Aaron McKenna - Publications

Affiliations: 
Genome Sciences University of Washington, Seattle, Seattle, WA 

56 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
2023 Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, et al. GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3 (Bethesda, Md.). PMID 37552705 DOI: 10.1093/g3journal/jkad177  0.492
2023 Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, et al. GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse ( ). Biorxiv : the Preprint Server For Biology. PMID 37066261 DOI: 10.1101/2023.04.03.535372  0.492
2022 Anderson DJ, Pauler FM, McKenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. PMID 35452605 DOI: 10.1016/j.cels.2022.03.006  0.524
2021 Brewer CM, Nelson BR, Wakenight P, Collins SJ, Okamura DM, Dong XR, Mahoney WM, McKenna A, Shendure J, Timms A, Millen KJ, Majesky MW. Adaptations in Hippo-Yap signaling and myofibroblast fate underlie scar-free ear appendage wound healing in spiny mice. Developmental Cell. PMID 34610329 DOI: 10.1016/j.devcel.2021.09.008  0.383
2021 Simeonov KP, Byrns CN, Clark ML, Norgard RJ, Martin B, Stanger BZ, Shendure J, McKenna A, Lengner CJ. Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states. Cancer Cell. PMID 34115987 DOI: 10.1016/j.ccell.2021.05.005  0.463
2019 Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure J. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic Acids Research. PMID 31165867 DOI: 10.1093/Nar/Gkz487  0.647
2018 McKenna A, Shendure J. FlashFry: a fast and flexible tool for large-scale CRISPR target design. Bmc Biology. 16: 74. PMID 29976198 DOI: 10.1186/S12915-018-0545-0  0.525
2018 Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nature Biotechnology. PMID 29608178 DOI: 10.1038/Nbt.4103  0.523
2017 Gasperini M, Findlay GM, McKenna A, Milbank JH, Lee C, Zhang MD, Cusanovich DA, Shendure J. CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions. American Journal of Human Genetics. PMID 28712454 DOI: 10.1016/J.Ajhg.2017.06.010  0.701
2017 Johnson CP, Kim IK, Esmaeli B, Amin-Mansour A, Treacy DJ, Carter SL, Hodis E, Wagle N, Seepo S, Yu X, Lane AM, Gragoudas ES, Vazquez F, Nickerson E, Cibulskis K, ... McKenna A, et al. Systematic genomic and translational efficiency studies of uveal melanoma. Plos One. 12: e0178189. PMID 28594900 DOI: 10.1371/Journal.Pone.0178189  0.462
2016 McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF, Shendure J. Whole organism lineage tracing by combinatorial and cumulative genome editing. Science (New York, N.Y.). PMID 27229144 DOI: 10.1126/Science.Aaf7907  0.566
2016 Allen EM, Robinson D, Morrissey C, Pritchard C, Imamovic A, Carter S, Rosenberg M, McKenna A, Wu YM, Cao X, Chinnaiyan A, Garraway L, Nelson PS. A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: Implications for precision cancer medicine. Oncotarget. PMID 27167109 DOI: 10.18632/Oncotarget.9184  0.494
2015 Brastianos PK, Carter SL, Santagata S, Cahill DP, Taylor-Weiner A, Jones RT, Van Allen EM, Lawrence MS, Horowitz PM, Cibulskis K, Ligon KL, Tabernero J, Seoane J, Martinez-Saez E, Curry WT, ... ... McKenna A, et al. Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. Cancer Discovery. PMID 26410082 DOI: 10.1158/2159-8290.Cd-15-0369  0.334
2015 Stachler MD, Taylor-Weiner A, Peng S, McKenna A, Agoston AT, Odze RD, Davison JM, Nason KS, Loda M, Leshchiner I, Stewart C, Stojanov P, Seepo S, Lawrence MS, Ferrer-Torres D, et al. Paired exome analysis of Barrett's esophagus and adenocarcinoma. Nature Genetics. 47: 1047-55. PMID 26192918 DOI: 10.1038/Ng.3343  0.456
2015 van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, ... ... McKenna A, et al. Prospective derivation of a living organoid biobank of colorectal cancer patients. Cell. 161: 933-45. PMID 25957691 DOI: 10.1016/J.Cell.2015.03.053  0.402
2015 Place CS, Kim IK, Esmaeli B, Amin-Mansour A, Treacy DJ, Carter SL, Hodis E, Wagle N, Seepo S, Yu X, Vazquez F, Nickerson E, Cibulskis K, McKenna A, Gabriel SB, et al. Abstract A1-15: Systematic genomic characterization of uveal melanoma Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-A1-15  0.482
