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A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery Creason, Allison; Haan, David; Dang, Kristen; Chiotti, Kami E.; Inkman, Matthew; Lamb, Andrew; Yu, Thomas; Hu, Yin; Norman, Thea C.; Buchanan, Alex; van Baren, Marijke J.; Spangler, Ryan; Rollins, M. Rick; Spellman, Paul T.; Rozanov, Dmitri; Zhang, Jin; Maher, Christopher A.; Caloian, Cristian; Watson, John D.; Uhrig, Sebastian; Haas, Brian J.; Jain, Miten; Akeson, Mark; Ahsen, Mehmet Eren; Stolovitzky, Gustavo; Guinney, Justin; Boutros, Paul C.; Stuart, Joshua M.; Ellrott, Kyle Share Save
Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival Gillani, Riaz; Seong, Bo Kyung A.; Crowdis, Jett; Conway, Jake R.; Dharia, Neekesh V.; Alimohamed, Saif; Haas, Brian J.; Han, Kyuho; Park, Jihye; Dietlein, Felix; He, Meng Xiao; Imamovic, Alma; Ma, Clement; Bassik, Michael C.; Boehm, Jesse S.; Vazquez, Francisca; Gusev, Alexander; Liu, David; Janeway, Katherine A.; McFarland, James M.; Stegmaier, Kimberly; Van Allen, Eliezer M. Share Save
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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
Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes Gevaert, Olivier; Nabian, Mohsen; Bakr, Shaimaa; Everaert, Celine; Shinde, Jayendra; Manukyan, Artur; Liefeld, Ted; Tabor, Thorin; Xu, Jishu; Lupberger, Joachim; Haas, Brian J.; Baumert, Thomas F.; Hernaez, Mikel; Reich, Michael; Quintana, Francisco J.; Uhlmann, Erik J.; Krichevsky, Anna M.; Mesirov, Jill P.; Carey, Vincent; Pochet, Nathalie Share Save
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Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution Leigh, Nicholas D.; Dunlap, Garrett S.; Johnson, Kimberly; Mariano, Rachelle; Oshiro, Rachel; Wong, Alan Y.; Bryant, Donald M.; Miller, Bess M.; Ratner, Alex; Chen, Andy; Ye, William W.; Haas, Brian J.; Whited, Jessica L. Share Save
SynerClust: a highly scalable, synteny-aware orthologue clustering tool Georgescu, Christophe H.; Manson, Abigail L.; Griggs, Alexander D.; Desjardins, Christopher A.; Pironti, Alejandro; Wapinski, Ilan; Abeel, Thomas; Haas, Brian J.; Earl, Ashlee M. Share Save
Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models Ng, Samuel Y.; Yoshida, Noriaki; Christie, Amanda L.; Ghandi, Mahmoud; Dharia, Neekesh V.; Dempster, Joshua; Murakami, Mark; Shigemori, Kay; Morrow, Sara N.; Van Scoyk, Alexandria; Cordero, Nicolas A.; Stevenson, Kristen E.; Puligandla, Maneka; Haas, Brian; Lo, Christopher; Meyers, Robin; Gao, Galen; Cherniack, Andrew; Louissaint, Abner, Jr.; Nardi, Valentina; Thorner, Aaron R.; Long, Henry; Qiu, Xintao; Morgan, Elizabeth A.; Dorfman, David M.; Fiore, Danilo; Jang, Julie; Epstein, Alan L.; Dogan, Ahmet; Zhang, Yanming; Horwitz, Steven M.; Jacobsen, Eric D.; Santiago, Solimar; Ren, Jian-Guo; Guerlavais, Vincent; Annis, D. Allen; Aivado, Manuel; Saleh, Mansoor N.; Mehta, Amitkumar; Tsherniak, Aviad; Root, David; Vazquez, Francisca; Hahn, William C.; Inghirami, Giorgio; Aster, Jon C.; Weinstock, David M.; Koch, Raphael Share Save
Revitalization of a Forward Genetic Screen Identifies Three New Regulators of Fungal Secondary Metabolism in the Genus Aspergillus Pfannenstiel, Brandon T.; Zhao, Xixi; Wortman, Jennifer; Wiemann, Philipp; Throckmorton, Kurt; Spraker, Joseph E.; Soukup, Alexandra A.; Luo, Xingyu; Lindner, Daniel L.; Lim, Fang Yun; Knox, Benjamin P.; Haas, Brian; Fischer, Gregory J.; Choera, Tsokyi; Butchko, Robert A. E.; Bok, Jin-Woo; Affeldt, Katharyn J.; Keller, Nancy P.; Palmer, Jonathan M. Share Save
