Cyriac Kandoth

Title(s)Assistant Adjunct Professor, Pathology and Laboratory Medicine
SchoolMedicine
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline. bioRxiv. 2024 Sep 07. Patel Y, Zhu C, Yamaguchi TN, Wang NK, Wiltsie N, Gonzalez AE, Winata HK, Zeltser N, Pan Y, Mootor MFE, Sanders T, Kandoth C, Fitz-Gibbon ST, Livingstone J, Liu LY, Carlin B, Holmes A, Oh J, Sahrmann J, Tao S, Eng S, Hugh-White R, Pashminehazar K, Park A, Beshlikyan A, Jordan M, Wu S, Tian M, Arbet J, Neilsen B, Bugh YZ, Kim G, Salmingo J, Zhang W, Haas R, Anand A, Hwang E, Neiman-Golden A, Steinberg P, Zhao W, Anand P, Tsai BL, Boutros PC. PMID: 39282325; PMCID: PMC11398472.
      View in: PubMed   Mentions:
    2. Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. JCO Clin Cancer Inform. 2022 02; 6:e2100144. de Bruijn I, Li X, Sumer SO, Gross B, Sheridan R, Ochoa A, Wilson M, Wang A, Zhang H, Lisman A, Abeshouse A, Zhang E, Thum A, Sadagopan A, Heins Z, Kandoth C, Rodenburg S, Tan S, Lukasse P, van Hagen S, Fijneman RJA, Meijer GA, Schultz N, Gao J. PMID: 35148171; PMCID: PMC8846305.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    3. Recurrent Mutations in Cyclin D3 Confer Clinical Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia. Clin Cancer Res. 2021 07 15; 27(14):4003-4011. Smith CC, Viny AD, Massi E, Kandoth C, Socci ND, Rapaport F, Najm M, Medina-Martinez JS, Papaemmanuil E, Tarver TC, Hsu HH, Le MH, West B, Bollag G, Taylor BS, Levine RL, Shah NP. PMID: 34103301; PMCID: PMC8282743.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    4. Poor survival after resection of early gastric cancer: extremes of survivorship analysis reveal distinct genomic profile. Br J Surg. 2020 01; 107(1):14-19. Datta J, Da Silva EM, Kandoth C, Song T, Russo AE, Hernandez JM, Taylor BS, Janjigian YY, Tang LH, Solit DB, Strong VE. PMID: 31763684; PMCID: PMC7453628.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    5. Coaltered Ras/B-raf and TP53 Is Associated with Extremes of Survivorship and Distinct Patterns of Metastasis in Patients with Metastatic Colorectal Cancer. Clin Cancer Res. 2020 03 01; 26(5):1077-1085. Datta J, Smith JJ, Chatila WK, McAuliffe JC, Kandoth C, Vakiani E, Frankel TL, Ganesh K, Wasserman I, Lipsyc-Sharf M, Guillem J, Nash GM, Paty PB, Weiser MR, Saltz LB, Berger MF, Jarnagin WR, Balachandran V, Kingham TP, Kemeny NE, Cercek A, Garcia-Aguilar J, Taylor BS, Viale A, Yaeger R, Solit DB, Schultz N, D'Angelica MI. PMID: 31719050; PMCID: PMC7056517.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    6. GNAQ Mutations in Diffuse and Solitary Choroidal Hemangiomas. Ophthalmology. 2019 05; 126(5):759-763. Francis JH, Milman T, Grossniklaus H, Albert D, Folberg R, Levitin G, Coupland S, Catalanotti F, Rabady D, Kandoth C, Busam K, Abramson D. PMID: 30537484; PMCID: PMC8425501.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    7. Regional differences in gallbladder cancer pathogenesis: Insights from a multi-institutional comparison of tumor mutations. Cancer. 2019 02 15; 125(4):575-585. Narayan RR, Creasy JM, Goldman DA, Gönen M, Kandoth C, Kundra R, Solit DB, Askan G, Klimstra DS, Basturk O, Allen PJ, Balachandran VP, D'Angelica MI, DeMatteo RP, Drebin JA, Kingham TP, Simpson AL, Abou-Alfa GK, Harding JJ, O'Reilly EM, Butte JM, Matsuyama R, Endo I, Jarnagin WR. PMID: 30427539; PMCID: PMC6636637.
