Li Lab

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Recent News)
Current revision (15:39, 18 December 2014) (view source)
(Recent News)
 
(74 intermediate revisions not shown.)
Line 6: Line 6:
<div style="float:left;margin-left:0.3em;margin-right:0.7em">
<div style="float:left;margin-left:0.3em;margin-right:0.7em">
-
== '''Wei Li's Computational Epigenomics Lab''' ==  
+
== '''Computational Epigenomics and Transcriptomics Lab (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]
Line 15: Line 15:
==Recent News==
==Recent News==
-
. 12/2012: [http://www.bcm.edu/news/item.cfm?newsID=6723 BCM News] and  [http://epigenie.com/danpos-reveals-dynamic-nucleosomes headline at Epigenie] about our recent work on nucleosome dynamics.
+
. 12/2014: We will receive a 3-year '''CPRIT R01''' grant to study 3`-UTR alterations in human cancers.
-
. 12/2012Kaifu's variomics paper with Xuewen Pan lab was accepted to '''Cell Reports'''.
+
. 12/2014Zheng Xia awarded '''Keck fellowship''' in Computational Cancer Biology.
-
. 12/2012:  Liguo and HJ's CPAT RNA coding potential prediction paper was accepted to '''Nucleic Acids Research'''.
+
. 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 [https://www.activemotif.com/catalog/1050/chip-exo ChIP-exo kit and service].
-
. 11/2012: Kaifu's nucleosome methodology paper DANPOS was accepted to '''Genome Research'''.
+
. 09/2013: Deqiang will start his tenure-track assistant professor position. Job well done. 
-
. 10/2012Kaifu's promoter nucleosome paper was accepted to '''Genome Research'''.
+
. 09/2013Zheng's prostate cancer RNA-seq paper with Dr. Balk at Harvard is accepted to '''Molecular Cancer Research '''. Yuanxin's work on H3K79 Methylation with Dr. Shi is accepted to '''Cell'''.
-
. 09/2012A '''NIH R01 grant''' was funded. We will work with Dr. Issa at Temple Univ. to understand DNA methylation in Cancer.
+
. 08/2013Zheng's DaPars 3'UTR Pan Cancer analysis paper is accepted in principle to '''Nature Communications''';
-
. 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.
+
. 08/2013: '''Three Collaboration CPRIT grants''' are funded: DNA methylation with Goodell lab, 3'UTR with Wagner lab and ZM11 with Shi lab.
-
. 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!
+
. 08/2014: Kaifu's "super promoter" paper is under review in '''Nature Genetics'''.  
-
. 08/2012A '''Mazzone Award ''' was funded. We will work with Dr. Balk at Harvard Medical School to understand the molecular features of aggressive prostate cancer.
+
. 06/2014Deqiang's Dnmt3a/3b double KO paper (with the Goodell Lab) is accepted to '''Cell Stem Cell '''.  
-
. 06/2012: Dr. Ira's Fun30 nucleosome remodeler paper was accepted to '''Nature'''. Kaifu is a co-author.
+
. 06/2014: Zheng's alternative splicing paper (with the Cooper Lab) is accepted to '''Molecular Cell '''.  
-
+
-
. 06/2012: Liguo's RNA-seq Quality Control paper was accepted to '''Bioinformatics'''.
+
-
. 06/2012A '''NIH R01 grant''' was funded. We will work with Dr. Goodell at BCM to understand DNA methylation in Hematopoietic Stem Cell.
+
. 02/2014Deqiang and Hyun Jung's HSC LncRNA paper (with the Goodell Lab) is in revision in '''Cell Stem Cell'''.  
-
. 04/2012A '''NIH R01 grant''' was funded. We will work with Dr. Dent at MD Anderson to define USP22 functions during mammalian development.
+
. 02/2014Zheng's collaborative work on alternative splicing in heart development is accepted to '''Nature Communications'''.  
-
. 04/2012Dr.Dean Tang's prostate cancer stem cell paper was accepted in '''Cell Stem Cell'''. Wei is a co-author.
+
. 02/2014Zheng'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.
-
. 02/2012Yuanxin's epigenetic paper with Katrin Chua lab at Stanford was accepted to '''Nature'''. Two years of hard work finally paid off!
+
. 02/2014Welcome our new postdoc Jianzhong Su and graduate student Xueqiu Lin.
-
. 02/2012Liguo Wang was offered a '''tenure-track Assistant Professor''' position at Mayo Clinic. Congratulations!
+
. 02/2014Deqiang'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:  Our collaborative work on Breast Cancer Epigenetics is accepted to '''Science Translational Medicine'''.
 +
 
 +
. 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.
 +
 
 +
. 12/2013: Kaifu's aging nucleosome paper is accepted to ''' Genes & Development'''
 +
 
