Zhenyu Xuan

Zhenyu Xuan

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Zhenyu Xuan

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Neuroprotection by Heat Shock Factor-1 (HSF1) and Trimerization-Deficient Mutant Identifies Novel Alterations in Gene Expression.

Sci Rep 2018 11 22;8(1):17255. Epub 2018 Nov 22.

Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA.

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http://dx.doi.org/10.1038/s41598-018-35610-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6250741PMC
November 2018

MTGIpick allows robust identification of genomic islands from a single genome.

Brief Bioinform 2018 05;19(3):361-373

Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA.

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http://dx.doi.org/10.1093/bib/bbw118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454522PMC
May 2018

Anaerobic Cysteine Degradation and Potential Metabolic Coordination in Salmonella enterica and Escherichia coli.

J Bacteriol 2017 08 25;199(16). Epub 2017 Jul 25.

Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA

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http://dx.doi.org/10.1128/JB.00117-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5527379PMC
August 2017

In Situ Capture of Chromatin Interactions by Biotinylated dCas9.

Cell 2017 Aug;170(5):1028-1043.e19

Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.08.003DOI Listing
August 2017

Anti-amnesic effect of extract and alkaloid fraction from aerial parts of Peganum harmala on scopolamine-induced memory deficits in mice.

J Ethnopharmacol 2017 May 23;204:95-106. Epub 2017 Apr 23.

Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, 1200 Cailun Rood, Shanghai 201203, China; Shanghai R&D Centre for Standardization of Chinese Medicines, 199 Guoshoujing Road, Shanghai 201203, China. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03788741173006
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http://dx.doi.org/10.1016/j.jep.2017.04.019DOI Listing
May 2017

TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells.

RNA Biol 2017 02 16;14(2):259-274. Epub 2016 Dec 16.

a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA.

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http://dx.doi.org/10.1080/15476286.2016.1270006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5324748PMC
February 2017

Deficiency of microRNA expands cell fate potential in pluripotent stem cells.

Science 2017 02 12;355(6325). Epub 2017 Jan 12.

Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94705, USA.

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http://dx.doi.org/10.1126/science.aag1927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6138252PMC
February 2017

The Swi3 protein plays a unique role in regulating respiration in eukaryotes.

Biosci Rep 2016 07 30;36(3). Epub 2016 Jun 30.

Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Mail Stop RL11, 800 W. Campbell Road, Richardson, TX 75080, U.S.A.

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http://dx.doi.org/10.1042/BSR20160083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5293592PMC
July 2016

De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles.

Nucleic Acids Res 2016 06 7;44(11):e106. Epub 2016 Apr 7.

Department of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department Automation, Tsinghua University, Beijing 100084, China

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http://dx.doi.org/10.1093/nar/gkw225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914103PMC
June 2016

The E3 ligase APC/C(Cdh1) promotes ubiquitylation-mediated proteolysis of PAX3 to suppress melanocyte proliferation and melanoma growth.

Sci Signal 2015 Sep 1;8(392):ra87. Epub 2015 Sep 1.

Department of Pharmacology and Experimental Therapeutics, Boston University Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA. Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 20032, P. R. China.

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http://dx.doi.org/10.1126/scisignal.aab1995DOI Listing
September 2015

Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures.

Authors:
Jin Gu Zhenyu Xuan

PLoS One 2013 20;8(11):e81032. Epub 2013 Nov 20.

MOE Key Laboratory of Bioinformatics; Bioinformatics Division/Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology, Department of Automation, Tsinghua University, Beijing, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081032PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3835731PMC
May 2015

Prioritization of cancer-related genomic variants by SNP association network.

Cancer Inform 2015 1;14(Suppl 2):57-70. Epub 2015 Apr 1.

Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, USA.

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http://dx.doi.org/10.4137/CIN.S17288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384763PMC
May 2015

PMA induces SnoN proteolysis and CD61 expression through an autocrine mechanism.

Cell Signal 2014 Jul 15;26(7):1369-78. Epub 2014 Mar 15.

Department of Biochemistry and Molecular Biology, Medical School, United States; Program of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, United States. Electronic address:

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http://dx.doi.org/10.1016/j.cellsig.2014.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074601PMC
July 2014

Long non-coding RNAs and complex human diseases.

Int J Mol Sci 2013 Sep 12;14(9):18790-808. Epub 2013 Sep 12.

Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.

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http://dx.doi.org/10.3390/ijms140918790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3794807PMC
September 2013

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.

