Quantifying tumor-infiltrating immune cells from transcriptomics data von Finotello, Francesca, Trajanoski, Zlatko

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Immunedeconv: An R Package for Unified Access to Computational Methods for Estimating Immune Cell Fractions from Bulk RNA-Sequencing Data von Sturm, Gregor, Finotello, Francesca, List, Markus

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Next-generation computational tools for interrogating cancer immunity von Finotello, Francesca, Rieder, Dietmar, Hackl, Hubert, Trajanoski, Zlatko

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Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology von Sturm, Gregor, Finotello, Francesca, Petitprez, Florent, Zhang, Jitao David, Baumbach, Jan, Fridman, Wolf H, List, Markus, Aneichyk, Tatsiana

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Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy von Efremova, Mirjana, Finotello, Francesca, Rieder, Dietmar, Trajanoski, Zlatko

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Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology von Finotello, Francesca, Eduati, Federica

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Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy von Yamazaki, Takahiro, Kirchmair, Alexander, Sato, Ai, Buqué, Aitziber, Rybstein, Marissa, Petroni, Giulia, Bloy, Norma, Finotello, Francesca, Stafford, Lena, Navarro Manzano, Esther, Ayala de la Peña, Francisco, García-Martínez, Elena, Formenti, Silvia C., Trajanoski, Zlatko, Galluzzi, Lorenzo

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Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution von Efremova, Mirjana, Rieder, Dietmar, Klepsch, Victoria, Charoentong, Pornpimol, Finotello, Francesca, Hackl, Hubert, Hermann-Kleiter, Natascha, Löwer, Martin, Baier, Gottfried, Krogsdam, Anne, Trajanoski, Zlatko

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Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data von Finotello, Francesca, Mayer, Clemens, Plattner, Christina, Laschober, Gerhard, Rieder, Dietmar, Hackl, Hubert, Krogsdam, Anne, Loncova, Zuzana, Posch, Wilfried, Wilflingseder, Doris, Sopper, Sieghart, Ijsselsteijn, Marieke, Brouwer, Thomas P, Johnson, Douglas, Xu, Yaomin, Wang, Yu, Sanders, Melinda E, Estrada, Monica V, Ericsson-Gonzalez, Paula, Charoentong, Pornpimol, Balko, Justin, de Miranda, Noel Filipe da Cunha Carvalho, Trajanoski, Zlatko

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Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma von Rohr-Udilova, Nataliya, Klinglmüller, Florian, Schulte-Hermann, Rolf, Stift, Judith, Herac, Merima, Salzmann, Martina, Finotello, Francesca, Timelthaler, Gerald, Oberhuber, Georg, Pinter, Matthias, Reiberger, Thomas, Jensen-Jarolim, Erika, Eferl, Robert, Trauner, Michael

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Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism von Fadista, João, Vikman, Petter, Laakso, Emilia Ottosson, Mollet, Inês Guerra, Esguerra, Jonathan Lou, Taneera, Jalal, Storm, Petter, Osmark, Peter, Ladenvall, Claes, Prasad, Rashmi B., Hansson, Karin B., Finotello, Francesca, Uvebrant, Kristina, Ofori, Jones K., Di Camillo, Barbara, Krus, Ulrika, Cilio, Corrado M., Hansson, Ola, Eliasson, Lena, Rosengren, Anders H., Renström, Erik, Wollheim, Claes B., Groop, Leif

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Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene von Sambo, Francesco, Finotello, Francesca, Lavezzo, Enrico, Baruzzo, Giacomo, Masi, Giulia, Peta, Elektra, Falda, Marco, Toppo, Stefano, Barzon, Luisa, Di Camillo, Barbara

