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SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data Zhang, Diane; Segerstolpe, Asa; Slyper, Michal; Waldman, Julia; Murray, Evan; Strasser, Robert; Watter, Jan; Cohen, Ofir; Ashenberg, Orr; Abravanel, Daniel; Jane-Valbuena, Judit; Mages, Simon; Lako, Ana; Helvie, Karla; Rozenblatt-Rosen, Orit; Rodig, Scott; Chen, Fei; Wagle, Nikhil; Regev, Aviv; Klughammer, Johanna Share Save
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features Klughammer, Johanna; Abravanel, Daniel L.; Segerstolpe, Asa; Blosser, Timothy R.; Goltsev, Yury; Cui, Yi; Goodwin, Daniel R.; Sinha, Anubhav; Ashenberg, Orr; Slyper, Michal; Vigneau, Sebastien; Jane-Valbuena, Judit; Alon, Shahar; Caraccio, Chiara; Chen, Judy; Cohen, Ofir; Cullen, Nicole; DelloStritto, Laura K.; Dionne, Danielle; Files, Janet; Frangieh, Allison; Helvie, Karla; Hughes, Melissa E.; Inga, Stephanie; Kanodia, Abhay; Lako, Ana; MacKichan, Colin; Mages, Simon; Moriel, Noa; Murray, Evan; Napolitano, Sara; Nguyen, Kyleen; Nitzan, Mor; Ortiz, Rebecca; Patel, Miraj; Pfaff, Kathleen L.; Porter, Caroline B. M.; Rotem, Asaf; Strauss, Sarah; Strasser, Robert; Thorner, Aaron R.; Turner, Madison; Wakiro, Isaac; Waldman, Julia; Wu, Jingyi; Zanudo, Jorge Gomez Tejeda; Zhang, Diane; Lin, Nancy U.; Tolaney, Sara M.; Winer, Eric P.; Boyden, Edward S.; Chen, Fei; Nolan, Garry P.; Rodig, Scott J.; Zhuang, Xiaowei; Rozenblatt-Rosen, Orit; Johnson, Bruce E.; Regev, Aviv; Wagle, Nikhil Share Save
Protective role for kidney TREM2high macrophages in obesity- and diabetes-induced kidney injury Subramanian, Ayshwarya; Vernon, Katherine A.; Zhou, Yiming; Marshall, Jamie L.; Alimova, Maria; Arevalo, Carlos; Zhang, Fan; Slyper, Michal; Waldman, Julia; Montesinos, Monica S.; Dionne, Danielle; Nguyen, Lan T.; Cuoco, Michael S.; Dubinsky, Dan; Purnell, Jason; Keller, Keith; Sturner, Samuel H.; Grinkevich, Elizabeth; Ghoshal, Ayan; Kotek, Amanda; Trivioli, Giorgio; Richoz, Nathan; Humphrey, Mary B.; Darby, Isabella G.; Miller, Sarah J.; Xu, Yingping; Weins, Astrid; Chloe-Villani, Alexandra; Chang, Steven L.; Kretzler, Matthias; Rosenblatt-Rosen, Orit; Shaw, Jillian L.; Zimmerman, Kurt A.; Clatworthy, Menna R.; Regev, Aviv; Greka, Anna 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
Spatio-molecular dissection of the breast cancer metastatic microenvironment Abravanel, Daniel L.; Klughammer, Johanna; Blosser, Timothy; Goltsev, Yury; Jiang, Sizun; Bai, Yunjao; Murray, Evan; Alon, Shahar; Cui, Yi; Goodwin, Daniel R.; Sinha, Anubhav; Cohen, Ofir; Slyper, Michal; Ashenberg, Orr; Dionne, Danielle; Jane-Valbuena, Judit; Porter, Caroline BM.; Segerstolpe, Asa; Waldman, Julia; Vigneau, Sebastien; Helvie, Karla; Frangieh, Allison; DelloStritto, Laura; Patel, Miraj; We, Jingyi; Pfaff, Kathleen; Cullen, Nicole; Lako, Ana; Turner, Madison; Wakiro, Isaac; Napolitano, Sara; Kanodia, Abhay; Ortiz, Rebecca; MacKichan, Colin; Inga, Stephanie; Chen, Judy; Thorner, Aaron R.; Rotem, Asaf; Rodig, Scott; Chen, Fei; Boyden, Edward S.; Nolan, Garry P.; Zhuang, Xiaowei; Rozenblatt-Rosen, Orit; Johnson, Bruce E.; Regev, Aviv; Wagle, Nikhil Share Save
Joint single-cell measurements of nuclear proteins and RNA in vivo Chung, Hattie; Parkhurst, Christopher N.; Magee, Emma M.; Phillips, Devan; Habibi, Ehsan; Chen, Fei; Yeung, Bertrand Z.; Waldman, Julia; Artis, David; Regev, Aviv Share Save