Nucleic Acids Res 2012 Apr 6;40(7):e50. Epub 2012 Jan 6.

Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA.

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http://dx.doi.org/10.1093/nar/gkr1135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326300PMC
April 2012

Chaperonins facilitate KNOTTED1 cell-to-cell trafficking and stem cell function.

Science 2011 Aug;333(6046):1141-4

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1126/science.1205727DOI Listing
August 2011

Estimating developmental states of tumors and normal tissues using a linear time-ordered model.

BMC Bioinformatics 2011 Feb 11;12:53. Epub 2011 Feb 11.

Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3223864PMC
February 2011

Estimating the quality of reprogrammed cells using ES cell differentiation expression patterns.

PLoS One 2011 Jan 11;6(1):e15336. Epub 2011 Jan 11.

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015336PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023460PMC
January 2011

Understanding protein evolutionary rate by integrating gene co-expression with protein interactions.

BMC Syst Biol 2010 Dec 30;4:179. Epub 2010 Dec 30.

Department of Computer Science and Engineering, Shanghai Jiao Tong University, China.

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http://dx.doi.org/10.1186/1752-0509-4-179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022652PMC
December 2010

Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells.

J Cell Sci 2010 Nov 12;123(Pt 21):3734-44. Epub 2010 Oct 12.

Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Chemical and Life Sciences Laboratory, 601 South Goodwin Avenue, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1242/jcs.070466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481618PMC
November 2010

A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression.

EMBO J 2010 Sep 20;29(18):3082-93. Epub 2010 Aug 20.

Laboratoire de Biologie Cellulaire de la Synapse, Inserm 1024/CNRS 8197, Institut de Biologie de l'Ecole Normale Supérieure, Paris, France.

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http://dx.doi.org/10.1038/emboj.2010.199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944070PMC
September 2010

Updates to the RMAP short-read mapping software.

Bioinformatics 2009 Nov 7;25(21):2841-2. Epub 2009 Sep 7.

Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895571PMC
November 2009

Investigating repetitively matching short sequencing reads: the enigmatic nature of H3K9me3.

Epigenetics 2009 Oct 14;4(7):476-86. Epub 2009 Oct 14.

Zucker Hillside Hospital, North Shore-Long Island Jewish Health System, Glen Oaks, NY, USA.

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http://dx.doi.org/10.4161/epi.4.7.9809DOI Listing
October 2009

Sensitive and accurate detection of copy number variants using read depth of coverage.

Genome Res 2009 Sep 5;19(9):1586-92. Epub 2009 Aug 5.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.092981.109
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http://dx.doi.org/10.1101/gr.092981.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752127PMC
September 2009

Pharmacokinetics of forsythoside after intravenous administration in beagle dogs.

Eur J Drug Metab Pharmacokinet 2009 Apr-Jun;34(2):101-5

Laboratory of Pharmacokinetics, Shanghai University of Traditional Chinese Medicine, Shanghai, China.

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http://dx.doi.org/10.1007/BF03191158DOI Listing
August 2009

The transcriptome of human CD34+ hematopoietic stem-progenitor cells.

Proc Natl Acad Sci U S A 2009 May 30;106(20):8278-83. Epub 2009 Apr 30.

Department of Medicine, Division of Medical Genetics, Center for Functional Genomics, Evanston Northwestern Healthcare Research Institute, Northwestern University Feinberg School of Medicine, Evanston, IL 60201, USA.

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http://dx.doi.org/10.1073/pnas.0903390106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688877PMC
May 2009

High-resolution human core-promoter prediction with CoreBoost_HM.

Genome Res 2009 Feb 7;19(2):266-75. Epub 2008 Nov 7.

MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China.

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http://dx.doi.org/10.1101/gr.081638.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652208PMC
February 2009

Deregulation of scribble promotes mammary tumorigenesis and reveals a role for cell polarity in carcinoma.

Cell 2008 Nov;135(5):865-78

Cold Spring Harbor Laboratory, Watson School of Biological Sciences, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1016/j.cell.2008.09.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3015046PMC
November 2008

Poly A- transcripts expressed in HeLa cells.

PLoS One 2008 Jul 30;3(7):e2803. Epub 2008 Jul 30.

Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002803PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481391PMC
July 2008

Conservation of small RNA pathways in platypus.

Genome Res 2008 Jun 7;18(6):995-1004. Epub 2008 May 7.

