Yavaş, Gökhan, Koyutürk, Mehmet, Özsoyoğlu, Meral, Gould, Meetha P, LaFramboise, Thomas
Abstract Copy number variants (CNVs) have roles in human disease, and DNA microarrays are important tools for identifying them. In this paper, we frame CNV identification as an objective function...
Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions (2009)
Sos, Martin L., Michel, Kathrin, Zander, Thomas, Weiss, Jonathan, Frommolt, Peter, Peifer, Martin, ...
Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. (2009)
Sos, Martin L., Michel, Kathrin, Zander, Thomas, Weiss, Jonathan, Frommolt, Peter, Peifer, Martin, ...
Somatic genetic alterations in cancers have been linked with response to targeted therapeutics by creation of specific dependency on activated oncogenic signaling pathways. However, no tools...
Array manufacturers originally designed single nucleotide polymorphism (SNP) arrays to genotype human DNA at thousands of SNPs across the genome simultaneously. In the decade since their initial...
A flexible rank-based framework for detecting copy number aberrations from array data (2009)
LaFramboise, Thomas, Winckler, Wendy, Thomas, Roman K.
Motivation: DNA copy number aberration—both inherited and sporadic—is a significant contributor to a variety of human diseases. Copy number characterization is therefore an area of intense...
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns (2009)
Schnetz, Michael P., Bartels, Cynthia F., Shastri, Kuntal, Balasubramanian, Dheepa, Zentner, Gabriel E., Balaji, Ravishankar, ...
CHD7 is a member of the chromodomain helicase DNA binding domain family of ATP-dependent chromatin remodeling enzymes. De novo mutation of the CHD7 gene is a major cause of CHARGE syndrome, a genetic...
Assi , Guillaume, LaFramboise, Thomas, Platzer, Petra, Bertherat, J R Me, Stratakis, Constantine A., Eng, Charis
SNP arrays provide reliable genotypes and can detect chromosomal aberrations at a high resolution. However, tissue heterogeneity is currently a major limitation for somatic tissue analysis. We have...
MacConaill, Laura E, Aldred, Micheala A, Lu, Xincheng, LaFramboise, Thomas
Abstract Background The recent discovery of widespread copy number variation in humans has forced a shift away from the assumption of two copies per locus per cell throughout the autosomal genome. In...
Corrigendum: High-throughput oncogene mutation profiling in human cancer. (2007)
Thomas, Roman K, Baker, Alissa C, Debiasi, Ralph M, Winckler, Wendy, Laframboise, Thomas, Lin, William M, ...
Systematic efforts are underway to decipher the genetic changes associated with tumor initiation and progression1, 2. However, widespread clinical application of this information is hampered by an...
Laframboise, Thomas, Harrington, David, Weir, Barbara A.
Human cancer is largely driven by the acquisition of mutations. One class of such mutations is copy number polymorphisms, comprised of deviations from the normal diploid two copies of each autosomal...
MacConaill, Laura E, Aldred, Micheala A, Lu, Xincheng, LaFramboise, Thomas
BACKGROUND: The recent discovery of widespread copy number variation in humans has forced a shift away from the assumption of two copies per locus per cell throughout the autosomal genome. In...
High-throughput oncogene mutation profiling in human cancer (2007)
Thomas, Roman K., Baker, Alissa C., Debiasi, Ralph M., Winckler, Wendy, Laframboise, Thomas, Lin, William M., ...
Thomas, Roman K., Nickerson, Elizabeth, Simons, Jan F., Jänne, Pasi A., Tengs, Torstein, Yuza, Yuki, ...
Tengs, Torstein, Lee, Jeff C., Paez, J. Guillermo, Zhao, Xiaojun, LaFramboise, Thomas, Giannoukos, Georgia, ...
Laframboise, Thomas, Harrington, David, Weir, Barbara A.
Human cancer is largely driven by the acquisition of mutations. One class of such mutations is copy number polymorphisms, comprised of deviations from the normal diploid two copies of each autosomal...
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis (2005)
Thomas LaFramboise, Barbara A. Weir, Xiaojun Zhao, Rameen Beroukhim, Cheng Li, David Harrington, ...
Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly...
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis (2005)
Thomas LaFramboise, Barbara Weir, Xiaojun Zhao, Rameen Beroukhim, Cheng Li, David Harrington, ...
Amplification, deletion, and loss-of-heterozygosity (LOH) of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
Motivation: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
Motivation: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these...
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
Motivation: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these...
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
LaFramboise, Thomas, Weir, Barbara A, Zhao, Xiaojun, Beroukhim, Rameen, Li, Cheng, Harrington, David, ...
Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly...
Genomic representations using concatenates of Type IIB restriction endonuclease digestion fragments
Tengs, Torstein, LaFramboise, Thomas, Den, Robert B., Hayes, David N., Zhang, Jianhua, DebRoy, Saikat, ...
We have developed a method for genomic representation using Type IIB restriction endonucleases. Representation by concatenation of restriction digests, or RECORD, is an approach to sample the...
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
LaFramboise, Thomas, Weir, Barbara A, Zhao, Xiaojun, Beroukhim, Rameen, Li, Cheng, Harrington, David, ...
Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly...
Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation
MacConaill, Laura E, Aldred, Micheala A, Lu, Xincheng, LaFramboise, Thomas
Statistical Analysis of Genomic Tag Data
Thomas LaFramboise, D. Hayes, Torstein Tengs
We present a series of statistical solutions to challenges that commonly arise in the production and analysis of genomic tag libraries. Tag libraries are collections of fragments of DNA or RNA, with...
Assié, Guillaume, LaFramboise, Thomas, Platzer, Petra, Bertherat, Jérôme, Stratakis, Constantine A., Eng, Charis
SNP arrays provide reliable genotypes and can detect chromosomal aberrations at a high resolution. However, tissue heterogeneity is currently a major limitation for somatic tissue analysis. We have...
Predicting drug susceptibility of non–small cell lung cancers based on genetic lesions
Sos, Martin L., Michel, Kathrin, Zander, Thomas, Weiss, Jonathan, Frommolt, Peter, Peifer, Martin, ...
Somatic genetic alterations in cancers have been linked with response to targeted therapeutics by creation of specific dependency on activated oncogenic signaling pathways. However, no tools...
The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3′ mRNA processing factors
Rozenblatt-Rosen, Orit, Nagaike, Takashi, Francis, Joshua M., Kaneko, Syuzo, Glatt, Karen A., Hughes, Christina M., ...
The CDC73 tumor suppressor gene is mutationally inactivated in hereditary and sporadic parathyroid tumors. Its product, the Cdc73 protein, is a component of the RNA polymerase II and...
Array manufacturers originally designed single nucleotide polymorphism (SNP) arrays to genotype human DNA at thousands of SNPs across the genome simultaneously. In the decade since their initial...
Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns
Schnetz, Michael P., Bartels, Cynthia F., Shastri, Kuntal, Balasubramanian, Dheepa, Zentner, Gabriel E., Balaji, Ravishankar, ...
CHD7 is a member of the chromodomain helicase DNA binding domain family of ATP-dependent chromatin remodeling enzymes. De novo mutation of the CHD7 gene is a major cause of CHARGE syndrome, a genetic...