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Angela N. Brooks, Ph.D. - Publications

Affiliations: 
2011 Molecular & Cell Biology University of California, Berkeley, Berkeley, CA 
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54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Reggiardo RE, Maroli SV, Halasz H, Ozen M, Hrabeta-Robinson E, Behera A, Peddu V, Carrillo D, LaMontagne E, Whitehead L, Kim E, Malik S, Fernandes J, Marinov G, Collisson E, ... Brooks A, et al. Mutant KRAS regulates transposable element RNA and innate immunity via KRAB zinc-finger genes. Cell Reports. 40: 111104. PMID 35858545 DOI: 10.1016/j.celrep.2022.111104  0.392
2021 Thornton AM, Fang L, Lo A, McSharry M, Haan D, O'Brien C, Berger AH, Giannakis M, Brooks AN. eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants. Plos Computational Biology. 17: e1009132. PMID 34214079 DOI: 10.1371/journal.pcbi.1009132  0.349
2020 Goldman MJ, Craft B, Hastie M, Repečka K, McDade F, Kamath A, Banerjee A, Luo Y, Rogers D, Brooks AN, Zhu J, Haussler D. Visualizing and interpreting cancer genomics data via the Xena platform. Nature Biotechnology. PMID 32444850 DOI: 10.1038/S41587-020-0546-8  0.302
2020 Huang HH, Ferguson ID, Thornton AM, Bastola P, Lam C, Lin YT, Choudhry P, Mariano MC, Marcoulis MD, Teo CF, Malato J, Phojanakong PJ, Martin TG, Wolf JL, Wong SW, ... ... Brooks AN, et al. Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma. Nature Communications. 11: 1931. PMID 32321912 DOI: 10.1038/S41467-020-15521-4  0.382
2020 Tang AD, Soulette CM, van Baren MJ, Hart K, Hrabeta-Robinson E, Wu CJ, Brooks AN. Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns. Nature Communications. 11: 1438. PMID 32188845 DOI: 10.1038/S41467-020-15171-6  0.476
2020 Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, ... ... Brooks AN, et al. Genomic basis for RNA alterations in cancer. Nature. 578: 129-136. PMID 32025019 DOI: 10.1038/S41586-020-1970-0  0.491
2019 Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, ... ... Brooks AN, et al. Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods. PMID 31819268 DOI: 10.1038/S41592-019-0697-Z  0.364
2019 Workman RE, Tang AD, Tang PS, Jain M, Tyson JR, Razaghi R, Zuzarte PC, Gilpatrick T, Payne A, Quick J, Sadowski N, Holmes N, de Jesus JG, Jones KL, Soulette CM, ... ... Brooks AN, et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nature Methods. PMID 31740818 DOI: 10.1038/S41592-019-0617-2  0.41
2019 Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J. A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell. 178: 1465-1477.e17. PMID 31491388 DOI: 10.1016/J.Cell.2019.08.018  0.404
2019 Yin S, Gambe RG, Sun J, Martinez AZ, Cartun ZJ, Regis FFD, Wan Y, Fan J, Brooks AN, Herman SEM, Hacken ET, Taylor-Weiner A, Rassenti LZ, Ghia EM, Kipps TJ, et al. A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion. Cancer Cell. PMID 30712845 DOI: 10.1016/J.Ccell.2018.12.013  0.409
2018 Hacken ET, Valentin R, Regis FFD, Sun J, Yin S, Werner L, Deng J, Gruber M, Wong J, Zheng M, Gill AL, Seiler M, Smith P, Thomas M, Buonamici S, ... ... Brooks AN, et al. Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies. Jci Insight. 3. PMID 30282833 DOI: 10.1172/Jci.Insight.121438  0.343
2018 Li J, Choi PS, Chaffer CL, Labella K, Hwang JH, Giacomelli AO, Kim JW, Ilic N, Doench JG, Ly SH, Dai C, Hagel K, Hong AL, Gjoerup O, Goel S, ... ... Brooks AN, et al. An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer. Elife. 7. PMID 30059005 DOI: 10.7554/Elife.37184  0.474
