Li Lab

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== '''Wei Li's Computational Epigenomics Lab''' ==  
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== '''Computational Cancer Epigenomics and Transcriptomics (PI: Wei Li)''' ==  
[http://www.bcm.edu/cancercenter/ Dan L. Duncan Cancer Center], [http://www.bcm.edu/mcb/index.html Department of Molecular and Cellular Biology], [http://www.bcm.edu/ Baylor College of Medicine]
[http://www.bcm.edu/cancercenter/ Dan L. Duncan Cancer Center], [http://www.bcm.edu/mcb/index.html Department of Molecular and Cellular Biology], [http://www.bcm.edu/ Baylor College of Medicine]
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==Recent News==
==Recent News==
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. 11/2012: Liguo and HJ's CPAT RNA coding potential prediction paper was in minor revision at '''Nucleic Acids Research'''.
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. 08/2017: Xueqiu's scUMC DNA methylation paper was accepted to  '''Genome Biology'''.
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. 11/2012: Kaifu's nucleosome methodology paper DANPOS was accepted to '''Genome Research'''.
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. 07/2017: Jianzhong's DNA methylation editing paper was published in  '''Nature Communications'''.
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. 10/2012: Kaifu's promoter nucleosome paper was accepted to '''Genome Research'''.
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. 05/2017: Our TCGA Liver Cancer paper was accepted to '''Cell'''.
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. 09/2012: A '''NIH R01 grant''' was funded. We will work with Dr. Issa at Temple Univ. to understand DNA methylation in Cancer.
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. 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.
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. 08/2012: A mouse ES nucleosome paper from Kaestner lab at Upenn was accepted to '''Cell'''. Kaifu and Wei used DANPOS to analyze the data and were listed as co-authors.
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. 02/2017: Collaborative work with Xiaobing Shi and David Allis was accepted to '''Nature'''.
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. 08/2011: Dr. Benjamin Rodriguez will join us as a '''Postdoc Associate'''. Ben has PhD in Integrated Biomedical Science from the Ohio State Univ. Eric B. Rutledge, a BCM MD/PhD student,  joined us for his term 2 '''rotation'''. Welcome!
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. 12/2016: Graduate student Xueqiu Lin will start his postdoc position at Stanford.
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. 08/2012: A '''Mazzone Award ''' was funded. We will work with Dr. Balk at Harvard Medical School to understand the molecular features of aggressive prostate cancer.
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. 11/2016: Jianfeng Xu has passed his qualify exam. Congratulations!
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. 06/2012: Dr. Ira's Fun30 nucleosome remodeler paper was accepted to '''Nature'''. Kaifu is a co-author.
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. 08/2016: Welcome our new Postdoc Associates Drs. Xiaodong Cui, Jiejun Shi and Lei Li.
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. 06/2012: Liguo's RNA-seq Quality Control paper was accepted to '''Bioinformatics'''.
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. 06/2012: A '''NIH R01 grant''' was funded. We will work with Dr. Goodell at BCM to understand DNA methylation in Hematopoietic Stem Cell.
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. 08/16: Zheng Xia will start his '''tenure-track faculty position''' at Oregon Health & Science University (OHSU) with a million-dollar package. Congratulations!
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. 04/2012: A '''NIH R01 grant''' was funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.
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. 07/16: Wei has been '''promoted to Professor of Bioinformatics''' at Baylor College of Medicine.
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. 04/2012Dr.Dean Tang's prostate cancer stem cell paper was accepted in '''Cell Stem Cell'''. Wei is a co-author.
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. 06/16Xueqiu successfully defended her PhD thesis. '''Congratulations Dr. Lin'''.  
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. 02/2012: Yuanxin's epigenetic paper with Katrin Chua lab at Stanford was accepted to '''Nature'''. Two years of hard work finally paid off!
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. 06/16: A new paper w/ MG Lee @ MD Anderson was accepted to '''Molecular Cell'''.
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. 02/2012: Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
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. 04/16: Jianzhong's DNMT3A/TET2 paper (w/ Goodell lab) was accepted to '''Nature Genetics'''.  
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. 02/2012: Justin Park will join us as a Postdoc Associate. Justin will graduate in May with a PhD in Computer Science from Rice University. Welcome!
