Li Lab: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(242 intermediate revisions by 3 users not shown)
Line 1: Line 1:
<center>{{Template:Li Lab}}
{{Template:Li_Lab}}


<center>
<center>
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">


== '''A Genomic View of Epigenetic and Transcriptional Regulation''' ==
== '''Computational Epigenomics and Transcriptomics Lab (PI: Wei Li)''' ==  
 
 
Our lab is focused on the design and application of statistical and computational algorithms to elucidate global epigenetic and transcriptional regulatory mechanism, by interpreting and integrating data from ChIP-chip/seq, DNA methylation, Nucleosome positioning, Alternative splicing and Motif finding.
 
An elaborate system of epigenetic and transcription regulation is responsible for the morphological and behavioral complexity in higher eukaryotes. This regulatory system consists of diverse trans-acting protein factors, cis-acting regulatory DNA sequences and the underlying epigenomic background, such as histone modifications, DNA methylation and Nucleosome localizations. Recently, Chromatin ImmunoPrecipitation coupled with whole genome tiled microarray (ChIP-chip) and/or next-generation sequencing (Solexa, SOLiD and 454) has evolved as a powerful and unbiased technique to study this genome-wide regulatory system. The application of this technology to multiple factors and/or in multiple conditions allows biologists to study how transcription is differentially regulated in a combinatorial manner. However, it also poses great challenges for the development of effective algorithms, the key link between massive raw data and biological hypotheses.
 
We developed a series of algorithms to reliably detect and annotate ChIP-enriched regions using Next-generation sequencing (MACS; Genome Biology 2008) and Affymetrix whole-genome tiling arrays, including 1) Model-based Analysis of Tiling-arrays (MAT; PNAS 2006) and a hidden Markov model (Bioinformatics 2005) for ChIP-region detection, 2) extreme MApping of OligoNucleotide (xMAN; BMC Genomics 2008) for microarray probe mapping, 3) Cis-regulatory Element Annotation System (CEAS; NAR 2006) for ChIP-region annotation. Since the inception in early 2006, they have been adopted by hundreds of academic users and are now considered as the ChIP-chip data analysis standard in many labs.  We worked with ENCODE consortium to systematically analyze the performance variability introduced in ChIP-chip protocols, array platforms, and analysis methods (Genome Res. 2008). Furthermore, we are also in close collaboration with several labs on identifying global regulation targets of several key transcription factors, including Estrogen Receptor (Cell 2005; Nature Genetics 2006); Androgen Receptor (Molecular Cell 2007; Cell 2009) and FoxA1 (Cell 2008).
 
We are currently collaborating with many BCM laboratories to use the Next generation sequencing to study 1) Transcription factor binding (ChIP-seq); 2) DNA methylation at single nucleotide resolution (BS-seq); 3) Nucleosome positioning (Nu-seq); 4) Cancer specific alternative splicing junctions (RNA-seq).  My laboratory also plays an important role in the BCM Epigenomics Data Analysis and Coordination Center for a five-year $190 million [http://nihroadmap.nih.gov/epigenomics/fundedresearch.asp NIH Roadmap Epigenomics Program].
 
[http://sites.google.com/a/bcm.edu/lilab/ Lab Intranet]
 
[[Image:WeiLi.jpg‎]]
 
 
<html><script type="text/javascript">
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
</script>
<script type="text/javascript">
try {
var pageTracker = _gat._getTracker("UA-5924762-3");
pageTracker._trackPageview();
} catch(err) {}</script></html>
 


[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]


</div>
</div>


|width="30%" style="border: 1px solid #dddddd; color: #000; background-color: #dddddd"|
| rowspan="2" width="40%" style="border: 2px dashed #6688AA; background-color:#ffffff; padding:1em;" valign="top"|
<div style="clear: right; text-align: left; float: left; padding: .1em 1.5em .9em; ">


==Lab Members==
==Recent News==
. 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.


*[[UserName|Name]]
. 09/2013: Deqiang will start his tenure-track assistant professor position. Job well done. 
*[[UserName|Name]]
*[[UserName|Name]]
*[[UserName|Name]]
*[[UserName|Name]]


{|width="*"
. 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'''.
|
{| style="width: 100%; text-align:center;font-size:12px;font-variant: small-caps;width: 18px; " align="center"
|-


|}
. 08/2013:  Zheng's DaPars 3'UTR Pan Cancer analysis paper is accepted in principle to '''Nature Communications'''; Liguo's RSeQC paper is ranked No. 15 in the [http://bioinformatics.oxfordjournals.org/reports/most-cited Most-Cited Articles] in Bioinformatics as of August 1, 2014.


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


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


<br />
. 06/2014: Deqiang's Dnmt3a/3b double KO paper (with the Goodell Lab) is accepted to '''Cell Stem Cell '''.
|----
|}
|-
| style="border: 2px dashed #6688aa; background-color:#99CCFF; padding:1em;" valign="top"|


<div style="border-bottom: 1px dashed #9999CC;">
. 06/2014: Zheng's alternative splicing paper (with the Cooper Lab) is accepted to '''Molecular Cell '''.
===Header===


</div>
. 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'''.


