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LaFramboise Lab

Publications

Publications

1: Somasundaram S, Forrest ME, Moinova H, Cohen A, Varadan V, LaFramboise T, Markowitz S, Khalil AM. The DNMT1-associated lincRNA DACOR1 reprograms genome-wide DNA methylation in colon cancer. Clin Epigenetics. 2018 Oct 22;10(1):127. doi: 10.1186/s13148-018-0555-3. PubMed PMID: 30348202; PubMed Central PMCID: PMC6196572.

2: Nagata Y, Narumi S, Guan Y, Przychodzen BP, Hirsch CM, Makishima H, Shima H, Aly M, Pastor V, Kuzmanovic T, Radivoyevitch T, Adema V, Awada H, Yoshida K, Li S, Sole F, Hanna R, Jha BK, LaFramboise T, Ogawa S, Sekeres MA, Wlodarski MW, Cammenga J, Maciejewski JP. Germline loss-of-function SAMD9 and SAMD9L alterations in adult myelodysplastic syndromes. Blood. 2018 Nov 22;132(21):2309-2313. doi: 10.1182/blood-2017-05-787390. Epub 2018 Oct 15. PubMed PMID: 30322869; PubMed Central PMCID: PMC6251008.

3: Grandhi S, Gould L, Wang J, Grandhi A, LaFramboise T. Mitochondrial genomics in the cancer cell line encyclopedia and a scoring method to effectively pair cell lines for cytoplasmic hybridization. Mitochondrion. 2018 Jul 31. pii: S1567-7249(17)30330-6. doi: 10.1016/j.mito.2018.07.005. [Epub ahead of print] PubMed PMID: 30075297.

4: Hirsch CM, Nazha A, Kneen K, Abazeed ME, Meggendorfer M, Przychodzen BP, Nadarajah N, Adema V, Nagata Y, Goyal A, Awada H, Asad MF, Visconte V, Guan Y, Sekeres MA, Olinski R, Jha BK, LaFramboise T, Radivoyevitch T, Haferlach T, Maciejewski JP. Consequences of mutant TET2 on clonality and subclonal hierarchy. Leukemia. 2018 Aug;32(8):1751-1761. doi: 10.1038/s41375-018-0150-9. Epub 2018 May 24. PubMed PMID: 29795413.

5: Forrest ME, Saiakhova A, Beard L, Buchner DA, Scacheri PC, LaFramboise T, Markowitz S, Khalil AM. Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis. Sci Rep. 2018 May 9;8(1):7324. doi: 10.1038/s41598-018-25530-5. PubMed PMID: 29743621; PubMed Central PMCID: PMC5943353.

6: Yehia L, Ni Y, Sesock K, Niazi F, Fletcher B, Chen HJL, LaFramboise T, Eng C. Unexpected cancer-predisposition gene variants in Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome patients without underlying germline PTEN mutations. PLoS Genet. 2018 Apr 23;14(4):e1007352. doi: 10.1371/journal.pgen.1007352. eCollection 2018 Apr. PubMed PMID: 29684080; PubMed Central PMCID: PMC5933810.

7: Moinova HR, LaFramboise T, Lutterbaugh JD, Chandar AK, Dumot J, Faulx A, Brock W, De la Cruz Cabrera O, Guda K, Barnholtz-Sloan JS, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Thota PN, Willis JE, Chak A, Markowitz SD. Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett's esophagus. Sci Transl Med. 2018 Jan 17;10(424). pii: eaao5848. doi: 10.1126/scitranslmed.aao5848. PubMed PMID: 29343623; PubMed Central PMCID: PMC5789768.

8: Bosworth CM, Grandhi S, Gould MP, LaFramboise T. Detection and quantification of mitochondrial DNA deletions from next-generation sequence data. BMC Bioinformatics. 2017 Oct 16;18(Suppl 12):407. doi: 10.1186/s12859-017-1821-7. PubMed PMID: 29072135; PubMed Central PMCID: PMC5657046.

9: Patel BJ, Przychodzen B, Thota S, Radivoyevitch T, Visconte V, Kuzmanovic T, Clemente M, Hirsch C, Morawski A, Souaid R, Saygin C, Nazha A, Demarest B, LaFramboise T, Sakaguchi H, Kojima S, Carraway HE, Ogawa S, Makishima H, Sekeres MA, Maciejewski JP. Genomic determinants of chronic myelomonocytic leukemia. Leukemia. 2017 Dec;31(12):2815-2823. doi: 10.1038/leu.2017.164. Epub 2017 May 30. PubMed PMID: 28555081.

