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COMPREHENSIVE FUNCTIONAL GENOMIC SCREENS REVEAL HUMAN TRANSCRIPTION FACTORS REQUIRED TO MAINTAIN GLIOBLASTOMA OLIGODENDROCYTE PROGENITOR CELL-LIKE IDENTITY Mihalas, Anca; Mitchell, Kelly; Arora, Sonali; Felton, Colette; Witkowski, Mikey; Abadilla, Aiden; Kuppers, Daniel; Brooks, Angela; Berger, Alice; Paddison, Patrick Share Save
SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing Bai, Gali; Dhillon, Namrita; Felton, Colette; Meissner, Brett; Saint-John, Brandon; Shelansky, Robert; Meyerson, Elliot; Hrabeta-Robinson, Eva; Hodjat, Babak; Boeger, Hinrich; Brooks, Angela N. Share Save
Steering research on mRNA splicing in cancer towards clinical translation Anczukow, Olga; Allain, Frederic H. -T.; Angarola, Brittany L.; Black, Douglas L.; Brooks, Angela N.; Cheng, Chonghui; Conesa, Ana; Crosse, Edie I.; Eyras, Eduardo; Guccione, Ernesto; Lu, Sydney X.; Neugebauer, Karla M.; Sehgal, Priyanka; Song, Xiao; Tothova, Zuzana; Valcarcel, Juan; Weeks, Kevin M.; Yeo, Gene W.; Thomas-Tikhonenko, Andrei Share Save
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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Pardo-Palacios, Francisco J.; Wang, Dingjie; Reese, Fairlie; Diekhans, Mark; Carbonell-Sala, Silvia; Williams, Brian; Loveland, Jane E.; De Maria, Maite; Adams, Matthew S.; Balderrama-Gutierrez, Gabriela; Behera, Amit K.; Gonzalez Martinez, Jose M.; Hunt, Toby; Lagarde, Julien; Liang, Cindy E.; Li, Haoran; Meade, Marcus Jerryd; Moraga Amador, David A.; Prjibelski, Andrey D.; Birol, Inanc; Bostan, Hamed; Brooks, Ashley M.; Celik, Muhammed Hasan; Chen, Ying; Du, Mei R. M.; Felton, Colette; Goeke, Jonathan; Hafezqorani, Saber; Herwig, Ralf; Kawaji, Hideya; Lee, Joseph; Li, Jian-Liang; Lienhard, Matthias; Mikheenko, Alla; Mulligan, Dennis; Nip, Ka Ming; Pertea, Mihaela; Ritchie, Matthew E.; Sim, Andre D.; Tang, Alison D.; Wan, Yuk Kei; Wang, Changqing; Wong, Brandon Y.; Yang, Chen; Barnes, If; Berry, Andrew E.; Capella-Gutierrez, Salvador; Cousineau, Alyssa; Dhillon, Namrita; Fernandez-Gonzalez, Jose M.; Ferrandez-Peral, Luis; Garcia-Reyero, Natalia; Goetz, Stefan; Hernandez-Ferrer, Carles; Kondratova, Liudmyla; Liu, Tianyuan; Martinez-Martin, Alessandra; Menor, Carlos; Mestre-Tomas, Jorge; Mudge, Jonathan M.; Panayotova, Nedka G.; Paniagua, Alejandro; Repchevsky, Dmitry; Ren, Xingjie; Rouchka, Eric; Saint-John, Brandon; Sapena, Enrique; Sheynkman, Leon; Smith, Melissa Laird; Suner, Marie-Marthe; Takahashi, Hazuki; Youngworth, Ingrid A.; Carninci, Piero; Denslow, Nancy D.; Guigo, Roderic; Hunter, Margaret E.; Maehr, Rene; Shen, Yin; Tilgner, Hagen U.; Wold, Barbara J.; Vollmers, Christopher; Frankish, Adam; Au, Kin Fai; Sheynkman, Gloria M.; Mortazavi, Ali; Conesa, Ana; Brooks, Angela N. Share Save
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DeepSea is an efficient deep-learning model for single-cell segmentation and tracking in time-lapse microscopy Zargari, Abolfazl; Lodewijk, Gerrald A.; Mashhadi, Najmeh; Cook, Nathan; Neudorf, Celine W.; Araghbidikashani, Kimiasadat; Hays, Robert; Kozuki, Sayaka; Rubio, Stefany; Hrabeta-Robinson, Eva; Brooks, Angela; Hinck, Lindsay; Shariati, S. Ali Share Save
