Research Topics
| Thomas LaFramboiseSummaryAffiliation: Case Western Reserve University Country: USA Publications
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Detail Information
Publications
A flexible rank-based framework for detecting copy number aberrations from array dataThomas LaFramboise
Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA
Bioinformatics 25:722-8. 2009..Copy number characterization is therefore an area of intense research. Probe hybridization-based arrays are important tools used to measure copy number in a high-throughput manner...- Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variationLaura E MacConaill
Dana Farber Cancer Institute, Boston, Massachusetts 02116, USA
BMC Genomics 8:211. 2007..In the presence of copy number variability, the individual may theoretically harbor any number of copies of each of the two SNP alleles... 
Frequency of germline genomic homozygosity associated with cancer casesGuillaume Assie
Genomic Medicine Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
JAMA 299:1437-45. 2008....- Epigenomic enhancer profiling defines a signature of colon cancerBatool Akhtar-Zaidi
Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
Science 336:736-9. 2012..We propose that reproducible changes in the epigenome at enhancer elements drive a specific transcriptional program to promote colon carcinogenesis... - Comparative analysis of algorithms for next-generation sequencing read alignmentMatthew Ruffalo
Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA
Bioinformatics 27:2790-6. 2011..However, for scientists who generate and use NGS data for their specific research projects, an important consideration is choosing the software that is most suitable for their application... - CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expressionMichael P Schnetz
Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
PLoS Genet 6:e1001023. 2010.... - An optimization framework for unsupervised identification of rare copy number variation from SNP array dataGokhan Yavas
Department of Electrical Engineering and Computer Science, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
Genome Biol 10:R119. 2009..Its performance compares favorably with currently available methods and it reveals previously unreported gains and losses... - Single nucleotide polymorphism arrays: a decade of biological, computational and technological advancesThomas LaFramboise
Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA
Nucleic Acids Res 37:4181-93. 2009..Even as emerging technologies seem poised to take over for at least some applications, researchers working with these new sources of data are adopting the computational approaches originally developed for SNP arrays... - Losing balance: Hardy-Weinberg disequilibrium as a marker for recurrent loss-of-heterozygosity in cancerKatherine Wilkins
Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
Hum Mol Genet 20:4831-9. 2011..Finally, we produce rate estimates that are generally higher than previously published, and provide evidence that the latter are likely underestimates... - Accurate estimation of short read mapping quality for next-generation genome sequencingMatthew Ruffalo
Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA
Bioinformatics 28:i349-i355. 2012.... - Characterizing mutational heterogeneity in a glioblastoma patient with double recurrenceGabrielle C Nickel
Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
PLoS ONE 7:e35262. 2012..As sequencing costs continue to decline and deep sequencing technology eventually moves into the clinic, this approach may provide guidance for treatment choices as we embark on the path to personalized cancer medicine... - Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patternsMichael P Schnetz
Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106, USA
Genome Res 19:590-601. 2009.... - A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degenerationTheru A Sivakumaran
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
PLoS ONE 6:e25598. 2011..We conclude that causal variation in this region potentially encompasses both regulatory effects at single markers and copy number... - SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samplesGuillaume Assie
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
Am J Hum Genet 82:903-15. 2008..SOMATICs is a ready-to-use open-source program that integrates all of these features into a simple format, comprehensively describing each chromosomal event...