10: Grandhi S, Bosworth C, Maddox W, Sensiba C, Akhavanfard S, Ni Y, LaFramboise T. Heteroplasmic shifts in tumor mitochondrial genomes reveal tissue-specific signals of relaxed and positive selection. Hum Mol Genet. 2017 Aug 1;26(15):2912-2922. doi: 10.1093/hmg/ddx172. PubMed PMID: 28475717; PubMed Central PMCID: PMC5886292.

11: Kenny TC, Hart P, Ragazzi M, Sersinghe M, Chipuk J, Sagar MAK, Eliceiri KW, LaFramboise T, Grandhi S, Santos J, Riar AK, Papa L, D'Aurello M, Manfredi G, Bonini MG, Germain D. Selected mitochondrial DNA landscapes activate the SIRT3 axis of the UPR(mt) to promote metastasis. Oncogene. 2017 Aug;36(31):4393-4404. doi: 10.1038/onc.2017.52. Epub 2017 Apr 3. PubMed PMID: 28368421; PubMed Central PMCID: PMC5542861.

12: Hirsch CM, Przychodzen BP, Radivoyevitch T, Patel B, Thota S, Clemente MJ, Nagata Y, LaFramboise T, Carraway HE, Nazha A, Sekeres MA, Makishima H, Maciejewski JP. Molecular features of early onset adult myelodysplastic syndrome. Haematologica. 2017 Jun;102(6):1028-1034. doi: 10.3324/haematol.2016.159772. Epub 2017 Mar 2. PubMed PMID: 28255022; PubMed Central PMCID: PMC5451334.

13: Niazi MKK, Keluo Yao, Zynger DL, Clinton SK, Chen J, Koyuturk M, LaFramboise T , Gurcan M. Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer. IEEE J Biomed Health Inform. 2017 Jul;21(4):1027-1038. doi: 10.1109/JBHI.2016.2565515. Epub 2016 May 10. Erratum in: IEEE J Biomed Health Inform. 2017 Sep;21(5):1473-1474. PubMed PMID: 28113734.

14: Hosono N, Makishima H, Mahfouz R, Przychodzen B, Yoshida K, Jerez A, LaFramboise T, Polprasert C, Clemente MJ, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Sanada M, Cui E, Verma AK, McDevitt MA, List AF, Saunthararajah Y, Sekeres MA, Boultwood J, Ogawa S, Maciejewski JP. Recurrent genetic defects on chromosome 5q in myeloid neoplasms. Oncotarget. 2017 Jan 24;8(4):6483-6495. doi: 10.18632/oncotarget.14130. PubMed PMID: 28031539; PubMed Central PMCID: PMC5351647.

15: Ni Y, Seballos S, Fletcher B, Romigh T, Yehia L, Mester J, Senter L, Niazi F, Saji M, Ringel MD, LaFramboise T, Eng C. Germline compound heterozygous poly-glutamine deletion in USF3 may be involved in predisposition to heritable and sporadic epithelial thyroid carcinoma. Hum Mol Genet. 2017 Jan 15;26(2):243-257. doi: 10.1093/hmg/ddw382. PubMed PMID: 28011713; PubMed Central PMCID: PMC5351935.

16: Makishima H, Yoshizato T, Yoshida K, Sekeres MA, Radivoyevitch T, Suzuki H, Przychodzen B, Nagata Y, Meggendorfer M, Sanada M, Okuno Y, Hirsch C, Kuzmanovic T, Sato Y, Sato-Otsubo A, LaFramboise T, Hosono N, Shiraishi Y, Chiba K, Haferlach C, Kern W, Tanaka H, Shiozawa Y, Gomez-Segui I, Husseinzadeh HD, Thota S, Guinta KM, Dienes B, Nakamaki T, Miyawaki S, Saunthararajah Y, Chiba S, Miyano S, Shih LY, Haferlach T, Ogawa S, Maciejewski JP. Dynamics of clonal evolution in myelodysplastic syndromes. Nat Genet. 2017 Feb;49(2):204-212. doi: 10.1038/ng.3742. Epub 2016 Dec 19. PubMed PMID: 27992414.

