Li Lab: Difference between revisions
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==Recent News== | ==Recent News== | ||
. 09/2015: Welcome our new Research Associate (and potential Graduate Student) YanBing Chen. | |||
. 08/2015: Kaifu's Cancer Big-data analysis paper is published in '''Nature Genetics'''. This work links broad H3K4me3 to pan-cancer tumor suppressors. See Nature Editor’s [http://blogs.nature.com/freeassociation/2015/08/methylation-marks-tumor-suppressors.html Blog] and Chinese Report in [http://www.ebiotrade.com/newsf/2015-8/2015825165005119.htm ebiotrade.com] | . 08/2015: Kaifu's Cancer Big-data analysis paper is published in '''Nature Genetics'''. This work links broad H3K4me3 to pan-cancer tumor suppressors. See Nature Editor’s [http://blogs.nature.com/freeassociation/2015/08/methylation-marks-tumor-suppressors.html Blog] and Chinese Report in [http://www.ebiotrade.com/newsf/2015-8/2015825165005119.htm ebiotrade.com] | ||
Revision as of 12:31, 6 October 2015
Computational Cancer Epigenomics and Transcriptomics (PI: Wei Li)Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine |
Recent News. 09/2015: Welcome our new Research Associate (and potential Graduate Student) YanBing Chen. . 08/2015: Kaifu's Cancer Big-data analysis paper is published in Nature Genetics. This work links broad H3K4me3 to pan-cancer tumor suppressors. See Nature Editor’s Blog and Chinese Report in ebiotrade.com . 07/2015: Wei will become a regular member of the NIH GCAT (Genomics, Computational Biology and Technology) study section. . 06/2015: Kaifu will start his tenure-track faculty position at Cornell University & Methodist Hospital. Congratulations! . 06/2015: We will receive a NEW NIH/NCI R01 grant (scored at 5%ile) to study 3`UTR alternations in human cancers. . 03/2015: Kaifu's MeCP2 mCH binding paper (w/ Zoghbi lab) is accepted to PNAS. . 3/2015: We received a NEW CPRIT grant. . 01/2015: Deqiang, HJ and Ben's HSC novel noncoding RNA paper is accepted to Cell Stem Cell -- the 100th paper we published. . 12/2014: Zheng Xia is awarded a Keck fellowship in Computational Cancer Biology. . 11/2014: Zheng's DaPars 3'UTR Pan Cancer analysis paper is published in Nature Communications. . 09/2014: Liguo's ChIP-exo methodology paper (MACE) is accepted to Nucleic Acids Research. MACE is recommended by Active Motif as the software solution for the company's new ChIP-exo kit and service. . 09/2014: Deqiang will start his tenure-track assistant professor position. Job well done. . 09/2014: Zheng's prostate cancer RNA-seq paper with Dr. Balk at Harvard is accepted to Molecular Cancer Research . . 09/2014: Yuanxin's work on H3K79 Methylation with Dr. Shi is accepted to Cell. . 08/2014: Three Collaborative CPRIT grants are funded: DNA methylation with Goodell lab, 3'UTR with Wagner lab and ZM11 with Shi lab. . 06/2014: Deqiang's Dnmt3a/3b double KO paper (w/ Goodell Lab) is accepted to Cell Stem Cell . . 06/2014: Zheng's alternative splicing paper (w/ Cooper Lab) is accepted to Molecular Cell . . 02/2014: Zheng's brain tumor 3'UTR regulator paper is accepted to Nature. This paper was initially rejected after review twice. We appealed twice with success and finally made it in the 3rd submission. . 02/2014: Welcome our new postdoc Jianzhong Su and graduate student Xueqiu Lin. . 02/2014: Deqiang's mouse HSC Aging Epigenomics paper is accepted in principle to Cell Stem Cell. . 01/2014: Deqiang's Methodology paper for the detection of differential DNA Methylation (MOABS) is accepted to Genome Biology. . 01/2014: Yuanxin and Zheng's ZM11 paper with Xiaobing Shi lab in MD Anderson is accepted to Nature. This work links transcription elongation to tumor suppression.
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Our lab is focused on the design and application of bioinformatics algorithms to elucidate global epigenetic mechanisms and transcription dynamics in normal development and diseases such as cancer. Since establishing the lab in early 2008, we have
We have developed a number of widely used algorithms to analyze next generation sequencing data from ChIP-seq (MACS, MACE), DNA methylation Bisulfite-seq (BSMAP/RRBSMAP, BSeQC, MOABS), nucleosome positioning MNase-seq (DANPOS), and RNA-seq (CPAT, RSeQC, DaPars). These algorithms have been broadly adopted by thousands of academic users. For example, the MACS algorithm has gathered >1900 citations since 2008. In collaboration with experimental biologists, we used these algorithms to gain novel biological insights from various biological processes and disease models.
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