<div style="border-bottom: 1px dashed #9999CC;">
. 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.
===Header===
</div>


|}
. 02/2014:  Welcome our new postdoc Jianzhong Su and graduate student Xueqiu Lin.
</center>
__NOTOC__


. 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'''.


== '''A Genomic View of Epigenetic and Transcriptional Regulation''' ==
. 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'''


Our lab is focused on the design and application of statistical and computational algorithms to elucidate global epigenetic and transcriptional regulatory mechanism, by interpreting and integrating data from ChIP-chip/seq, DNA methylation, Nucleosome positioning, Alternative splicing and Motif finding.
. 12/2013: We received a 5-year NIH/NHGRI '''R01''' grant (scored at 6 percentile in its first submission) to study DNA Methylation


An elaborate system of epigenetic and transcription regulation is responsible for the morphological and behavioral complexity in higher eukaryotes. This regulatory system consists of diverse trans-acting protein factors, cis-acting regulatory DNA sequences and the underlying epigenomic background, such as histone modifications, DNA methylation and Nucleosome localizations. Recently, Chromatin ImmunoPrecipitation coupled with whole genome tiled microarray (ChIP-chip) and/or next-generation sequencing (Solexa, SOLiD and 454) has evolved as a powerful and unbiased technique to study this genome-wide regulatory system. The application of this technology to multiple factors and/or in multiple conditions allows biologists to study how transcription is differentially regulated in a combinatorial manner. However, it also poses great challenges for the development of effective algorithms, the key link between massive raw data and biological hypotheses.
. 11/2013: Wei will serve on the Editorial Board of '''Molecular Endocrinology'''


We developed a series of algorithms to reliably detect and annotate ChIP-enriched regions using Next-generation sequencing (MACS; Genome Biology 2008) and Affymetrix whole-genome tiling arrays, including 1) Model-based Analysis of Tiling-arrays (MAT; PNAS 2006) and a hidden Markov model (Bioinformatics 2005) for ChIP-region detection, 2) extreme MApping of OligoNucleotide (xMAN; BMC Genomics 2008) for microarray probe mapping, 3) Cis-regulatory Element Annotation System (CEAS; NAR 2006) for ChIP-region annotation. Since the inception in early 2006, they have been adopted by hundreds of academic users and are now considered as the ChIP-chip data analysis standard in many labs.  We worked with ENCODE consortium to systematically analyze the performance variability introduced in ChIP-chip protocols, array platforms, and analysis methods (Genome Res. 2008). Furthermore, we are also in close collaboration with several labs on identifying global regulation targets of several key transcription factors, including Estrogen Receptor (Cell 2005; Nature Genetics 2006); Androgen Receptor (Molecular Cell 2007; Cell 2009) and FoxA1 (Cell 2008).
. 09/2013: Deqiang's DNA methylation Canyon paper is accepted to '''Nature Genetics'''.


We are currently collaborating with many BCM laboratories to use the Next generation sequencing to study 1) Transcription factor binding (ChIP-seq); 2) DNA methylation at single nucleotide resolution (BS-seq); 3) Nucleosome positioning (Nu-seq); 4) Cancer specific alternative splicing junctions (RNA-seq).  My laboratory also plays an important role in the BCM Epigenomics Data Analysis and Coordination Center for a five-year $190 million [http://nihroadmap.nih.gov/epigenomics/fundedresearch.asp NIH Roadmap Epigenomics Program].  
. 09/2013:  Xueqiu's bisulfite sequencing quality control paper (BSeQC) is accepted to '''Bioinformatics'''.


[http://sites.google.com/a/bcm.edu/lilab/ Lab Intranet]
. 08/2013:  Kadir's p53 paper is accepted to '''Nucleic Acids Research'''


[[Image:WeiLi.jpg‎]]
. 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.




<html><script type="text/javascript">
[[Image:Banner.jpg‎‎]]
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
</script>
<script type="text/javascript">
try {
var pageTracker = _gat._getTracker("UA-5924762-3");
pageTracker._trackPageview();
} catch(err) {}</script></html>


[http://openwetware.org/wiki/Li_Lab:news News Archive]


{|width="*"
|
{| style="width: 728px;  text-align:center;font-size:12px;font-variant: small-caps;width: 18px; " align="center"
|-


</div>
|}


|width="30%" style="border: 1px solid #dddddd; color: #000; background-color: #dddddd"|
<div style="clear: right; text-align: left; float: left; padding: .1em 1.5em .9em; ">


==Recent News==
<br />
. '''06/05/2009, New BMC Bioinformatics Paper'''


Yuanxin's paper titled 'BSMAP: whole genome Bisulfite Sequence MAPping program' has been accepted by '''BMC Bioinformatics'''. Congratulations Yuanxin!
<br />
|----
|}
|-
| style="border: 2px dashed #6688aa; background-color:#99CCFF; padding:1em;" valign="top"|


<div style="border-bottom: 1px dashed #9999CC;">


. '''06/04/2009, New Postdoc (joint with Prof. Xuewen Pan)'''
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 64 peer-reviewed papers in high profile journals, including Nature (4), Cell (6), Nature Genetics (3), Cell Stem Cell (3), Molecular Cell (2), Nature Communications (2), Science Translational Medicine (1), Cell Reports (2), Genome Research (6), Genome Biology (3), PNAS (3), Genes and Development, Nucleic Acids Research (3), Cancer Research, and Bioinformatics.