 +
. 12/2013: We received a 5-year NIH/NHGRI '''R01''' grant (scored at 6 percentile in its first submission) to study DNA Methylation
 +
 
 +
. 11/2013: Wei will serve on the Editorial Board of '''Molecular Endocrinology'''
 +
 
 +
. 09/2013:  Deqiang's DNA methylation Canyon paper is accepted to '''Nature Genetics'''.
 +
 
 +
. 09/2013:  Xueqiu's bisulfite sequencing quality control paper (BSeQC) is accepted to '''Bioinformatics'''.
 +
 
 +
. 08/2013:  Kadir's p53 paper is accepted to '''Nucleic Acids Research'''
 +
 
 +
. 01/2013:  [http://www.bcm.edu/news/item.cfm?newsID=6723 BCM News] and  [http://epigenie.com/danpos-reveals-dynamic-nucleosomes Epigenie Headline] about our recent work on nucleosome dynamics.
-
. 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!
 
[[Image:Banner.jpg‎‎]]
[[Image:Banner.jpg‎‎]]
Line 71: Line 88:
<div style="border-bottom: 1px dashed #9999CC;">
<div style="border-bottom: 1px dashed #9999CC;">
-
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.  
+
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 more than 66 peer-reviewed papers in high profile journals, such as Nature, Cell, Nature Genetics, Cell Stem Cell, Molecular Cell, Nature Communications, Genome Research, Genome Biology, PNAS, Genes and Development, Nucleic Acids Research, Cancer Research, and Bioinformatics.
 +
 
 +
We have developed a number of widely used algorithms to analyze next generation sequencing data from ChIP-seq (MACS, MACE, DyChIPS), 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 >1600 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.  
-
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).
+
* '''Nucleosome Organization''': Fragile nucleosome in stress-response, Promoter nucleosome with Tup1, Nucleosome dynamics in ES differentiation, and Global nucleosome loss in yeast aging.
-
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).
+
* '''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

. 12/2014: We will receive a 3-year CPRIT R01 grant to study 3`-UTR alterations in human cancers.

. 12/2014: Zheng Xia awarded Keck fellowship in Computational Cancer Biology.

. 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.

. 09/2013: Deqiang will start his tenure-track assistant professor position. Job well done.

. 09/2013: Zheng's prostate cancer RNA-seq paper with Dr. Balk at Harvard is accepted to Molecular Cancer Research . Yuanxin's work on H3K79 Methylation with Dr. Shi is accepted to Cell.

. 08/2013: Zheng's DaPars 3'UTR Pan Cancer analysis paper is accepted in principle to Nature Communications;

. 08/2013: Three Collaboration CPRIT grants are funded: DNA methylation with Goodell lab, 3'UTR with Wagner lab and ZM11 with Shi lab.

. 08/2014: Kaifu's "super promoter" paper is under review in Nature Genetics.

. 06/2014: Deqiang's Dnmt3a/3b double KO paper (with the Goodell Lab) is accepted to Cell Stem Cell .

. 06/2014: Zheng's alternative splicing paper (with the Cooper Lab) is accepted to Molecular Cell .

. 02/2014: Deqiang and Hyun Jung's HSC LncRNA paper (with the Goodell Lab) is in revision in Cell Stem Cell.

. 02/2014: Zheng's collaborative work on alternative splicing in heart development is accepted to Nature Communications.

. 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: Our collaborative work on Breast Cancer Epigenetics is accepted to Science Translational Medicine.

. 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.

. 12/2013: Kaifu's aging nucleosome paper is accepted to Genes & Development

. 12/2013: We received a 5-year NIH/NHGRI R01 grant (scored at 6 percentile in its first submission) to study DNA Methylation

. 11/2013: Wei will serve on the Editorial Board of Molecular Endocrinology

. 09/2013: Deqiang's DNA methylation Canyon paper is accepted to Nature Genetics.

. 09/2013: Xueqiu's bisulfite sequencing quality control paper (BSeQC) is accepted to Bioinformatics.

. 08/2013: Kadir's p53 paper is accepted to Nucleic Acids Research

. 01/2013: BCM News and Epigenie Headline about our recent work on nucleosome dynamics.


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 more than 66 peer-reviewed papers in high profile journals, such as Nature, Cell, Nature Genetics, Cell Stem Cell, Molecular Cell, Nature Communications, Genome Research, Genome Biology, PNAS, Genes and Development, Nucleic Acids Research, Cancer Research, and Bioinformatics.

We have developed a number of widely used algorithms to analyze next generation sequencing data from ChIP-seq (MACS, MACE, DyChIPS), 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 >1600 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


Image:WeiLi.jpg‎


Personal tools