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. 04/16: Wei has been selected as a recipient of the 2016 [https://www.bcm.edu/news/awards-honors-faculty-staff/2016-debakey-research-award-science  '''Michael E. DeBakey, M.D., Excellence in Research Award''']
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. 11/2011: Yuanxin's RRBSMAP paper was accepted to '''Bioinformatics'''.  
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. 04/16: Yuanxin has been offered a '''tenure-track faculty position''' at The University of Texas Health Science Center at Houston (UTHealth). Congratulations!
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. 09/2011Wei Li was promoted to tenured '''Associate Professor''' at BCM. Cheers!
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. 03/2016Ben's enhancer hypomethylation paper (w/ Goodell lab) was accepted to '''Cancer Cell'''.  
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. 09/2011Deqiang's DNA methylation paper with Peggy Goodell lab was accepted to '''Nature Genetics'''.
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. 02/2016Yuanxin's SIRT6 paper (w/ Chua lab at Stanford) was accepted to '''Nature Structural & Molecular Biology'''
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. 08/2011: Kaifu's NSD2 epigenetic paper with Or Gozani lab at Stanford was accepted to '''Molecular Cell'''.
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. 01/2016: Welcome our new Postdoc Associate Dr. Jie Lyu.
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. 08/2011A '''NIH R01 grant''' was funded. We will work with Dr. Wang at the Ohio State University to understand the role of histone methylations in prostate cancer.
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. 12/2015Yuanxin's G9a paper (w/ Shi lab at MD Anderson) was accepted to '''Nature Communications. '''
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. 07/2011Liguo's FoxA1 cistrome paper was accepted to '''Cancer Research'''.
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. 12/2015Kaifu's UTX paper (w/ Lee lab at MD Anderson) was accepted to '''Nucleic Acids Research '''.  
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. 07/2011: See our '''[http://www.genomeweb.com/node/973004 Genomic Regulation Technical Guide]''' on Genome Technology magazine
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. 11/2015: We received a new '''NIH/NCI R01''' grant (scored at 5%ile) to study 3`UTR alternations in human cancers. 
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. 07/2011: Dr. Zheng Xia will join us as a postdoc fellow. Zheng has PhD in Control Theory and Engineering Computer Science from Zhejiang University in China. Welcome!
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. 09/2015: Welcome our new Research Associate (and potential Graduate Student) YanBing Cheng.
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. 05/2011: Dr.Bert O'Malley's coregulator network paper was published in '''Cell'''. Wei is a co-author on the paper.
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. 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 [http://blogs.nature.com/freeassociation/2015/08/methylation-marks-tumor-suppressors.html Blog], [http://cancerdiscovery.aacrjournals.org/content/early/2015/09/01/2159-8290.CD-RW2015-166.abstract Cancer Discovery], [http://www.ebiotrade.com/newsf/2015-8/2015825165005119.htm ebiotrade.com] (in Chinese), [http://fromthelabs.bcm.edu/2015/10/15/novel-epigenetic-signature-for-tumor-suppressors-in-normal-cells-found/ BCM news] and [http://cancer.osu.edu/news-and-media/news/studies-suggest-new-ways-to-inhibit-oncogenes-enhance-tumor-suppressor-activity OSU news]; and an error we found in a [http://www.cell.com/cell/fulltext/S0092-8674(15)01407-5 Cell paper].
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. 04/2011Liguo's Prostate Cancer RNA-seq paper was officially accepted to  '''PNAS'''.
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. 07/2015Wei will become a regular member of the '''NIH GCAT''' (Genomics, Computational Biology and Technology) study section.
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. 03/2011: Our Texas '''CPRIT Multi-Investigator grant''' was funded with a total direct cost of ~$10M for 5 years. This project will bring together a "dream team" in cancer epigenetic researchWe will direct the bioinformatics component for LONESTAR.  
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. 06/2015: Kaifu will start his '''tenure-track faculty''' position at Cornell University & Methodist Hospital. Congratulations!
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. 03/2015: Kaifu's MeCP2 mCH binding paper (w/ Zoghbi lab) is accepted to '''PNAS'''.
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. 3/2015: We received a NEW '''CPRIT''' grant.   
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. 01/2015:  Deqiang, HJ and Ben's HSC novel noncoding RNA paper is accepted to '''Cell Stem Cell''' -- the 100th paper we published.
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. 01/2011:  Yuanxin's fragile nucleosome paper was accepted to  '''Genome Research'''.
 