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics Muus, Christoph; Luecken, Malte D.; Eraslan, Gokcen; Sikkema, Lisa; Waghray, Avinash; Heimberg, Graham; Kobayashi, Yoshihiko; Vaishnav, Eeshit Dhaval; Subramanian, Ayshwarya; Smillie, Christopher; Jagadeesh, Karthik A.; Duong, Elizabeth Thu; Fiskin, Evgenij; Triglia, Elena Torlai; Ansari, Meshal; Cai, Peiwen; Lin, Brian; Buchanan, Justin; Chen, Sijia; Shu, Jian; Haber, Adam L.; Chung, Hattie; Montoro, Daniel T.; Adams, Taylor; Aliee, Hananeh; Allon, Samuel J.; Andrusivova, Zaneta; Angelidis, Ilias; Ashenberg, Orr; Bassler, Kevin; Becavin, Christophe; Benhar, Inbal; Bergenstrahle, Joseph; Bergenstrahle, Ludvig; Bolt, Liam; Braun, Emelie; Bui, Linh T.; Callori, Steven; Chaffin, Mark; Chichelnitskiy, Evgeny; Chiou, Joshua; Conlon, Thomas M.; Cuoco, Michael S.; Cuomo, Anna S. E.; Deprez, Marie; Duclos, Grant; Fine, Denise; Fischer, David S.; Ghazanfar, Shila; Gillich, Astrid; Giotti, Bruno; Gould, Joshua; Guo, Minzhe; Gutierrez, Austin J.; Habermann, Arun C.; Harvey, Tyler; He, Peng; Hou, Xiaomeng; Hu, Lijuan; Hu, Yan; Jaiswal, Alok; Ji, Lu; Jiang, Peiyong; Kapellos, Theodoros S.; Kuo, Christin S.; Larsson, Ludvig; Leney-Greene, Michael A.; Lim, Kyungtae; Litvinukova, Monika; Ludwig, Leif S.; Lukassen, Soeren; Luo, Wendy; Maatz, Henrike; Madissoon, Elo; Mamanova, Lira; Manakongtreecheep, Kasidet; Leroy, Sylvie; Mayr, Christoph H.; Mbano, Ian M.; McAdams, Alexi M.; Nabhan, Ahmad N.; Nyquist, Sarah K.; Penland, Lolita; Poirion, Olivier B.; Poli, Sergio; Qi, CanCan; Queen, Rachel; Reichart, Daniel; Rosas, Ivan; Schupp, Jonas C.; Shea, Conor, V; Shi, Xingyi; Sinha, Rahul; Sit, Rene, V; Slowikowski, Kamil; Slyper, Michal; Smith, Neal P.; Sountoulidis, Alex; Strunz, Maximilian; Sullivan, Travis B.; Sun, Dawei; Talavera-Lopez, Carlos; Tan, Peng; Tantivit, Jessica; Travaglini, Kyle J.; Tucker, Nathan R.; Vernon, Katherine A.; Wadsworth, Marc H.; Waldman, Julia; Wang, Xiuting; Xu, Ke; Yan, Wenjun; Zhao, William; Ziegler, Carly G. K. Share Save
Nuclei multiplexing with barcoded antibodies for single-nucleus genomics (vol 163, pg 447, 2021) Gaublomme, Jellert T.; Li, Bo; McCabe, Cristin; Knecht, Abigail; Yang, Yiming; Drokhlyansky, Eugene; Van Wittenberghe, Nicholas; Waldman, Julia; Dionne, Danielle; Nguyen, Lan; De Jager, Philip L.; Yeung, Bertrand; Zhao, Xinfang; Habib, Naomi; Rozenblatt-Rosen, Orit; Regev, Aviv Share Save
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors (vol 26, pg 792, 2020) Slyper, Michal; Porter, Caroline B. M.; Ashenberg, Orr; Waldman, Julia; Drokhlyansky, Eugene; Wakiro, Isaac; Smillie, Christopher; Smith-Rosario, Gabriela; Wu, Jingyi; Dionne, Danielle; Vigneau, Sebastien; Jane-Valbuena, Judit; Tickle, Timothy L.; Napolitano, Sara; Su, Mei-Ju; Patel, Anand G.; Karlstrom, Asa; Gritsch, Simon; Nomura, Masashi; Waghray, Avinash; Gohil, Satyen H.; Tsankov, Alexander M.; Jerby-Arnon, Livnat; Cohen, Ofir; Klughammer, Johanna; Rosen, Yanay; Gould, Joshua; Nguyen Lan; Hofree, Matan; Tramontozzi, Peter J.; Li, Bo; Wu, Catherine J.; Izar, Benjamin; Haq, Rizwan; Hodi, F. Stephen; Yoon, Charles H.; Hata, Aaron N.; Baker, Suzanne J.; Suva, Mario L.; Bueno, Raphael; Stover, Elizabeth H.; Clay, Michael R.; Dyer, Michael A.; Collins, Natalie B.; Matulonis, Ursula A.; Wagle, Nikhil; Johnson, Bruce E.; Rotem, Asaf; Rozenblatt-Rosen, Orit; Regev, Aviv Share Save