17: Overman MJ, Morris V, Moinova H, Manyam G, Ensor J, Lee MS, Eng C, Kee B, Fogelman D, Shroff RT, LaFramboise T, Mazard T, Feng T, Hamilton S, Broom B, Lutterbaugh J, Issa JP, Markowitz SD, Kopetz S. Phase I/II study of azacitidine and capecitabine/oxaliplatin (CAPOX) in refractory CIMP-high metastatic colorectal cancer: evaluation of circulating methylated vimentin. Oncotarget. 2016 Oct 11;7(41):67495-67506. doi: 10.18632/oncotarget.11317. PubMed PMID: 27542211; PubMed Central PMCID: PMC5341892.

18: Savel D, LaFramboise T, Grama A, Koyuturk M. Pluribus-Exploring the Limits of Error Correction Using a Suffix Tree. IEEE/ACM Trans Comput Biol Bioinform. 2017 Nov-Dec;14(6):1378-1388. doi: 10.1109/TCBB.2016.2586060. Epub 2016 Jun 29. PubMed PMID: 27362987; PubMed Central PMCID: PMC5754272.

19: Hao Y, Samuels Y, Li Q, Krokowski D, Guan BJ, Wang C, Jin Z, Dong B, Cao B, Feng X, Xiang M, Xu C, Fink S, Meropol NJ, Xu Y, Conlon RA, Markowitz S, Kinzler KW, Velculescu VE, Brunengraber H, Willis JE, LaFramboise T, Hatzoglou M, Zhang GF, Vogelstein B, Wang Z. Oncogenic PIK3CA mutations reprogram glutamine metabolism in colorectal cancer. Nat Commun. 2016 Jun 20;7:11971. doi: 10.1038/ncomms11971. PubMed PMID: 27321283; PubMed Central PMCID: PMC4915131.

20: Gould MP, Bosworth CM, McMahon S, Grandhi S, Grimberg BT, LaFramboise T. PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing. PLoS One. 2015 Oct 21;10(10):e0139253. doi: 10.1371/journal.pone.0139253. eCollection 2015. Erratum in: PLoS One. 2016 May 31;11(5):e0156884. PubMed PMID: 26488301; PubMed Central PMCID: PMC4619561.

21: Ruffalo M, Husseinzadeh H, Makishima H, Przychodzen B, Ashkar M, Koyuturk M, Maciejewski JP, LaFramboise T. Whole-exome sequencing enhances prognostic classification of myeloid malignancies. J Biomed Inform. 2015 Dec;58:104-113. doi: 10.1016/j.jbi.2015.10.003. Epub 2015 Oct 8. PubMed PMID: 26453823.

22: Ni Y, Seballos S, Ganapathi S, Gurin D, Fletcher B, Ngeow J, Nagy R, Kloos RT, Ringel MD, LaFramboise T, Eng C. Germline and somatic SDHx alterations in apparently sporadic differentiated thyroid cancer. Endocr Relat Cancer. 2015 Apr;22(2):121-30. doi: 10.1530/ERC-14-0537. PubMed PMID: 25694510; PubMed Central PMCID: PMC4335266.

23: Liu Y, Koyuturk M, Maxwell S, Xiang M, Veigl M, Cooper RS, Tayo BO, Li L, LaFramboise T, Wang Z, Zhu X, Chance MR. Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing. BMC Genomics. 2014 Aug 16;15:685. doi: 10.1186/1471-2164-15-685. PubMed PMID: 25129063; PubMed Central PMCID: PMC4148959.

24: Yava? G, Koyuturk M, Gould MP, McMahon S, LaFramboise T. DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads. BMC Genomics. 2014 Mar 5;15:175. doi: 10.1186/1471-2164-15-175. PubMed PMID: 24597945; PubMed Central PMCID: PMC4234483.

25: McMahon S, LaFramboise T. Mutational patterns in the breast cancer mitochondrial genome, with clinical correlates. Carcinogenesis. 2014 May;35(5):1046-54. doi: 10.1093/carcin/bgu012. Epub 2014 Jan 18. PubMed PMID: 24442641; PubMed Central PMCID: PMC4004206.

26: 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. 2013 Jan 31;152(3):633-41. doi: 10.1016/j.cell.2012.12.034. Review. PubMed PMID: 23374354; PubMed Central PMCID: PMC4165609.

27: Ruffalo M, Koyuturk M, Ray S, LaFramboise T. Accurate estimation of short read mapping quality for next-generation genome sequencing. Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408. PubMed PMID: 22962451; PubMed Central PMCID: PMC3436835.

