DF/HCC Program Affiliation

Biostatistics

Research Abstract

We develop analysis methods and software for high-throughput microarray and sequencing data, and apply these methods to cancer and neuroscience studies. We use gene expression arrays, SNP arrays, and microRNA platforms for integrative analysis of genomic alteration patterns in human diseases such as cancer. We also develop and maintain the dChip software for microarray analysis, which has been cited more than 1600 times.

Publications

• Avet-Loiseau H, Li C, Magrangeas F, Gouraud W, Charbonnel C, Harousseau JL, Attal M, Marit G, Mathiot C, Facon T, Moreau P, Anderson KC, Campion L, Munshi NC, Minvielle S.Prognostic significance of copy-number alterations in multiple myeloma.J Clin Oncol
  19687334
• Li C,Kim SW,Rai D,Bolla AR,Adhvaryu S,Kinney MC,Robetorye RS,Aguiar RC.Copy number abnormalities, MYC activity and the genetic fingerprint of normal B-cells mechanistically define the microRNA profile of DLBCL.Blood 2009 Mar 10.
  19278952
• Li C.Automating dChip: toward reproducible sharing of microarray data analysis.BMC Bioinformatics 2008 May 8;9(1):231.
  18466620
• Li C, Beroukhim R, Weir BA, Winckler W, Garraway LA, Sellers WR, Meyerson M.Major copy proportion analysis of tumor samples using SNP arrays.BMC Bioinformatics 2008;9:204.
  18426588
• 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.Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide S
  16699594
• Johnson WE, Rabinovic A, Li C.Adjusting batch effects in microarray expression data using Empirical Bayes methods.Biostatistics 2006 Apr 21.
  16632515
• Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR.Integrative genomic analyses identify MITF as a lineage survival onc
  16001072