Publications


In bioRxiv

2018

  • Nanopore native RNA sequencing of a human poly(A) transcriptome
    Rachael E. Workman*, Alison D. Tang*, Paul S. Tang*, Miten Jain*, John R. Tyson*, Philip C. Zuzarte, Timothy Gilpatrick, Roham Razaghi, Joshua Quick, Norah Sadowski, Nadine Holmes, Jaqueline Goes de Jesus, Karen L. Jones, Terrance P. Snutch, Nicholas Loman, Benedict Paten, Matthew Loose, Jared T. Simpson, Hugh E. Olsen**, Angela N. Brooks**, Mark Akeson2**#, Winston Timp1**#
    https://doi.org/10.1101/459529 *Contributed equally to the work, **Co-lead the project, #Corresponding authors.
  • Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns
    Alison D. Tang, Cameron M. Soulette, Marijke J van Baren, Kevyn Hart, Eva Hrabeta-Robinson, Catherine J. Wu, Angela N. Brooks
    https://doi.org/10.1101/410183 
  • The UCSC Xena Platform for cancer genomics data visualization and interpretation
    Mary Goldman, Brian Craft, Akhil Kamath, Angela N Brooks, Jingchun Zhu, David Haussler
    https://doi.org/10.1101/326470
  • Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
    PCAWG Transcriptome Core Group; Claudia Calabrese*, Natalie R. Davidson*, Nuno A. Fonseca*, Yao He*, André Kahles*, Kjong-Van Lehmann*, Fenglin Liu*, Yuichi Shiraishi*, Cameron M. Soulette*, Lara Urban*; Deniz Demircioğlu, Liliana Greger, Siliang Li, Dongbing Liu, Junjun Zhang, Marc D. Perry, Linda Xiang, Fan Zhang, Peter Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina Yung, Shida Zhu, PCAWG Transcriptome Working Group, Philip Awadalla, Chad J. Creighton, Matthew Meyerson, B.F. Francis Ouellette, Kui Wu, Huangming Yang, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network, Alvis Brazma#§, Angela N. Brooks#§, Jonathan Göke#, Gunnar Rätsch#§, Roland F. Schwarz#, Oliver Stegle#, Zemin Zhang#
    https://doi.org/10.1101/183889  *equal contribution, # co-senior author, §co-corresponding authors

Peer-Reviewed

2018

  • Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies
    Ten Hacken E, 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, Ghia EM, Kim E, Rassenti LZ, Burger JA, Kipps TJ, Meyerson ML, Bachireddy P, Wang L, Reed R, Neuberg D, Carrasco RD, Brooks AN, Letai A, Davids MS, Wu CJ
    JCI Insight. 2018 Oct 4;3(19). pii: 121438. doi: 10.1172/jci.insight.121438. [link]
  • An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer
    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, Ge JY, Root DE, Zhao JJ, Brooks AN, Weinberg RA, Hahn WC
    eLife Jul 30;7.pii: e37184. doi: 10.7554/eLife.37184. [link]

2017

  • A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles
    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, Khan M, Wadden D, Smith IC, Lam D, Liberzon A, Toder C, Bagul M, Orzechowski M, Enache OM, Piccioni F, Johnson SA, Lyons NJ, Berger AH, Shamji AF, Brooks AN, Vrcic A, Flynn C, Rosains J, Takeda DY, Hu R, Davison D, Lamb J, Ardlie K, Hogstrom L, Greenside P, Gray NS, Clemons PA, Silver S, Wu X, Zhao WN, Read-Button W, Wu X, Haggarty SJ, Ronco LV, Boehm JS, Schreiber SL, Doench JG, Bittker JA, Root DE, Wong B, Golub TR
    Cell, Nov 30;171(6):1437-1452.e17.[link]
  • RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation
    Carlson SM, Soulette CM, Yang Z, Elias JE, Brooks AN, Gozani O.
    J Biol Chem, Aug 11;292(32):13381-13390. doi: 10.1074/jbc.M117.784371 [link]
  • MET exon 14 mutation encodes an actionable therapeutic target in lung adenocarcinoma
    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.
    Cancer Research, May 18. pii: canres.1944.2016. [link]

2016

  • Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia
    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, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ.
    Cancer Cell, Nov 14;30(5):750-763 [link]
  • High-throughput Phenotyping of Lung Cancer Somatic Mutations
    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, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS.
    Cancer Cell, Aug 8;30(2):214-28 [link]
  • Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
    Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G, Artyomov MN, Schreiber R, Govindan R, Meyerson M
    Nature Genetics, Jun;48(6):607-16.

