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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 IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets IL-27驱动的转录网络识别T辅助细胞亚群中IL-10表达的调控因子 Zhang, Huiyuan; Madi, Asaf; Yosef, Nir; Chihara, Norio; Awasthi, Amit; Pot, Caroline; Lambden, Conner; Srivastava, Amitabh; Burkett, Patrick R.; Nyman, Jackson; Christian, Elena; Etminan, Yasaman; Lee, Annika; Stroh, Helene; Xia, Junrong; Karwacz, Katarzyna; Thakore, Pratiksha I.; Acharya, Nandini; Schnell, Alexandra; Wang, Chao; Apetoh, Lionel; Rozenblatt-Rosen, Orit; Anderson, Ana C.; Regev, Aviv; Kuchroo, Vijay K. 分享 收藏
Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView (OCT, 10.1038/s41587-024-02391-0, 2024) 基于图像的多路复用混合筛选方法在原代细胞和组织中的应用（PerturbView, OCT, 10.1038/s41587-024-02391-0, 2024） Kudo, Takamasa; Meireles, Ana M.; Moncada, Reuben; Chen, Yushu; Wu, Ping; Gould, Joshua; Hu, Xiaoyu; Kornfeld, Opher; Jesudason, Rajiv; Foo, Conrad; Hockendorf, Burkhard; Corrada Bravo, Hector; Town, Jason P.; Wei, Runmin; Rios, Antonio; Chandrasekar, Vineethkrishna; Heinlein, Melanie; Chuong, Amy S.; Cai, Shuangyi; Lu, Cherry Sakura; Coelho, Paula; Mis, Monika; Celen, Cemre; Kljavin, Noelyn; Jiang, Jian; Richmond, David; Thakore, Pratiksha; Benito-Gutierrez, Elia; Geiger-Schuller, Kathryn; Hleap, Jose Sergio; Kayagaki, Nobuhiko; Melo, Felipe; Mcginnis, Lisa; Li, Bo; Singh, Avtar; Garraway, Levi; Rozenblatt-Rosen, Orit; Regev, Aviv; Lubeck, Eric 分享 收藏
Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView 具有扰动视图的原代细胞和组织中基于图像的多路复用合并屏幕 Kudo, Takamasa; Meireles, Ana M.; Moncada, Reuben; Chen, Yushu; Wu, Ping; Gould, Joshua; Hu, Xiaoyu; Kornfeld, Opher; Jesudason, Rajiv; Foo, Conrad; Hockendorf, Burkhard; Bravo, Hector Corrada; Town, Jason P.; Wei, Runmin; Rios, Antonio; Chandrasekar, Vineethkrishna; Heinlein, Melanie; Chuong, Amy S.; Cai, Shuangyi; Lu, Cherry Sakura; Coelho, Paula; Mis, Monika; Celen, Cemre; Kljavin, Noelyn; Jiang, Jian; Richmond, David; Thakore, Pratiksha; Benito-Gutierrez, Elia; Geiger-Schuller, Kathryn; Hleap, Jose Sergio; Kayagaki, Nobuhiko; Melo, Felipe; McGinnis, Lisa; Li, Bo; Singh, Avtar; Garraway, Levi; Rozenblatt-Rosen, Orit; Regev, Aviv; Lubeck, Eric 分享 收藏
BACH2 regulates diversification of regulatory and proinflammatory chromatin states in TH17 cells BACH2调节TH17细胞中调节性和促炎性染色质状态的多样化 Thakore, Pratiksha I.; Schnell, Alexandra; Huang, Linglin; Zhao, Maryann; Hou, Yu; Christian, Elena; Zaghouani, Sarah; Wang, Chao; Singh, Vasundhara; Singaraju, Anvita; Krishnan, Rajesh Kumar; Kozoriz, Deneen; Ma, Sai; Sankar, Venkat; Notarbartolo, Samuele; Buenrostro, Jason D.; Sallusto, Federica; Patsopoulos, Nikolaos A.; Rozenblatt-Rosen, Orit; Kuchroo, Vijay K.; Regev, Aviv 分享 收藏
