Chun-Xiao Song

Chun-Xiao Song

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Chun-Xiao Song

Chun-Xiao Song

Publications by authors named "Chun-Xiao Song"

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47Publications

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Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.

Nat Biotechnol 2019 04 25;37(4):424-429. Epub 2019 Feb 25.

Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1038/s41587-019-0041-2DOI Listing
April 2019

Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate.

Chem Commun (Camb) 2019 Feb;55(16):2328-2331

Ludwig Institute for Cancer Research and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.

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http://dx.doi.org/10.1039/c9cc00274jDOI Listing
February 2019

Glucose and glutamine availability regulate HepG2 transcriptional responses to low oxygen.

Wellcome Open Res 2018 26;3:126. Epub 2018 Sep 26.

Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK.

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https://wellcomeopenresearch.org/articles/3-126/v1
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http://dx.doi.org/10.12688/wellcomeopenres.14839.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178907PMC
September 2018

Simultaneously Monitoring Immune Response and Microbial Infections during Pregnancy through Plasma cfRNA Sequencing.

Clin Chem 2017 Nov 13;63(11):1695-1704. Epub 2017 Sep 13.

Departments of Bioengineering and Applied Physics, Stanford University, and Chan Zuckerberg Biohub, Stanford, CA;

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http://dx.doi.org/10.1373/clinchem.2017.273888DOI Listing
November 2017

Quantitation and mapping of the epigenetic marker 5-hydroxymethylcytosine.

Bioessays 2017 05 23;39(5). Epub 2017 Mar 23.

Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.

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http://dx.doi.org/10.1002/bies.201700010DOI Listing
May 2017

Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation.

Proc Natl Acad Sci U S A 2016 Apr 28;113(16):4338-43. Epub 2016 Mar 28.

Department of Bioengineering, Stanford University, Stanford, CA 94305; Department of Applied Physics, Stanford University, Stanford, CA 94305; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305

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http://dx.doi.org/10.1073/pnas.1600223113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843451PMC
April 2016

Identification of MLL-fusion/MYC⊣miR-26⊣TET1 signaling circuit in MLL-rearranged leukemia.

Cancer Lett 2016 Mar 11;372(2):157-65. Epub 2016 Jan 11.

Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45219, USA. Electronic address:

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http://dx.doi.org/10.1016/j.canlet.2015.12.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809417PMC
March 2016

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics.

Cell Res 2015 Mar 16;25(3):386-9. Epub 2015 Jan 16.

Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1038/cr.2015.5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349244PMC
March 2015

Detection of mismatched 5-hydroxymethyluracil in DNA by selective chemical labeling.

Methods 2015 Jan 15;72:16-20. Epub 2014 Nov 15.

Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 E. 57th Street, Chicago, IL 60637, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.11.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300242PMC
January 2015

5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.

Mol Cell 2014 Oct 25;56(2):286-297. Epub 2014 Sep 25.

Ludwig Institute for Cancer Research, La Jolla, CA 92093-0653, USA; Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, University of California, San Diego School of Medicine, La Jolla, CA 92093. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.08.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319980PMC
October 2014

Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions.

PLoS Comput Biol 2013 5;9(12):e1003367. Epub 2013 Dec 5.

Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854512PMC
August 2014

Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis.

Nat Commun 2013 ;4:1995

State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China.

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http://dx.doi.org/10.1038/ncomms2995DOI Listing
December 2013

Potential functional roles of DNA demethylation intermediates.

Trends Biochem Sci 2013 Oct 8;38(10):480-4. Epub 2013 Aug 8.

Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1016/j.tibs.2013.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4013277PMC
October 2013

Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing.

Nat Commun 2013 ;4:1517

Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1038/ncomms2527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679896PMC
June 2013

HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis.

Proc Natl Acad Sci U S A 2013 Jun 28;110(24):9920-5. Epub 2013 May 28.

Ben May Department for Cancer Research, Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1073/pnas.1305172110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683728PMC
June 2013

Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA.

J Am Chem Soc 2013 Jun 17;135(25):9315-7. Epub 2013 Jun 17.

Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.

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http://dx.doi.org/10.1021/ja4044856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3727251PMC
June 2013

Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming.

Cell 2013 Apr 18;153(3):678-91. Epub 2013 Apr 18.

Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/j.cell.2013.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3657391PMC
April 2013

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation.

Genome Res 2013 Feb 2;23(2):352-64. Epub 2012 Oct 2.

Department of Bioengineering, University of California, San Diego, California 92093, USA.

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http://dx.doi.org/10.1101/gr.144949.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561876PMC
February 2013

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.

Nat Protoc 2012 Dec 29;7(12):2159-70. Epub 2012 Nov 29.

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1038/nprot.2012.137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641661PMC
December 2012

Mapping recently identified nucleotide variants in the genome and transcriptome.

Nat Biotechnol 2012 Nov;30(11):1107-16

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1038/nbt.2398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3537840PMC
November 2012

Selective capture of 5-hydroxymethylcytosine from genomic DNA.

J Vis Exp 2012 Oct 5(68). Epub 2012 Oct 5.

Department of Human Genetics, Emory University School of Medicine.

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http://dx.doi.org/10.3791/4441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3490294PMC
October 2012

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription.

Nat Struct Mol Biol 2012 Aug 22;19(8):831-3. Epub 2012 Jul 22.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nsmb.2346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3414690PMC
August 2012

5-Hydroxymethylcytosine (5-hmC) Specific Enrichment.

Bio Protoc 2012 Aug;2(15)

Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4956340PMC
http://dx.doi.org/10.21769/bioprotoc.242DOI Listing
August 2012

Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.

Cell 2012 Jun 17;149(6):1368-80. Epub 2012 May 17.

Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/j.cell.2012.04.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589129PMC
June 2012

[Effects of extremely low frequency electromagnetic radiation on cardiovascular system of workers].

Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2012 Mar;30(3):194-5

Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun 130021, China.

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March 2012

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine.

Nat Methods 2011 Nov 20;9(1):75-7. Epub 2011 Nov 20.

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.

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http://dx.doi.org/10.1038/nmeth.1779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646335PMC
November 2011

Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(α)I.

Bioorg Med Chem Lett 2011 Sep 9;21(17):5075-7. Epub 2011 Apr 9.

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.1016/j.bmcl.2011.03.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156281PMC
September 2011

Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes.

Acc Chem Res 2011 Sep 3;44(9):709-17. Epub 2011 May 3.

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1021/ar2000502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646476PMC
September 2011

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA.

Science 2011 Sep 4;333(6047):1303-7. Epub 2011 Aug 4.

Group of DNA Metabolism, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.1126/science.1210944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462231PMC
September 2011

Targeting MgrA-mediated virulence regulation in Staphylococcus aureus.

Chem Biol 2011 Aug;18(8):1032-41

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/j.chembiol.2011.05.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163066PMC
August 2011

Detection of 5-hydroxymethylcytosine in DNA by transferring a keto-glucose by using T4 phage β-glucosyltransferase.

Chembiochem 2011 Jul 7;12(11):1682-5. Epub 2011 Jun 7.

Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.

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http://dx.doi.org/10.1002/cbic.201100278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065167PMC
July 2011

Syntheses of two 5-hydroxymethyl-2'-deoxycytidine phosphoramidites with TBDMS as the 5-hydroxymethyl protecting group and their incorporation into DNA.

J Org Chem 2011 May 14;76(10):4182-8. Epub 2011 Apr 14.

Department of Chemistry, The University of Chicago, 929 E. 57th St., Chicago, Illinois, 60637 United States.

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http://dx.doi.org/10.1021/jo200566dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031239PMC
May 2011

Direct functionalization of benzylic C-Hs with vinyl acetates via Fe-catalysis.

Chem Commun (Camb) 2009 Oct 7(40):6002-4. Epub 2009 Sep 7.

Beijing National Laboratory of Molecular Sciences (BNLMS) and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China.

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http://dx.doi.org/10.1039/b911031cDOI Listing
October 2009

Intra/intermolecular direct allylic alkylation via Pd(II)-catalyzed allylic C-H activation.

J Am Chem Soc 2008 Oct 9;130(39):12901-3. Epub 2008 Sep 9.

Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering and Green Chemistry Center, Peking University, Beijing 100871, China.

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http://dx.doi.org/10.1021/ja803452pDOI Listing
October 2008