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Chunxiao Song, Ph.D. - Publications

Affiliations: 
2013 Chemistry University of Chicago, Chicago, IL 
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66 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Irie N, Lee SM, Lorenzi V, Xu H, Chen J, Inoue M, Kobayashi T, Sancho-Serra C, Drousioti E, Dietmann S, Vento-Tormo R, Song CX, Surani MA. DMRT1 regulates human germline commitment. Nature Cell Biology. PMID 37709822 DOI: 10.1038/s41556-023-01224-7  0.306
2023 Chen X, Xu H, Shu X, Song CX. Mapping epigenetic modifications by sequencing technologies. Cell Death and Differentiation. PMID 37658169 DOI: 10.1038/s41418-023-01213-1  0.364
2022 Liu Y, Song CX. TAPS: The Development of a Direct and Base-Resolution Sequencing Method for DNA Methylation. Acs Chemical Biology. 17: 2683-2685. PMID 36194499 DOI: 10.1021/acschembio.2c00746  0.358
2022 Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX. Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology. Nucleic Acids Research. PMID 35849350 DOI: 10.1093/nar/gkac612  0.342
2021 Cheng J, Siejka-Zielińska P, Liu Y, Chandran A, Kriaucionis S, Song CX. Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection. Nucleic Acids Research. PMID 33905495 DOI: 10.1093/nar/gkab291  0.343
2020 Zhao LY, Song J, Liu Y, Song CX, Yi C. Mapping the epigenetic modifications of DNA and RNA. Protein & Cell. PMID 32440736 DOI: 10.1007/S13238-020-00733-7  0.594
2020 Liu Y, Cheng J, Siejka-Zielińska P, Weldon C, Roberts H, Lopopolo M, Magri A, D'Arienzo V, Harris JM, McKeating JA, Song CX. Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS. Genome Biology. 21: 54. PMID 32127008 DOI: 10.1186/S13059-020-01969-6  0.446
2019 Yuan F, Bi Y, Zhang JY, Zhou YL, Zhang XX, Song CX. 5-Carboxylcytosine is resistant towards phosphodiesterase I digestion: implications for epigenetic modification quantification by mass spectrometry. Rsc Advances. 9: 29010-29014. PMID 35528408 DOI: 10.1039/c9ra04375f  0.343
2019 Nesterova TB, Wei G, Coker H, Pintacuda G, Bowness JS, Zhang T, Almeida M, Bloechl B, Moindrot B, Carter EJ, Alvarez Rodrigo I, Pan Q, Bi Y, Song CX, Brockdorff N. Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation. Nature Communications. 10: 3129. PMID 31311937 DOI: 10.1038/S41467-019-11171-3  0.327
2019 Li C, Dong L, Su R, Bi Y, Qing Y, Deng X, Zhou Y, Hu C, Yu M, Huang H, Jiang X, Li X, He X, Zou D, Shen C, ... ... Song C, et al. Homoharringtonine exhibits potent anti-tumor effect and modulates DNA epigenome in acute myeloid leukemia by targeting SP1/TET1/5hmC. Haematologica. PMID 30975912 DOI: 10.3324/Haematol.2018.208835  0.32
2019 Liu Y, Siejka-Zielińska P, Velikova G, Bi Y, Yuan F, Tomkova M, Bai C, Chen L, Schuster-Böckler B, Song CX. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nature Biotechnology. PMID 30804537 DOI: 10.1038/s41587-019-0041-2  0.348
2019 Yuan F, Bi Y, Siejka-Zielinska P, Zhou YL, Zhang XX, Song CX. Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate. Chemical Communications (Cambridge, England). PMID 30723849 DOI: 10.1039/C9Cc00274J  0.324
2019 Weng H, Huang H, Huang H, Yu Z, Siejka-Zielinska P, Chen Z, Prince E, Shen C, Li Z, Song C, Zhao Y, Chen J. TET1 Modulates DNA Replication in Leukemia Cells Via a Catalytic-Independent Mechanism through Cooperating with KAT8 Blood. 134: 1249-1249. DOI: 10.1182/Blood-2019-127321  0.402
2019 Liu Y, Siejka P, Velikova G, Bi Y, Tomkova M, Schuster-Boeckler B, Song C. Abstract 825: TAPS: A bisulfite-free, base-resolution and quantitative sequencing method for cytosine modifications Cancer Research. 79: 825-825. DOI: 10.1158/1538-7445.Am2019-825  0.45