      View in: PubMed   Mentions: 25     Fields:    Translation:Humans
    8. The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers. Cancer Cell. 2018 09 10; 34(3):427-438.e6. Razavi P, Chang MT, Xu G, Bandlamudi C, Ross DS, Vasan N, Cai Y, Bielski CM, Donoghue MTA, Jonsson P, Penson A, Shen R, Pareja F, Kundra R, Middha S, Cheng ML, Zehir A, Kandoth C, Patel R, Huberman K, Smyth LM, Jhaveri K, Modi S, Traina TA, Dang C, Zhang W, Weigelt B, Li BT, Ladanyi M, Hyman DM, Schultz N, Robson ME, Hudis C, Brogi E, Viale A, Norton L, Dickler MN, Berger MF, Iacobuzio-Donahue CA, Chandarlapaty S, Scaltriti M, Reis-Filho JS, Solit DB, Taylor BS, Baselga J. PMID: 30205045; PMCID: PMC6327853.
      View in: PubMed   Mentions: 461     Fields:    Translation:HumansCells
    9. Genetic and epigenetic evolution as a contributor to WT1-mutant leukemogenesis. Blood. 2018 09 20; 132(12):1265-1278. Pronier E, Bowman RL, Ahn J, Glass J, Kandoth C, Merlinsky TR, Whitfield JT, Durham BH, Gruet A, Hanasoge Somasundara AV, Rampal R, Melnick A, Koche RP, Taylor BS, Levine RL. PMID: 30064973; PMCID: PMC6148447.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    10. Integrative omics analyses broaden treatment targets in human cancer. Genome Med. 2018 07 27; 10(1):60. Sengupta S, Sun SQ, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, Payne SH, Fenyö D, Townsend RR, Dipersio JF, Chen F, Ding L. PMID: 30053901; PMCID: PMC6064051.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    11. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 04 05; 173(2):321-337.e10. Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. PMID: 29625050; PMCID: PMC6070353.
      View in: PubMed   Mentions: 1387     Fields:    Translation:HumansCells
    12. Tumor Evolution and Drug Response in Patient-Derived Organoid Models of Bladder Cancer. Cell. 2018 04 05; 173(2):515-528.e17. Lee SH, Hu W, Matulay JT, Silva MV, Owczarek TB, Kim K, Chua CW, Barlow LJ, Kandoth C, Williams AB, Bergren SK, Pietzak EJ, Anderson CB, Benson MC, Coleman JA, Taylor BS, Abate-Shen C, McKiernan JM, Al-Ahmadie H, Solit DB, Shen MM. PMID: 29625057; PMCID: PMC5890941.
      View in: PubMed   Mentions: 354     Fields:    Translation:HumansAnimalsCells
    13. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 03 28; 6(3):271-281.e7. Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L, MC3 Working Group, Cancer Genome Atlas Research Network. PMID: 29596782; PMCID: PMC6075717.
      View in: PubMed   Mentions: 420     Fields:    Translation:Humans
    14. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell. 2018 01 08; 33(1):151. Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT, TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. PMID: 29316429.
      View in: PubMed   Mentions: 57     Fields:    
    15. Accelerating Discovery of Functional Mutant Alleles in Cancer. Cancer Discov. 2018 02; 8(2):174-183. Chang MT, Bhattarai TS, Schram AM, Bielski CM, Donoghue MTA, Jonsson P, Chakravarty D, Phillips S, Kandoth C, Penson A, Gorelick A, Shamu T, Patel S, Harris C, Gao J, Sumer SO, Kundra R, Razavi P, Li BT, Reales DN, Socci ND, Jayakumaran G, Zehir A, Benayed R, Arcila ME, Chandarlapaty S, Ladanyi M, Schultz N, Baselga J, Berger MF, Rosen N, Solit DB, Hyman DM, Taylor BS. PMID: 29247016; PMCID: PMC5809279.
      View in: PubMed   Mentions: 195     Fields:    Translation:Humans
    16. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell. 2017 08 14; 32(2):204-220.e15. Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT, TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. PMID: 28810145; PMCID: PMC5619925.
      View in: PubMed   Mentions: 393     Fields:    Translation:HumansCells
    17. Patterns and functional implications of rare germline variants across 12 cancer types. Nat Commun. 2015 Dec 22; 6:10086. Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, Dipersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L. PMID: 26689913; PMCID: PMC4703835.