2014 Perry JA, Kiezun A, Tonzi P, Van Allen EM, Carter SL, Baca SC, Cowley GS, Bhatt AS, Rheinbay E, Pedamallu CS, Helman E, Taylor-Weiner A, McKenna A, DeLuca DS, Lawrence MS, et al. Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Proceedings of the National Academy of Sciences of the United States of America. 111: E5564-73. PMID 25512523 DOI: 10.1073/Pnas.1419260111  0.484
2014 Crompton BD, Stewart C, Taylor-Weiner A, Alexe G, Kurek KC, Calicchio ML, Kiezun A, Carter SL, Shukla SA, Mehta SS, Thorner AR, de Torres C, Lavarino C, Suñol M, McKenna A, et al. The genomic landscape of pediatric Ewing sarcoma. Cancer Discovery. 4: 1326-41. PMID 25186949 DOI: 10.1158/2159-8290.Cd-13-1037  0.426
2014 Pugh TJ, Yu W, Yang J, Field AL, Ambrogio L, Carter SL, Cibulskis K, Giannikopoulos P, Kiezun A, Kim J, McKenna A, Nickerson E, Getz G, Hoffher S, Messinger YH, et al. Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences. Oncogene. 33: 5295-302. PMID 24909177 DOI: 10.1038/Onc.2014.150  0.368
2014 Van Allen EM, Wagle N, Stojanov P, Perrin DL, Cibulskis K, Marlow S, Jane-Valbuena J, Friedrich DC, Kryukov G, Carter SL, McKenna A, Sivachenko A, Rosenberg M, Kiezun A, Voet D, et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nature Medicine. 20: 682-8. PMID 24836576 DOI: 10.1038/Nm.3559  0.338
2014 McFadden DG, Papagiannakopoulos T, Taylor-Weiner A, Stewart C, Carter SL, Cibulskis K, Bhutkar A, McKenna A, Dooley A, Vernon A, Sougnez C, Malstrom S, Heimann M, Park J, Chen F, et al. Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. Cell. 156: 1298-311. PMID 24630729 DOI: 10.1016/J.Cell.2014.02.031  0.48
2014 Lohr JG, Stojanov P, Carter SL, Cruz-Gordillo P, Lawrence MS, Auclair D, Sougnez C, Knoechel B, Gould J, Saksena G, Cibulskis K, McKenna A, Chapman MA, Straussman R, Levy J, et al. Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy. Cancer Cell. 25: 91-101. PMID 24434212 DOI: 10.1016/J.Ccr.2013.12.015  0.453
2014 Ojesina AI, Lichtenstein L, Freeman SS, Pedamallu CS, Imaz-Rosshandler I, Pugh TJ, Cherniack AD, Ambrogio L, Cibulskis K, Bertelsen B, Romero-Cordoba S, Treviño V, Vazquez-Santillan K, Guadarrama AS, Wright AA, ... ... McKenna A, et al. Landscape of genomic alterations in cervical carcinomas. Nature. 506: 371-5. PMID 24390348 DOI: 10.1038/Nature12881  0.403
2014 Kim Y, Hammerman PS, Kim J, Yoon JA, Lee Y, Sun JM, Wilkerson MD, Pedamallu CS, Cibulskis K, Yoo YK, Lawrence MS, Stojanov P, Carter SL, McKenna A, Stewart C, et al. Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 32: 121-8. PMID 24323028 DOI: 10.1200/Jco.2013.50.8556  0.397
2014 Wagle N, Van Allen EM, Treacy DJ, Frederick DT, Cooper ZA, Taylor-Weiner A, Rosenberg M, Goetz EM, Sullivan RJ, Farlow DN, Friedrich DC, Anderka K, Perrin D, Johannessen CM, McKenna A, et al. MAP kinase pathway alterations in BRAF-mutant melanoma patients with acquired resistance to combined RAF/MEK inhibition. Cancer Discovery. 4: 61-8. PMID 24265154 DOI: 10.1158/2159-8290.Cd-13-0631  0.316
2014 Van Allen EM, Wagle N, Sucker A, Treacy DJ, Johannessen CM, Goetz EM, Place CS, Taylor-Weiner A, Whittaker S, Kryukov GV, Hodis E, Rosenberg M, Mckenna A, Cibulskis K, Farlow D, et al. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma Cancer Discovery. 4: 94-109. PMID 24265153 DOI: 10.1158/2159-8290.Cd-13-0617  0.336
2014 Crompton B, Stewart C, Taylor-Weiner A, Alexa G, Kurek K, Calicchio M, Kiezun A, Carter S, Shukla S, Mehta S, Thorner A, Torres Cd, Lavarino C, Sunol M, McKenna A, et al. Abstract 999: The genomic landscape of pediatric Ewing sarcoma Cancer Research. 74: 999-999. DOI: 10.1158/1538-7445.Am2014-999  0.496
2014 Brennan C, Verhaak R, McKenna A, Campos B, Noushmehr H, Salama S, Zheng S, Chakravarty D, Sanborn J, Berman S, Beroukhim R, Bernard B, Wu C, Genovese G, Shmulevich I, et al. The Somatic Genomic Landscape of Glioblastoma Cell. 157: 753. DOI: 10.1016/J.Cell.2014.04.004  0.379