A single-cell landscape of high-grade serous ovarian cancer Izar, Benjamin; Tirosh, Itay; Stover, Elizabeth H.; Wakiro, Isaac; Cuoco, Michael S.; Alter, Idan; Rodman, Christopher; Leeson, Rachel; Su, Mei-Ju; Shah, Parin; Iwanicki, Marcin; Walker, Sarah R.; Kanodia, Abhay; Melms, Johannes C.; Mei, Shaolin; Lin, Jia-Ren; Porter, Caroline B. M.; Slyper, Michal; Waldman, Julia; Jerby-Arnon, Livnat; Ashenberg, Orr; Brinker, Titus J.; Mills, Caitlin; Rogava, Meri; Vigneau, Sebastien; Sorger, Peter K.; Garraway, Levi A.; Konstantinopoulos, Panagiotis A.; Liu, Joyce F.; Matulonis, Ursula; Johnson, Bruce E.; Rozenblatt-Rosen, Orit; Rotem, Asaf; Regev, Aviv Share Save
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors Slyper, Michal; Porter, Caroline B. M.; Ashenberg, Orr; Waldman, Julia; Drokhlyansky, Eugene; Wakiro, Isaac; Smillie, Christopher; Smith-Rosario, Gabriela; Wu, Jingyi; Dionne, Danielle; Vigneau, Sebastien; Jane-Valbuena, Judit; Tickle, Timothy L.; Napolitano, Sara; Su, Mei-Ju; Patel, Anand G.; Karlstrom, Asa; Gritsch, Simon; Nomura, Masashi; Waghray, Avinash; Gohil, Satyen H.; Tsankov, Alexander M.; Jerby-Arnon, Livnat; Cohen, Ofir; Klughammer, Johanna; Rosen, Yanay; Gould, Joshua; Lan Nguyen; Hofree, Matan; Tramontozzi, Peter J.; Li, Bo; Wu, Catherine J.; Izar, Benjamin; Haq, Rizwan; Hodi, F. Stephen; Yoon, Charles H.; Hata, Aaron N.; Baker, Suzanne J.; Suva, Mario L.; Bueno, Raphael; Stover, Elizabeth H.; Clay, Michael R.; Dyer, Michael A.; Collins, Natalie B.; Matulonis, Ursula A.; Wagle, Nikhil; Johnson, Bruce E.; Rotem, Asaf; Rozenblatt-Rosen, Orit; Regev, Aviv Share Save
A joint atlas of single-cell and bulk RNA-seq in metastatic breast cancer allows inference of oncogenic and drug-resistant transcriptional programs in malignant cells and the tumor microenvironment Cohen, Ofir; Abravanel, Daniel; Slyper, Michal; Klughammer, Johanna; Jane-Valbuena, Judit; Helvie, Karla; Dellostritto, Laura; Frangieh, Allison; Vigneau, Sebastien; Wu, Jingyi; Mayorga, Angie; Waldman, Julia; Nguyen, Lan; Dionne, Danielle; Ashenberg, Orr; Hofree, Matan; Cuoco, Mike; Rodman, Christopher; Winer, Eric P.; Lin, Nancy; Johnson, Bruce; Rotem, Asaf; Rozenblatt-Rosen, Orit; Regev, Aviv; Wagle, Nikhil Share Save
Molecular subtypes and resistance programs in pancreatic ductal adenocarcinoma elucidated with single-nucleus RNA-seq Hwang, William L.; Jagadeesh, Karthik A.; Ashenberg, Orr; Drokhlyansky, Eugene; Eng, George; Van Wittenberghe, Nicholas; Freed-Pastor, William; Rodriguez, Clifton; Dionne, Danielle; Waldman, Julia; Cuoco, Michael; Tsankov, Alexander; Lambden, Connor; Porter, Caroline; Schenkel, Jason; Lambert, Laurens; Ciprani, Debora; Aguirre, Andrew J.; Mino-Kenudson, Mari; Hong, Theodore S.; Rozenblatt-Rosen, Orit; Castillo, Carlos Fernandez-Del; Liss, Andrew S.; Regev, Aviv; Jacks, Tyler E. Share Save
Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation Subramanian, Ayshwarya; Sidhom, Eriene-Heidi; Emani, Maheswarareddy; Vernon, Katherine; Sahakian, Nareh; Zhou, Yiming; Kost-Alimova, Maria; Slyper, Michal; Waldman, Julia; Dionne, Danielle; Nguyen, Lan T.; Weins, Astrid; Marshall, Jamie L.; Rosenblatt-Rosen, Orit; Regev, Aviv; Greka, Anna Share Save
Nuclei multiplexing with barcoded antibodies for single-nucleus genomics Gaublomme, Jellert T.; Li, Bo; McCabe, Cristin; Knecht, Abigail; Yang, Yiming; Drokhlyansky, Eugene; Van Wittenberghe, Nicholas; Waldman, Julia; Dionne, Danielle; Nguyen, Lan; De Jager, Philip L.; Yeung, Bertrand; Zhao, Xinfang; Habib, Naomi; Rozenblatt-Rosen, Orit; Regev, Aviv Share Save
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