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== '''Welcome to the Computational Genomics Lab''' ==  
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[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]
<h3>About Us</h3>
#[[Knight:Lab Members | Lab Members]]
#[[Knight:Contact | Contact]]
#[[SynBERC:MIT/Lab video tours|Video]] (Knight & Endy labs)
#[[Knight:Projects | Projects]]
#[[Knight:Publications | Publications]]


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<h3>Technical Info</h3>
==Recent News==
#[[Knight:Equipment | Equipment]]
. '''05/2010, New Paper'''
#[[Knight:Materials | Materials]]
#[[Knight:Protocols | Protocols]]


A paper titled "Histone modifications and chromatin organization in prostate cancer" has been accepted by Epigenomics.
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<h3>Internal</h3>
 
#[[Knight:Freezer | Freezer Inventory]]
. '''02/2010, New Paper'''
#[[Knight:Fridge | Fridge Inventory]]
 
#[[Knight:Dyes | Dyes Inventory]]
A paper titled  "New syntax to describe local continuous structure-sequence information for recognizing new pre-miRNAs" has been accepted by Journal of Theoretical Biology .
#[[Knight:Orders | Orders]]
 
#[[Knight:Punchlist | Punchlist]]
 
#[[Knight:Safety | Safety]]
. '''01/2010, New Grant'''
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A Texas CPRIT grant was funded. We will use ChIP-seq and RNA-seq to analyze Androgen Receptor (AR) function in Prostate Cancer with Dr. Weigel at BCM.
 
 
. '''01/2010, New Grant'''
 
A planning award for the Lonestar Oncology Network for EpigeneticS Therapy And Research (LONESTAR) was funded. This project will bring together a "dream team" in epigenetics research from UT Southwestern, Baylor College of Medicine, and M.D. Anderson.  We will direct the bioinformatics component for LONESTAR.
 
 
. '''01/2010, New Postdoc'''
 
Deqiang Sun will join us as a postdoc fellow. Deqiang has a PhD in Condensed Matter Physics from Texas A&M University.  Welcome!
 
 
. '''01/2010, [http://www.aacr.org/home/scientists/meetings--workshops/special-conferences/cancer-epigenetics.aspx Conference on Cancer Epigenetics]'''
 
Wei Li is an invited speaker in the American Association for Cancer Research (AACR) Special Conference on Cancer Epigenetics at Puerto Rico.
 
 
. '''12/24/2009, New Paper'''
 
Dr.Bert O'Malley's paper, Global Characterization of Transcriptional Impact of the SRC-3 Coregulator, has been accepted by '''Molecular Endocrinology'''. Liguo and Wei are co-authors on the paper.
 
 
. '''12/08/2009, New Paper'''
 
Liguo's paper titled 'A Statistical Method for the Detection of Alternative Splicing Using RNA-seq' has been accepted by '''PLoS ONE'''. Congratulations Liguo!
 
 
. '''11/13/2009, New Grant'''
 
Wei Li received a '''New Investigator Award''' from the Department of Defense (DOD) Prostate Cancer Research Program (PCRP). Cheers!
 
 
. '''11/07/2009, Keynote Presentation'''
 
Wei Li gave a Keynote Presentation at the Symposium on Advances in Cell Signaling, Cancer Prevention and Therapy at South Padre Island, Texas.
 
 
. '''09/29/2009, New Grant'''
 
A prestigious NIH Challenge grant was funded. We will use ChIP-seq to analyze RXRa binding in mouse liver with Dr. Karpen at Texas Children's Hospital.
 
 
. '''09/17/2009, New Grant'''
 
A two-year $2.5 million NIH Grand Opportunity (GO) grant was funded. We will study aging epigenomics with Drs. Darlington and Goodell at BCM.
 
 
. '''09/15/2009, New Grant'''
 
A prestigious NIH Challenge grant was funded. We will use RNA-seq to characterize patient cardiac progenitors with Dr. Pu at Harvard Medical School.
 
 
. '''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!
 
 
. '''03/26/2009, New Cell Paper'''
 
A paper titled 'Reprogrammed Androgen Receptor Function in Androgen-Independent Prostate Cancer' has finally been accepted by '''Cell'''.
 
 
 
[http://openwetware.org/wiki/Li_Lab:news News Archive]
 
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<h3>Related sites</h3>
#[http://www.csail.mit.edu/biographies/PI/bioprint.php?PeopleID=2033 Biography]
#[http://people.csail.mit.edu/tk/ Website]
#[http://web.archive.org/web/20040202103232/http://www.ai.mit.edu/people/tk/tk.html Old page]
#[http://dictionary.reference.com/search?q=Tom%20Knight Dictionary.com entry]
#[[Wikipedia:Tom Knight | Wikipedia page]]
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<font size=4>'''Recent changes'''</font>{{Special:Recentchanges/Knight}}
 
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== '''A Genomic View of Epigenetic and Transcriptional Regulation''' ==
 
 
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 and histone modifications (ChIP-seq); 2) DNA methylation at single nucleotide resolution (Bisulfite-seq); 3) Nucleosome remodeling (Mnase-seq); 4) Alternative splicing (RNA-seq).  My laboratory also plays an important role in the BCM Epigenomics Data Analysis and Coordination Center for a five-year [http://nihroadmap.nih.gov/epigenomics/referenceepigenomeconsortium.asp NIH Roadmap Epigenomics Program].
 
[http://sites.google.com/a/bcm.edu/lilab/ Lab Intranet]
 
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Revision as of 04:59, 18 November 2013

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CSAIL logo
Knight Lab



About Us

  1. Lab Members
  2. Contact
  3. Video (Knight & Endy labs)
  4. Projects
  5. Publications

Technical Info

  1. Equipment
  2. Materials
  3. Protocols

Internal

  1. Freezer Inventory
  2. Fridge Inventory
  3. Dyes Inventory
  4. Orders
  5. Punchlist
  6. Safety

Related sites

  1. Biography
  2. Website
  3. Old page
  4. Dictionary.com entry
  5. Wikipedia page

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Recent changes

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18 April 2024

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17 April 2024

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16 April 2024

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