2015

  • Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma
    The Cancer Genome Atlas Research Network
    N Engl J Med, Nov 4.DOI: 10.1056/NEJMoa1505917
  • Regulation of alternative splicing in Drosophila by 56 RNA binding proteins
    Brooks AN, Duff MO,  May G, Yang L, Bolisetty M,  Landolin J, Wan K, Sandler J, Celniker SE,  Graveley BR, Brenner SE
    Genome Research, Nov;25(11):1771-80. doi: 10.1101/gr.192518.115.

2014

  • Comprehensive Molecular Profiling of Lung Adenocarcinoma
    The Cancer Genome Atlas Research Network
    Nature, 511(7511):543-50. doi: 10.1038/nature13385
  • SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas
    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, Ligon KL, Liu XS, Marto JA, Meyerson M, Bass AJ
    J Clin Invest, 124(4):1636-1645. doi:10.1172/JCI71545
  • A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events
    Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinksi M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M
    PLOS ONE, 9(1): e87361. doi:10.1371/journal.pone.0087361

2012

  • Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing
    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 M S, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Janne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, and Meyerson M
    Cell, 150, 1107–1120

2011

  • Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans
    Brooks AN*, Aspden JL*, Podgornaia AI, Rio DC, Brenner SE
    RNA, Oct:17(10):1884-94
  • The Developmental Transcriptome of Drosophila melanogaster
    Graveley BR*, Brooks AN*, Carlson JW*, Duff MO*, Landolin J*, Yang L*, Arieri C, van Baren MJ, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin AD, Li R, Lin W, Mattiuzzo N, Miller D, Sturgill D, Tuch B, Zaleski C, Zhang D, Blancette M, Clough E, Dudoit S, Eads B, Green RE, Hammonds A, Kapranov P, Langton L, Malone J, Perrimon N, Sandler J, Wan K, Willingham A, Zhang Y, Zou Y , Andrews J, Brenner SE, Brent M, Cherbas P, Gingeras TR, Hoskins RA, Kaufman T, Oliver B, Celniker SE
    Nature, Mar 24;471(7339):473-9
  • Conservation of an RNA Regulatory Map between Drosophila and Mammals
    Brooks AN*, Yang L*, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, and Graveley BR
    Genome Research, 21:193-202

2010

  • Identification of functional elements and regulatory circuits by Drosophila modENCODE
    The modENCODE Consortium, 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, Robine N, Washington NL, Stefano LD, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyneko A, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov A, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine H, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell S, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz Y, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SCR, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda M, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russel S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M
    Science, 330 (6012):1787-1797

2009

  • Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members
    Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC
    Molecular Cell, 33(4):438-49

2007

  • Evolution of genes and genomes on the Drosophila phylogeny
    Drosophila 12 Genomes Consortium.
    Nature, 450(7167):203-18

2006

  • Structural basis for double- stranded RNA processing by Dicer
    Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA.
    Science, 311(5758):195-8

2005

  • The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
    Schattner P, Brooks AN, Lowe TM
    Nucleic Acids Research, 33 (Web Server issue): W686-9

* equal contribution

Additional Publications

2014

  • Breaking Down RET Breakpoints in Lung Adenocarcinoma
    Watanabe H, Brooks AN, Meyerson M
    J Thorac Oncol, 9(5):590-2 (editorial)

2013

  • The Cancer Genome Atlas Pan-Cancer analysis project
    Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM
    Nature Genetics, Oct;45(10):1113-20

2009

  • Unlocking the secrets of the genome
    modENCODE Consortium
    Nature, 459:927-930

2007

  • The coupling of alternative splicing and nonsense- mediated mRNA decay
    Lareau LF, Brooks AN, Soergel DA, Meng Q, Brenner SE
    Advances in Experimental Medicine and Biology, 623:190-211 (review)