      View in: PubMed   Mentions: 160     Fields:    Translation:Humans
    18. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun. 2015 Dec 09; 6:10001. Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG. PMID: 26647970; PMCID: PMC4682041.
      View in: PubMed   Mentions: 156     Fields:    Translation:Humans
    19. Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Nat Biotechnol. 2016 Feb; 34(2):155-63. Chang MT, Asthana S, Gao SP, Lee BH, Chapman JS, Kandoth C, Gao J, Socci ND, Solit DB, Olshen AB, Schultz N, Taylor BS. PMID: 26619011; PMCID: PMC4744099.
      View in: PubMed   Mentions: 420     Fields:    Translation:Humans
    20. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 08; 163(2):506-19. Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA, TCGA Research Network, Perou CM. PMID: 26451490; PMCID: PMC4603750.
      View in: PubMed   Mentions: 962     Fields:    Translation:HumansCells
    21. Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015 Jul; 11(7):e1004274. Griffith M, Griffith OL, Smith SM, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK. PMID: 26158448; PMCID: PMC4497734.
      View in: PubMed   Mentions: 54     Fields:    Translation:Humans
    22. Transcriptomic Responses of the Heart and Brain to Anoxia in the Western Painted Turtle. PLoS One. 2015; 10(7):e0131669. Keenan SW, Hill CA, Kandoth C, Buck LT, Warren DE. PMID: 26147940; PMCID: PMC4493013.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    23. Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma. Pac Symp Biocomput. 2015; 44-55. Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G. PMID: 25592567; PMCID: PMC4333684.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    24. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14; 158(4):929-944. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MDM, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. PMID: 25109877; PMCID: PMC4152462.
      View in: PubMed   Mentions: 746     Fields:    Translation:HumansCells
    25. Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun. 2014; 5:3156. Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L. PMID: 24448499; PMCID: PMC4025965.
      View in: PubMed   Mentions: 164     Fields:    Translation:HumansCells
    26. Mutational landscape and significance across 12 major cancer types. Nature. 2013 Oct 17; 502(7471):333-339. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MDM, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L. PMID: 24132290; PMCID: PMC3927368.
      View in: PubMed   Mentions: 2277     Fields:    Translation:HumansCells
    27. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep. 2013 Oct 02; 3:2650. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N. PMID: 24084849; PMCID: PMC3788361.
      View in: PubMed   Mentions: 297     Fields:    Translation:HumansCells
    28. Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. Nat Genet. 2013 Oct; 45(10):1121-6. Omberg L, Ellrott K, Yuan Y, Kandoth C, Wong C, Kellen MR, Friend SH, Stuart J, Liang H, Margolin AA. PMID: 24071850; PMCID: PMC3950337.
      View in: PubMed   Mentions: 66     Fields:    Translation:Humans
    29. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 02; 497(7447):67-73. Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. PMID: 23636398; PMCID: PMC3704730.
      View in: PubMed   Mentions: 2302     Fields:    Translation:HumansCells
    30. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013 05 30; 368(22):2059-74. Cancer Genome Atlas Research Network, Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G. PMID: 23634996; PMCID: PMC3767041.
      View in: PubMed   Mentions: 2528     Fields:    Translation:HumansCells
    31. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet. 2013 Jun; 45(6):602-12. Zhang J, Wu G, Miller CP, Tatevossian RG, Dalton JD, Tang B, Orisme W, Punchihewa C, Parker M, Qaddoumi I, Boop FA, Lu C, Kandoth C, Ding L, Lee R, Huether R, Chen X, Hedlund E, Nagahawatte P, Rusch M, Boggs K, Cheng J, Becksfort J, Ma J, Song G, Li Y, Wei L, Wang J, Shurtleff S, Easton J, Zhao D, Fulton RS, Fulton LL, Dooling DJ, Vadodaria B, Mulder HL, Tang C, Ochoa K, Mullighan CG, Gajjar A, Kriwacki R, Sheer D, Gilbertson RJ, Mardis ER, Wilson RK, Downing JR, Baker SJ, Ellison DW, St. Jude Children’s Research Hospital–Washington University Pediatric Cancer Genome Project. PMID: 23583981; PMCID: PMC3727232.
