Thomas LaFramboise

Summary

Affiliation: Case Western Reserve University
Country: USA

Publications

  1. ncbi request reprint DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads
    Gokhan Yavas
    Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    BMC Genomics 15:175. 2014
  2. ncbi request reprint Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing
    Yu Liu
    Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
    BMC Genomics 15:685. 2014
  3. pmc A flexible rank-based framework for detecting copy number aberrations from array data
    Thomas LaFramboise
    Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA
    Bioinformatics 25:722-8. 2009
  4. pmc Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation
    Laura E MacConaill
    Dana Farber Cancer Institute, Boston, Massachusetts 02116, USA
    BMC Genomics 8:211. 2007
  5. ncbi request reprint Frequency of germline genomic homozygosity associated with cancer cases
    Guillaume Assie
    Genomic Medicine Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
    JAMA 299:1437-45. 2008
  6. pmc CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression
    Michael P Schnetz
    Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
    PLoS Genet 6:e1001023. 2010
  7. pmc Accurate estimation of short read mapping quality for next-generation genome sequencing
    Matthew Ruffalo
    Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA
    Bioinformatics 28:i349-i355. 2012
  8. pmc Epigenomic enhancer profiling defines a signature of colon cancer
    Batool Akhtar-Zaidi
    Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
    Science 336:736-9. 2012
  9. ncbi request reprint Comparative analysis of algorithms for next-generation sequencing read alignment
    Matthew Ruffalo
    Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA
    Bioinformatics 27:2790-6. 2011
  10. pmc An optimization framework for unsupervised identification of rare copy number variation from SNP array data
    Gokhan Yavas
    Department of Electrical Engineering and Computer Science, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    Genome Biol 10:R119. 2009

Collaborators

Detail Information

Publications17

  1. ncbi request reprint DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads
    Gokhan Yavas
    Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    BMC Genomics 15:175. 2014
    ..In this paper, we propose a new method, Distribution Based detection of Duplication Boundaries (DB2), for accurate detection of tandem duplication breakpoints, an important class of structural variation, with high precision and recall...
  2. ncbi request reprint Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing
    Yu Liu
    Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
    BMC Genomics 15:685. 2014
    ..However, there is no study to investigate the distribution, evolution and functionality of those sequences in human populations...
  3. pmc A flexible rank-based framework for detecting copy number aberrations from array data
    Thomas 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...
  4. pmc Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation
    Laura 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...
  5. ncbi request reprint Frequency of germline genomic homozygosity associated with cancer cases
    Guillaume Assie
    Genomic Medicine Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
    JAMA 299:1437-45. 2008
    ....
  6. pmc CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression
    Michael P Schnetz
    Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
    PLoS Genet 6:e1001023. 2010
    ....
  7. pmc Accurate estimation of short read mapping quality for next-generation genome sequencing
    Matthew Ruffalo
    Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA
    Bioinformatics 28:i349-i355. 2012
    ..Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants...
  8. pmc Epigenomic enhancer profiling defines a signature of colon cancer
    Batool 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...
  9. ncbi request reprint Comparative analysis of algorithms for next-generation sequencing read alignment
    Matthew 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...
  10. pmc An optimization framework for unsupervised identification of rare copy number variation from SNP array data
    Gokhan 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...
  11. pmc Losing balance: Hardy-Weinberg disequilibrium as a marker for recurrent loss-of-heterozygosity in cancer
    Katherine 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...
  12. pmc Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances
    Thomas 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...
  13. pmc Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis
    Thomas LaFramboise
    Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
    PLoS Genet 6:e1001086. 2010
    ..Our results support the notion that combining germline and tumor genetic data can identify regions relevant to cancer biology...
  14. pmc Characterizing mutational heterogeneity in a glioblastoma patient with double recurrence
    Gabrielle 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...
  15. pmc A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degeneration
    Theru 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...
  16. pmc SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples
    Guillaume 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...
  17. pmc Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns
    Michael P Schnetz
    Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106, USA
    Genome Res 19:590-601. 2009
    ....