2019 Payne K, Velikova G, Song C, Nankivell P, Mehanna H. High-throughput methylation profiling of cell-free plasma DNA in head and neck cancer: a pilot study British Journal of Oral & Maxillofacial Surgery. 57. DOI: 10.1016/J.Bjoms.2019.10.292  0.378
2017 Song CX, Yin S, Ma L, Wheeler A, Chen Y, Zhang Y, Liu B, Xiong J, Zhang W, Hu J, Zhou Z, Dong B, Tian Z, Jeffrey SS, Chua MS, et al. 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages. Cell Research. PMID 28820176 DOI: 10.1038/Cr.2017.106  0.362
2017 Qing Y, Tian Z, Bi Y, Wang Y, Long J, Song CX, Diao J. Quantitation and mapping of the epigenetic marker 5-hydroxymethylcytosine. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 28332209 DOI: 10.1002/Bies.201700010  0.418
2016 Yang YA, Zhao JC, Fong KW, Kim J, Li S, Song C, Song B, Zheng B, He C, Yu J. FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function. Nucleic Acids Research. PMID 27257062 DOI: 10.1093/Nar/Gkw498  0.569
2016 Song CX, Diao J, Brunger AT, Quake SR. Simultaneous single-molecule epigenetic imaging of DNA methylation and hydroxymethylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 27035984 DOI: 10.1073/Pnas.1600223113  0.5
2016 Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, ... Song C, et al. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. 12: 1-222. PMID 26799652 DOI: 10.1080/15548627.2015.1100356  0.557
2016 Huang H, Jiang X, Wang J, Li Y, Song CX, Chen P, Li S, Gurbuxani S, Arnovitz S, Wang Y, Weng H, Neilly MB, He C, Li Z, Chen J. Identification of MLL-fusion/MYC⊣miR-26⊣TET1 signaling circuit in MLL-rearranged leukemia. Cancer Letters. PMID 26791235 DOI: 10.1016/J.Canlet.2015.12.032  0.341
2015 Kang X, Song C, Du X, Zhang C, Liu Y, Liang L, He J, Lamb K, Shen WH, Yin Y. PTEN stabilizes TOP2A and regulates the DNA decatenation. Scientific Reports. 5: 17873. PMID 26657567 DOI: 10.1038/srep17873  0.324
2015 Fu Y, Liu H, Song C, Zhang F, Liu Y, Wu J, Wen X, Liang C, Ma K, Li L, Zhang X, Shao X, Sun Y, Du Y, Song Y. Mangiferin regulates cognitive deficits and heme oxygenase-1 induced by lipopolysaccharide in mice. International Immunopharmacology. PMID 26558697 DOI: 10.1016/j.intimp.2015.10.035  0.337
2015 Song C, Zhang S, Huang H. Choosing a suitable method for the identification of replication origins in microbial genomes. Frontiers in Microbiology. 6: 1049. PMID 26483774 DOI: 10.3389/fmicb.2015.01049  0.3
2015 Xu D, Zhang J, Shi Z, Song C, Zheng X, Zhang Y, Hao Y, Dong H, Wei L, El-Mahallawy HS, Kelly P, Xiong W, Wang H, Li J, Zhang X, et al. Molecular detection of vector-borne agents in dogs from ten provinces of China. Parasites & Vectors. 8: 501. PMID 26428085 DOI: 10.1186/s13071-015-1120-y  0.335
2015 Lu X, Han D, Zhao BS, Song CX, Zhang LS, Doré LC, He C. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Research. 25: 386-9. PMID 25591929 DOI: 10.1038/Cr.2015.5  0.691
2015 Yu M, Song CX, He C. Detection of mismatched 5-hydroxymethyluracil in DNA by selective chemical labeling. Methods (San Diego, Calif.). 72: 16-20. PMID 25462560 DOI: 10.1016/J.Ymeth.2014.11.007  0.545
2014 Tsai YP, Chen HF, Chen SY, Cheng WC, Wang HW, Shen ZJ, Song C, Teng SC, He C, Wu KJ. TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator. Genome Biology. 15: 513. PMID 25517638 DOI: 10.1186/S13059-014-0513-0  0.504
2014 Hon GC, Song CX, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao SQ, Wang BA, Kuan S, Edsall LE, Zhao BS, Xu GL, He C, et al. 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Molecular Cell. 56: 286-97. PMID 25263596 DOI: 10.1016/J.Molcel.2014.08.026  0.712
2014 Shen L, Song CX, He C, Zhang Y. Mechanism and function of oxidative reversal of DNA and RNA methylation. Annual Review of Biochemistry. 83: 585-614. PMID 24905787 DOI: 10.1146/Annurev-Biochem-060713-035513  0.564
