Publications


Peer-Reviewed

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)