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Chen Laboratory

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PI:Kaifu Chen, PhD

Assistant Professor: 07/2015 - present
The Methodist Hospital Research Institute, Houston, Texas, United States
Weill Cornell Medical College, Cornell University, New York, United States

Instructor: 12/2013 - 07/2015
Postdoctoral Associate: 09/2009 - 12/2013
Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States

Ph.D. in Genomics: 09/2004 - 09/2009
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China

Dr. Chen received his undergraduate training in Biophysics from 2000 to 2004 in the renown Nankai University, where he studied in both the Physics and the Biology institutes. Thereafter he was admitted as a Ph.D. student to the Beijing Institute of Genomics, which is the first genome center in China and has accomplished many famous genomic researches, e.g., the Human Genome Project. Dr. Chen spent 4 years on the Trichomonas Vaginalis Genome Project, in which he experienced the growing of their research team from 3 to dozens of scientists, and soon become the bioinformatics group leader. Dr. Chen was one of the 10 scientists selected out from Beijing Institute of Genomics in August 2008 to build a new genome center in Saudi Arabia and initiate the international Date Palm Genome Project. Due to their significant contribution, Dr. Chen and his colleagues were visited and highly appreciated by the former Chinese President Hu Jintao in February 2009.

Dr. Chen developed the first tool for genome analysis based on Power Spectrum Density algorithm, and discovered a 121bp periodicity in nucleotide composition along T. Vaginalis DNA sequence. He successfully proved that the periodicity is a genomic signature of nucleosome positions in chromatin, and further proved that similar periodicity exists in each other genome, with unit size ranges from 165, 175, to 193bp in Yeast, Worm, and Human, respectively. This is the third sequence periodicity discovered in genome sequence, with the earlier other two being the 3bp and the 10bp periodicities, which served as critical clues in discovering the amino acid codes and DNA double-strands helix structure, respectively.

Promoted by the exciting study on genomic signature of nucleosome positions, an important epigenetic mechanism, Dr. Chen went to Baylor College of Medicine in September 2009 to focus on computational epigenetic research. He developed DANPOS, the first statistical framework for comparing nucleosome organization between different conditions based on MNase-Seq data. Dr. Chen further improved DANPOS to provide new methodology for histone modification ChIP-Seq analysis, and used this tool to gain novel biomedical insight by revisiting tons of published high throughput sequencing data. This innovative research strategy promoted Dr. Chen to discover for the first time that epigenetic signature, such as broad H3K4me3, can serve as robust clue for cancer gene discovery.

Dr. Chen has also been collaborating closely with over a dozen of fantastic wet-bench laboratories, e.g., the labs of Dr. Or Gozani, Dr. Sharon Dent, Dr. Klaus H. Kaestner, Dr. Jessica Tyler, and Dr. Huda Zoghbi. Findings from those researches have been published in over 20 articles in high impact journals, e.g., Nature, Cell, PNAS, Genome Research, Molecular Cell, Genes & Development.

POSTDOCS

Multiple postdoctoral fellows are coming …