28: Zhang Z, Lee JC, Lin L, Olivas V, Au V, LaFramboise T, Abdel-Rahman M, Wang X, Levine AD, Rho JK, Choi YJ, Choi CM, Kim SW, Jang SJ, Park YS, Kim WS, Lee DH, Lee JS, Miller VA, Arcila M, Ladanyi M, Moonsamy P, Sawyers C, Boggon TJ, Ma PC, Costa C, Taron M, Rosell R, Halmos B, Bivona TG. Activation of the AXL kinase causes resistance to EGFR-targeted therapy in lung cancer. Nat Genet. 2012 Jul 1;44(8):852-60. doi: 10.1038/ng.2330. PubMed PMID: 22751098; PubMed Central PMCID: PMC3408577.

29: Nickel GC, Barnholtz-Sloan J, Gould MP, McMahon S, Cohen A, Adams MD, Guda K, Cohen M, Sloan AE, LaFramboise T. Characterizing mutational heterogeneity in a glioblastoma patient with double recurrence. PLoS One. 2012;7(4):e35262. doi: 10.1371/journal.pone.0035262. Epub 2012 Apr 20. PubMed PMID: 22536362; PubMed Central PMCID: PMC3335059.

30: Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, Myeroff L, Lutterbaugh J, Jarrar A, Kalady MF, Willis J, Moore JH, Tesar PJ, LaFramboise T, Markowitz S, Lupien M, Scacheri PC. Epigenomic enhancer profiling defines a signature of colon cancer. Science. 2012 May 11;336(6082):736-9. doi: 10.1126/science.1217277. Epub 2012 Apr 12. PubMed PMID: 22499810; PubMed Central PMCID: PMC3711120.

31: Dewal N, Hu Y, Freedman ML, LaFramboise T, Pe'er I. Calling amplified haplotypes in next generation tumor sequence data. Genome Res. 2012 Feb;22(2):362-74. doi: 10.1101/gr.122564.111. Epub 2011 Nov 16. PubMed PMID: 22090379; PubMed Central PMCID: PMC3266043.

32: Sivakumaran TA, Igo RP Jr, Kidd JM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachey NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KE, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, LaFramboise T, Sen P, Aarthi M, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis GR, Klein R, Klein BE, Nickerson DA, Eichler EE, Iyengar SK. A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degeneration. PLoS One. 2011;6(10):e25598. doi: 10.1371/journal.pone.0025598. Epub 2011 Oct 12. Erratum in: PLoS One. 2018 Dec 20;13(12):e0209943. PubMed PMID: 22022419; PubMed Central PMCID: PMC3192039.

33: Wilkins K, LaFramboise T. Losing balance: Hardy-Weinberg disequilibrium as a marker for recurrent loss-of-heterozygosity in cancer. Hum Mol Genet. 2011 Dec 15;20(24):4831-9. doi: 10.1093/hmg/ddr422. Epub 2011 Sep 14. PubMed PMID: 21920941; PubMed Central PMCID: PMC3221535.

34: Ruffalo M, LaFramboise T, Koyuturk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19. PubMed PMID: 21856737.

35: LaFramboise T, Dewal N, Wilkins K, Pe'er I, Freedman ML. Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis. PLoS Genet. 2010 Sep 2;6(9):e1001086. doi: 10.1371/journal.pgen.1001086. PubMed PMID: 20824129; PubMed Central PMCID: PMC2932683.

36: Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, LaFramboise T, Tesar P, Wei CL, Scacheri PC. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet. 2010 Jul 15;6(7):e1001023. doi: 10.1371/journal.pgen.1001023. PubMed PMID: 20657823; PubMed Central PMCID: PMC2904778.

37: Zhang Z, Kobayashi S, Borczuk AC, Leidner RS, LaFramboise T, Levine AD, Halmos B. Dual specificity phosphatase 6 (DUSP6) is an ETS-regulated negative feedback mediator of oncogenic ERK signaling in lung cancer cells. Carcinogenesis. 2010 Apr;31(4):577-86. doi: 10.1093/carcin/bgq020. Epub 2010 Jan 22. PubMed PMID: 20097731; PubMed Central PMCID: PMC2847094.

38: Dewal N, Freedman ML, LaFramboise T, Pe'er I. Power to detect selective allelic amplification in genome-wide scans of tumor data. Bioinformatics. 2010 Feb 15;26(4):518-28. doi: 10.1093/bioinformatics/btp694. Epub 2009 Dec 23. PubMed PMID: 20031965; PubMed Central PMCID: PMC2852215.