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Stress-induced inflammation evoked by immunogenic cell death is blunted by the IRE1α kinase inhibitor KIRA6 through HSP60 targeting von Rufo, Nicole, Korovesis, Dimitris, Van Eygen, Sofie, Derua, Rita, Garg, Abhishek D., Finotello, Francesca, Vara-Perez, Monica, Rožanc, Jan, Dewaele, Michael, de Witte, Peter A., Alexopoulos, Leonidas G., Janssens, Sophie, Sinkkonen, Lasse, Sauter, Thomas, Verhelst, Steven H. L., Agostinis, Patrizia

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Editorial: Multi-omic Data Integration in Oncology von Finotello, Francesca, Calura, Enrica, Risso, Davide, Hautaniemi, Sampsa, Romualdi, Chiara

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The highly selective and oral phosphoinositide 3-kinase delta (PI3K-δ) inhibitor roginolisib induces apoptosis in mesothelioma cells and increases immune effector cell composition von Kalla, Claudia, Ott, German, Finotello, Francesca, Niewola-Staszkowska, Karolina, Conza, Giusy Di, Lahn, Michael, van der Veen, Lars, Schüler, Julia, Falkenstern-Ge, Roger, Kopecka, Joanna, Riganti, Chiara

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Single cell dynamics of tumor specificity vs bystander activity in CD8+ T cells define the diverse immune landscapes in colorectal cancer von Borràs, Daniel Morales, Verbandt, Sara, Ausserhofer, Markus, Sturm, Gregor, Lim, Jinyeong, Verge, Gil Arasa, Vanmeerbeek, Isaure, Laureano, Raquel S., Govaerts, Jannes, Sprooten, Jenny, Hong, Yourae, Wall, Rebecca, De Hertogh, Gert, Sagaert, Xavier, Bislenghi, Gabriele, D’Hoore, André, Wolthuis, Albert, Finotello, Francesca, Park, Woong-Yang, Naulaerts, Stefan, Tejpar, Sabine, Garg, Abhishek D.

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A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer von Mason, Mike, Lapuente-Santana, Óscar, Halkola, Anni S, Wang, Wenyu, Mall, Raghvendra, Xiao, Xu, Kaufman, Jacob, Fu, Jingxin, Pfeil, Jacob, Banerjee, Jineta, Chung, Verena, Chang, Han, Chasalow, Scott D, Lin, Hung Ying, Chai, Rongrong, Yu, Thomas, Finotello, Francesca, Mirtti, Tuomas, Mäyränpää, Mikko I, Bao, Jie, Verschuren, Emmy W, Ahmed, Eiman I, Ceccarelli, Michele, Miller, Lance D, Monaco, Gianni, Hendrickx, Wouter R L, Sherif, Shimaa, Yang, Lin, Tang, Ming, Gu, Shengqing Stan, Zhang, Wubing, Zhang, Yi, Zeng, Zexian, Das Sahu, Avinash, Liu, Yang, Yang, Wenxian, Bedognetti, Davide, Tang, Jing, Eduati, Federica, Laajala, Teemu D, Geese, William J, Guinney, Justin, Szustakowski, Joseph D, Vincent, Benjamin G, Carbone, David P

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The scverse project provides a computational ecosystem for single-cell omics data analysis von Virshup, Isaac, Bredikhin, Danila, Heumos, Lukas, Palla, Giovanni, Sturm, Gregor, Gayoso, Adam, Kats, Ilia, Koutrouli, Mikaela, Berger, Bonnie, Pe'er, Dana, Regev, Aviv, Teichmann, Sarah A, Finotello, Francesca, Wolf, F Alexander, Yosef, Nir, Stegle, Oliver, Theis, Fabian J

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Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion von Lapuente-Santana, Óscar, Sturm, Gregor, Kant, Joan, Ausserhofer, Markus, Zackl, Constantin, Zopoglou, Maria, McGranahan, Nicholas, Rieder, Dietmar, Trajanoski, Zlatko, da Cunha Carvalho de Miranda, Noel Filipe, Eduati, Federica, Finotello, Francesca

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Deconvoluting tumor-infiltrating immune cells from RNA-seq data using quanTIseq von Plattner, Christina, Finotello, Francesca, Rieder, Dietmar

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