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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
Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease Linna-Kuosmanen, Suvi; Schmauch, Eloi; Galani, Kyriakitsa; Ojanen, Johannes; Boix, Carles A.; Ord, Tiit; Toropainen, Anu; Singha, Prosanta K.; Moreau, Pierre R.; Harju, Kristiina; Blazeski, Adriana; Segerstolpe, Asa; Lahtinen, Veikko; Hou, Lei; Kang, Kai; Meibalan, Elamaran; Agudelo, Leandro Z.; Kokki, Hannu; Halonen, Jari; Jalkanen, Juho; Gunn, Jarmo; Macrae, Calum A.; Hollmen, Maija; Hartikainen, Juha E. K.; Kaikkonen, Minna U.; Garcia-Cardena, Guillermo; Tavi, Pasi; Kiviniemi, Tuomas; Kellis, Manolis Share Save
Translational genetics identifies a phosphorylation switch in CARD9 required for innate inflammatory responses Brandt, Marta; Cao, Zhifang; Krishna, Chirag; Reedy, Jennifer L.; Gu, Xiebin; Dutko, Richard A.; Oliver, Blayne A.; Tusi, Betsabeh Khoramian; Park, Jihye; Richey, Lauren; Segerstolpe, Asa; Litwiler, Scott; Creasey, Elizabeth A.; Carey, Kimberly L.; Vyas, Jatin M.; Graham, Daniel B.; Xavier, Ramnik J. Share Save
Genetic vulnerability to Crohn's disease reveals a spatially resolved epithelial restitution program Nakata, Toru; Li, Chenhao; Mayassi, Toufic; Lin, Helen; Ghosh, Koushik; Segerstolpe, Asa; Diamond, Emma L.; Herbst, Paula; Biancalani, Tommaso; Gaddam, Shreya; Parkar, Saurabh; Lu, Ziqing; Jaiswal, Alok; Li, Bihua; Creasey, Elizabeth A.; Lefkovith, Ariel; Daly, Mark J.; Graham, Daniel B.; Xavier, Ramnik J. Share Save
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A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration Subramanian, Elaiyaraja; Elewa, Ahmed; Brito, Goncalo; Kumar, Anoop; Segerstolpe, Asa; Karampelias, Christos; Bjorklund, Asa; Sandberg, Rickard; Echeverri, Karen; Lui, Weng-Onn; Andersson, Olov; Simon, Andras Share Save
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 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
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Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity Andrews, Tallulah S.; Atif, Jawairia; Liu, Jeff C.; Perciani, Catia T.; Ma, Xue-Zhong; Thoeni, Cornelia; Slyper, Michal; Eraslan, Gokcen; Segerstolpe, Asa; Manuel, Justin; Chung, Sai; Winter, Erin; Cirlan, Iulia; Khuu, Nicholas; Fischer, Sandra; Rozenblatt-Rosen, Orit; Regev, Aviv; McGilvray, Ian D.; Bader, Gary D.; MacParland, Sonya A. Share Save
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram Biancalani, Tommaso; Scalia, Gabriele; Buffoni, Lorenzo; Avasthi, Raghav; Lu, Ziqing; Sanger, Aman; Tokcan, Neriman; Vanderburg, Charles R.; Segerstolpe, Asa; Zhang, Meng; Avraham-Davidi, Inbal; Vickovic, Sanja; Nitzan, Mor; Ma, Sai; Subramanian, Ayshwarya; Lipinski, Michal; Buenrostro, Jason; Brown, Nik Bear; Fanelli, Duccio; Zhuang, Xiaowei; Macosko, Evan Z.; Regev, Aviv Share Save
Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma Jerby-Arnon, Livnat; Neftel, Cyril; Shore, Marni E.; Weisman, Hannah R.; Mathewson, Nathan D.; McBride, Matthew J.; Haas, Brian; Izar, Benjamin; Volorio, Angela; Boulay, Gaylor; Cironi, Luisa; Richman, Alyssa R.; Broye, Liliane C.; Gurski, Joseph M.; Luo, Christina C.; Mylvaganam, Ravindra; Nguyen, Lan; Mei, Shaolin; Melms, Johannes C.; Georgescu, Christophe; Cohen, Ofir; Buendia-Buendia, Jorge E.; Segerstolpe, Asa; Sud, Malika; Cuoco, Michael S.; Labes, Danny; Gritsch, Simon; Zollinger, Daniel R.; Ortogero, Nicole; Beechem, Joseph M.; Petur Nielsen, G.; Chebib, Ivan; Nguyen-Ngoc, Tu; Montemurro, Michael; Cote, Gregory M.; Choy, Edwin; Letovanec, Igor; Cherix, Stephane; Wagle, Nikhil; Sorger, Peter K.; Haynes, Alex B.; Mullen, John T.; Stamenkovic, Ivan; Rivera, Miguel N.; Kadoch, Cigall; Wucherpfennig, Kai W.; Rozenblatt-Rosen, Orit; Suva, Mario L.; Riggi, Nicolo; Regev, Aviv Share Save
Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination (Aug, 10.1038/s41467-020-17740-1, 2020) Muhl, Lars; Genove, Guillem; Leptidis, Stefanos; Liu, Jianping; He, Liqun; Mocci, Giuseppe; Sun, Ying; Gustafsson, Sonja; Buyandelger, Byambajav; Chivukula, Indira V.; Segerstolpe, Asa; Raschperger, Elisabeth; Hansson, Emil M.; Bjoerkegren, Johan L. M.; Peng, Xiao-Rong; Vanlandewijck, Michael; Lendahl, Urban; Betsholtz, Christer Share Save
Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination Muhl, Lars; Genove, Guillem; Leptidis, Stefanos; Liu, Jianping; He, Liqun; Mocci, Giuseppe; Sun, Ying; Gustafsson, Sonja; Buyandelger, Byambajav; Chivukula, Indira, V; Segerstolpe, Asa; Raschperger, Elisabeth; Hansson, Emil M.; Bjorkegren, Johan L. M.; Peng, Xiao-Rong; Vanlandewijck, Michael; Lendahl, Urban; Betsholtz, Christer Share Save
A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover Malenczyk, Katarzyna; Girach, Fatima; Szodorai, Edit; Storm, Petter; Segerstolpe, Asa; Tortoriello, Giuseppe; Schnell, Robert; Mulder, Jan; Romanov, Roman A.; Borok, Erzsebet; Piscitelli, Fabiana; Di Marzo, Vincenzo; Szabo, Gabor; Sandberg, Rickard; Kubicek, Stefan; Lubec, Gert; Hokfelt, Tomas; Wagner, Ludwig; Groop, Leif; Harkany, Tibor Share Save
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