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A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients Pita-Juarez, Yered; Karagkouni, Dimitra; Kalavros, Nikolaos; Melms, Johannes C.; Niezen, Sebastian; Delorey, Toni M.; Essene, Adam L.; Brook, Olga R.; Pant, Deepti; Skelton-Badlani, Disha; Naderi, Pourya; Huang, Pinzhu; Pan, Liuliu; Hether, Tyler; Andrews, Tallulah S.; Ziegler, Carly G. K.; Reeves, Jason; Myloserdnyy, Andriy; Chen, Rachel; Nam, Andy; Phelan, Stefan; Liang, Yan; Gregory, Mark; He, Shanshan; Patrick, Michael; Rane, Tushar; Wardhani, Aster; Amin, Amit Dipak; Biermann, Jana; Hibshoosh, Hanina; Veregge, Molly; Kramer, Zachary; Jacobs, Christopher; Yalcin, Yusuf; Phillips, Devan; Slyper, Michal; Subramanian, Ayshwarya; Ashenberg, Orr; Bloom-Ackermann, Zohar; Tran, Victoria M.; Gomez, James; Sturm, Alexander; Zhang, Shuting; Fleming, Stephen J.; Warren, Sarah; Beechem, Joseph; Hung, Deborah; Babadi, Mehrtash; Padera Jr, Robert F.; Macparland, Sonya A.; Bader, Gary D.; Imad, Nasser; Solomon, Isaac H.; Miller, Eric; Riedel, Stefan; Porter, Caroline B. M.; Villani, Alexandra-Chloe; Tsai, Linus T. -Y.; Hide, Winston; Szabo, Gyongyi; Hecht, Jonathan; Rozenblatt-Rosen, Orit; Shalek, Alex K.; Izar, Benjamin; Popov, Yury V.; Jiang, Z. Gordon; Vlachos, Ioannis S. Share Save
Spatially resolved analysis of pancreatic cancer identifies therapy-associated remodeling of the tumor microenvironment Shiau, Carina; Cao, Jingyi; Gong, Dennis; Gregory, Mark T.; Caldwell, Nicholas J.; Yin, Xunqin; Cho, Jae-Won; Wang, Peter L.; Su, Jennifer; Wang, Steven; Reeves, Jason W.; Kim, Tae Kyung; Kim, Youngmi; Guo, Jimmy A.; Lester, Nicole A.; Bae, Jung Woo; Zhao, Ryan; Schurman, Nathan; Barth, Jamie L.; Ganci, Maria L.; Weissleder, Ralph; Jacks, Tyler; Qadan, Motaz; Hong, Theodore S.; Wo, Jennifer Y.; Roberts, Hannah; Beechem, Joseph M.; Fernandez-del Castillo, Carlos; Mino-Kenudson, Mari; Ting, David T.; Hemberg, Martin; Hwang, William L. Share Save
The spatially resolved single-cell atlas of the tumor immune architecture revealed the central role of IFN-alpha and plasmacytoid dendritic cells in triple-negative breast cancer in the Mayo Clinic cohort and FinXX trial Chumsri, Saranya; Liu, Yi; Ma, Yaohua; Carter, Jodi; Gregory, Mark; Church, Sarah; Reeves, Jason; Brauer, Heather Ann; Warren, Sarah; Joensuu, Heikki; Perez, Edith; Leon-Ferre, Roberto; Hillman, David; Boughey, Judy; Ingle, James; Kalari, Krishna; Couch, Fergus; Goetz, Matthew; Knutson, Keith; Thompson, E. Share Save
Uncover spatial signatures of tumor microenvironment and oncogenic pathways using 6,000-plex single-cell spatial molecular imaging on FFPE skin squamous cell carcinoma Patrick, Michael; He, Shanshan; Ilcisin, Saskia; Kroeppler, David; Danaher, Patrick; Reeves, Jason; Gregory, Mark; Zhai, Haiyan; Rhodes, Michael; Beechem, Joseph Share Save
Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis Cao, Jingyi; Shiau, Carina; Gong, Dennis; Gregory, Mark T.; Yin, Xunqin; Cho, Jae-Won; Wang, Peter L.; Su, Jennifer; Reeves, Jason W.; Guo, Jimmy A.; Lester, Nicole A.; Bae, Jung Woo; Zhao, Ryan; Hemberg, Martin; Hwang, William L. Share Save
