Publications

Preprints

2024

• Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing
  Bai G*, Dhillon N*, Felton C*, Meissner B*, Saint-John B*, Shelansky R*, Meyerson E, Hrabeta-Robinson E, Hodjat B, Boeger H#, Brooks AN#. *equal contribution, #co-corresponding. bioRxiv [Preprint]. 2024 Mar 22:2024.03.20.585815. doi: https://doi.org/10.1101/2024.03.20.585815

2023

• Detection of alternative isoforms of gene fusions from long-read RNA-seq with FLAIR-fusion
  Colette Felton, Alison D Tang, Binyamin A Knisbacher, Catherine J Wu, Angela N Brooks
  bioRxiv 2022.08.01.502364; doi: https://doi.org/10.1101/2022.08.01.502364

2022

• Identification of cancer drivers from tumor-only RNA-seq with RNA-VACAY
  Jon Akutagawa, Allysia J Mak, Julie L Aspden, Angela N Brooks
  bioRxiv 2022.05.10.491431; doi: https://doi.org/10.1101/2022.05.10.491431

Peer-Reviewed

2024

• Detecting haplotype-specific transcript variation in long reads with FLAIR2
  Tang AD, Felton C, Hrabeta-Robinson E, Volden R, Vollmers C, Brooks AN. Genome Biol. 2024 Jul 2;25(1):173. doi: 10.1186/s13059-024-03301-y. PMID: 38956576; PMCID: PMC11218413. [link]
• Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
  Pardo-Palacios FJ*, Wang D*, Reese F*, Diekhans M*, Carbonell-Sala S*, Williams B*, Loveland JE**, De María M**, Adams MS**, Balderrama-Gutierrez G**, Behera AK**, Gonzalez JM**, Hunt T**, Lagarde J**, Liang CE**, Li H**, Sheynkman L**, Prjibelski AD**, Jerryd Meade M, Moraga Amador, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C#, Frankish A#, Fai Au K#, Sheynkman GM#, Mortazavi A#, Conesa A#, Brooks AN#. *equal contribution, **equal contribution, #co-corresponding. Nat Methods. 2024 Jun 7. doi: 10.1038/s41592-024-02298-3. PMID: 37546854; PMCID: PMC10402094. [link]

2023

• Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations
  Soulette CM, Hrabeta-Robinson E, Arevalo C, Felton C, Tang AD, Marin MG, Brooks AN. Life Sci Alliance. 2023 Jul 24;6(10):e202000641. doi: 10.26508/lsa.202000641 [link]

Micropublications

• MET exon 14 skipping is overexpressed in an allele-specific manner in lung adenocarcinoma primary samples
  Durham M, Vadde S, Brooks AN. microPublication Biology. 10.17912/micropub.biology.000957 [link]

2022

• An expression-based variant impact phenotyping protocol to predict the impact of gene variants in cell lines
  Thornton AM, Tumu M, Brooks AN. STAR Protocols 2022. https://doi.org/10.1016/j.xpro.2022.101651 [link]

• Cell Painting predicts impact of lung cancer variants
  Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, Singh S. Mol Biol Cell. 2022 May 15;33(6):ar49. doi: 10.1091/mbc.E21-11-0538. Epub 2022 Mar 30. PMID: 35353015. [link]

• SRSF1 governs progenitor-specific alternative splicing to maintain adult epithelial tissue homeostasis and renewal
  Yu T, Cazares O, Tang AD, Kim HY, Wald T, Verma A, Liu Q, Barcellos-Hoff MH, Floor SN, Jung HS, Brooks AN, Klein OD. Dev Cell. 2022 Feb 22:S1534-5807(22)00036-3. doi: 10.1016/j.devcel.2022.01.011.PMID: 35202586. [link]

2021

• eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants
  Thornton AM, Fang L, Lo A, McSharry M, Haan D, O’Brien C, Berger AH*, Giannakis M*, Brooks AN*#. PLoS Comput Biol. 2021 Jul 2;17(7):e1009132. doi: 10.1371/journal.pcbi.1009132. PMID: 34214079; PMCID: PMC8281988. *co-senior, #corresponding [link]