Pan-cancer mapping of single CD8+T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity Tooley, Katherine; Jerby, Livnat; Escobar, Giulia; Krovi, S. Harsha; Mangani, Davide; Dandekar, Gitanjali; Cheng, Hanning; Madi, Asaf; Goldschmidt, Ella; Lambden, Conner; Krishnan, Rajesh K.; Rozenblatt-Rosen, Orit; Regev, Aviv; Anderson, Ana C. 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
Enhancing TCR T cell function in solid tumors through in vivo combinatorial screens and single-cell analysis Polyak, Dina; Fuhriman, Jessica; Susanto, Josephine; Merrell, Allyson; Simon, Mandi; Oh, Catherine; Cordazo, Andrew; DeTomasso, David; Tocchini, Carla; Sail, Vibhavari; Cui, Eric; Milush, Jeff; Gray-Rupp, Levi; Galvin, Brendan; Murriel, Christopher; Zheng, Grace; Boroughs, Angela C.; Thakore, Pratiksha; Oh, Soyoung; Freimer, Jake; Chen, Bob; Eidenschenk, Celine; Wheeler, Emily; Levine, Jacob; Huetter, Jan-Christian; Schartner, Jill; Geiger-Schuller, Katie; Rozenblatt-Rosen, Orit; Rutz, Sascha; Mellman, Ira; Haining, W. Nicholas 分享 收藏
Pooled CRISPR screening coupled with single-cell sequencing identifies modifiers of CAR T cell state in the context of chronic antigen stimulation Joshi, Sahil; Wozniak, Glenn; Gagnon, John; Vucci, Kristina; Merrell, Allyson; Simon, Mandi; Oh, Catherine; Cardozo, Andrew; DeTomaso, David; Chow, Julie; Zheng, Grace; Boroughs, Angela; Joho, Keith; Thakore, Pratiksha; Oh, Soyoung; Freimer, Jake; Cass, Ashley; Sail, Vibhavari; Tocchini, Carla; Sandoval, Marian; Liu, Andrea; Cui, Eric; Drever, Matt; Galvin, Brendan; Milush, Jeff; Gray-Rupp, Levi; Wheeler, Emily; Chen, Bob; Levine, Jacob; Eidenschenk, Celine; Schartner, Jill; Geiger-Schuller, Katie; Huetter, Jan-Christian; Rutz, Sascha; Rozenblatt-Rosen, Orit; Mellman, Ira; Haining, W. Nicholas 分享 收藏
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain 阿尔茨海默氏病大脑中遗传变异的细胞亚型特异性影响 Fujita, Masashi; Gao, Zongmei; Zeng, Lu; Mccabe, Cristin; White, Charles C.; Ng, Bernard; Green, Gilad Sahar; Rozenblatt-Rosen, Orit; Phillips, Devan; Amir-Zilberstein, Liat; Lee, Hyo; Pearse, Richard V.; Khan, Atlas; Vardarajan, Badri N.; Kiryluk, Krzysztof; Ye, Chun Jimmie; Klein, Hans-Ulrich; Wang, Gao; Regev, Aviv; Habib, Naomi; Schneider, Julie A.; Wang, Yanling; Young-Pearse, Tracy; Mostafavi, Sara; Bennett, David A.; Menon, Vilas; De Jager, Philip L. 分享 收藏