39: Yavas G, Koyuturk M, Ozsoyolu M, Gould MP, LaFramboise T. COKGEN: a software for the identification of rare copy number variation from SNP microarrays. Pac Symp Biocomput. 2010:371-82. PubMed PMID: 19908389.

40: Yavas G, Koyuturk M, Ozsoyo?lu M, Gould MP, LaFramboise T. An optimization framework for unsupervised identification of rare copy number variation from SNP array data. Genome Biol. 2009;10(10):R119. doi: 10.1186/gb-2009-10-10-r119. Epub 2009 Oct 23. PubMed PMID: 19849861; PubMed Central PMCID: PMC2784334.

41: LaFramboise T. Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res. 2009 Jul;37(13):4181-93. doi: 10.1093/nar/gkp552. Epub 2009 Jul 1. PubMed PMID: 19570852; PubMed Central PMCID: PMC2715261.

42: Sos ML, Michel K, Zander T, Weiss J, Frommolt P, Peifer M, Li D, Ullrich R, Koker M, Fischer F, Shimamura T, Rauh D, Mermel C, Fischer S, Stuckrath I, Heynck S, Beroukhim R, Lin W, Winckler W, Shah K, LaFramboise T, Moriarty WF, Hanna M, Tolosi L, Rahnenfuhrer J, Verhaak R, Chiang D, Getz G, Hellmich M, Wolf J, Girard L, Peyton M, Weir BA, Chen TH, Greulich H, Barretina J, Shapiro GI, Garraway LA, Gazdar AF, Minna JD, Meyerson M, Wong KK, Thomas RK. Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. J Clin Invest. 2009 Jun;119(6):1727-40. doi: 10.1172/JCI37127. Epub 2009 May 18. PubMed PMID: 19451690; PubMed Central PMCID: PMC2689116.

43: Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Zentner GE, Balaji R, Zhang X, Song L, Wang Z, LaFramboise T, Crawford GE, Scacheri PC. Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res. 2009 Apr;19(4):590-601. doi: 10.1101/gr.086983.108. Epub 2009 Feb 27. PubMed PMID: 19251738; PubMed Central PMCID: PMC2665778.

44: LaFramboise T, Winckler W, Thomas RK. A flexible rank-based framework for detecting copy number aberrations from array data. Bioinformatics. 2009 Mar 15;25(6):722-8. doi: 10.1093/bioinformatics/btp063. Epub 2009 Jan 28. PubMed PMID: 19176555; PubMed Central PMCID: PMC2732300.

45: Rozenblatt-Rosen O, Nagaike T, Francis JM, Kaneko S, Glatt KA, Hughes CM, LaFramboise T, Manley JL, Meyerson M. The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors. Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):755-60. doi: 10.1073/pnas.0812023106. Epub 2009 Jan 9. PubMed PMID: 19136632; PubMed Central PMCID: PMC2615665.

46: Assie G, LaFramboise T, Platzer P, Eng C. Frequency of germline genomic homozygosity associated with cancer cases. JAMA. 2008 Mar 26;299(12):1437-45. doi: 10.1001/jama.299.12.1437. PubMed PMID: 18364486.

47: Assie G, LaFramboise T, Platzer P, Bertherat J, Stratakis CA, Eng C. SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples. Am J Hum Genet. 2008 Apr;82(4):903-15. doi: 10.1016/j.ajhg.2008.01.012. Epub 2008 Mar 20. PubMed PMID: 18355774; PubMed Central PMCID: PMC2427213.

48: Zhang X, Guo C, Chen Y, Shulha HP, Schnetz MP, LaFramboise T, Bartels CF, Markowitz S, Weng Z, Scacheri PC, Wang Z. Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. Nat Methods. 2008 Feb;5(2):163-5. doi: 10.1038/nmeth1170. Epub 2008 Jan 6. PubMed PMID: 18176569; PubMed Central PMCID: PMC2435063.

49: Macconaill LE, Aldred MA, Lu X, LaFramboise T. Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation. BMC Genomics. 2007 Jul 3;8:211. PubMed PMID: 17608949; PubMed Central PMCID: PMC1934372.

50: Minami Y, Shimamura T, Shah K, LaFramboise T, Glatt KA, Liniker E, Borgman CL, Haringsma HJ, Feng W, Weir BA, Lowell AM, Lee JC, Wolf J, Shapiro GI, Wong KK, Meyerson M, Thomas RK. The major lung cancer-derived mutants of ERBB2 are oncogenic and are associated with sensitivity to the irreversible EGFR/ERBB2 inhibitor HKI-272. Oncogene. 2007 Jul 26;26(34):5023-7. Epub 2007 Feb 19. PubMed PMID: 17311002.

