A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters
Demircioğlu, Deniz, Cukuroglu, Engin, Kindermans, Martin, Nandi, Tannistha, Calabrese, Claudia, Fonseca, Nuno A., Kahles, André, Lehmann, Kjong-Van, Stegle, Oliver, Brazma, Alvis, Brooks, Angela N., Rätsch, Gunnar, Tan, Patrick, Göke, Jonathan
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Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma
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Published in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2015)
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Published in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2015)
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Prediction of homologous recombination deficiency from routine histology with attention-based multiple instance learning in nine different tumor types
Loeffler, Chiara Maria Lavinia, El Nahhas, Omar S M, Muti, Hannah Sophie, Carrero, Zunamys I, Seibel, Tobias, van Treeck, Marko, Cifci, Didem, Gustav, Marco, Bretz, Kevin, Gaisa, Nadine T, Lehmann, Kjong-Van, Leary, Alexandra, Selenica, Pier, Reis-Filho, Jorge S, Ortiz-Bruechle, Nadina, Kather, Jakob Nikolas
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
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Published in Nature (London) (06.02.2020)
Published in Nature (London) (06.02.2020)
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Author Correction: Learning single-cell perturbation responses using neural optimal transport
Bunne, Charlotte, Stark, Stefan G., Gut, Gabriele, del Castillo, Jacobo Sarabia, Levesque, Mitch, Lehmann, Kjong-Van, Pelkmans, Lucas, Krause, Andreas, Rätsch, Gunnar
Published in Nature methods (01.11.2023)
Published in Nature methods (01.11.2023)
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Buffering of Genetic Regulatory Networks in Drosophila melanogaster
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Published in Genetics (Austin) (01.07.2016)
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Direct prediction of Homologous Recombination Deficiency from routine histology in ten different tumor types with attention-based Multiple Instance Learning: a development and validation study
Loeffler, Chiara Maria Lavinia, El Nahhas, Omar S M, Muti, Hannah Sophie, Seibel, Tobias, Cifci, Didem, van Treeck, Marko, Gustav, Marco, Carrero, Zunamys I, Gaisa, Nadine T, Lehmann, Kjong-Van, Leary, Alexandra, Selenica, Pier, Reis-Filho, Jorge S, Bruechle, Nadina Ortiz, Kather, Jakob Nikolas
Published in medRxiv : the preprint server for health sciences (10.03.2023)
Published in medRxiv : the preprint server for health sciences (10.03.2023)
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Journal Article
A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
Deniz Demircio lu, Kindermans, Martin, Nandi, Tannistha, Cukuroglu, Engin, Calabrese, Claudia, Fonseca, Nuno A, Kahles, Andre, Lehmann, Kjong, Stegle, Oliver, Pcawg Transcriptome Working Group, Icgc/tcga Pan-Cancer Analysis Of Whole Genomes Network, Alvis Brazma, Brooks, Angela, Gunnar R tsch, Tan, Patrick, Jonathan G ke
Published in bioRxiv (02.05.2018)
Published in bioRxiv (02.05.2018)
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Paper
Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico, Wala, Jeremiah A., Shapira, Ofer, Tiao, Grace, Hornshøj, Henrik, Hess, Julian M., Juul, Randi Istrup, Lin, Ziao, Feuerbach, Lars, Sabarinathan, Radhakrishnan, Madsen, Tobias, Kim, Jaegil, Mularoni, Loris, Shuai, Shimin, Lanzós, Andrés, Herrmann, Carl, Maruvka, Yosef E., Shen, Ciyue, Amin, Samirkumar B., Bandopadhayay, Pratiti, Bertl, Johanna, Boroevich, Keith A., Busanovich, John, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Craft, David, Dhingra, Priyanka, Diamanti, Klev, Fonseca, Nuno A., Gonzalez-Perez, Abel, Guo, Qianyun, Hamilton, Mark P., Haradhvala, Nicholas J., Hong, Chen, Isaev, Keren, Johnson, Todd A., Juul, Malene, Kahles, Andre, Kahraman, Abdullah, Kim, Youngwook, Komorowski, Jan, Kumar, Kiran, Kumar, Sushant, Lee, Donghoon, Lehmann, Kjong-Van, Li, Yilong, Liu, Eric Minwei, Lochovsky, Lucas, Park, Keunchil, Pich, Oriol, Roberts, Nicola D., Saksena, Gordon, Schumacher, Steven E., Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stewart, Chip, Tamborero, David, Tubio, Jose M. C., Umer, Husen M., Uusküla-Reimand, Liis, Wadelius, Claes, Wadi, Lina, Yao, Xiaotong, Zhang, Cheng-Zhong, Zhang, Jing, Haber, James E., Hobolth, Asger, Imielinski, Marcin, Kellis, Manolis, Lawrence, Michael S., von Mering, Christian, Nakagawa, Hidewaki, Raphael, Benjamin J., Rubin, Mark A., Sander, Chris, Stein, Lincoln D., Stuart, Joshua M., Tsunoda, Tatsuhiko, Wheeler, David A., Johnson, Rory, Reimand, Jüri, Gerstein, Mark, Khurana, Ekta, Campbell, Peter J., López-Bigas, Núria, Weischenfeldt, Joachim, Beroukhim, Rameen, Martincorena, Iñigo, Pedersen, Jakob Skou, Getz, Gad
Published in Nature (London) (2023)
Published in Nature (London) (2023)
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Abstract 389: Integrating diverse transcriptomic alterations to identify cancer-relevant genes
Davidson, Natalie R., Brazma, Alvis, Brooks, Angela N., Calabrese, Claudia, Fonseca, Nuno A., Goke, Jonathan, He, Yao, Hu, Xueda, Kahles, Andre, Lehmann, Kjong-Van, Liu, Fenglin, Rätsch, Gunnar, Li, Siliang, Schwarz, Roland F., Yang, Mingyu, Zhang, Zemin, Zhang, Fan, Zheng, Liangtao
Published in Cancer research (Chicago, Ill.) (01.07.2017)
Published in Cancer research (Chicago, Ill.) (01.07.2017)
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Abstract SY10-02: Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants
Amin, Samirkumar, Awadalla, Philip, Biankin, Andrew, Boutros, Paul, Brazma, Alvis, Brooks, Angela Norie, Calabrese, Claudia, Chang, David, Chateigner, Aurélien, Chen, Ken, Chong, Zechen, Craft, Brian, Creighton, Chad, Demircioğlu, Deniz, Fonseca, Nuno, Frenkel-Morgenstern, Milana, Getz, Gad, Göke, Jonathan, Goldman, Mary, Greger, Liliana, Haider, Syed, He, Yao, Hoadley, Katherine, Ji, Yuan, Kahles, Andre, Khurana, Ekta, Korbel, Jan, Lehmann, Kjong, Liang, Han, Liu, Fenglin, Marin, Maximillian, Meyerson, Matthew, Ojesina, Akinyemi, Ouellette, Francis, Pedamallu, Chandra, Perry, Marc, Rätsch, Gunnar, Schwarz, Roland, Shiraishi, Yuichi, Soulette, Cameron, Stegle, Oliver, Tan, Patrick, Valencia, Alfonso, Xiang, Linda, Yung, Christina, Zhang, Junjun, Zhang, Fan, Zhang, Zemin, Zhu, Jingchun
Published in Cancer research (Chicago, Ill.) (01.07.2017)
Published in Cancer research (Chicago, Ill.) (01.07.2017)
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scROSHI: robust supervised hierarchical identification of single cells
Prummer, Michael, Bertolini, Anne, Bosshard, Lars, Barkmann, Florian, Yates, Josephine, Boeva, Valentina, Stekhoven, Daniel, Singer, Franziska
Published in NAR genomics and bioinformatics (01.06.2023)
Published in NAR genomics and bioinformatics (01.06.2023)
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