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Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics Avraham-Davidi, Inbal; Mages, Simon; Klughammer, Johanna; Moriel, Noa; Imada, Shinya; Hofree, Matan; Murray, Evan; Chen, Jonathan; Pelka, Karin; Mehta, Arnav; Boland, Genevieve M.; Delorey, Toni; Caplan, Leah; Dionne, Danielle; Strasser, Robert; Lalakova, Jana; Niesnerova, Anezka; Xu, Hao; Rouault, Morgane; Tirosh, Itay; Nir, Hacohen; Chen, Fei; Yilmaz, Omer; Roper, Jatin; Rozenblatt-Rosen, Orit; Nitzan, Mor; Regev, Aviv Share Save
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
B cells are associated with aggressive Cases of Cutaneous T cell Lymphoma and a distinct spatio-temporal composition of the tumor microenviroenment Oganesian, S.; Rudelius, M.; Piontek, G.; Posch, C.; Weigert, O.; Heide, M.; Krebs, S.; Blum, H.; Klughammer, J.; Mages, S.; Watter, J.; Kirmaier, M.; Hadzic, A.; Funk, M.; Tu, J.; Carboniero, A.; Vona, L.; von Bergwelt-Baildon, M.; Theurich, S. Share Save
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UNC93B1 variants underlie TLR7-dependent autoimmunity Wolf, Christine; Lim, Ee Lyn; Mokhtari, Mohammad; Kind, Barbara; Odainic, Alexandru; Lara-Villacanas, Eusebia; Koss, Sarah; Mages, Simon; Menzel, Katharina; Engel, Kerstin; Dueckers, Gregor; Bernbeck, Benedikt; Schneider, Dominik T.; Siepermann, Kathrin; Niehues, Tim; Goetzke, Carl Christoph; Durek, Pawel; Minden, Kirsten; Doerner, Thomas; Stittrich, Anna; Szelinski, Franziska; Guerra, Gabriela Maria; Massoud, Mona; Bieringer, Markus; Mann, Carina C. de Oliveira; Beltran, Eduardo; Kallinich, Tilmann; Mashreghi, Mir-Farzin; Schmidt, Susanne V.; Latz, Eicke; Klughammer, Johanna; Majer, Olivia; Lee-Kirsch, Min Ae Share Save
Radiomic features define risk and are linked to DNA methylation attributes in primary CNS lymphoma Nenning, Karl-Heinz; Gesperger, Johanna; Furtner, Julia; Nemc, Amelie; Roetzer-Pejrimovsky, Thomas; Choi, Seung-Won; Mitter, Christian; Leber, Stefan L.; Hofmanninger, Johannes; Klughammer, Johanna; Erguener, Bekir; Bauer, Marlies; Brada, Martina; Chong, Kyuha; Brandner-Kokalj, Tanisa; Freyschlag, Christian F.; Grams, Astrid; Haybaeck, Johannes; Hoenigschnabl, Selma; Hoffermann, Markus; Iglseder, Sarah; Kiesel, Barbara; Kitzwoegerer, Melitta; Kleindienst, Waltraud; Marhold, Franz; Moser, Patrizia; Oberndorfer, Stefan; Pinggera, Daniel; Scheichel, Florian; Sherif, Camillo; Stockhammer, Guenther; Stultschnig, Martin; Thome, Claudius; Trenkler, Johannes; Urbanic-Purkart, Tadeja; Weis, Serge; Widhalm, Georg; Wuertz, Franz; Preusser, Matthias; Baumann, Bernhard; Simonitsch-Klupp, Ingrid; Nam, Do-Hyun; Bock, Christoph; Langs, Georg; Woehrer, Adelheid Share Save
TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics Mages, Simon; Moriel, Noa; Avraham-Davidi, Inbal; Murray, Evan; Watter, Jan; Chen, Fei; Rozenblatt-Rosen, Orit; Klughammer, Johanna; Regev, Aviv; Nitzan, Mor Share Save
Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species Klughammer, Johanna; Romanovskaia, Daria; Nemc, Amelie; Posautz, Annika; Seid, Charlotte A.; Schuster, Linda C.; Keinath, Melissa C.; Lugo Ramos, Juan Sebastian; Kosack, Lindsay; Evankow, Ann; Printz, Dieter; Kirchberger, Stefanie; Erguener, Bekir; Datlinger, Paul; Fortelny, Nikolaus; Schmidl, Christian; Farlik, Matthias; Skjaerven, Kaja; Bergthaler, Andreas; Liedvogel, Miriam; Thaller, Denise; Burger, Pamela A.; Hermann, Marcela; Distel, Martin; Distel, Daniel L.; Kuebber-Heiss, Anna; Bock, Christoph 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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Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states Chaligne, Ronan; Gaiti, Federico; Silverbush, Dana; Schiffman, Joshua S.; Weisman, Hannah R.; Kluegel, Lloyd; Gritsch, Simon; Deochand, Sunil D.; Castro, L. Nicolas Gonzalez; Richman, Alyssa R.; Klughammer, Johanna; Biancalani, Tommaso; Muus, Christoph; Sheridan, Caroline; Alonso, Alicia; Izzo, Franco; Park, Jane; Rozenblatt-Rosen, Orit; Regev, Aviv; Suva, Mario L.; Landau, Dan A. Share Save
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation Min, Josine L.; Hemani, Gibran; Hannon, Eilis; Dekkers, Koen F.; Castillo-Fernandez, Juan; Luijk, Rene; Carnero-Montoro, Elena; Lawson, Daniel J.; Burrows, Kimberley; Suderman, Matthew; Bretherick, Andrew D.; Richardson, Tom G.; Klughammer, Johanna; Iotchkova, Valentina; Sharp, Gemma; Al Khleifat, Ahmad; Shatunov, Aleksey; Iacoangeli, Alfredo; McArdle, Wendy L.; Ho, Karen M.; Kumar, Ashish; Soderhall, Cilia; Soriano-Tarraga, Carolina; Giralt-Steinhauer, Eva; Kazmi, Nabila; Mason, Dan; McRae, Allan F.; Corcoran, David L.; Sugden, Karen; Kasela, Silva; Cardona, Alexia; Day, Felix R.; Cugliari, Giovanni; Viberti, Clara; Guarrera, Simonetta; Lerro, Michael; Gupta, Richa; Bollepalli, Sailalitha; Mandaviya, Pooja; Zeng, Yanni; Clarke, Toni-Kim; Walker, Rosie M.; Schmoll, Vanessa; Czamara, Darina; Ruiz-Arenas, Carlos; Rezwan, Faisal, I; Marioni, Riccardo E.; Lin, Tian; Awaloff, Yvonne; Germain, Marine; Aissi, Dylan; Zwamborn, Ramona; van Eijk, Kristel; Dekker, Annelot; van Dongen, Jenny; Hottenga, Jouke-Jan; Willemsen, Gonneke; Xu, Cheng-Jian; Barturen, Guillermo; Catala-Moll, Francesc; Kerick, Martin; Wang, Carol; Melton, Phillip; Elliott, Hannah R.; Shin, Jean; Bernard, Manon; Yet, Idil; Smarts, Melissa; Gorrie-Stone, Tyler; Shaw, Chris; Al Chalabi, Ammar; Ring, Susan M.; Pershagen, Goran; Melen, Erik; Jimenez-Conde, Jordi; Roquer, Jaume; Lawlor, Deborah A.; Wright, John; Martin, Nicholas G.; Montgomery, Grant W.; Moffitt, Terrie E.; Poulton, Richie; Esko, Tonu; Milani, Lili; Metspalu, Andres; Perry, John R. B.; Ong, Ken K.; Wareham, Nicholas