Kaifu Chen has accepted our postdoc offer. Kaifu has a PhD in Genomics and Bioinformatics from Beijing Institute of Genomics, Chinese Academy of Sciences. Welcome Kaifu!
We developed a number of widely used algorithms to analyze next generation sequencing data from Chromatin Factor 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 >1000 citations since 2008.  


In collaboration with experimental biologists, we used these algorithms to gain novel biological insights from various biological processes and disease models.


. '''04/30/2009, New Postdoc (joint with Prof. Huda Zoghbi)'''
* 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.


Peng Yu has accepted our postdoc offer. Peng will soon finish his PhD in computer engineering at the University of Texas at Austin, and join our lab this summer. Welcome Peng!
* DNA Methylation: Dnmt3a in HSC differentiation, DNA methylation Canyon, HSC aging.  


* Nucleosome Organization: fragile nucleosome in gene poising, promoter nucleosome with Tup1, nucleosome dynamics in ES differentiation, global nucleosome loss in aging.


. '''03/26/2009, New Cell Paper'''
* Transcriptome: chimeric RNA in prostate cancer,  Long non-coding RNA in HSC, 3’UTR deletion in cancer and their master regulators.


A paper titled 'Reprogrammed Androgen Receptor Function in Androgen-Independent Prostate Cancer' has finally been accepted by '''Cell'''.
[http://sites.google.com/a/bcm.edu/lilab/ Lab Intranet]
[http://openwetware.org/wiki/Li_Lab openwetware]
</div>




. '''03/20/2009, [http://cancerepigenome.pbwiki.com/ Cancer Epigenomics Workshop]'''
<div style="border-bottom: 1px dashed #9999CC;">
[[Image:WeiLi.jpg‎]]
</div>


Please join us on May 2nd (Saturday) 2009 at MD Anderson Cancer Center. This meeting is organized by Steffi Oesterreich, Wei Li and Jean-Pierre Issa.
|}
</center>
<html>
<script type="text/javascript">


  var _gaq = _gaq || [];
  _gaq.push(['_setAccount', 'UA-5924762-2']);
  _gaq.push(['_trackPageview']);


. '''03/18/2009, New Student'''
  (function() {
    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
  })();


Julia Kristine Blackmore, a PhD student in BCM MCB dept.,  will be doing a two-month rotation in our lab.
</script>
</html>


 
__NOTOC__
. '''03/16/2009, New Course'''
 
[http://sites.google.com/site/mcbseminar/ 320-466 MCB Seminar]
 
 
 
. '''01/21/2009, New Paper'''
 
A paper titled 'Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis' has been accepted by '''PNAS'''.
 
 
 
 
 
 
 
 
 
</div>
</div>

Revision as of 07:05, 7 September 2014

Home        People        Publications        Collaborations        Software        Positions        Contact       


Computational Epigenomics and Transcriptomics Lab (PI: Wei Li)

Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine

Recent News

. 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; Liguo's RSeQC paper is ranked No. 15 in the Most-Cited Articles in Bioinformatics as of August 1, 2014.

. 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.


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 64 peer-reviewed papers in high profile journals, including Nature (4), Cell (6), Nature Genetics (3), Cell Stem Cell (3), Molecular Cell (2), Nature Communications (2), Science Translational Medicine (1), Cell Reports (2), Genome Research (6), Genome Biology (3), PNAS (3), Genes and Development, Nucleic Acids Research (3), Cancer Research, and Bioinformatics.

We developed a number of widely used algorithms to analyze next generation sequencing data from Chromatin Factor 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 >1000 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: Dnmt3a in HSC differentiation, DNA methylation Canyon, HSC aging.
  • Nucleosome Organization: fragile nucleosome in gene poising, promoter nucleosome with Tup1, nucleosome dynamics in ES differentiation, global nucleosome loss in aging.
  • Transcriptome: chimeric RNA in prostate cancer, Long non-coding RNA in HSC, 3’UTR deletion in cancer and their master regulators.


Lab Intranet openwetware


<html> <script type="text/javascript"> 

 var _gaq = _gaq || [];
 _gaq.push(['_setAccount', 'UA-5924762-2']);
 _gaq.push(['_trackPageview']);

 (function() {
   var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
   ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
   var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
 })();

</script> </html>


Retrieved from "https://openwetware.org/mediawiki/index.php?title=Li_Lab&oldid=816974"