2018 Wang L, Yin S, Martinez Az, Regis FF, Brooks A, Herman SEM, Ten Hacken E, Obeng E, Campagna D, Fleming MD, Ebert BL, Wiestner A, Leshchiner I, Getz G, Carrasco RD, et al. Integrated Genomic and Proteomic Analysis of Murine CLL-like Cells Reveals SF3B1 Mutation to Impact DNA Damage Response and BCR Signaling Blood. 132: 947-947. DOI: 10.1182/Blood-2018-99-117691  0.483
2017 Subramanian A, Narayan R, Corsello SM, Peck DD, Natoli TE, Lu X, Gould J, Davis JF, Tubelli AA, Asiedu JK, Lahr DL, Hirschman JE, Liu Z, Donahue M, Julian B, ... ... Brooks AN, et al. A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell. 171: 1437-1452.e17. PMID 29195078 DOI: 10.1016/J.Cell.2017.10.049  0.353
2017 Carlson SM, Soulette CM, Yang Z, Elias JE, Brooks AN, Gozani O. RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation. The Journal of Biological Chemistry. PMID 28655759 DOI: 10.1074/Jbc.M117.784371  0.449
2017 Lu X, Peled N, Greer J, Wu W, Choi P, Berger AH, Wong S, Jen KY, Seo Y, Hann B, Brooks A, Meyerson M, Collisson EA. MET exon 14 mutation encodes an actionable therapeutic target in lung adenocarcinoma. Cancer Research. PMID 28522754 DOI: 10.1158/0008-5472.Can-16-1944  0.401
2017 Li J, Choi P, Chaffer C, Labella K, Kim JW, Doench J, Dai C, Giacomelli A, Ly SH, Hwang J, Hong A, Ilic N, Gjoerup O, Meyerson M, Brooks A, et al. Abstract A36: Genome-scale ORF screening to identify modulators of the epithelial-to-mesenchymal transition Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-A36  0.439
2017 Amin S, Awadalla P, Biankin A, Boutros P, Brazma A, Brooks AN, Calabrese C, Chang D, Chateigner A, Chen K, Chong Z, Craft B, Creighton C, Demircioğlu D, Fonseca N, et al. Abstract SY10-02: Pan-cancer study of recurrent and heterogeneous RNA aberrations and association with whole-genome variants Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Sy10-02  0.419
2017 Li J, Choi P, Chaffer C, Labella K, Kim JW, Doench J, Dai C, Giacomelli A, Ly SH, Hwang J, Hong A, Ilic N, Gjoerup O, Meyerson M, Brooks A, et al. Abstract 5020: A genome-scale ORF screen reveals an alternative splicing program that regulates mesenchymal and stem-like cell states in breast cancer Cancer Research. 77: 5020-5020. DOI: 10.1158/1538-7445.Am2017-5020  0.4
2017 Davidson NR, Brazma A, Brooks AN, Calabrese C, Fonseca NA, Goke J, He Y, Hu X, Kahles A, Lehmann K, Liu F, Rätsch G, Li S, Schwarz RF, Yang M, et al. Abstract 389: Integrating diverse transcriptomic alterations to identify cancer-relevant genes Cancer Research. 77: 389-389. DOI: 10.1158/1538-7445.Am2017-389  0.448
2017 Beale H, Lam DL, Vivian J, Newton Y, Shah AT, Bjork I, Goldstein T, Brooks AN, Stuart J, Salama S, Sweet-Cordero EA, Haussler D, Morozova O. Abstract 2466: Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing Cancer Research. 77: 2466-2466. DOI: 10.1158/1538-7445.Am2017-2466  0.409
2017 Wang L, Sun J, Taylor-Weiner A, Kim J, Cartun ZJ, Brooks AN, Neuberg D, Fleming MD, Ebert BL, Getz G, Carrasco R, Wu CJ. Abstract 2449: Transcriptome and whole-genome sequencing analysis of a novel murine model of chronic lymphocytic leukemia Cancer Research. 77: 2449-2449. DOI: 10.1158/1538-7445.Am2017-2449  0.461
2016 Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, et al. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell. PMID 27818134 DOI: 10.1016/J.Ccell.2016.10.005  0.428
2016 Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, et al. High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell. PMID 27478040 DOI: 10.1016/J.Ccell.2016.06.022  0.438
2016 Wang L, Gambe R, Sun J, Shukla S, Kim J, Brooks AN, Neuberg DS, Fleming MD, Ebert BL, Carrasco RD, Wu CJ. Genome-Wide Analysis of a Novel Murine Model of Chronic Lymphocytic Leukemia Blood. 128: 967-967. DOI: 10.1182/Blood.V128.22.967.967  0.492