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A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors Bryant, Donald M.; Johnson, Kimberly; DiTommaso, Tia; Tickle, Timothy; Couger, Matthew Brian; Payzin-Dogru, Duygu; Lee, Tae J.; Leigh, Nicholas D.; Kuo, Tzu-Hsing; Davis, Francis G.; Bateman, Joel; Bryant, Sevara; Guzikowski, Anna R.; Tsai, Stephanie L.; Coyne, Steven; Ye, William W.; Freeman, Robert M., Jr.; Peshkin, Leonid; Tabin, Clifford J.; Regev, Aviv; Haas, Brian J.; Whited, Jessica L. Share Save
Fast and accurate fusion transcript detection using the Trinity Cancer Transcriptome Analysis Toolkit Haas, Brian; Tickle, Timothy; Pochet, Nathalie; Sun, Jing; Hsu, Peggy; Stewart, Chip; Ganote, Carrie; Fulton, Ben; Wu, Catherine; Regev, Aviv Share Save
Leveraging transcriptomic and genomic data to better select models for preclinical oncology therapeutic development to identify cell lines most similar to patient tumors Cha, Yoonjeong; Labradorf, Adam; -Rogers, Joseph Perez; Haas, Brian; Lysaght, Andrew; Weiner, Brian; Towfic, Fadi; Fowler, Kevin; Zeskind, Benjamin; Kolitz, Sarah; Vardarajan, Badri; Artyomov, Maxim; Kusko, Rebecca L. Share Save
Neutron-induced fission cross section of 237Np in the keV to MeV range at the CERN n_TOF facility Diakaki, M.; Karadimos, D.; Vlastou, R.; Kokkoris, M.; Demetriou, P.; Skordis, E.; Tsinganis, A.; Abbondanno, U.; Aerts, G.; Alvarez, H.; Alvarez-Velarde, F.; Andriamonje, S.; Andrzejewski, J.; Assimakopoulos, P.; Audouin, L.; Badurek, G.; Baumann, P.; Becvar, F.; Berthoumieux, E.; Calviani, M.; Calvino, F.; Cano-Ott, D.; Capote, R.; de Albornoz, A. Carrillo; Cennini, P.; Chepel, V.; Chiaveri, E.; Colonna, N.; Cortes, G.; Couture, A.; Cox, J.; David, S.; Dolfini, R.; Domingo-Pardo, C.; Dorochenko, A.; Dridi, W.; Duran, I.; Eleftheriadis, Ch.; Embid-Segura, M.; Ferrant, L.; Ferrari, A.; Ferreira-Marques, R.; Fitzpatrick, L.; Frais-Koelbl, H.; Fuji, K.; Furman, W.; Goncalves, I.; Gallino, R.; Gonzalez-Romero, E.; Goverdovski, A.; Gramegna, F.; Griesmayer, E.; Guerrero, C.; Gunsing, F.; Haas, B.; Haight, R.; Heil, M.; Herrera-Martinez, A.; Igashira, M.; Ioannidis, K.; Isaev, S.; Jericha, E.; Kadi, Y.; Kaeppeler, F.; Karamanis, D.; Kerveno, M.; Ketlerov, V.; Koehler, P.; Kolokolov, D.; Konovalov, V.; Krticka, M.; Lamboudis, C.; Leeb, H.; Lindote, A.; Lopes, I.; Lozano, M.; Lukic, S.; Marganiec, J.; Marques, L.; Marrone, S.; Massimi, C.; Mastinu, P.; Mengoni, A.; Milazzo, P. M.; Moreau, C.; Mosconi, M.; Neves, F.; Oberhummer, H.; O'Brien, S.; Oshima, M.; Pancin, J.; Papadopoulos, C.; Paradela, C.; Patronis, N.; Pavlik, A.; Pavlopoulos, P.; Perrot, L.; Plag, R.; Plompen, A.; Plukis, A.; Poch, A.; Pretel, C.; Quesada, J.; Rauscher, T.; Reifarth, R.; Rosetti, M.; Rubbia, C.; Rudolf, G.; Rullhusen, P.; Salgado, J.; Sarchiapone, L.; Savvidis, I.; Sedysheva, M.; Stamoulis, K.; Stephan, C.; Tagliente, G.; Tain, J. L.; Tassan-Got, L.; Tavora, L.; Terlizzi, R.; Vannini, G.; Vaz, P.; Ventura, A.; Villamarin, D.; Vincente, M. C.; Vlachoudis, V.; Voss, F.; Wendler, H.; Wiescher, M.; Wisshak, K. Share Save
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