Jamie; Lee, Charlotte; Xu, Qiong; Hochart, Guillaume; Jacobson, Connor A.; Yapp, Clarence; Schapiro, Denis; Sorger, Peter K.; Seeley, Erin H.; Navin, Nicholas; Downey, Robert J.; Michor, Franziska Share Save
The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution Nirmal, Ajit J.; Maliga, Zoltan; Vallius, Tuulia; Quattrochi, Brian; Chen, Alyce A.; Jacobson, Connor A.; Pelletier, Roxanne J.; Yapp, Clarence; Arias-Camison, Raquel; Chen, Yu-An; Lian, Christine G.; Murphy, George F.; Santagata, Sandro; Sorger, Peter K. Share Save
MITI minimum information guidelines for highly multiplexed tissue images Schapiro, Denis; Yapp, Clarence; Sokolov, Artem; Reynolds, Sheila M.; Chen, Yu-An; Sudar, Damir; Xie, Yubin; Muhlich, Jeremy; Arias-Camison, Raquel; Arena, Sarah; Taylor, Adam J.; Nikolov, Milen; Tyler, Madison; Lin, Jia-Ren; Burlingame, Erik A.; Chang, Young H.; Farhi, Samouil L.; Thorsson, Vesteinn; Venkatamohan, Nithya; Drewes, Julia L.; Pe'er, Dana; Gutman, David A.; Herrmann, Markus D.; Gehlenborg, Nils; Bankhead, Peter; Roland, Joseph T.; Herndon, John M.; Snyder, Michael P.; Angelo, Michael; Nolan, Garry; Swedlow, Jason R.; Schultz, Nikolaus; Merrick, Daniel T.; Mazzili, Sarah A.; Cerami, Ethan; Rodig, Scott J.; Santagata, Sandro; Sorger, Peter K. Share Save
High-dimensional, single-cell analysis and transcriptional profiling reveal novel correlatives of response to PARP inhibition plus PD-1 blockade in triple-negative breast cancer Guerriero, Jennifer L.; Baker, Gregory J.; Lin, Jia-Ren; Chen, Yu-An; Pastorello, Ricardo; Vallius, Tuulia; Davis, Janae; Yapp, Clarence; Church, Sarah E.; Miller, Eric; Farkkila, Anniina; Vinayak, Shaveta; Telli, Melinda L.; Fulci, Giulia; D'Andrea, Alan; Shapiro, Geoffrey I.; Tolaney, Sara M.; Santagata, Sandro; Sorger, Peter K.; Mittendorf, Elizabeth A. Share Save
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging Schapiro, Denis; Sokolov, Artem; Yapp, Clarence; Chen, Yu-An; Muhlich, Jeremy L.; Hess, Joshua; Creason, Allison L.; Nirmal, Ajit J.; Baker, Gregory J.; Nariya, Maulik K.; Lin, Jia-Ren; Maliga, Zoltan; Jacobson, Connor A.; Hodgman, Matthew W.; Ruokonen, Juha; Farhi, Samouil L.; Abbondanza, Domenic; McKinley, Eliot T.; Persson, Daniel; Betts, Courtney; Sivagnanam, Shamilene; Regev, Aviv; Goecks, Jeremy; Coffey, Robert J.; Coussens, Lisa M.; Santagata, Sandro; Sorger, Peter K. Share Save
Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 severity Inde, Zintis; Croker, Ben A.; Yapp, Clarence; Joshi, Gaurav N.; Spetz, Johan; Fraser, Cameron; Qin, Xingping; Xu, Le; Deskin, Brian; Ghelfi, Elisa; Webb, Gabrielle; Carlin, Aaron F.; Zhu, Yanfang Peipei; Leibel, Sandra L.; Garretson, Aaron F.; Clark, Alex E.; Duran, Jason M.; Pretorius, Victor; Crotty-Alexander, Laura E.; Li, Chendi; Lee, Jamie Casey; Sodhi, Chhinder; Hackam, David J.; Sun, Xin; Hata, Aaron N.; Kobzik, Lester; Miller, Jeffrey; Park, Jin-Ah; Brownfield, Douglas; Jia, Hongpeng; Sarosiek, Kristopher A. Share Save
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Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer (vol 11, pg 1459, 2020) Farkkila, Anniina; Gulhan, Doga C.; Casado, Julia; Jacobson, Connor A.; Huy Nguyen; Kochupurakkal, Bose; Maliga, Zoltan; Yapp, Clarence; Chen, Yu-An; Schapiro, Denis; Zhou, Yinghui; Graham, Julie R.; Dezube, Bruce J.; Munster, Pamela; Santagata, Sandro; Garcia, Elizabeth; Rodig, Scott; Lako, Ana; Chowdhury, Dipanjan; Shapiro, Geoffrey I.; Matulonis, Ursula A.; Park, Peter J.; Hautaniemi, Sampsa; Sorger, Peter K.; Swisher, Elizabeth M.; D'Andrea, Alan D.; Konstantinopoulos, Panagiotis A. Share Save
Control of Synaptic Specificity by Establishing a Relative Preference for Synaptic Partners (vol 103, pg 865, 2019) Xu, Chundi; Theisen, Emma; Maloney, Ryan; Peng, Jing; Santiago, Ivan; Yapp, Clarence; Werkhoven, Zachary; Rumbaut, Elijah; Shum, Bryan; Tarnogorska, Dorota; Borycz, Jolanta; Tan, Liming; Courgeon, Maximilien; Griffin, Tessa; Levin, Raina; Meinertzhagen, Ian A.; de Bivort, Benjamin; Drugowitsch, Jan; Pecot, Matthew Y. Share Save
Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer Farkkila, Anniina; Gulhan, Doga C.; Casado, Julia; Jacobson, Connor A.; Nguyen, Huy; Kochupurakkal, Bose; Maliga, Zoltan; Yapp, Clarence; Chen, Yu-An; Schapiro, Denis; Zhou, Yinghui; Graham, Julie R.; Dezube, Bruce J.; Munster, Pamela; Santagata, Sandro; Garcia, Elizabeth; Rodig, Scott; Lako, Ana; Chowdhury, Dipanjan; Shapiro, Geoffrey, I; Matulonis, Ursula A.; Park, Peter J.; Hautaniemi, Sampsa; Sorger, Peter K.; Swisher, Elizabeth M.; D'Andrea, Alan D.; Konstantinopoulos, Panagiotis A. Share Save
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