Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap von Reimand, Jüri, Isserlin, Ruth, Voisin, Veronique, Kucera, Mike, Tannus-Lopes, Christian, Rostamianfar, Asha, Wadi, Lina, Meyer, Mona, Wong, Jeff, Xu, Changjiang, Merico, Daniele, Bader, Gary D.

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g:Profiler-a web server for functional interpretation of gene lists (2016 update) von Reimand, Jüri, Arak, Tambet, Adler, Priit, Kolberg, Liis, Reisberg, Sulev, Peterson, Hedi, Vilo, Jaak

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Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin von Ocsenas, Oliver, Reimand, Jüri

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Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers von Reimand, Jüri, Bader, Gary D

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Impact of outdated gene annotations on pathway enrichment analysis von Wadi, Lina, Meyer, Mona, Weiser, Joel, Stein, Lincoln D, Reimand, Jüri

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The mutational landscape of phosphorylation signaling in cancer von Reimand, Jüri, Wagih, Omar, Bader, Gary D.

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MIMP: predicting the impact of mutations on kinase-substrate phosphorylation von Wagih, Omar, Reimand, Jüri, Bader, Gary D

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Evolutionary constraint and disease associations of post-translational modification sites in human genomes von Reimand, Jüri, Wagih, Omar, Bader, Gary D

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Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes von Lee, Christian A., Abd-Rabbo, Diala, Reimand, Juri

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Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders von Uusküla-Reimand, Liis, Hou, Huayun, Samavarchi-Tehrani, Payman, Rudan, Matteo Vietri, Liang, Minggao, Medina-Rivera, Alejandra, Mohammed, Hisham, Schmidt, Dominic, Schwalie, Petra, Young, Edwin J, Reimand, Jüri, Hadjur, Suzana, Gingras, Anne-Claude, Wilson, Michael D

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ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins von Krassowski, Michal, Paczkowska, Marta, Cullion, Kim, Huang, Tina, Dzneladze, Irakli, Ouellette, B F Francis, Yamada, Joseph T, Fradet-Turcotte, Amelie, Reimand, Jüri

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Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance von Marcotte, Richard, Sayad, Azin, Brown, Kevin R., Sanchez-Garcia, Felix, Reimand, Jüri, Haider, Maliha, Virtanen, Carl, Bradner, James E., Bader, Gary D., Mills, Gordon B., Pe’er, Dana, Moffat, Jason, Neel, Benjamin G.

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Directional integration and pathway enrichment analysis for multi-omics data von Slobodyanyuk, Mykhaylo, Bahcheli, Alexander T., Klein, Zoe P., Bayati, Masroor, Strug, Lisa J., Reimand, Jüri

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Human phospho‐signaling networks of SARS‐CoV‐2 infection are rewired by population genetic variants von Pellegrina, Diogo, Bahcheli, Alexander T, Krassowski, Michal, Reimand, Jüri

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Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity von Meyer, Mona, Reimand, Jüri, Lan, Xiaoyang, Head, Renee, Zhu, Xueming, Kushida, Michelle, Bayani, Jane, Pressey, Jessica C., Lionel, Anath C., Clarke, Ian D., Cusimano, Michael, Squire, Jeremy A., Scherer, Stephen W., Bernstein, Mark, Woodin, Melanie A., Bader, Gary D., Dirks, Peter B.

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Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups von Pajtler, Kristian W., Witt, Hendrik, Sill, Martin, Jones, David T.W., Hovestadt, Volker, Kratochwil, Fabian, Wani, Khalida, Tatevossian, Ruth, Punchihewa, Chandanamali, Johann, Pascal, Reimand, Jüri, Warnatz, Hans-Jörg, Ryzhova, Marina, Mack, Steve, Ramaswamy, Vijay, Capper, David, Schweizer, Leonille, Sieber, Laura, Wittmann, Andrea, Huang, Zhiqin, van Sluis, Peter, Volckmann, Richard, Koster, Jan, Versteeg, Rogier, Fults, Daniel, Toledano, Helen, Avigad, Smadar, Hoffman, Lindsey M., Donson, Andrew M., Foreman, Nicholas, Hewer, Ekkehard, Zitterbart, Karel, Gilbert, Mark, Armstrong, Terri S., Gupta, Nalin, Allen, Jeffrey C., Karajannis, Matthias A., Zagzag, David, Hasselblatt, Martin, Kulozik, Andreas E., Witt, Olaf, Collins, V. Peter, von Hoff, Katja, Rutkowski, Stefan, Pietsch, Torsten, Bader, Gary, Yaspo, Marie-Laure, von Deimling, Andreas, Lichter, Peter, Taylor, Michael D., Gilbertson, Richard, Ellison, David W., Aldape, Kenneth, Korshunov, Andrey, Kool, Marcel, Pfister, Stefan M.

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Comprehensive identification of mutational cancer driver genes across 12 tumor types von Tamborero, David, Gonzalez-Perez, Abel, Perez-Llamas, Christian, Deu-Pons, Jordi, Kandoth, Cyriac, Reimand, Jüri, Lawrence, Michael S., Getz, Gad, Bader, Gary D., Ding, Li, Lopez-Bigas, Nuria

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Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1 von Kauko, Otto, Imanishi, Susumu Y., Kulesskiy, Evgeny, Yetukuri, Laxman, Laajala, Teemu Daniel, Sharma, Mukund, Pavic, Karolina, Aakula, Anna, Rupp, Christian, Jumppanen, Mikael, Haapaniemi, Pekka, Ruan, Luyao, Yadav, Bhagwan, Suni, Veronika, Varila, Taru, Corthals, Garry L., Reimand, Jüri, Wennerberg, Krister, Aittokallio, Tero, Westermarck, Jukka

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Pathway and network analysis of cancer genomes von Creixell, Pau, Reimand, Jüri, Haider, Syed, Wu, Guanming, Shibata, Tatsuhiro, Vazquez, Miguel, Mustonen, Ville, Gonzalez-Perez, Abel, Pearson, John, Sander, Chris, Raphael, Benjamin J, Marks, Debora S, Ouellette, B F Francis, Valencia, Alfonso, Bader, Gary D, Boutros, Paul C, Stuart, Joshua M, Linding, Rune, Lopez-Bigas, Nuria, Stein, Lincoln D

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g:Profiler—a web server for functional interpretation of gene lists (2011 update) von Reimand, Jüri, Arak, Tambet, Vilo, Jaak

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