Systematic benchmarking of single-cell ATAC-sequencing protocols 单细胞ATAC测序方案的系统基准测试 De Rop, Florian V.; Hulselmans, Gert; Flerin, Chris; Soler-Vila, Paula; Rafels, Albert; Christiaens, Valerie; Gonzalez-Blas, Carmen Bravo; Marchese, Domenica; Caratu, Ginevra; Poovathingal, Suresh; Rozenblatt-Rosen, Orit; Slyper, Michael; Luo, Wendy; Muus, Christoph; Duarte, Fabiana; Shrestha, Rojesh; Bagdatli, S. Tansu; Corces, M. Ryan; Mamanova, Lira; Knights, Andrew; Meyer, Kerstin B.; Mulqueen, Ryan; Taherinasab, Akram; Maschmeyer, Patrick; Pezoldt, Jörn; Lambert, Camille Lucie Germaine; Iglesias, Marta; Najle, Sebastian R.; Dossani, Zain Y.; Martelotto, Luciano G.; Burkett, Zach; Lebofsky, Ronald; Martin-Subero, Jose Ignacio; Pillai, Satish; Sebe-Pedros, Arnau; Deplancke, Bart; Teichmann, Sarah A.; Ludwig, Leif S.; Braun, Theodore P.; Adey, Andrew C.; Greenleaf, William J.; Buenrostro, Jason D.; Regev, Aviv; Aerts, Stein; Heyn, Holger 分享 收藏
An integrated cell atlas of the lung in health and disease 健康和疾病中肺的综合细胞图谱 Sikkema, Lisa; Ramirez-Suastegui, Ciro; Strobl, Daniel C.; Gillett, Tessa E.; Zappia, Luke; Madissoon, Elo; Markov, Nikolay S.; Zaragosi, Laure-Emmanuelle; Ji, Yuge; Ansari, Meshal; Arguel, Marie-Jeanne; Apperloo, Leonie; Banchero, Martin; Becavin, Christophe; Berg, Marijn; Chichelnitskiy, Evgeny; Chung, Mei-i; Collin, Antoine; Gay, Aurore C. A.; Gote-Schniering, Janine; Kashani, Baharak Hooshiar; Inecik, Kemal; Jain, Manu; Kapellos, Theodore S.; Kole, Tessa M.; Leroy, Sylvie; Mayr, Christoph H.; Oliver, Amanda J.; von Papen, Michael; Peter, Lance; Taylor, Chase J.; Walzthoeni, Thomas; Xu, Chuan; Bui, Linh T.; De Donno, Carlo; Dony, Leander; Faiz, Alen; Guo, Minzhe; Gutierrez, Austin J.; Heumos, Lukas; Huang, Ni; Ibarra, Ignacio L.; Jackson, Nathan D.; Murthy, Preetish Kadur Lakshminarasimha; Lotfollahi, Mohammad; Tabib, Tracy; Talavera-Lopez, Carlos; Travaglini, Kyle J.; Wilbrey-Clark, Anna; Worlock, Kaylee B.; Yoshida, Masahiro; van den Berge, Maarten; Bosse, Yohan; Desai, Tushar J.; Eickelberg, Oliver; Kaminski, Naftali; Krasnow, Mark A.; Lafyatis, Robert; Nikolic, Marko Z.; Powell, Joseph E.; Rajagopal, Jayaraj; Rojas, Mauricio; Rozenblatt-Rosen, Orit; Seibold, Max A.; Sheppard, Dean; Shepherd, Douglas P.; Sin, Don D.; Timens, Wim; Tsankov, Alexander M.; Whitsett, Jeffrey; Xu, Yan; Banovich, Nicholas E.; Barbry, Pascal; Duong, Thu Elizabeth; Falk, Christine S.; Meyer, Kerstin B.; Kropski, Jonathan A.; Pe'er, Dana; Schiller, Herbert B.; Tata, Purushothama Rao; Schultze, Joachim L.; Teichmann, Sara A.; Misharin, Alexander, V; Nawijn, Martijn C.; Luecken, Malte D.; Theis, Fabian J.; Chen, Yuexin; Hagood, James S.; Agami, Ahmed; Horvath, Peter; Lundeberg, Joakim; Marquette, Charles-Hugo; Pryhuber, Gloria; Samakovlis, Chistos; Sun, Xin; Ware, Lorraine B.; Zhang, Kun 分享 收藏
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