Spatial Atlas of Human Anatomy (SAHA): A subcellular, multiscale spatial odyssey of immune and gastrointestinal tissues and tumors Park, Jiwoon; Gregorio, Roberto; Hissong, Erika; Patel, Sanjay; Robinson, Brian; Socciarelli, Fabio; Metzger, Evenlyn; Liang, Yan; Reeves, Jason; Beechem, Joseph; Elemento, Olivier; Alonso, Alicia; Houlihan, Shauna; Schwartz, Robert; Mason, Christopher E. Share Save
Deep spatial immunophenotyping of lymphoid aggregates in pancreatic cancer using multi-omic integration of ultra high-plex proteomics and transcriptomics Gong, Dennis; Cao, Jingyi; Wang, Peter; Jhaveri, Niyati; Hou, Yue; Cheikh, Bassem B.; Ji, HaYeun; Gregory, Mark; Reeves, Jason; Patrick, Michael; Shiau, Carina; Su, Jennifer; Guo, Jimmy A.; Beechem, Joseph M.; Hemberg, Martin; Hwang, William L.; Park, Ryan Share Save
Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy Chen, Jonathan H.; Nieman, Linda T.; Spurrell, Maxwell; Jorgji, Vjola; Elmelech, Liad; Richieri, Peter; Xu, Katherine H.; Madhu, Roopa; Parikh, Milan; Zamora, Izabella; Mehta, Arnav; Nabel, Christopher S.; Freeman, Samuel S.; Pirl, Joshua D.; Lu, Chenyue; Meador, Catherine B.; Barth, Jaimie L.; Sakhi, Mustafa; Tang, Alexander L.; Sarkizova, Siranush; Price, Colles; Fernandez, Nicolas F.; Emanuel, George; He, Jiang; Van Raay, Katrina; Reeves, Jason W.; Yizhak, Keren; Hofree, Matan; Shih, Angela; Sade-Feldman, Moshe; Boland, Genevieve M.; Pelka, Karin; Aryee, Martin J.; Mino-Kenudson, Mari; Gainor, Justin F.; Korsunsky, Ilya; Hacohen, Nir Share Save
Spatially-constrained optimal transport interaction analysis reveals therapy-associated remodeling in the pancreatic cancer microenvironment Shiau, Carina; Cao, Jingyi; Gregory, Mark T.; Gong, Dennis; Yin, Xunqin; Cho, Jae-Won; Wang, Peter L.; Su, Jennifer; Wang, Steven; Reeves, Jason W.; Kim, Tae Kyung; Kim, Youngmi; Guo, Jimmy A.; Lester, Nicole A.; Barth, Jamie L.; Jacks, Tyler; Hong, Theodore S.; Beechem, Joseph M.; Fernandez-del Castillo, Carlos; Mino-Kenudson, Mari; Ting, David T.; Hemberg, Martin; Hwang, William L. Share Save
Distinct cancer-intrinsic mechanisms mediate nerve recruitment/outgrowth versus perineural invasion Hwang, William L.; Su, Jennifer; Shiau, Carina; Wang, Peter L.; Guo, Jimmy A.; Lester, Nicole A.; Barth, Jaimie L.; Hoffman, Hannah I.; Divakar, Prajan; Reeves, Jason W.; Miller, Eric; Beechem, Joseph M.; Aguirre, Andrew J.; Zheng, Lei; Ting, David T.; Mino-Kenudson, Mari; Jacks, Tyler Share Save
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Spatial insights into tumor immune evasion illuminated with 1000-plex RNA profiling with CosMx Spatial Molecular Imager Williams, Claire; Reeves, Jason W.; Danaher, Patrick; He, Shanshan; Kim, Sean; Patrick, Michael; Preciado, Julian; Gregory, Mark; Reitz, Zach; Jenkins, Justin; Liu, Rachel; Murphy, Sarah; Kang, Christine; Hartman, Byron; Devgan, Vikram; Rhodes, Michael; Beechem, Joseph Share Save
Spatially resolved expression of T cell receptors elucidates spatial relationships between T cells, immune infiltration, and cancer-associated pathways van Raay, Katrina; Kriner, Michelle; Reeves, Jason; Piazza, Erin; Kaplan, Hargita; Vivian, John; Fernandez, Francis; Hoang, Margaret; Beechem, Joseph Share Save
