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micronuclAI enables automated quantification of micronuclei for assessment of chromosomal instability Ibarra-Arellano, Miguel A.; Caprio, Lindsay A.; Hada, Aroj; Stotzem, Niklas; Cai, Luke L.; Shah, Shivem B.; Walsh, Zachary H.; Melms, Johannes C.; Wuenneman, Florian; Bestak, Kresimir; Mansaray, Ibrahim; Izar, Benjamin; Schapiro, Denis Share Save
Identification of an embryonic differentiation stage marked by Sox1 and FoxA2 co-expression using combined cell tracking and high dimensional protein imaging Arekatla, Geethika; Skylaki, Stavroula; Suarez, David Corredor; Jackson, Hartland; Schapiro, Denis; Engler, Stefanie; Auler, Markus; Ortega, German Camargo; Hastreiter, Simon; Reimann, Andreas; Loeffler, Dirk; Bodenmiller, Bernd; Schroeder, Timm Share Save
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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
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment Hwang, William L.; Jagadeesh, Karthik A.; Guo, Jimmy A.; Hoffman, Hannah, I; Yadollahpour, Payman; Reeves, Jason W.; Mohan, Rahul; Drokhlyansky, Eugene; Van Wittenberghe, Nicholas; Ashenberg, Orr; Farhi, Samouil L.; Schapiro, Denis; Divakar, Prajan; Miller, Eric; Zollinger, Daniel R.; Eng, George; Schenkel, Jason M.; Su, Jennifer; Shiau, Carina; Yu, Patrick; Freed-Pastor, William A.; Abbondanza, Domenic; Mehta, Arnav; Gould, Joshua; Lambden, Conner; Porter, Caroline B. M.; Tsankov, Alexander; Dionne, Danielle; Waldman, Julia; Cuoco, Michael S.; Lan Nguyen; Delorey, Toni; Phillips, Devan; Barth, Jaimie L.; Kem, Marina; Rodrigues, Clifton; Ciprani, Debora; Roldan, Jorge; Zelga, Piotr; Jorgji, Vjola; Chen, Jonathan H.; Ely, Zackery; Zhao, Daniel; Fuhrman, Kit; Fropf, Robin; Beechem, Joseph M.; Loeffler, Jay S.; Ryan, David P.; Weekes, Colin D.; Ferrone, Cristina R.; Qadan, Motaz; Aryee, Martin J.; Jain, Rakesh K.; Neuberg, Donna S.; Wo, Jennifer Y.; Hong, Theodore S.; Xavier, Ramnik; Aguirre, Andrew J.; Rozenblatt-Rosen, Orit; Mino-Kenudson, Mari; Fernandez-del Castillo, Carlos; Liss, Andrew S.; Ting, David T.; Jacks, Tyler; Regev, Aviv Share Save
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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
Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium Vickovic, Sanja; Schapiro, Denis; Carlberg, Konstantin; Lotstedt, Britta; Larsson, Ludvig; Hildebrandt, Franziska; Korotkova, Marina; Hensvold, Aase H.; Catrina, Anca, I; Sorger, Peter K.; Malmstrom, Vivianne; Regev, Aviv; Stahl, Patrik L. 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
Evolution of delayed resistance to immunotherapy in a melanoma responder Liu, David; Lin, Jia-Ren; Robitschek, Emily J.; Kasumova, Gyulnara G.; Heyde, Alex; Shi, Alvin; Kraya, Adam; Zhang, Gao; Moll, Tabea; Frederick, Dennie T.; Chen, Yu-An; Wang, Shu; Schapiro, Denis; Ho, Li-Lun; Bi, Kevin; Sahu, Avinash; Mei, Shaolin; Miao, Benchun; Sharova, Tatyana; Alvarez-Breckenridge, Christopher; Stocking, Jackson H.; Kim, Tommy; Fadden, Riley; Lawrence, Donald; Hoang, Mai P.; Cahill, Daniel P.; Malehmir, Mohsen; Nowak, Martin A.; Brastianos, Priscilla K.; Lian, Christine G.; Ruppin, Eytan; Izar, Benjamin; Herlyn, Meenhard; Van Allen, Eliezer M.; Nathanson, Katherine; Flaherty, Keith T.; Sullivan, Ryan J.; Kellis, Manolis; Sorger, Peter K.; Boland, Genevieve M. Share Save
Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells Gerosa, Luca; Chidley, Christopher; Frohlich, Fabian; Sanchez, Gabriela; Lim, Sang Kyun; Muhlich, Jeremy; Chen, Jia-Yun; Vallabhaneni, Sreeram; Baker, Gregory J.; Schapiro, Denis; Atanasova, Mariya, I; Chylek, Lily A.; Shi, Tujin; Yi, Lian; Nicora, Carrie D.; Claas, Allison; Ng, Thomas S. C.; Kohler, Rainer H.; Lauffenburger, Douglas A.; Weissleder, Ralph; Miller, Miles A.; Qian, Wei-Jun; Wiley, H. Steven; Sorger, Peter K. Share Save
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
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
ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells Gerosa, Luca; Chidley, Christopher; Froehlich, Fabian; Sanchez, Gabriela; Lim, Sang Kyun; Muhlich, Jeremy; Chen, Jia-Yun; Baker, Gregory J.; Schapiro, Denis; Shi, Tujin; Yi, Lian; Nicora, Carrie D.; Qian, Wei-Jun; Wiley, H. Steven; Sorger, Peter Share Save
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High-definition spatial transcriptomics for in situ tissue profiling Vickovic, Sanja; Eraslan, Gokcen; Salmen, Fredrik; Klughammer, Johanna; Stenbeck, Linnea; Schapiro, Denis; Aijo, Tarmo; Bonneau, Richard; Bergenstrahle, Ludvig; Navarro, Jose Fernandez; Gould, Joshua; Griffin, Gabriel K.; Borg, Ake; Ronaghi, Mostafa; Frisen, Jonas; Lundeberg, Joakim; Regev, Aviv; Stahl, Patrik L. Share Save
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