2016 Wang L, Gambe R, Fan J, Brooks AN, Sun J, Neuberg D, Kharchenko P, Meyerson M, Fleming MD, Ebert BL, Carrasco R, Wu CJ. Abstract 669: Compound heterozygous Sf3b1-K700E mutation and Atm deletion in B cells leads to CLL in mice Cancer Research. 76: 669-669. DOI: 10.1158/1538-7445.Am2016-669  0.482
2016 Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Kaplan N, et al. Abstract 4368: High-throughput phenotyping of lung cancer somatic mutations Cancer Research. 76: 4368-4368. DOI: 10.1158/1538-7445.Am2016-4368  0.466
2016 Wang L, Brooks A, Gambe R, Fan J, Sun J, Hergert S, Wan Y, Neuberg D, Kharchenko P, Meyerson M, Fleming M, Ebert B, Wu C. From Human Genetic to Mouse Model: SF3B1 Mutation and its Impact on Chronic Lymphocytic Leukemia Clinical Lymphoma Myeloma and Leukemia. 16: S52. DOI: 10.1016/J.Clml.2016.07.076  0.324
2015 Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Celniker SE, Graveley BR, Brenner SE. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Research. PMID 26294686 DOI: 10.1101/Gr.192518.115  0.434
2015 Albiges L, Murray B, Brooks A, Cherniack A, Berger A, Creighton CJ, Ricketts C, Bottaro DP, Srinivasan R, Schmidt LS, Meyerson M, Spellman P, Linehan WM, Choueiri TK. Distinct MET alterations to induce a common phenotype and to define a MET-driven subset of papillary RCC: Results from the Cancer Genome Atlas (TCGA) Kidney Renal Papillary (KIRP) Working Group. Journal of Clinical Oncology. 33: 4521-4521. DOI: 10.1200/Jco.2015.33.15_Suppl.4521  0.432
2015 Wang L, Gambe R, Fan J, Wan Y, Brooks AN, Sun J, Obeng EA, Neuberg DS, Meyerson M, Fleming MD, Ebert BL, Carrasco RD, Wu CJ. Expressionof Sf3b1- K700Ein Murine B Cells Causes Pre-mRNA Splicing and Altered B Cell Differentiation and Function Blood. 126: 366-366. DOI: 10.1182/Blood.V126.23.366.366  0.447
2015 Fan J, Wang L, Brooks AN, Wan Y, Neuberg DS, Rassenti LZ, Ghia EM, Kipps TJ, Brown JR, Li S, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Comprehensive Bulk and Single Cell Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia Blood. 126: 2906-2906. DOI: 10.1182/Blood.V126.23.2906.2906  0.504
2015 Berger A, Brooks A, Wu X, Hogstrom L, Tirosh I, Piccioni F, Bagul M, Zhu C, Shretha Y, Root D, Tamayo P, Sakai R, Wong B, Subramanian A, Golub T, et al. Abstract PR12: High-throughput gene expression profiling as a generalizable assay for determination of mutation impact on gene function Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-Pr12  0.465
2015 Berger AH, Kim E, Brooks A, Ilic N, Shrestha Y, Tseng Y, Wu X, Zou L, Kamburov A, Yang X, Zhu C, Keskula P, Seepo S, Hong A, Kantoff P, et al. Abstract PR07: Towards precision functional genomics via next-generation functional mapping of cancer variants Cancer Research. 75: 957-957. DOI: 10.1158/1538-7445.Transcagen-Pr07  0.426
2015 Berger A, Brooks A, Wu X, Hogstrom L, Tirosh I, Piccioni F, Bagul M, Zhu C, Shretha Y, Root D, Tamayo P, Sakai R, Wong B, Subramanian A, Golub T, et al. Abstract PR04: High-throughput gene expression profiling as a generalizable assay for determination of mutation impact on gene function Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr04  0.461
2015 Brooks AN, Ge Y, Chau K, Freeman SS, Saksena G, Pedamallu CS, Meyerson M. Abstract B2-21: Identification of somatic RNA splicing alterations in human cancers Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B2-21  0.511
2015 Berger A, Kim E, Brooks A, Shrestha Y, Tseng Y, Wu X, Ilic N, Zou L, Kamburov A, Yang X, Zhu C, Keskula P, Seepo S, Hong A, Doench J, et al. Abstract 957: Towards precision functional genomics via next-generation functional mapping of cancer variants Molecular and Cellular Biology. DOI: 10.1158/1538-7445.Am2015-957  0.329
