Papers citing dChip (Li and Wong 2001 PNAS) (1322+)

Papers citing dChipSNP (Lin et al. 2004 Bioinformatics) (123+)

Selected Applications

Cheng Li (2008) Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics. 9:231. (PubMed)

Cheng Li, Rameen Beroukhim, Barbara A. Weir, Wendy Winckler, Levi A. Garraway, William R. Sellers, Matthew Meyerson (2008) Major copy proportion analysis of tumor samples using SNP arrays. BMC Bioinformatics. 9:204. (PubMed)

Beroukhim R^†, Lin M^†, Park Y, Hao K, Zhao X, Garraway LA, Fox EA, Hochberg EP, Mellinghoff IK, Hofer MD, Descazeaud A, Rubin MA, Meyerson M, Wong WH, Sellers WR*, Li C* (2006) Inferring Loss-of-Heterozygosity From Tumor-only Samples Using High-Density Oligonucleotide SNP Arrays. PLoS Computational Biology. 2(5): e41. (PubMed, dChip usage, ^†Joint first authors)

Igor Leykin, Ke Hao, Junsheng Cheng, Nicole Meyer, Martin R Pollak, Richard JH Smith, Wing Hung Wong, Carsten Rosenow*, Cheng Li* (2005) Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data. BMC Genetics. 6:7. (PubMed, Software, dChip usage)

Ming Lin, Lee-Jen Wei, William R. Sellers, Marshall Lieberfarb, Wing Hung Wong*, and Cheng Li* (2004) dChipSNP: Significance Curve and Clustering of SNP-Array-Based Loss-of-Heterozygosity Data. Bioinformatics. 20: 1233-1240. (PubMed, Journal, Data and Software, dChip usage)

Sheng Zhong, Cheng Li* and Wing Hung Wong* (2003) ChipInfo: Software for Extracting Gene Annotation and Gene Ontology Information for Microarray Analysis. Nucleic Acids Research. Vol. 31, 3483-3486. (PubMed, Journal, Software, dChip usage)

Cheng Li and Wing Hung Wong (2003) DNA-Chip Analyzer (dChip). In The analysis of gene expression data: methods and software. Edited by G Parmigiani, ES Garrett, R Irizarry and SL Zeger. Springer, New York. 120-141. (Book site)

Cheng Li and Wing Hung Wong (2001b) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application, Genome Biology 2(8): research0032.1-0032.11 (PubMed)

Cheng Li and Wing Hung Wong (2001a) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection, Proc. Natl. Acad. Sci. Vol. 98, 31-36. (PubMed, Journal)