Research Department

Biostatistics and Computational Biology

Area of Research

Biography

Dr. Li received his PhD from the University of California, Los Angeles, in 2001. Later that same year, he joined Dana-Farber Cancer Institute and the Harvard School of Public Health as a postdoctoral fellow. He was appointed Assistant Professor of Biostatistics in 2002 and Associate Professor of Biostatistics in 2008. He has played a seminal role in the development of model-based analysis of oligonucleotide microarrays and the microarray software package dChip.

Research

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. We collaborate with many experimental research labs that study cancer and neurological diseases.

Select Publications

• Lu T, Pan Y, Kao SY, Li C, Kohane I, Chan J, Yankner BA. Gene regulation and DNA damage in the aging human brain. Nature 2004;429:883-91.
• 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 oncogene amplified in malignant melanoma. Nature 2005;436:117-22.
• 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. 113(26):6681-90.
• Li C. Automating dChip: toward reproducible sharing of microarray data analysis. BMC Bioinformatics. 2008; 9:231.
• 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.
• Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics. 2007; 8(1):118-127
• 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 Tumor-only Samples Using High-Density Oligonucleotide SNP Arrays. PLoS Computational Biology. 2006; 2(5): e41.

Trainees

• Amin, Samir B., MBBS
• Yan, Zhenyu, PhD
• Shah, Parantu K., PhD