2014 Watanabe H, Brooks AN, Meyerson M. Breaking down RET breakpoints in lung adenocarcinoma. Journal of Thoracic Oncology : Official Publication of the International Association For the Study of Lung Cancer. 9: 590-2. PMID 24722148 DOI: 10.1097/Jto.0000000000000168  0.395
2014 Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis JM, Pedamallu CS, DeLuca DS, Brooks AN, Wang S, Que J, Rustgi AK, Wong KK, et al. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas. The Journal of Clinical Investigation. 124: 1636-45. PMID 24590290 DOI: 10.1172/Jci71545  0.384
2014 Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M. A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. Plos One. 9: e87361. PMID 24498085 DOI: 10.1371/Journal.Pone.0087361  0.501
2014 Berger AH, Brooks AN, Imielinski M, Cherniack A, Duke F, Kaplan N, Wala J, Meyerson M. Abstract PR08:NF1,MET, andRIT1mutations are RAS-pathway driver events in lung adenocarcinoma Molecular Cancer Research. 12. DOI: 10.1158/1557-3125.Rasonc14-Pr08  0.429
2014 Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis JM, Pedamallu CS, Deluca DS, Brooks AN, Que J, Rustgi AK, Wong K, Ligon KL, et al. Abstract 1391: SOX2-p63 interaction and genomic co-localization in squamous cell carcinomas Cancer Research. 74: 1391-1391. DOI: 10.1158/1538-7445.Am2014-1391  0.379
2013 Wan Y, Brooks AN, Wang L, Sougnez C, Zhang W, Wong J, Landau D, Kotliar D, Deluca D, Brown JR, Reed R, Getz G, Meyerson M, Wu CJ. SF3B1 Mutation Alters The Selection Of 3' RNA Splice Sites In Chronic Lymphocytic Leukemia Blood. 122: 117-117. DOI: 10.1182/Blood.V122.21.117.117  0.402
2013 Brooks AN, Wan Y, Choi P, Jing R, DeLuca DS, Sougnez C, Chmielecki J, Imielinski M, Getz G, Wu CJ, Meyerson M. Abstract 3150: Characterizing the effects of somatic mutations in splice factors on the transcriptome. Cancer Research. 73: 3150-3150. DOI: 10.1158/1538-7445.Am2013-3150  0.382
2012 Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, ... ... Brooks A, et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell. 150: 1107-20. PMID 22980975 DOI: 10.1016/J.Cell.2012.08.029  0.421
2011 Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. Rna (New York, N.Y.). 17: 1884-94. PMID 21865603 DOI: 10.1261/Rna.2696311  0.614
2011 Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. PMID 21179090 DOI: 10.1038/Nature09715  0.461
2011 Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research. 21: 193-202. PMID 20921232 DOI: 10.1101/Gr.108662.110  0.467
2010 Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... Brooks AN, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374  0.418
2009 Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Molecular Cell. 33: 438-49. PMID 19250905 DOI: 10.1016/J.Molcel.2009.01.022  0.601
2007 Lareau LF, Brooks AN, Soergel DA, Meng Q, Brenner SE. The coupling of alternative splicing and nonsense-mediated mRNA decay. Advances in Experimental Medicine and Biology. 623: 190-211. PMID 18380348 DOI: 10.1007/978-0-387-77374-2_12  0.405
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Brooks AN, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.399
2006 Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. Structural basis for double-stranded RNA processing by Dicer. Science (New York, N.Y.). 311: 195-8. PMID 16410517 DOI: 10.1126/Science.1121638  0.329
2005 Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research. 33: W686-9. PMID 15980563 DOI: 10.1093/Nar/Gki366  0.396
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