A complete pipeline for high-plex spatial proteomic profiling and analysis on the cosmx™ spatial molecular imager and atom™ spatial informatics platform Phan-Everson, Tien; Lewis, Zachary; Ong, Giang; Liang, Yan; Brown, Emily; Pan, Liuliu; Wardhani, Aster; Korukonda, Mithra; Brown, Carl; Dunaway, Dwayne; Zhao, Edward; McGuire, Dan; Woo, Sangsoon; Rosenbloom, Alyssa; Filanoski, Brian; Meredith, Rhonda; Chantranuvatana, Kan; Birditt, Brian; Yi, Hye Son; Piazza, Erin; Reeves, Jason; Lyssand, John; Devgan, Vik; Rhodes, Michael; Geiss, Gary; Beechem, Joseph Share Save
Mechanisms of therapeutic resistance in pancreatic cancer identified by single-cell spatial transcriptomics and genetically-engineered stromal tumoroids Shiau, Carina; Cao, Jingyi; Gregory, Mark; Kim, Tae Kyung; Kim, Youngmi; Reeves, Jason W.; Wang, Peter L.; Wang, Steven; Lester, Nicole A.; Su, Jennifer; Guo, Jimmy; Beechem, Joseph M.; Ting, David T.; Hemberg, Martin; Hwang, William L. Share Save
Single cell spatial molecular imaging of 76-plex proteins in clinical cancer samples in response to personalized treatment Lewis, Zachary R.; Birditt, Brian; Brown, Emily; Chantranuvatana, Kan; Filanoski, Brian; Corless, Chris; Phan-Everson, Tien; Geiss, Gary; Hether, Tyler; Hobbs, Evie; Johnson, Brett; Kelley, Taylor; Lopez, Charles; Meredith, Rhonda; Olson, Anastasiya; Ong, Giang; Korukonda, Mithra; Piazza, Erin; Reeves, Jason; Rosenbloom, Alyssa; Siex, Kiara; Yi, Hye Son; Zhao, Edward; Beechem, Joseph M.; Mills, Gordon Share Save
Path to the holy grail of spatial biology: Spatial single-cell whole transcriptomes using 6000-plex spatial molecular imaging on FFPE tissue He, Shanshan; Patrick, Michael; Reeves, Jason W.; Danaher, Patrick; Preciado, Julian; Phan, Joseph; Piazza, Erin; Reitz, Zachary; Wu, Lidan; Khafizov, Rustem; Zhai, Haiyan; Rhodes, Michael; Ruff, David; Beechem, Joseph Share Save
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A PHASE I STUDY OF PERSONALIZED ADOPTIVE TCR T CELL THERAPY IN PATIENTS WITH SOLID TUMORS: SAFETY, EFFICACY, AND T CELL TRAFFICKING TO TUMORS OF NON-VIRALLY GENE EDITED T CELLS Foy, Susan; Jacoby, Kyle; Bota, Daniela; Hunter, Theresa; Schoenfeld, Adam; Pan, Zheng; Stawiski, Eric; Ma, Yan; Lu, William; Peng, Songming; Wang, Clifford; Yuen, Benjamin; Dalmas, Olivier; Heeringa, Katharine; Sennino, Barbara; Conroy, Andy; Bethune, Michael; Mende, Ines; White, William; Kukreja, Monica; Gunturu, Swetha; Humphrey, Emily; Hussaini, Adeel; An, Duo; Quach, Boi; Ng, Alphonsus; Lu, Yue; Smith, Chad; Campbell, Katie; Anaya, Daniel; Skrdlant, Lindsey; Huang, Eva; Mendoza, Ventura; Mathur, Jyoti; Dengler, Luke; Purandare, Bhamini; Moot, Robert; Yi, Michael; Funke, Roel; Sibley, Alison; Stallings-Schmitt, Todd; Oh, David; Chmielowski, Bartosz; Abedi, Mehrdad; Yuan, Yuan; Sosman, Jeff; Lee, Sylvia; Williams, Claire; Kim, Sean; Keefe, Matthwe; Leon, Michael; Kim, Youngmi; Reeves, Jason; Goldman, Wes; Baltimore, David; Heath, James; Franzusoff, Alex; Ribas, Antoni; Rao, Arati; Mandl, Stefanie Share Save
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