Li Lab

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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 . 05/2017: Our TCGA Liver Cancer paper was accepted to Cell. . 02/2017: Our Research Center for Cancer Systems Biology (CCSB U54) grant was funded by NCI, in collaboration with Qianben Wang, Victor Jin and Tim Huang. . 02/2017: Collaborative work with Xiaobing Shi and David Allis was accepted to Nature. . 12/2016: Graduate student Xueqiu Lin will start his postdoc position at Stanford. . 11/2016: Jianfeng Xu has passed his qualify exam. Congratulations! . 08/2016: Welcome our new Postdoc Associates Drs. Xiaodong Cui, Jiejun Shi and Lei Li. . 08/16: Zheng Xia will start his tenure-track faculty position at Oregon Health & Science University (OHSU) with a million-dollar package. Congratulations! . 07/16: Wei has been promoted to Professor of Bioinformatics at Baylor College of Medicine. . 06/16: Xueqiu successfully defended her PhD thesis. Congratulations Dr. Lin. . 06/16: A new paper w/ MG Lee @ MD Anderson was accepted to Molecular Cell. . 04/16: Jianzhong's DNMT3A/TET2 paper (w/ Goodell lab) was accepted to Nature Genetics. . 04/16: Wei has been selected as a recipient of the 2016 Michael E. DeBakey, M.D., Excellence in Research Award . 04/16: Yuanxin has been offered a tenure-track faculty position at The University of Texas Health Science Center at Houston (UTHealth). Congratulations! . 03/2016: Ben's enhancer hypomethylation paper (w/ Goodell lab) was accepted to Cancer Cell. . 02/2016: Yuanxin's SIRT6 paper (w/ Chua lab at Stanford) was accepted to Nature Structural & Molecular Biology . 01/2016: Welcome our new Postdoc Associate Dr. Jie Lyu. . 12/2015: Yuanxin's G9a paper (w/ Shi lab at MD Anderson) was accepted to Nature Communications. . 12/2015: Kaifu's UTX paper (w/ Lee lab at MD Anderson) was accepted to Nucleic Acids Research . . 11/2015: We received a new NIH/NCI R01 grant (scored at 5%ile) to study 3`UTR alternations in human cancers. . 09/2015: Welcome our new Research Associate (and potential Graduate Student) YanBing Cheng. . 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 reports in Nature Editor’s Blog, Cancer Discovery, ebiotrade.com (in Chinese), BCM news and OSU news; and an error we found in a Cell paper. . 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! . 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. News Archive

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 Published >95 peer-reviewed papers through solid methodology development and extensive collaboration research, including >37 in Nature, Science and Cell series. Been well-funded by NIH and Texas CPRIT with total external funding >$1.0 million per year. Dr Li is the PI on the following 3 major grants: NIH R01HG007538 (2013-2018) and R01CA193466 (2015-2020); CPRIT RP150292 (2015-2018). Mentored the first 5 postdoc trainees to start their tenure track faculty positions in prestigious research institutions in the US. 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 >3000 citations since 2008. In collaboration with experimental biologists, we used these algorithms to gain novel biological insights from various biological processes and disease models. Chromatin Factors: ER in breast cancer, AR in prostate cancer, FoxA1 pioneer factor, Atoh1 in neuron development, NSD2 in oncogenic programming, SIRT7 in cancer transformation, ZM11 in transcription elongation, and p53 in ES differentiation.. DNA Methylation: DNA methylation Canyon, Epigenetic changes in HSC aging, Dnmt3a in HSC differentiation and cancer transformation. Nucleosome Organization: Fragile nucleosome in stress-response, Promoter nucleosome with Tup1, Nucleosome dynamics in ES differentiation, and Global nucleosome loss in yeast aging. Transcriptome: chimeric RNA in prostate cancer, Long non-coding RNA in HSC, 3’UTR deletion in cancer and its master regulator CFIm25. . Lab Intranet openwetware

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