2013 Francis JM, Kiezun A, Ramos AH, Serra S, Pedamallu CS, Qian ZR, Banck MS, Kanwar R, Kulkarni AA, Karpathakis A, Manzo V, Contractor T, Philips J, Nickerson E, Pho N, ... ... McKenna A, et al. Somatic mutation of CDKN1B in small intestine neuroendocrine tumors. Nature Genetics. 45: 1483-6. PMID 24185511 DOI: 10.1038/Ng.2821  0.412
2013 Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, et al. The somatic genomic landscape of glioblastoma. Cell. 155: 462-77. PMID 24120142 DOI: 10.1016/J.Cell.2013.09.034  0.483
2013 Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, Brennan CW, Yung WK, Weinstein JN, Aldape KD, Sulman EP, et al. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes & Development. 27: 1462-72. PMID 23796897 DOI: 10.1101/Gad.213686.113  0.458
2013 Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 499: 214-8. PMID 23770567 DOI: 10.1038/Nature12213  0.473
2013 Ramkissoon LA, Horowitz PM, Craig JM, Ramkissoon SH, Rich BE, Schumacher SE, McKenna A, Lawrence MS, Bergthold G, Brastianos PK, Tabak B, Ducar MD, Van Hummelen P, MacConaill LE, Pouissant-Young T, et al. Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1. Proceedings of the National Academy of Sciences of the United States of America. 110: 8188-93. PMID 23633565 DOI: 10.1073/Pnas.1300252110  0.375
2013 Dulak AM, Stojanov P, Peng S, Lawrence MS, Fox C, Stewart C, Bandla S, Imamura Y, Schumacher SE, Shefler E, McKenna A, Carter SL, Cibulskis K, Sivachenko A, Saksena G, et al. Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity. Nature Genetics. 45: 478-86. PMID 23525077 DOI: 10.1038/Ng.2591  0.503
2013 Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, Sougnez C, Stewart C, Sivachenko A, Wang L, Wan Y, Zhang W, Shukla SA, Vartanov A, Fernandes SM, et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell. 152: 714-26. PMID 23415222 DOI: 10.1016/J.Cell.2013.01.019  0.415
2013 Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell. 152: 633-41. PMID 23374354 DOI: 10.1016/J.Cell.2012.12.034  0.343
2013 Brastianos PK, Horowitz PM, Santagata S, Jones RT, McKenna A, Getz G, Ligon KL, Palescandolo E, Van Hummelen P, Ducar MD, Raza A, Sunkavalli A, Macconaill LE, Stemmer-Rachamimov AO, Louis DN, et al. Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations. Nature Genetics. 45: 285-9. PMID 23334667 DOI: 10.1038/Ng.2526  0.459
2013 Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, et al. The genetic landscape of high-risk neuroblastoma. Nature Genetics. 45: 279-84. PMID 23334666 DOI: 10.1038/Ng.2529  0.467
2013 Chmielecki J, Crago AM, Rosenberg M, O'Connor R, Walker SR, Ambrogio L, Auclair D, McKenna A, Heinrich MC, Frank DA, Meyerson M. Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors. Nature Genetics. 45: 131-2. PMID 23313954 DOI: 10.1038/Ng.2522  0.348
2013 Brastianos P, Horowitz PM, Santagata S, Jones RT, McKenna A, Getz G, Ligon K, Hummelen PV, Ducar M, Raza A, Sunkavalli A, MacConaill L, Stemmer-Rachamimov A, Louis DN, Hahn WC, et al. Abstract 803: Genomic sequencing of meningiomas reveals oncogenic SMO and AKT1 mutations. Cancer Research. 73: 803-803. DOI: 10.1158/1538-7445.Am2013-803  0.486
2013 Carter SL, Landau D, Stojanov P, McKenna A, Cibulskis K, Lawrence MS, Lohr J, Stevenson K, Neuberg D, Meyerson M, Wu CJ, Getz G. Abstract 4600: Analysis of clonal evolution in cancer using whole exome sequence data reveals that subclonal driver mutations predict poor prognosis in chronic lymphocytic leukemia. Cancer Research. 73: 4600-4600. DOI: 10.1158/1538-7445.Am2013-4600  0.445
2013 Pugh TJ, Yu W, Yang J, Ambrogio L, Carter SL, Kiezun A, McKenna A, Giannikopoulos P, Getz G, Messinger Y, Meyerson M, Hill DA. Abstract 3806: Progressive biallelic loss of TP53 is associated with progression of pleuropulmonary blastoma initiated by germline loss and somatic mutation of DICER1. Cancer Research. 73: 3806-3806. DOI: 10.1158/1538-7445.Am2013-3806  0.446
