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Publications

Peer-reviewed Publications

2016

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. 11317
See PubMed abstract

Savel D, LaFramboise T, Grama A, Koyuturk M.
"Pluribus - Exploring the Limits of Error Correction Using a Suffix Tree."
J IEEE/ACM Trans Comput Biol Bioinform. PP(99):1
See PubMed abstract

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.7:11971
See PubMed abstract

Niazi MK, Yao K, Zynger D, Clinton S, Chen J, Koyuturk M, LaFramboise T, Gurcan M.
"Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer."
J Biomed Health InformPP(99):1
See PubMed abstract

2015

Gould MP, Bosworth CM, McMahon S, Grandhi S, Grimerg BT, LaFramboise T.
"PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing"
PLoS One 10(10):e0139253
See PubMed abstract

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 58:104-13
See PubMed abstract

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 22(22):121-30
See PubMed abstract

2014

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 15:685
See PubMed abstract

Yavas 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 15:175
See PubMed abstract

McMahon S, LaFramboise T
"Mutational patterns in the breast cancer mitochondrial genome, with clinical correlates"
Carcinogenesis 35(5):1046-54
See PubMed abstract

2013

Li Q, Seo J-H, Stranger B, McKenna A, Pe'er I, LaFramboise T, Brown M, Tuyekucheva S, Freedman ML
"Integrative eQTL-based analyses reveal the biology of breast cancer risk loci"
Cell 152(3):633-41
See Cell abstract

2012

Ibrahim J, LaFramboise T
"Exploring correlations among copy number variants"
Open Journal of Genetics 2:131-135
See SCIRP abstract

Ruffalo M, Kyutürk M, Ray S, LaFramboise T
"Accurate estimation of short read mapping quality for next-generation genome sequencing"
Bioinformatics 28(18):i349-i355
See Pubmed abstract

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"
Nature Genetics 44(8):852-860
See Pubmed abstract

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 336(6082):736-9
See Science abstract

Nickel G, Barnholtz-Sloan J, Gould M, 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 7(4)
See PLoS abstract

Dewal N, Hu Y, Freedman ML, LaFramboise T, Pe'er I
"Calling amplified haplotypes in next generation tumor sequence data"
Genome Research 22(2):362-74
See Pubmed abstract

2011

Wilkins K, and LaFramboise T.
"Losing Balance: Hardy-Weinberg Disequilibrium as a Marker for recurrent Loss-of-Heterozygosity in Cancer"
Human Molecular Genetics (2011)4
See Pubmed abstract

Sivakumaran TA, Igo RP, Kidd LM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachy NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KL, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, LaFramboise T, Sen P, Aarthi P, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis G, Klein R, Klein BEK, Nickerson DA, Eichler EE, Iygengar SK
"A 32 kb Critical Region Excluding Y402H in CFH Mediates Risk for Age-Related Macular Degeneration"
PLoS One 6(10):e25598
See PLoS abstract

Ruffalo M, LaFramboise T, Koyutürk M.
"Comparative Analysis of Algorithms for Next-Generation Sequencing read Alignment"
Bioinformatics 27(20):2790-6
See Bioinformatics abstract

2010

Yavas G, Koyutürk M, LaFramboise T
"Optimization algorithms for identification and genotyping of copy number polymorphisms in human populations"
PRIB'10
See SpringerLink abstract

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 Genetics 6(9)
See PubMed abstract

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 Genetics 6(7)
See PubMed abstract

Yavas G, Koyutürk M, LaFramboise T
"Optimization Algorithms for identification and genotyping of copy number polymorphisms in human populations"
In Proceedings of 5th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB '10) LNCS 6282:74-85
See full paper

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 31(4)577-86
See PubMed abstract

Dewal N, Freedman ML, LaFramboise T, Pe'er I
"Power to Detect Selective Allelic Amplification in Genome-wide Scans of Tumor Data"
Bioinformatics 26(4):518-28
See PubMed abstract