      View in: PubMed   Mentions: 421     Fields:    Translation:HumansAnimalsCells
    32. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol. 2013 Mar 28; 14(3):R28. Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. PMID: 23537068; PMCID: PMC4054807.
      View in: PubMed   Mentions: 126     Fields:    Translation:HumansAnimalsCells
    33. Clonal diversity of recurrently mutated genes in myelodysplastic syndromes. Leukemia. 2013 Jun; 27(6):1275-82. Walter MJ, Shen D, Shao J, Ding L, White BS, Kandoth C, Miller CA, Niu B, McLellan MD, Dees ND, Fulton R, Elliot K, Heath S, Grillot M, Westervelt P, Link DC, DiPersio JF, Mardis E, Ley TJ, Wilson RK, Graubert TA. PMID: 23443460; PMCID: PMC3736571.
      View in: PubMed   Mentions: 151     Fields:    Translation:Humans
    34. Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Nat Commun. 2013; 4:2730. Hamilton MP, Rajapakshe K, Hartig SM, Reva B, McLellan MD, Kandoth C, Ding L, Zack TI, Gunaratne PH, Wheeler DA, Coarfa C, McGuire SE. PMID: 24220575; PMCID: PMC3868236.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansCells
    35. Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. Genome Res. 2013 Mar; 23(3):431-9. Gutmann DH, McLellan MD, Hussain I, Wallis JW, Fulton LL, Fulton RS, Magrini V, Demeter R, Wylie T, Kandoth C, Leonard JR, Guha A, Miller CA, Ding L, Mardis ER. PMID: 23222849; PMCID: PMC3589532.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    36. The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012 Jul 20; 150(2):264-78. Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, Hundal J, Cook LL, Swift GW, Reed JP, Alldredge PA, Wylie TN, Walker JR, Watson MA, Heath SE, Shannon WD, Varghese N, Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, DiPersio JF, Ding L, Mardis ER, Wilson RK. PMID: 22817890; PMCID: PMC3407563.
      View in: PubMed   Mentions: 821     Fields:    Translation:HumansCells
    37. MuSiC: identifying mutational significance in cancer genomes. Genome Res. 2012 Aug; 22(8):1589-98. Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L. PMID: 22759861; PMCID: PMC3409272.
      View in: PubMed   Mentions: 364     Fields:    Translation:Humans
    38. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012 Jun 10; 486(7403):353-60. Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER. PMID: 22722193; PMCID: PMC3383766.
      View in: PubMed   Mentions: 549     Fields:    Translation:HumansCells
    39. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics. 2012 Jul 15; 28(14):1923-4. Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, Jones SJ, Marra MA, Ley TJ, Mardis ER, Wilson RK, Weinstein JN, Ding L. PMID: 22563071; PMCID: PMC3389765.
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    40. PathScan: a tool for discerning mutational significance in groups of putative cancer genes. Bioinformatics. 2011 Jun 15; 27(12):1595-602. Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L. PMID: 21498403; PMCID: PMC3106187.
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    41. Recurrent DNMT3A mutations in patients with myelodysplastic syndromes. Leukemia. 2011 Jul; 25(7):1153-8. Walter MJ, Ding L, Shen D, Shao J, Grillot M, McLellan M, Fulton R, Schmidt H, Kalicki-Veizer J, O'Laughlin M, Kandoth C, Baty J, Westervelt P, DiPersio JF, Mardis ER, Wilson RK, Ley TJ, Graubert TA. PMID: 21415852; PMCID: PMC3202965.
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    42. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010 Dec 16; 363(25):2424-33. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O'Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, Swift GW, Reed JP, Alldredge PA, Wylie T, Walker J, Kalicki J, Watson MA, Heath S, Shannon WD, Varghese N, Nagarajan R, Westervelt P, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Wilson RK. PMID: 21067377; PMCID: PMC3201818.
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    43. A framework for automated enrichment of functionally significant inverted repeats in whole genomes. BMC Bioinformatics. 2010 Oct 07; 11 Suppl 6:S20. Kandoth C, Ercal F, Frank RL. PMID: 20946604; PMCID: PMC3026368.
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    44. Validation of an NSP-based (negative selection pattern) gene family identification strategy. BMC Bioinformatics. 2008 Aug 12; 9 Suppl 9:S2. Frank RL, Kandoth C, Ercal F. PMID: 18793465; PMCID: PMC2537573.
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