Mutant KRAS regulates transposable element RNA and innate immunity via KRAB zinc-finger genes Reggiardo, Roman E.; Maroli, Sreelakshmi Velandi; Halasz, Haley; Ozen, Mehmet; Hrabeta-Robinson, Eva; Behera, Amit; Peddu, Vikas; Carrillo, David; LaMontagne, Erin; Whitehead, Lila; Kim, Eejung; Malik, Shivani; Fernandes, Jason; Marinov, Georgi; Collisson, Eric; Brooks, Angela; Demirci, Utkan; Kim, Daniel H. Share Save
SRSF1 governs progenitor-specific alternative splicing to maintain adult epithelial tissue homeostasis and renewal Yu, Tingsheng; Cazares, Oscar; Tang, Alison D.; Kim, Hyun-Yi; Wald, Tomas; Verma, Adya; Liu, Qi; Barcellos-Hoff, Mary Helen; Floor, Stephen N.; Jung, Han-Sung; Brooks, Angela N.; Klein, Ophir D. Share Save
Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2 Robinson, Elektra K.; Jagannatha, Pratibha; Covarrubias, Sergio; Cattle, Matthew; Smaliy, Valeriya; Safavi, Rojin; Shapleigh, Barbara; Abu-Shumays, Robin; Jain, Miten; Cloonan, Suzanne M.; Akeson, Mark; Brooks, Angela N.; Carpenter, Susan Share Save
Visualizing and interpreting cancer genomics data via the Xena platform Goldman, Mary J.; Craft, Brian; Hastie, Mim; Repecka, Kristupas; McDade, Fran; Kamath, Akhil; Banerjee, Ayan; Luo, Yunhai; Rogers, Dave; Brooks, Angela N.; Zhu, Jingchun; Haussler, David Share Save
Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma Huang, Hector H.; Ferguson, Ian D.; Thornton, Alexis M.; Bastola, Prabhakar; Lam, Christine; Lin, Yu-Hsiu T.; Choudhry, Priya; Mariano, Margarette C.; Marcoulis, Makeba D.; Teo, Chin Fen; Malato, Julia; Phojanakong, Paul J.; Martin, Thomas G., III; Wolf, Jeffrey L.; Wong, Sandy W.; Shah, Nina; Hann, Byron; Brooks, Angela N.; Wiita, Arun P. Share Save
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Butler enables rapid cloud-based analysis of thousands of human genomes (vol 79, pg 134, 2019) Yakneen, Sergei; Waszak, Sebastian M.; Gertz, Michael; Korbel, Jan O.; Aminou, Brice; Bartolome, Javier; Boroevich, Keith A.; Boyce, Rich; Brooks, Angela N.; Buchanan, Alex; Buchhalter, Ivo; Butler, Adam P.; Byrne, Niall J.; Cafferkey, Andy; Campbell, Peter J.; Chen, Zhaohong; Cho, Sunghoon; Choi, Wan; Clapham, Peter; Davis-Dusenbery, Brandi N.; De La Vega, Francisco M.; Demeulemeester, Jonas; Dow, Michelle T.; Dursi, Lewis Jonathan; Eils, Juergen; Eils, Roland; Ellrott, Kyle; Farcas, Claudiu; Favero, Francesco; Fayzullaev, Nodirjon; Ferretti, Vincent; Flicek, Paul; Fonseca, Nuno A.; Gelpi, Josep Ll.; Getz, Gad; Gibson, Bob; Grossman, Robert L.; Harismendy, Olivier; Heath, Allison P.; Heinold, Michael C.; Hess, Julian M.; Hofmann, Oliver; Hong, Jongwhi H.; Hudson, Thomas J.; Hutter, Barbara; Hutter, Carolyn M.; Hubschmann, Daniel; Imoto, Seiya; Ivkovic, Sinisa; Jeon, Seung-Hyup; Jiao, Wei; Jung, Jongsun; Kabbe, Rolf; Kahles, Andre; Kerssemakers, Jules N. A.; Kim, Hyung-Lae; Kim, Hyunghwan; Kim, Jihoon; Kim, Youngwook; Kleinheinz, Kortine; Koscher, Michael; Koures, Antonios; Kovacevic, Milena; Lawerenz, Chris; Leshchiner, Ignaty; Liu, Jia; Livitz, Dimitri; Mihaiescu, George L.; Mijalkovic, Sanja; Lazic, Ana Mijalkovic; Miyano, Satoru; Miyoshi, Naoki; Nahal-Bose, Hardeep