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SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data SlideCNA: 从slide-seq-like空间转录组学数据中检测空间拷贝数改变 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 分享 收藏
B-cell-specific checkpoint molecules that regulate anti-tumour immunity (vol 619, pg 348, 2023) B细胞特异性检查点分子对肿瘤免疫的调控（vol 619, pg 348, 2023） Bod, Lloyd; Kye, Yoon-Chul; Shi, Jingwen; Triglia, Elena Torlai; Schnell, Alexandra; Fessler, Johannes; Ostrowski, Stephen M.; Von-Franque, Max Y.; Kuchroo, Juhi R.; Barilla, Rocky M.; Zaghouani, Sarah; Christian, Elena; Delorey, Toni Marie; Mohib, Kanishka; Xiao, Sheng; Slingerland, Nadine; Giuliano, Christopher J.; Ashenberg, Orr; Li, Zhaorong; Rothstein, David M.; Fisher, David E.; Rozenblatt-Rosen, Orit; Sharpe, Arlene H.; Quintana, Francisco J.; Apetoh, Lionel; Regev, Aviv; Kuchroo, Vijay K. 分享 收藏
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients 单核和空间转录组图谱揭示了COVID-19患者肝脏中的拓扑结构、功能及再生性器官损伤 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. 分享 收藏
An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission 食道细胞图谱揭示了活动性嗜酸性食管炎和缓解期间的动态重新布线 Ding, Jiarui; Garber, John J.; Uchida, Amiko; Lefkovith, Ariel; Carter, Grace T.; Vimalathas, Praveen; Canha, Lauren; Dougan, Michael; Staller, Kyle; Yarze, Joseph; Delorey, Toni M.; Rozenblatt-Rosen, Orit; Ashenberg, Orr; Graham, Daniel B.; Deguine, Jacques; Regev, Aviv; Xavier, Ramnik J. 分享 收藏
The landscape of immune dysregulation in Crohn's disease revealed through single-cell transcriptomic profiling in the ileum and colon (vol 56, pg 444, 2023) Kong, Lingjia; Pokatayev, Vladislav; Lefkovith, Ariel; Carter, Grace T.; Creasey, Elizabeth A.; Krishna, Chirag; Subramanian, Sathish; Kochar, Bharati; Ashenberg, Orr; Lau, Helena; Ananthakrishnan, Ashwin N.; Graham, Daniel B.; Deguine, Jacques; Xavier, Ramnik J. 分享 收藏
The landscape of immune dysregulation in Crohn?s disease revealed through single-cell transcriptomic profiling in the ileum and colon 通过回肠和结肠中的单细胞转录组分析揭示了克罗恩病的免疫失调景观 Kong, Lingjia; Pokatayev, Vladislav; Lefkovith, Ariel; Carter, Grace T.; Creasey, Elizabeth A.; Krishna, Chirag; Subramanian, Sathish; Kochar, Bharati; Ashenberg, Orr; Lau, Helena; Ananthakrishnan, Ashwin N.; Graham, Daniel B.; Deguine, Jacques; Xavier, Ramnik J. 分享 收藏
Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade Kaur, Gurman; Porter, Caroline B. M.; Ashenberg, Orr; Lee, Jack; Riesenfeld, Samantha J.; Hofree, Matan; Aggelakopoulou, Maria; Subramanian, Ayshwarya; Kuttikkatte, Subita Balaram; Attfield, Kathrine E.; Desel, Christiane A. E.; Davies, Jessica L.; Evans, Hayley G.; Avraham-Davidi, Inbal; Nguyen, Lan T.; Dionne, Danielle A.; Neumann, Anna E.; Jensen, Lise Torp; Barber, Thomas R.; Soilleux, Elizabeth; Carrington, Mary; McVean, Gil; Rozenblatt-Rosen, Orit; Regev, Aviv; Fugger, Lars 分享 收藏
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment 胰腺癌的单核和空间转录组分析确定与新辅助治疗相关的多细胞动力学 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 分享 收藏
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics 跨组织和人口统计学的SARS-CoV-2进入基因的单细胞荟萃分析 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. 分享 收藏
A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq Scrna-seq揭示了人类CAR T细胞中带有4-1BB信号传导域的独特转录程序 Boroughs, Angela C.; Larson, Rebecca C.; Marjanovic, Nemanja D.; Gosik, Kirk; Castano, Ana P.; Porter, Caroline B. M.; Lorrey, Selena J.; Ashenberg, Orr; Jerby, Livnat; Hofree, Matan; Smith-Rosario, Gabriela; Morris, Robert; Gould, Joshua; Riley, Lauren S.; Berger, Trisha R.; Riesenfeld, Samantha J.; Rozenblatt-Rosen, Orit; Choi, Bryan D.; Regev, Aviv; Maus, Marcela V. 分享 收藏
Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq Cumulus为大规模单细胞和单核rna-seq提供基于云的数据分析 Li, Bo; Gould, Joshua; Yang, Yiming; Sarkizova, Siranush; Tabaka, Marcin; Ashenberg, Orr; Rosen, Yanay; Slyper, Michal; Kowalczyk, Monika S.; Villani, Alexandra-Chloe; Tickle, Timothy; Hacohen, Nir; Rozenblatt-Rosen, Orit; Regev, Aviv 分享 收藏
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 分享 收藏
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 分享 收藏
Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes Lavaert, Marieke; Liang, Kai Ling; Vandamme, Niels; Park, Jong-Eun; Roels, Juliette; Kowalczyk, Monica S.; Li, Bo; Ashenberg, Orr; Tabaka, Marcin; Dionne, Danielle; Tickle, Timothy L.; Slyper, Michal; Rozenblatt-Rosen, Orit; Vandekerckhove, Bart; Leclercq, Georges; Regev, Aviv; Van Vlierberghe, Pieter; Guilliams, Martin; Teichmann, Sarah A.; Saeys, Yvan; Taghon, Tom 分享 收藏
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 分享 收藏
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 分享 收藏
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. 分享 收藏
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