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.073056.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2413167PMC
June 2008

Scanning the human genome at kilobase resolution.

Genome Res 2008 May 21;18(5):751-62. Epub 2008 Feb 21.

Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, Illinois 60201, USA.

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http://dx.doi.org/10.1101/gr.068304.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336809PMC
May 2008

Using quality scores and longer reads improves accuracy of Solexa read mapping.

BMC Bioinformatics 2008 Feb 28;9:128. Epub 2008 Feb 28.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11274, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-9-128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335322PMC
February 2008

Prediction of transcription start sites based on feature selection using AMOSA.

Comput Syst Bioinformatics Conf 2007 ;6:183-93

Bioinformatics Division, TNLIST and Department of Automation, Tsinghua Univ., Beijing 100084, China.

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December 2007

Genome-wide in situ exon capture for selective resequencing.

Nat Genet 2007 Dec 4;39(12):1522-7. Epub 2007 Nov 4.

Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://rulai.cshl.edu/xuan/publication/hybridSelectionSolexa
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http://www.nature.com/doifinder/10.1038/ng.2007.42
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http://dx.doi.org/10.1038/ng.2007.42DOI Listing
December 2007

A biochemical approach to identifying microRNA targets.

Proc Natl Acad Sci U S A 2007 Dec 27;104(49):19291-6. Epub 2007 Nov 27.

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1073/pnas.0709971104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2148283PMC
December 2007

Boosting with stumps for predicting transcription start sites.

Genome Biol 2007 ;8(2):R17

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1186/gb-2007-8-2-r17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852414PMC
July 2007

A microRNA component of the p53 tumour suppressor network.

Nature 2007 Jun 6;447(7148):1130-4. Epub 2007 Jun 6.

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nature05939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4590999PMC
June 2007

Critical roles for Dicer in the female germline.

Genes Dev 2007 Mar;21(6):682-93

Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gad.1521307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820942PMC
March 2007

Pan-genome isolation of low abundance transcripts using SAGE tag.

FEBS Lett 2006 Dec 14;580(28-29):6721-9. Epub 2006 Nov 14.

Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, IL 60201, USA.

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http://dx.doi.org/10.1016/j.febslet.2006.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1791009PMC
December 2006

Genome-wide promoter extraction and analysis in human, mouse, and rat.

Genome Biol 2005 1;6(8):R72. Epub 2005 Aug 1.

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1186/gb-2005-6-8-r72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1273639PMC
July 2006

Computational prediction of methylation status in human genomic sequences.

Proc Natl Acad Sci U S A 2006 Jul 3;103(28):10713-6. Epub 2006 Jul 3.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1073/pnas.0602949103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1502297PMC
July 2006

DNA motifs in human and mouse proximal promoters predict tissue-specific expression.

Proc Natl Acad Sci U S A 2006 Apr 10;103(16):6275-80. Epub 2006 Apr 10.

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1073/pnas.0508169103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458868PMC
April 2006

Regulating gene expression through RNA nuclear retention.

Cell 2005 Oct;123(2):249-63

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1016/j.cell.2005.08.033DOI Listing
October 2005

TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

Nucleic Acids Res 2005 Jan;33(Database issue):D103-7

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1093/nar/gki004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539958PMC
January 2005

From worm to human: bioinformatics approaches to identify FOXO target genes.

Mech Ageing Dev 2005 Jan;126(1):209-15

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1016/j.mad.2004.09.021DOI Listing
January 2005

Computational comparison of two mouse draft genomes and the human golden path.

Genome Biol 2003 5;4(1):R1. Epub 2002 Dec 5.

Cold Spring Harbor Laboratory, New York, NY 11724, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151282PMC
http://dx.doi.org/10.1186/gb-2002-4-1-r1DOI Listing
March 2003

The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis.

Genes Dev 2002 Nov;16(21):2733-42

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://www.genesdev.org/cgi/doi/10.1101/gad.1026102
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http://dx.doi.org/10.1101/gad.1026102DOI Listing
November 2002

GFScan: a gene family search tool at genomic DNA level.

Genome Res 2002 Jul;12(7):1142-9

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.220102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186623PMC
July 2002

A complete sequence of the T. tengcongensis genome.

Genome Res 2002 May;12(5):689-700

Beijing Genomics Institute/Genomics and Bioinformatics Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China.

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http://dx.doi.org/10.1101/gr.219302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186588PMC
May 2002