Thomas Laframboise
Assistant Professor
Ph.D. Training Faculty
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Department of Genetics
School of Medicine
Case Western Reserve University
Biomedical Research Building 630
2109 Adelbert Road
Cleveland, Ohio 44106-4955
Tel: (216) 368-0150
Fax: (216) 368-3432
E-mail: thomas.laframboise@case.edu
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About Thomas Laframboise
Tom LaFramboise earned his B.S. from the University of Michigan at Ann Arbor and his Ph.D. from the University of Illinois at Urbana-Champaign, both degrees being in theoretical mathematics. Subsequently, he spent several years as Assistant and Associate Professor in the mathematics department at Marietta College in Marietta, OH. In 2002, Tom decided to retrain in biostatistics, earning a Master’s degree at the Harvard School of Public Health, which led to a postdoctoral position in cancer genomics in the laboratory of Matthew Meyerson at the Dana-Farber Cancer Institute and the Broad Institute of Harvard/MIT. He joined the department in August 2006.
Research
Broadly, Dr. LaFramboise is interested in developing and applying computational tools to identify molecular variants - both inherited and somatic - that contribute to cancer and related diseases in humans. His postdoctoral work centered around the statistical modeling of data from SNP microarrays to detect DNA copy number changes in tumors. Dr. LaFramboise has written a number of R software packages designed to draw biological inferences from genomic data. His group is currently working to mine high-dimensional SNP array data for inherited variants that predispose the cell to genomic instability. Related interests include the detection of germline copy number polymorphisms, their relevance in association studies, and developing statistical methodologies to optimize power in such studies.
Selected Publications
| Yavaş G, Koyutürk M, Ozsoyoğlu M, Gould MP, Laframboise T (2010) | | Cokgen: a software for the identification of rare copy number variation from SNP microarrays. | | Pac Symp Biocomput;:371-82 | | See PubMed abstract |
| Yavas G, Koyuturk M, Ozsoyoglu M, Gould M, Laframboise T (2009) | | An Optimization Framework for Unsupervised Identification of Rare Copy Number Variation from SNP Array Data. | | Genome Biol;10(10):R119 | | See PubMed abstract |
| LaFramboise T (2009) | | Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. | | Nucleic Acids Res;37(13):4181-93 | | 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, Rahnenführer 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 (2009) | | Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. | | J Clin Invest;: | | See PubMed abstract |
| LaFramboise T, Winckler W, Thomas RK (2009) | | 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 (2009) | | The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors. | | Proc Natl Acad Sci U S A;: | | See PubMed abstract |
| Assié G, LaFramboise T, Platzer P, Bertherat J, Stratakis CA, Eng C (2008) | | SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples. | | Am J Hum Genet;82(4):903-15 | | See PubMed abstract |
| Assié G, LaFramboise T, Platzer P, Eng C (2008) | | Frequency of germline genomic homozygosity associated with cancer cases. | | JAMA;299(12):1437-45 | | 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 (2008) | | Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. | | Nat Methods;5(2):163-5 | | See PubMed abstract |
| Macconaill LE, Aldred MA, Lu X, Laframboise T (2007) | | Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation. | | BMC Genomics;8(1):211 | | 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 (2007) | | High-throughput oncogene mutation profiling in human cancer | | Nature Genetics;(In Press) | |
| 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 (2007) | | The major lung cancer-derived mutants of ERBB2 are oncogenic and are associated with sensitivity to the irreversible EGFR/ ERBB2 inhibitor HKI-272 | | Oncogene;(In Press) | |
| Tengs T, Lee JC, Guillermo Paez J, Zhao X, LaFramboise T, Giannoukos G, Thomas RK (2006) | | 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 (2006) | | Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing | | Nat Med;12(7):852-855 | | See PubMed abstract |
| LaFramboise T, Harrington D, Weir BA (2006) | | PLASQ: A Generalized Linear Model-Based Procedure to Determine Allelic Dosage in Cancer Cells from SNP Array Data | | Biostatistics; | | See PubMed abstract |
| LaFramboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington D, Sellers WR, Meyerson M. (2005) | | Allele-specific amplification in cancer revealed by SNP array analysis | | PLoS Comput Biol;1(6):e65 | | See PubMed abstract |
| Zhao, X., Weir, B., LaFramboise, T., Lin, M., Beroukhim, R., Garraway, L., Beheshti, J., Lee, J., Naoki, K., Chen, F., et al. (2005) | | Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis | | Cancer Research;65: 5561 - 5570 | | See PubMed abstract |
| Balasubramanian R, LaFramboise T, Scholtens D, Gentleman R. (2004) | | 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. (2004) | | Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments | | Nucleic Acids Res;32(15):e121 | | See PubMed abstract |
| LaFramboise TL, Hayes DN, Tengs T. (2004) | | Statistical analysis of genomic tag data | | Stat Appl Genet Mol Biol;3(1):Article34 | | See PubMed abstract |
| Contributing author to Comprehensive Dictionary of Mathematics (2001) | | | CRC Press.; | |
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