• Inflammation Drives Alternative First Exon usage to Regulate Immune Genes including a Novel Iron Regulated Isoform of Aim2
  Robinson EK*, Jagannatha P*, Covarrubias S, Cattle M, Smaliy V, Safavi R, Shapleigh B, Abu-Shumays R, Jain M, Cloonan SM, Akeson M, Brooks AN#, Carpenter S#. Elife. 2021 May 28;10:e69431. doi: 10.7554/eLife.69431. PMID: 34047695; PMCID: PMC8260223. *equal contribution, #co-corresponding [link]
• Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment.
  Trujillo CA, Rice ES, Schaefer NK, Chaim IA, Wheeler EC, Madrigal AA, Buchanan J, Preissl S, Wang A, Negraes PD, Szeto RA, Herai RH, Huseynov A, Ferraz MSA, Borges FS, Kihara AH, Byrne A, Marin M, Vollmers C, Brooks AN, Lautz JD, Semendeferi K, Shapiro B, Yeo GW, Smith SEP, Green RE, Muotri AR. Science. 2021 Feb 12;371(6530):eaax2537. doi: 10.1126/science.aax2537. PMID: 33574182; PMCID: PMC8006534. [link]

2020

• Visualizing and interpreting cancer genomics data via the Xena platform.
  Goldman MJ, Craft B, Hastie M, Repečka K, McDade F, Kamath A, Banerjee A, Luo Y, Rogers D, Brooks AN, Zhu J, Haussler D. Nat Biotechnol. 2020 Jun;38(6):675-678. doi: 10.1038/s41587-020-0546-8. PMID: 32444850. [link]

• Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma
  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 3rd, Wolf JL, Wong SW, Shah N, Hann B, Brooks AN, Wiita AP.  Nat Commun. 2020 Apr 22;11(1):1931. doi: 10.1038/s41467-020-15521-4. PMID: 32321912; PMCID: PMC7176739. [link]

• Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns
  Tang AD, Soulette CM, van Baren MJ, Hart K, Hrabeta-Robinson E, Wu CJ, Brooks AN.
  Nature Communications. 2020 Mar 18;11(1):1438. doi: 10.1038/s41467-020-15171-6. [link]

• Genomic basis for RNA alterations in cancer
  PCAWG Transcriptome Core Group*, 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, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A§**, Brooks AN§**, Göke J**, Rätsch G§**, Schwarz RF**, Stegle O**, Zhang Z**; PCAWG Consortium. *equal contribution, **co-senior, §co-corresponding Nature. 2020 Feb;578(7793):129-136. doi: 10.1038/s41586-020-1970-0. [link]

2019

• Nanopore native RNA sequencing of a human poly(A) transcriptome
  Rachael E. Workman*, Alison D. Tang*, Paul S. Tang*, Miten Jain*, John R. Tyson*, Roham Razaghi*, Philip C. Zuzarte, Timothy Gilpatrick, Alexander Payne, Joshua Quick, Norah Sadowski, Nadine Holmes, Jaqueline Goes de Jesus, Karen L. Jones, Cameron M. Soulette, Terrance P. Snutch, Nicholas Loman, Benedict Paten, Matthew Loose, Jared T. Simpson, Hugh E. Olsen**, Angela N. Brooks**, Mark Akeson**#, Winston Timp**# *Contributed equally to the work, **Co-lead the project, #Corresponding authors.
  Nature Methods. 2019 Dec; 16(12):1297-1305. doi: 10.1038/s41592-019-0617-2 [link]

• A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters
  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.
  Cell. 2019 Sep 5; 178(6):1465-1477.e17. doi: 10.1016/j.cell.2019.08.018. [link]

• A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion
  Yin S, Gambe RG, Sun J, Martinez AZ, Cartun ZJ, Regis FFD, Wan Y, Fan J, Brooks AN, Herman SEM, Ten Hacken E, Taylor-Weiner A, Rassenti LZ, Ghia EM, Kipps TJ, Obeng EA, Cibulskis CL, Neuberg D, Campagna DR, Fleming MD, Ebert BL, Wiestner A, Leshchiner I, DeCaprio JA, Getz G, Reed R, Carrasco RD, Wu CJ, Wang L
  Cancer Cell. 2019 Feb 11;35(2):283-296.e5. doi: 10.1016/j.ccell.2018.12.013. [link]

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. [link]

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)