51: Thomas RK, Baker AC, Debiasi RM, Winckler W, LaFramboise T, Lin WM, Wang M, Feng W, Zander T, MacConaill L, Lee JC, Nicoletti R, Hatton C, Goyette M, Girard L, Majmudar K, Ziaugra L, Wong KK, Gabriel S, Beroukhim R, Peyton M, Barretina J, Dutt A, Emery C, Greulich H, Shah K, Sasaki H, Gazdar A, Minna J, Armstrong SA, Mellinghoff IK, Hodi FS, Dranoff G, Mischel PS, Cloughesy TF, Nelson SF, Liau LM, Mertz K, Rubin MA, Moch H, Loda M, Catalona W, Fletcher J, Signoretti S, Kaye F, Anderson KC, Demetri GD, Dummer R, Wagner S, Herlyn M, Sellers WR, Meyerson M, Garraway LA. High-throughput oncogene mutation profiling in human cancer. Nat Genet. 2007 Mar;39(3):347-51. Epub 2007 Feb 11. Erratum in: Nat Genet. 2007 Apr;39(4):567. Macconnaill, Laura E [corrected to MacConaill, Laura]. PubMed PMID: 17293865.

52: Thomas RK, Nickerson E, Simons JF, Janne PA, Tengs T, Yuza Y, Garraway LA, LaFramboise T, Lee JC, Shah K, O'Neill K, Sasaki H, Lindeman N, Wong KK, Borras AM, Gutmann EJ, Dragnev KH, DeBiasi R, Chen TH, Glatt KA, Greulich H, Desany B, Lubeski CK, Brockman W, Alvarez P, Hutchison SK, Leamon JH, Ronan MT, Turenchalk GS, Egholm M, Sellers WR, Rothberg JM, Meyerson M. Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med. 2006 Jul;12(7):852-5. Epub 2006 Jun 25. Erratum in: Nat Med. 2006 Oct;12(10):1220. PubMed PMID: 16799556.

53: LaFramboise T, Harrington D, Weir BA. PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data. Biostatistics. 2007 Apr;8(2):323-36. Epub 2006 Jun 20. PubMed PMID: 16787995.

54: LaFramboise TL, Hayes DN, Tengs T. Statistical analysis of genomic tag data. Stat Appl Genet Mol Biol. 2004;3:Article34. Epub 2004 Dec 8. PubMed PMID: 16646814.

55: LaFramboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington D, Sellers WR, Meyerson M. Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol. 2005 Nov;1(6):e65. Epub 2005 Nov 25. PubMed PMID: 16322765; PubMed Central PMCID: PMC1289392.

56: Tengs T, Lee JC, Paez JG, Zhao X, LaFramboise T, Giannoukos G, Thomas RK. A transforming MET mutation discovered in non-small cell lung cancer using microarray-based resequencing. Cancer Lett. 2006 Aug 8;239(2):227-33. Epub 2005 Sep 19. PubMed PMID: 16171945.

57: Zhao X, Weir BA, LaFramboise T, Lin M, Beroukhim R, Garraway L, Beheshti J, Lee JC, Naoki K, Richards WG, Sugarbaker D, Chen F, Rubin MA, Janne PA, Girard L, Minna J, Christiani D, Li C, Sellers WR, Meyerson M. Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res. 2005 Jul 1;65(13):5561-70. PubMed PMID: 15994928.

58: Tengs T, LaFramboise T, Den RB, Hayes DN, Zhang J, DebRoy S, Gentleman RC, O'Neill K, Birren B, Meyerson M. Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments. Nucleic Acids Res. 2004 Aug 25;32(15):e121. PubMed PMID: 15329383; PubMed Central PMCID: PMC516078.

59: Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R. A graph-theoretic approach to testing associations between disparate sources of functional genomics data. Bioinformatics. 2004 Dec 12;20(18):3353-62. Epub 2004 Jul 15. PubMed PMID: 15256415.

60: LaFramboise TL, Hayes DN, Tengs T. Statistical analysis of genomic tag data. Stat Appl Genet Mol Biol. 2004;3:Article34. Epub 2004 Dec 8. PubMed PMID: 16646814. Last update on: 10th March 2019