2013 Allen EMV, Wagle N, Keizun A, Kryukov G, McKenna A, Huang F, Hiller E, Rainville I, Auclair D, Ambrogio L, Gray S, Joffe S, Getz G, Garber J, Garraway L. Abstract 2570: An integrated germline analysis platform for comprehensive clinical cancer genomics. Cancer Research. 73: 2570-2570. DOI: 10.1158/1538-7445.Am2013-2570  0.419
2013 Horowitz P, Brastianos P, Santagata S, Jones R, McKenna A, Getz G, Ligon K, Palescandolo E, Ducar M, MacConaill L, Stemmer-Rachamimov A. Novel Oncogenic SMO and AKT1 Mutations in Meningiomas Journal of Neurological Surgery Part B: Skull Base. 74. DOI: 10.1055/S-0033-1336194  0.384
2012 Hammerman PS, Voet D, Lawrence MS, Jing R, Cibulskis K, Sivachenko A, Stojanov P, McKenna A, Lander ES, Gabriel S, Getz G, Imielinski M, Helman E, Hernandez B, Pho NH, et al. Comprehensive genomic characterization of squamous cell lung cancers Nature. 489: 519-525. PMID 22960745 DOI: 10.1038/Nature11404  0.442
2012 Pugh TJ, Weeraratne SD, Archer TC, Pomeranz Krummel DA, Auclair D, Bochicchio J, Carneiro MO, Carter SL, Cibulskis K, Erlich RL, Greulich H, Lawrence MS, Lennon NJ, McKenna A, Meldrim J, et al. Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature. 488: 106-10. PMID 22820256 DOI: 10.1038/Nature11329  0.468
2012 Muzny DM, Bainbridge MN, Chang K, Dinh HH, Drummond JA, Fowler G, Kovar CL, Lewis LR, Morgan MB, Newsham IF, Reid JG, Santibanez J, Shinbrot E, Trevino LR, Wu YQ, ... ... McKenna A, et al. Comprehensive molecular characterization of human colon and rectal cancer Nature. 487: 330-337. PMID 22810696 DOI: 10.1038/Nature11252  0.503
2012 Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, et al. Absolute quantification of somatic DNA alterations in human cancer. Nature Biotechnology. 30: 413-21. PMID 22544022 DOI: 10.1038/Nbt.2203  0.483
2012 Brastianos PK, Horowitz P, Santagata S, Jones RT, McKenna A, Ligon K, Palescandolo E, Van Hummelen P, Getz G, Hahn WC, Dunn IF, Beroukhim R. Genomic characterization of meningiomas. Journal of Clinical Oncology. 30: 2020-2020. DOI: 10.1200/Jco.2012.30.15_Suppl.2020  0.477
2012 Landau D, Carter S, Stojanov P, Stevenson KE, Mckenna A, Lawrence M, Sougnez C, Sivachenko A, Wang L, Zhang W, Sachet S, Vartanov AR, Fernandes SM, Cibulskis K, Tesar B, et al. The Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia Blood. 120: 5-5. DOI: 10.1182/Blood.V120.21.5.5  0.433
2012 Hodis E, Watson I, Theurillat J, Zou L, Place C, Nickerson E, Auclair D, Cibulskis K, Sivachenko A, Kryukov G, Stransky N, Ramos AH, Voet D, Lawrence MS, Stojanov P, ... ... McKenna A, et al. Abstract 5056: A glimpse into the somatic mutation landscape of melanoma through exome sequencing of 121 tumor-normal pairs Cancer Research. 72: 5056-5056. DOI: 10.1158/1538-7445.Am2012-5056  0.487
2011 Cibulskis K, McKenna A, Fennell T, Banks E, DePristo M, Getz G. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics (Oxford, England). 27: 2601-2. PMID 21803805 DOI: 10.1093/Bioinformatics/Btr446  0.334
2011 Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence MS, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, et al. The mutational landscape of head and neck squamous cell carcinoma. Science (New York, N.Y.). 333: 1157-60. PMID 21798893 DOI: 10.1126/Science.1208130  0.461
2011 DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics. 43: 491-8. PMID 21478889 DOI: 10.1038/Ng.806  0.397
2011 Cibulskis K, McKenna A, Fennell T, Getz G. Abstract 48: Detecting and controlling for physical contamination in next-generation sequencing cancer studies Cancer Research. 71: 48-48. DOI: 10.1158/1538-7445.Am2011-48  0.441
2005 El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran AN, Ghedin E, Worthey EA, Delcher AL, Blandin G, Westenberger SJ, Caler E, Cerqueira GC, Branche C, Haas B, ... ... McKenna A, et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (New York, N.Y.). 309: 409-15. PMID 16020725 DOI: 10.1126/Science.1112631  0.309
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