Now showing items 1-14 of 14

    • Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis 

      LaFramboise, Thomas; Weir, Barbara Ann; Zhao, Xiaojun; Beroukhim, Rameen; Li, Cheng; Harrington, David Paul; Sellers, William R; Meyerson, Matthew Langer (Public Library of Science, 2005)
      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 high resolution. Similarly, ...
    • Automating dChip: Toward Reproducible Sharing of Microarray Data Analysis 

      Li, Cheng (BioMed Central, 2008)
      Background: During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis ...
    • canEvolve: A Web Portal for Integrative Oncogenomics 

      Samur, Mehmet Kemal; Yan, Zhenyu; Wang, Xujun; Cao, Qingyi; Munshi, Nikhil C.; Li, Cheng; Shah, Parantu K. (Public Library of Science, 2013)
      Background & objective: Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual ...
    • Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data 

      Leykin, Igor; Hao, Ke; Cheng, Junsheng; Meyer, Nicole; Pollak, Martin Russell; Smith, Richard JH; Wong, Wing Hung; Rosenow, Carsten; Li, Cheng (BioMed Central, 2005)
      Background: The identification of disease-associated genes using single nucleotide polymorphisms (SNPs) has been increasingly reported. In particular, the Affymetrix Mapping 10 K SNP microarray platform uses one PCR primer ...
    • Computational inference of mRNA stability from histone modification and transcriptome profiles 

      Wang, Chengyang; Tian, Rui; Zhao, Qian; Xu, Han; Meyer, Clifford; Li, Cheng; Zhang, Yong; Liu, Xiaole Shirley (Oxford University Press, 2012)
      Histone modifications play important roles in regulating eukaryotic gene expression and have been used to model expression levels. Here, we present a regression model to systematically infer mRNA stability by comparing ...
    • Genome-Wide Analysis of Neuroblastomas using High-Density Single Nucleotide Polymorphism Arrays 

      Attiyeh, Edward F.; Moreau, Lisa A.; Fortina, Paolo; Maris, John M.; George, Rani E.; Li, Shuli; Neuberg, Donna S.; Li, Cheng; Fox, Edward Alvin; Meyerson, Matthew Langer; Diller, Lisa Robin; Look, A. Thomas (Public Library of Science, 2007)
      Background: Neuroblastomas are characterized by chromosomal alterations with biological and clinical significance. We analyzed paired blood and primary tumor samples from 22 children with high-risk neuroblastoma for loss ...
    • Global Gene Expression Profiling in Whole-Blood Samples From Individuals Exposed to Metal Fumes 

      Wang, Zhaoxi; Neuburg, Donna; Li, Cheng; Su, Li; Kim, Jee Young; Chen, Jiu Chiuan; Christiani, David C. (National Institute of Environmental Health Sciences, 2005)
      Accumulating evidence demonstrates that particulate air pollutants can cause both pulmonary and airway inflammation. However, few data show that particulates can induce systemic inflammatory responses. We conducted an ...
    • Identifying Rare Variants Using a Bayesian Regression Approach 

      Yan, Aimin; Laird, Nan M.; Li, Cheng (BioMed Central, 2011)
      Recent advances in next-generation sequencing technologies have made it possible to generate large amounts of sequence data with rare variants in a cost-effective way. Statistical methods that test variants individually ...
    • Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays 

      Park, Yuhyun; Hao, Ke; Zhao, Xiaojun; Mellinghoff, Ingo K; Hofer, Matthias D; Descazeaud, Aurelien; Rubin, Mark A; Sellers, William R; Bourne, Philip; Beroukhim, Rameen; Lin, Ming; Garraway, Levi Alexander; Fox, Edward Alvin; Hochberg, Ephraim Paul; Meyerson, Matthew Langer; Wong, Wing H; Li, Cheng (Public Library of Science, 2006)
      Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on genotyping tumor and ...
    • Integrative analysis of gene and miRNA expression profiles with transcription factor–miRNA feed-forward loops identifies regulators in human cancers 

      Yan, Zhenyu; Shah, Parantu K.; Amin, Samir B.; Samur, Mehmet K.; Huang, Norman; Wang, Xujun; Misra, Vikas; Ji, Hongbin; Gabuzda, Dana Helga; Li, Cheng (Oxford University Press, 2012)
      We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI ...
    • Major Copy Proportion Analysis of Tumor Samples Using SNP Arrays 

      Li, Cheng; Beroukhim, Rameen; Weir, Barbara Ann; Winckler, Wendy; Garraway, Levi Alexander; Sellers, William R; Meyerson, Matthew Langer (BioMed Central, 2008)
      Background: Single nucleotide polymorphisms (SNPs) are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been developed for high-throughput ...
    • Model-based Analysis of Oligonucleotide Arrays: Model Validation, Design Issues and Standard Error Application 

      Li, Cheng; Hung Wong, Wing (BioMed Central, 2001)
      Background: A model-based analysis of oligonucleotide expression arrays we developed previously uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based ...
    • A Plasma Biomarker Signature of Immune Activation in HIV Patients on Antiretroviral Therapy 

      Kamat, Anupa U; Misra, Vikas; Cassol, Edana; Ancuta, Petronela; Yan, Zhenyu; Li, Cheng; Morgello, Susan; Gabuzda, Dana Helga (Public Library of Science, 2012)
      Background: Immune activation is a strong predictor of disease progression in HIV infection. Combinatorial plasma biomarker signatures that represent surrogate markers of immune activation in both viremic and aviremic HIV ...
    • The Polyoma Virus Large T Binding Protein p150 Is a Transcriptional Repressor of c-MYC 

      Sung, Chang Kyoo; Yim, Hyungshin; Gu, Hongcang; Li, Dawei; Andrews, Erik; Duraisamy, Sekhar; Li, Cheng; Drapkin, Ronny I.; Benjamin, Thomas L. (Public Library of Science, 2012)
      p150, product of the SALL2 gene, is a binding partner of the polyoma virus large T antigen and a putative tumor suppressor. p150 binds to the nuclease hypersensitive element of the c-MYC promoter and represses c-MYC ...