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The Chen Lab is a system biology research group interested in computational modeling of cell identity regulation in development and diseases.


The most important discovery in the lab is that the cell identity genes as a unique group are distinct from other genes in the molecular mechanisms to regulate their expression (Kaifu Chen, et al, Nature Genetics 2015; Shilpa Dhar, et al, Molecular Cell 2018; Dongyu Zhao, et al, Manuscript Submitted). This finding provided insight into the molecular regulation of normal cell identities in development and dysregulation of cell identity in diseases, particularly in cancers. The finding further laid the foundation for us to develop bioinformatics technique to uncover cell identity regulators and cancer driver genes. The technique has been proved to successfully recapture known cancer driver genes, and further, overcome critical constraint on current technologies by successfully identifying many cancer driver genes that were not detectable by conventional mutation analysis. These cancer driver genes led to new therapeutic targets and diagnostic markers as have been verified in cell, xenograft, and PDX models (Sen Zhu, et al, Nature Communications, 2018; Qipeng Liu, et al, IJC 2018; Sen Zhu, et al, Submitted) and thus, will benefit numerous cancer patients.


Major research directions in the lab include:

  • Develop bioinformatics techniques to gain novel biomedical insight into genome, epigenome, and transcriptome data.
  • Study expression regulation mechanisms on the basis of cutting-edge bioinformatics methods, and in combination with genomic, molecular, cellular, and animal experiments.


Science.jpg




Recent news:

January, 2019:

  • Jie and Bo's paper in collaboration with the Fang and Bai labs is accepted to Science. Jie developed a new bioinformatics tool CAGREfor this project and successfully applied it to the genomic data interpretation. Congratulations!

December, 2018:

  • Dr. Xin Wang joined the group as a new postdoc, welcome onboard!
  • Dr. Trinh Tat joined the group as a new postdoc, she will receive joint postdoctoral training in the Kiss and Chen labs, welcome onboard!
  • Guangyu's paper in collaboration with Qipeng and Qiaqia is accepted to the International Journal of Cancer. Cheers

October, 2018:

  • Bo's paper in collaboration with Yang under supervision of Greg was accepted to Nature. Bo developed a new bioinformatics tool FAID for this project and successfully applied it to the genomic data interpretation. Bo is a co-first author, Guangyu is a co-author, and Kaifu is the co-coressponding author, Cheers!
  • Dongyu received the Moran Foundation Award, a $2,000 addition to paycheck. Congratulations!

September, 2018:

  • Kaifu received the Houston Methodist Career Cornerstone Award. Cheers!

August, 2018:

  • Bo's paper for aging research based on Ribo-Seq data in collaboration with Zheng was accepted to Elife. Cheers!
  • Dr. Min Zhang joined the group as a new postdoc, welcome onboard!

July, 2018:

  • Kaifu was assigned as the founding Director to develop a Center for Bioinformatics and Computational Biology. The center will thrive to a size of 4-6 faculties in the following 5 years.
  • Dr. Yanqiang Li joined the group as a new postdoc, welcome onboard!

June, 2018:

  • Kaifu was promoted to Associate Professor, many thanks to hard workings of the fantastic team in the past 3 years!
  • Kaifu received an Houston Methodist Award For Excellence in Peer-reviewed Publication for the discovery of the key role for MLL4 in establishing Broad H3K4me3 and Super enhancers at tumor suppressor genes (Zhao, et al, Molecular Cell 2018)

May, 2018:

  • Dr. Yiwen Bu, who published a paper in Nature Cell Biology very recently, joined the group as a new postdoc, welcome onboard!

April, 2018:

  • Dongyu's paper with Shilpa et al got accepted to Molecular Cell, the 19th paper published by the new lab, cheers!
  • Kaifu received an Houston Methodist Award For Excellence in Peer-reviewed Publication for the discovery of the a novel role for BMI1 in regulating AR signaling in prostate cancer (Zhao, et al, Nature Communications 2018)

Dec, 2017:

  • Dongyu's paper in collaboration with Sen et al was accepted to Nature Communications, the 16th paper published by the new lab, Cheers!

September, 2017:

  • Dr. Guangyu Wang joined the group as a new postdoc, welcome onboard!

May, 2017:

  • Houston Methodist is named one of “America’s Best Employers” by Forbes magazine for the second year in a row.
  • Dr. Lei La will be a visiting scholar in the lab for 1 year. Dr. La is an Associate Professor at the Southern Medical University Nanfang Hospital ( a top hospital in China). Welcome!

April, 2017:

  • Kaifu provided a talk in the EB / ASBMB annual meeting 2017.
  • Dongyu's first-authorship manuscript for prostate cancer research is submitted, fingers crossed!
  • Dongyu's first-authorship manuscript for brain cancer research is submitted, fingers crossed!

March, 2017:

  • Kaifu become a member of the NCI-Funded Interdisciplinary Approaches to Cancer Metastasis Workshop, and will work together with the workshop to develop highly innovative and collaborative projects on cancer metastasis.
  • A manuscript is accepted by Elife. Alin and Kaifu help the collaborators interpret the 17 sets of RNA-Seq data. Cheers!

February, 2017:

  • A manuscript is accepted by the Nature Chemical Biology journal, Jie conducted the RNA-Seq analysis for this project. Cheers!

January, 2017:

  • Dr. Guangyu Wang from Beijing Institute of Genomiocs will join the lab as a postdoc soon, welcome!
  • Ms. Karen Lai from UT Austin will be an undergraduate intern in the lab this summer, welcome!

December, 2016:

  • A manuscript is accepted by the Science journal, Kaifu helps supervising the MNase-Seq and ChIP-Seq analysis and is a co-author. Cheers!

November, 2016:

  • Alin will start his tenure-track faculty position (assistant professor of statistics) at the Manhattan College. Congratulations!
  • Bo has joined the lab. Welcome onboard!

September, 2016

  • A manuscript is accepted to the Journal of the American Heart Association, Jie and Kaifu are co-authors, cheers!
  • A manuscript is accepted to the Nucleic Acids Research, Kaifu is a co-author, cheers!
  • Dr. Qingshu Meng will be visiting the lab for 1 year. Dr. Meng has outstanding background in Genomics research, and is a group leader at Beijing Institute of Genomics. Welcome!

August, 2016

  • Kaifu will be an adjunt assistant professor of Texas A&M.
  • Dr. Bo Xia from Georgia Tech will join the lab as a fresh postdoc soon. Dr. Xia is a PhD of biology and Master of computer science. Welcome!

April, 2016

  • Jie's paper was accepted by Molecular Cell, congratulations!

April, 2016

  • New postdoc position opening.
  • Jie's co-first authorship manuscript is under revision at Molecular Cell (IF 14), fingers crossed!

December, 2015

  • Kaifu's new manuscript was accepted to the Nucleic Acids Research, thank Alin for his help with the revision work!
  • A manuscript was accepted to the Molecular and Cellular Biology, thank Dongyu for his help with the revision work!

November, 2015

  • Dr. Jie Lu has joined the lab as postdoctoral Fellow, welcome onboard!

October, 2015

  • Dr. Dongyu Zhao has joined the lab as postdoctoral Fellow, welcome onboard!

September, 2015

August, 2015

  • Kaifu's data-revisiting paper is accepted to Nature Genetics.
  • Kaifu's MeCP2 mCH-binding paper (with Dr. Zoghbi lab) has been accepted to PNAS.





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