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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
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features 跨临床病理特征的转移性乳腺癌活检的多模态单细胞和空间表达图 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 分享 收藏
A gene expression meta-analysis identifies microenvironment differences in cellular composition and cell-cell interactions associated with breast cancer invasion Officer, Adam; Dempsey, Andre; Hasteh, Farnaz; Slyper, Michal; Segerstolpe, Asa; Klughammer, Joanna; Jane-Valbuena, Judit; Rozenblatt-Rosen, Orit; Murrow, Lyndsay; Gartner, Zev; Regev, Aviv; Yau, Christina; Tamayo, Pablo; Harismendy, Olivier 分享 收藏
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 分享 收藏
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies Keshishian, Hasmik; McDonald, E. Robert; Mundt, Filip; Melanson, Randy; Krug, Karsten; Porter, Dale A.; Wallace, Luke; Forestier, Dominique; Rabasha, Bokang; Marlow, Sara E.; Jane-Valbuena, Judit; Todres, Ellen; Specht, Harrison; Robinson, Margaret Lea; Beltran, Pierre M. Jean; Babur, Ozgun; Olive, Meagan E.; Golji, Javad; Kuhn, Eric; Burgess, Michael; MacMullan, Melanie A.; Rejtar, Tomas; Wang, Karen; Mani, D. R.; Satpathy, Shankha; Gillette, Michael A.; Sellers, William R.; Carr, Steven A. 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 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
A Curated Resource for Phosphosite- specific Signature Analysis 用于磷矿特定特征分析的精选资源 Krug, Karsten; Mertins, Philipp; Zhang, Bin; Hornbeck, Peter; Raju, Rajesh; Ahmad, Rushdy; Szucs, Matthew; Mund, Filip; Forestier, Dominique; Jane-Valbuena, Judit; Keshishian, Hasmik; Gillette, Michael A.; Tamayo, Pablo; Mesirov, Jill P.; Jaffe, Jacob D.; Carr, Steven A.; Mani, D. R. 分享 收藏
Randomized trial of 10 days of decitabine ± bortezomib in untreated older patients with AML: CALGB 11002 (Alliance) Roboz, Gail J.; Mandrekar, Sumithra J.; Desai, Pinkal; Laumann, Kristina; Walker, Alison R.; Wang, Eunice S.; Kolitz, Jonathan E.; Powell, Bayard L.; Attar, Eyal C.; Stock, Wendy; Bloomfield, Clara D.; Kohlschmidt, Jessica; Mrozek, Krzysztof; Hassane, Duane C.; Garraway, Levi; Jane-Valbuena, Judit; Baltay, Michele; Tracy, Adam; Marcucci, Guido; Stone, Richard M.; Larson, Richard A. 分享 收藏
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Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-sequencing Izar, Benjamin; Tirsh, Itay; Prakadan, Sanjay; Wadsworth, Marc; Treacy, Daniel; Trombetta, John; Rotem, Asaf; Lian, Christine; Murphy, George; Fallahi-Sichani, Mohammad; Dutton-Regester, Ken; Lin, Jia-Ren; Jane-Valbuena, Judit; Rozenblatt-Rosen, Orit; Yoon, Charles; Shalek, Alex; Regev, Aviv; Garraway, Levi 分享 收藏
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Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine 福尔马林固定石蜡包埋肿瘤标本全外显子组测序及临床解读指导精准肿瘤医学 Van Allen, Eliezer M.; Wagle, Nikhil; Stojanov, Petar; Perrin, Danielle L.; Cibulskis, Kristian; Marlow, Sara; Jane-Valbuena, Judit; Friedrich, Dennis C.; Kryukov, Gregory; Carter, Scott L.; McKenna, Aaron; Sivachenko, Andrey; Rosenberg, Mara; Kiezun, Adam; Voet, Douglas; Lawrence, Michael; Lichtenstein, Lee T.; Gentry, Jeff G.; Huang, Franklin W.; Fostel, Jennifer; Farlow, Deborah; Barbie, David; Gandhi, Leena; Lander, Eric S.; Gray, Stacy W.; Joffe, Steven; Janne, Pasi; Garber, Judy; MacConaill, Laura; Lindeman, Neal; Rollins, Barrett; Kantoff, Philip; Fisher, Sheila A.; Gabriel, Stacey; Getz, Gad; Garraway, Levi A. 分享 收藏
The ETS factor ETV1 is an oncogene in melanoma Jane-Valbuena, Judit; Widlund, Hans; Perner, Sven; Johnson, Laura; Dibner, Aurora; Lin, William; Baker, Alissa; Nazarian, Rosalynn; Vijayendran, Krishna; Sellers, William; Hahn, William; Duncan, Lyn; Rubin, Mark; Fisher, David; Garraway, Levi A. 分享 收藏
An Oncogenic Role for ETV1 in Melanoma Jane-Valbuena, Judit; Widlund, Hans R.; Perner, Sven; Johnson, Laura A.; Dibner, Aurora C.; Lin, William M.; Baker, Alissa C.; Nazarian, Rosalynn M.; Vijayendran, Krishna G.; Sellers, William R.; Hahn, William C.; Duncan, Lyn M.; Rubin, Mark A.; Fisher, David E.; Garraway, Levi A. 分享 收藏
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