J.; Matullo, Giuseppe; Sacerdote, Carlotta; Panico, Salvatore; Caspi, Avshalom; Arseneault, Louise; Gagnon, France; Ollikainen, Miina; Kaprio, Jaakko; Felix, Janine F.; Rivadeneira, Fernando; Tiemeier, Henning; van IJzendoorn, Marinus H.; Uitterlinden, Andre G.; Jaddoe, Vincent W. V.; Hale, Chris; McIntosh, Andrew M.; Evans, Kathryn L.; Murray, Alison; Raikkonen, Katri; Lahti, Jari; Nohr, Ellen A.; Sorensen, Thorkild I. A.; Hansen, Torben; Morgen, Camilla S.; Binder, Elisabeth B.; Lucae, Susanne; Gonzalez, Juan Ramon; Bustamante, Mariona; Sunyer, Jordi; Holloway, John W.; Karmaus, Wilfried; Zhang, Hongmei; Deary, Ian J.; Wray, Naomi R.; Starr, John M.; Beekman, Marian; VanHeemst, Diana; Slagboom, P. Eline; Morange, Pierre-Emmanuel; Tregouet, David-Alexandre; Veldink, Jan H.; Davies, Gareth E.; de Geus, Eco J. C.; Boomsma, Dorret, I; Vonk, Judith M.; Brunekreef, Bert; Koppelman, Gerard H.; Alarcon-Riquelme, Marta E.; Huang, Rae-Chi; Pennell, Craig E.; van Meurs, Joyce; Ikram, M. Arfan; Hughes, Alun D.; Tillin, Therese; Chaturvedi, Nish; Pausova, Zdenka; Paus, Tomas; Spector, Timothy D.; Kumari, Meena; Schalkwyk, Leonard C.; Visscher, Peter M.; Smith, George Davey; Bock, Christoph; Gaunt, Tom R.; Bell, Jordana T.; Heijmans, Bastiaan T.; Mill, Jonathan; Relton, Caroline L. 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 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
High-definition spatial transcriptomics for in situ tissue profiling Vickovic, Sanja; Eraslan, Gokcen; Salmen, Fredrik; Klughammer, Johanna; Stenbeck, Linnea; Schapiro, Denis; Aijo, Tarmo; Bonneau, Richard; Bergenstrahle, Ludvig; Navarro, Jose Fernandez; Gould, Joshua; Griffin, Gabriel K.; Borg, Ake; Ronaghi, Mostafa; Frisen, Jonas; Lundeberg, Joakim; Regev, Aviv; Stahl, Patrik L. Share Save
The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space Klughammer, Johanna; Kiesel, Barbara; Roetzer, Thomas; Fortelny, Nikolaus; Nemc, Amelie; Nenning, Karl-Heinz; Furtner, Julia; Sheffield, Nathan C.; Datlinger, Paul; Peter, Nadine; Nowosielski, Martha; Augustin, Marco; Mischkulnig, Mario; Stroebel, Thomas; Alpar, Donat; Erguener, Bekir; Senekowitsch, Martin; Moser, Patrizia; Freyschlag, Christian F.; Kerschbaumer, Johannes; Thome, Claudius; Grams, Astrid E.; Stockhammer, Guenther; Kitzwoegerer, Melitta; Oberndorfer, Stefan; Marhold, Franz; Weis, Serge; Trenkler, Johannes; Buchroithner, Johanna; Pichler, Josef; Haybaeck, Johannes; Krassnig, Stefanie; Ali, Kariem Mahdy; von Campe, Gord; Payer, Franz; Sherif, Camillo; Preiser, Julius; Hauser, Thomas; Winkler, Peter A.; Kleindienst, Waltraud; Wuertz, Franz; Brandner-Kokalj, Tanisa; Stultschnig, Martin; Schweiger, Stefan; Dieckmann, Karin; Preusser, Matthias; Langs, Georg; Baumann, Bernhard; Knosp, Engelbert; Widhalm, Georg; Marosi, Christine; Hainfellner, Johannes A.; Woehrer, Adelheid; Bock, Christoph Share Save
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