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. 01/2011:  Yuanxin and Liguo's  Atoh1 targetome paper was accepted to  '''PNAS'''.
 
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Our lab is focused on the design and application of bioinformatics algorithms to elucidate global regulatory mechanism by integrating data from ChIP-seq, DNA methylation, Nucleosome positioning, and RNA-seq. We are also working with bench and clinical collaborators to understand epigenetic gene regulation and transcription dynamics in various biological processes and disease models.  
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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
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* '''Published''' >95 peer-reviewed papers through solid methodology development and extensive collaboration research, including >37 in '''Nature, Science and Cell''' series.
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* '''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).
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* '''Mentored''' the first 5 postdoc trainees to start their tenure track faculty positions in prestigious research institutions in the US.
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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.
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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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* '''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..
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* '''DNA Methylation''': DNA methylation Canyon, Epigenetic changes in HSC aging, Dnmt3a in HSC differentiation and cancer transformation.  
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We have developed a number of widely used algorithms to detect and annotate genome-wide cis-regulatory regions, including MAT ('''PNAS''' 2006) for analyzing ChIP-chip experiments on genome tiling arrays, MACS ('''Genome Biology''' 2008) for model based analysis of ChIP-seq, BSMAP/RRBSMAP ('''BMC Bioinformatics''' 2009; '''Bioinformatics''' 2012) for DNA methylation analysis using Bisulfite-seq, and fragile nucleosomes ('''Genome Re'''s 2011) using MNase-seq. These algorithms have gathered thousands of academic users worldwide and hundreds of citations, including > 50 papers in Cell and Nature series. We are currently working on bioinformatics development for 1) Transcription factor binding and histone modifications (ChIP-seq); 2) DNA methylation at single nucleotide resolution (Bisulfite-seq); 3) Nucleosome dynamics (Mnase-seq); 4) Alternative splicing (RNA-seq).
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* '''Nucleosome Organization''': Fragile nucleosome in stress-response, Promoter nucleosome with Tup1, Nucleosome dynamics in ES differentiation, and Global nucleosome loss in yeast aging.
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We have extensive experience in collaborative research including androgen and estrogen receptors in prostate and breast cancers ('''Cell''' 2005; '''Nature Genetics''' 2006; '''Molecular Cell''' 2007; '''Cell''' 2009), epigenetic regulation by histone modifications ('''Cell''' 2008; '''PNAS''' 2011; '''Cancer Res.''' 2011; '''Molecular Cell''' 2011; '''Nature''' 2012), nucleosome positioning ('''Genome Res.''' 2011), DNA methylation ('''Nature Genetics''' 2012) and novel chimerical RNAs in prostate cancer ('''PNAS''' 2011).
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* '''Transcriptome''': chimeric RNA in prostate cancer, Long non-coding RNA in HSC, 3’UTR deletion in cancer and its master regulator CFIm25. .
   
   

Current revision

Home        People        Publications        Collaborations        Software        Positions        Contact       


Recent News

. 08/2017: Xueqiu's scUMC DNA methylation paper was accepted to Genome Biology.

. 07/2017: Jianzhong's DNA methylation editing paper was published in Nature Communications.

. 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.


Image:Banner.jpg‎‎

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. .


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Image:WeiLi.jpg‎


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