K.; Nakagawa, Hidewaki; Nastic, Mia; Newhouse, Steven J.; Nicholson, Jonathan; O'Connor, Brian D.; Ocana, David; Ohi, Kazuhiro; Ohno-Machado, Lucila; Omberg, Larsson; Ouellette, B. F. Francis; Paramasivam, Nagarajan; Perry, Marc D.; Pihl, Todd D.; Prinz, Manuel; Puiggros, Montserrat; Radovic, Petar; Raine, Keiran M.; Rheinbay, Esther; Rosenberg, Mara; Royo, Romina; Ratsch, Gunnar; Saksena, Gordon; Schlesner, Matthias; Shorser, Solomon I.; Short, Charles; Sofia, Heidi J.; Spring, Jonathan; Stein, Lincoln D.; Struck, Adam J.; Tiao, Grace; Tijanic, Nebojsa; Torrents, David; Van Loo, Peter; Vazquez, Miguel; Vicente, David; Wala, Jeremiah A.; Wang, Zhining; Waszak, Sebastian M.; Weischenfeldt, Joachim; Werner, Johannes; Williams, Ashley; Woo, Youngchoon; Wright, Adam J.; Xiang, Qian; Yang, Liming; Yuen, Denis; Yung, Christina K.; Zhang, Junjun; Korbel, Jan O. Share Save
Nanopore native RNA sequencing of a human poly(A) transcriptome (vol 16, pg, 1297, 2019) Workman, Rachael E.; Tang, Alison D.; Tang, Paul S.; Jain, Miten; Tyson, John R.; Razaghi, Roham; Zuzarte, Philip C.; Gilpatrick, Timothy; Payne, Alexander; Quick, Joshua; Sadowski, Norah; Holmes, Nadine; de Jesus, Jaqueline Goes; Jones, Karen L.; Soulette, Cameron M.; Snutch, Terrance P.; Loman, Nicholas; Paten, Benedict; Loose, Matthew; Simpson, Jared T.; Olsen, Hugh E.; Brooks, Angela N.; Akeson, Mark; Timp, Winston Share Save
Nanopore native RNA sequencing of a human poly(A) transcriptome Workman, Rachael E.; Tang, Alison D.; Tang, Paul S.; Jain, Miten; Tyson, John R.; Razaghi, Roham; Zuzarte, Philip C.; Gilpatrick, Timothy; Payne, Alexander; Quick, Joshua; Sadowski, Norah; Holmes, Nadine; de Jesus, Jaqueline Goes; Jones, Karen L.; Soulette, Cameron M.; Snutch, Terrance P.; Loman, Nicholas; Paten, Benedict; Loose, Matthew; Simpson, Jared T.; Olsen, Hugh E.; Brooks, Angela N.; Akeson, Mark; Timp, Winston Share Save
Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies ten Hacken, Elisa; Valentin, Rebecca; Regis, Fara Faye D.; Sun, Jing; Yin, Shanye; Werner, Lillian; Deng, Jing; Gruber, Michaela; Wong, Jessica; Zheng, Mei; Gill, Amy L.; Seiler, Michael; Smith, Peter; Thomas, Michael; Buonamici, Silvia; Ghia, Emanuela M.; Kim, Ekaterina; Rassenti, Laura Z.; Burger, Jan A.; Kipps, Thomas J.; Meyerson, Matthew L.; Bachireddy, Pavan; Wang, Lili; Reed, Robin; Neuberg, Donna; Carrasco, Ruben D.; Brooks, Angela N.; Letai, Anthony; Davids, Matthew S.; Wu, Catherine J. Share Save
An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer Li, Ji; Choi, Peter S.; Chaffer, Christine L.; Labella, Katherine; Hwang, Justin H.; Giacomelli, Andrew O.; Kim, Jong Wook; Ilic, Nina; Doench, John G.; Ly, Seav Huong; Dai, Chao; Hagel, Kimberly; Hong, Andrew L.; Gjoerup, Ole; Goel, Shom; Ge, Jennifer Y.; Root, David E.; Zhao, Jean J.; Brooks, Angela N.; Weinberg, Robert A.; Hahn, William C. Share Save
MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma Lu, Xinyuan; Peled, Nir; Greer, John; Wu, Wei; Choi, Peter; Berger, Alice H.; Wong, Sergio; Jen, Kuang-Yu; Seo, Youngho; Hann, Byron; Brooks, Angela; Meyerson, Matthew; Collisson, Eric A. Share Save
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