MET exon 14 skipping is overexpressed in an allele-specific manner in lung adenocarcinoma primary samples

por Durham, Megan, Vadde, Swetha, Brooks, Angela N
Publicado 2023

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

por Schattner, Peter, Brooks, Angela N., Lowe, Todd M.
Publicado 2005

An expression-based variant impact phenotyping protocol to predict the impact of gene variants in cell lines

por Thornton, Alexis M., Tumu, Manoj, Brooks, Angela N.
Publicado 2022

Detecting haplotype-specific transcript variation in long reads with FLAIR2

por Tang, Alison D., Hrabeta-Robinson, Eva, Volden, Roger, Vollmers, Christopher, Brooks, Angela N.
Publicado 2023

Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations

por Soulette, Cameron M, Hrabeta-Robinson, Eva, Arevalo, Carlos, Felton, Colette, Tang, Alison D, Marin, Maximillian G, Brooks, Angela N
Publicado 2023

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

por Tang, Alison D., Soulette, Cameron M., van Baren, Marijke J., Hart, Kevyn, Hrabeta-Robinson, Eva, Wu, Catherine J., Brooks, Angela N.
Publicado 2020

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants

por Thornton, Alexis M., Fang, Lishan, Lo, April, McSharry, Maria, Haan, David, O’Brien, Casey, Berger, Alice H., Giannakis, Marios, Brooks, Angela N.
Publicado 2021

Cell Painting predicts impact of lung cancer variants

por Caicedo, Juan C., Arevalo, John, Piccioni, Federica, Bray, Mark-Anthony, Hartland, Cathy L., Wu, Xiaoyun, Brooks, Angela N., Berger, Alice H., Boehm, Jesse S., Carpenter, Anne E., Singh, Shantanu
Publicado 2022

Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

por Brooks, Angela N., Duff, Michael O., May, Gemma, Yang, Li, Bolisetty, Mohan, Landolin, Jane, Wan, Ken, Sandler, Jeremy, Booth, Benjamin W., Celniker, Susan E., Graveley, Brenton R., Brenner, Steven E.
Publicado 2015

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2

por 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
Publicado 2021

A Pan-Cancer Analysis of Transcriptome Changes Associated with Somatic Mutations in U2AF1 Reveals Commonly Altered Splicing Events

por Brooks, Angela N., Choi, Peter S., de Waal, Luc, Sharifnia, Tanaz, Imielinski, Marcin, Saksena, Gordon, Pedamallu, Chandra Sekhar, Sivachenko, Andrey, Rosenberg, Mara, Chmielecki, Juliann, Lawrence, Michael S., DeLuca, David S., Getz, Gad, Meyerson, Matthew
Publicado 2014

Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma

por 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., Wolf, Jeffrey L., Wong, Sandy W., Shah, Nina, Hann, Byron, Brooks, Angela N., Wiita, Arun P.
Publicado 2020

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer

por 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
Publicado 2018

Nanopore native RNA sequencing of a human poly(A) transcriptome

por 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
Publicado 2019

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

por Campbell, Joshua D., Alexandrov, Anton, Kim, Jaegil, Wala, Jeremiah, Berger, Alice H., Pedamallu, Chandra Sekhar, Shukla, Sachet A., Guo, Guangwu, Brooks, Angela N., Murray, Bradley A., Imielinski, Marcin, Hu, Xin, Ling, Shiyun, Akbani, Rehan, Rosenberg, Mara, Cibulskis, Carrie, Ramachandran, Aruna, Collisson, Eric A., Kwiatkowski, David J., Lawrence, Michael S., Weinstein, John N., Verhaak, Roel G. W., Wu, Catherine J., Hammerman, Peter S., Cherniack, Andrew D., Getz, Gad, Artyomov, Maxim N., Schreiber, Robert, Govindan, Ramaswamy, Meyerson, Matthew
Publicado 2016

The Developmental Transcriptome of Drosophila melanogaster

por Graveley, Brenton R., Brooks, Angela N., Carlson, Joseph W., Duff, Michael O., Landolin, Jane M., Yang, Li, Artieri, Carlo G., van Baren, Marijke J., Boley, Nathan, Booth, Benjamin W., Brown, James B., Cherbas, Lucy, Davis, Carrie A., Dobin, Alex, Li, Renhua, Lin, Wei, Malone, John H., Mattiuzzo, Nicolas R., Miller, David, Sturgill, David, Tuch, Brian B., Zaleski, Chris, Zhang, Dayu, Blanchette, Marco, Dudoit, Sandrine, Eads, Brian, Green, Richard E., Hammonds, Ann, Jiang, Lichun, Kapranov, Phil, Langton, Laura, Perrimon, Norbert, Sandler, Jeremy E., Wan, Kenneth H., Willingham, Aarron, Zhang, Yu, Zou, Yi, Andrews, Justen, Bickel, Peter J., Brenner, Steven E., Brent, Michael R., Cherbas, Peter, Gingeras, Thomas R., Hoskins, Roger A., Kaufman, Thomas C., Oliver, Brian, Celniker, Susan E.
Publicado 2010

Genomic basis for RNA alterations in cancer

por Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, Zhang, Zemin
Publicado 2020

Author Correction: Genomic basis for RNA alterations in cancer

por Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, Zhang, Zemin
Publicado 2023

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

por Pardo-Palacios, Francisco J., Wang, Dingjie, Reese, Fairlie, Diekhans, Mark, Carbonell-Sala, Sílvia, Williams, Brian, Loveland, Jane E., De María, Maite, Adams, Matthew S., Balderrama-Gutierrez, Gabriela, Behera, Amit K., Gonzalez, Jose M., Hunt, Toby, Lagarde, Julien, Liang, Cindy E., Li, Haoran, Jerryd Meade, Marcus, Moraga Amador, David A., Prjibelski, Andrey D., Birol, Inanc, Bostan, Hamed, Brooks, Ashley M., Hasan Çelik, Muhammed, Chen, Ying, Du, Mei R,M., Felton, Colette, Göke, Jonathan, Hafezqorani, Saber, Herwig, Ralf, Kawaji, Hideya, Lee, Joseph, Liang Li, Jian, Lienhard, Matthias, Mikheenko, Alla, Mulligan, Dennis, Ming Nip, Ka, Pertea, Mihaela, Ritchie, Matthew E., Sim, Andre D., Tang, Alison D., Kei Wan, Yuk, Wang, Changqing, Wong, Brandon Y., Yang, Chen, Barnes, If, Berry, Andrew, Capella, Salvador, Dhillon, Namrita, Fernandez-Gonzalez, Jose M., Ferrández-Peral, Luis, Garcia-Reyero, Natàlia, Goetz, Stefan, Hernández-Ferrer, Carles, Kondratova, Liudmyla, Liu, Tianyuan, Martinez-Martin, Alessandra, Menor, Carlos, Mestre-Tomás, Jorge, Mudge, Jonathan M., Panayotova, Nedka G., Paniagua, Alejandro, Repchevsky, Dmitry, Rouchka, Eric, Saint-John, Brandon, Sapena, Enrique, Sheynkman, Leon, Laird Smith, Melissa, Suner, Marie-Marthe, Takahashi, Hazuki, Youngworth, Ingrid Ashley., Carninci, Piero, Denslow, Nancy D., Guigó, Roderic, Hunter, Margaret E., Tilgner, Hagen U., Wold, Barbara J., Vollmers, Christopher, Frankish, Adam, Fai Au, Kin, Sheynkman, Gloria M., Mortazavi, Ali, Conesa, Ana, Brooks, Angela N.
Publicado 2023