Yavas G, Koyutürk M, Ozsoyoğlu M, Gould M, Laframboise T
"Cokgen: a software for the identification of rare copy number variation from SNP microarrays"
Pacific Symposium on Biocomputng 2010:371-82.
See PubMed abstract

2009

Yavas G, Koyutürk M, Ozsoyoğlu M, Gould M, Laframboise T
"An Optimization Framework for Unsupervised Identification of Rare Copy Number Variation from SNP Array Data"
Genome Biology 10(10):R119
See PubMed abstract

Laframboise T
"Single nucleotide polymorphism arrays: A decade of biological, computational and technological advances"
Nucleic Acids Research 37(13)4184-93
See PubMed abstract

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, Stückrath I, Heynck S, Beroukhim R, Lin W, Winckler W, Shah K, Laframboise T, Moriarty WF, Hanna M, Tolosi L, Rahnenürer 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"
Journal of Clinical Investigation 119(6)1727-40
See PubMed abstract

Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Balaji R, LaFramboise T, Crawford G, Scacheri PC
"Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns"
Genome Research 9(4):590-601.
See PubMed abstract

LaFramboise T, Winckler W, Thomas RK
"A Flexible Rank-Based Framework for Detecting Copy Number Aberrations from Array Data"
Bioinformatics 25(6):722-8.
See PubMed abstract

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 106:755-60.
See PubMed abstract

2008

Assié G, LaFramboise T, Platzer P, Eng C
"Frequency of germline genomic homozygosity associated with cancer cases"
Journal of the American Medical Association 299(12):1437-45
See PubMed abstract

Assié 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 sample"
American Journal of Human Genetics 82(4):903-15
See PubMed abstract

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"
Nature Methods 5(2):163-5
See PubMed abstract

2007

Macconaill LE, Aldred MA, Lu X, LaFramboise T
"Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation"
BMC Genomics 8:211
See PubMed abstract

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 <26(34)>:5023-7
See Pubmed abstract

Thomas RK, Baker AC, DeBiasi RM, Winckler W, LaFramboise T, Lin WM, Feng W, Wang M, MacConnaill LE, 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 AF, 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"
Nature Genetics 39(3):347-51
See Pubmed abstract

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 8(2):323-36
See PubMed abstract

2006

Tengs T, Lee JC, Guillermo Paez J, 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 239(2):227-33
See PubMed abstract

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 12(7):852-855
See Pubmed abstract

2005

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 Letters 239(2)227-33
See Pubmed abstract

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 Computational Biology 1:6
See PubMed abstract

Zhao X, Weir B, LaFramboise T, Lin M, Beroukhim R, Garraway L, Beheshti J, Lee JC, Naoki K, Chen F, Rubin MA, Janne PA, Girard L, Minna J, Christiani DC, Li C, Sellers WC, Meyerson M
"Genome-wide analysis of genomic alterations in human lung cancers by single nucleotide polymorphism array"
Cancer Research 65: 5561 - 5570
See PubMed abstract

2004

LaFramboise TL, Hayes DN, Tengs T.
"Statistical analysis of genomic tag data"
Statistical Applications in Genetics and Molecular Biology 3(1):Article34
See PubMed abstract

Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R.
"A graph-theoretic approach to testing associations between disparate sources of functional genomics data",
Bioinformatics 20:3353-62.
See PubMed abstract

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. 32(15):e121.
See PubMed abstract

Miscellaneous

Microarray Analysis Trouble Shooting Guide
Engineering and Science Review Article

Bebek C, Koyutürk M, LaFramboise T, Raphael BJ Chance MR.
POST-NGS: INTERPRETATION AND ANALYSIS OF NEXT GENERATION SEQUENCING DATA FOR BASIC AND TRANSLATIONAL SCIENCE.
Pac Symp Biocomput 2013 18:307-309.

Invited commentary (with Balazs Halmos and Rom Leidner)
"Predictave markers of Esophageal cancer--in search of the main charAKTers"
American Journal of Hematology/Oncology (September 17. 2009).

Contributing author, Dictionary of Classical and Theoretical Mathematics (2001). Cavagnaro and Haight, eds. CRC Press, New York