2014 Wen L, Li X, Yan L, Tan Y, Li R, Zhao Y, Wang Y, Xie J, Zhang Y, Song C, Yu M, Liu X, Zhu P, Li X, Hou Y, et al. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain. Genome Biology. 15: R49. PMID 24594098 DOI: 10.1186/Gb-2014-15-3-R49  0.521
2014 Madzo J, Liu H, Rodriguez A, Vasanthakumar A, Sundaravel S, Caces DB, Looney TJ, Zhang L, Lepore JB, Macrae T, Duszynski R, Shih AH, Song CX, Yu M, Yu Y, et al. Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Cell Reports. 6: 231-44. PMID 24373966 DOI: 10.1016/J.Celrep.2013.11.044  0.465
2014 Hon G, Song C, Jin F, Selvaraj S, Lee AY, Yen C, Ye Z, Mao S, Wang B, Kuan S, Edsall L, Zhao BS, Xu G, He C, Ren B. Abstract 460: Base resolution epigenomic analysis reveals a role for Tet2 in modulating enhancer activity Molecular and Cellular Biology. 74: 460-460. DOI: 10.1158/1538-7445.Am2014-460  0.742
2013 Chen CC, Xiao S, Xie D, Cao X, Song CX, Wang T, He C, Zhong S. Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. Plos Computational Biology. 9: e1003367. PMID 24339764 DOI: 10.1371/Journal.Pcbi.1003367  0.512
2013 Song CX, He C. Potential functional roles of DNA demethylation intermediates. Trends in Biochemical Sciences. 38: 480-4. PMID 23932479 DOI: 10.1016/J.Tibs.2013.07.003  0.576
2013 Huang H, Jiang X, Li Z, Li Y, Song CX, He C, Sun M, Chen P, Gurbuxani S, Wang J, Hong GM, Elkahloun AG, Arnovitz S, Wang J, Szulwach K, et al. TET1 plays an essential oncogenic role in MLL-rearranged leukemia. Proceedings of the National Academy of Sciences of the United States of America. 110: 11994-9. PMID 23818607 DOI: 10.1073/Pnas.1310656110  0.369
2013 Gan H, Wen L, Liao S, Lin X, Ma T, Liu J, Song CX, Wang M, He C, Han C, Tang F. Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis. Nature Communications. 4: 1995. PMID 23759713 DOI: 10.1038/Ncomms2995  0.585
2013 Lu X, Song CX, Szulwach K, Wang Z, Weidenbacher P, Jin P, He C. Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA. Journal of the American Chemical Society. 135: 9315-7. PMID 23758547 DOI: 10.1021/Ja4044856  0.556
2013 Sun M, Song CX, Huang H, Frankenberger CA, Sankarasharma D, Gomes S, Chen P, Chen J, Chada KK, He C, Rosner MR. HMGA2/TET1/HOXA9 signaling pathway regulates breast cancer growth and metastasis. Proceedings of the National Academy of Sciences of the United States of America. 110: 9920-5. PMID 23716660 DOI: 10.1073/Pnas.1305172110  0.363
2013 Wang T, Wu H, Li Y, Szulwach KE, Lin L, Li X, Chen IP, Goldlust IS, Chamberlain SJ, Dodd A, Gong H, Ananiev G, Han JW, Yoon YS, Rudd MK, ... ... Song CX, et al. Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency. Nature Cell Biology. 15: 700-11. PMID 23685628 DOI: 10.1038/Ncb2748  0.486
2013 Song CX, Szulwach KE, Dai Q, Fu Y, Mao SQ, Lin L, Street C, Li Y, Poidevin M, Wu H, Gao J, Liu P, Li L, Xu GL, Jin P, et al. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell. 153: 678-91. PMID 23602153 DOI: 10.1016/J.Cell.2013.04.001  0.66
2013 Zhang L, Szulwach KE, Hon GC, Song CX, Park B, Yu M, Lu X, Dai Q, Wang X, Street CR, Tan H, Min JH, Ren B, Jin P, He C. Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nature Communications. 4: 1517. PMID 23443545 DOI: 10.1038/Ncomms2527  0.512
2013 Yu P, Xiao S, Xin X, Song CX, Huang W, McDee D, Tanaka T, Wang T, He C, Zhong S. Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation. Genome Research. 23: 352-64. PMID 23033340 DOI: 10.1101/Gr.144949.112  0.535
2012 Szulwach KE, Song CX, He C, Jin P. 5-Hydroxymethylcytosine (5-hmC) Specific Enrichment. Bio-Protocol. 2. PMID 27453898  0.477
2012 Yu M, Hon GC, Szulwach KE, Song CX, Jin P, Ren B, He C. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nature Protocols. 7: 2159-70. PMID 23196972 DOI: 10.1038/Nprot.2012.137  0.477
2012 Song CX, Yi C, He C. Mapping recently identified nucleotide variants in the genome and transcriptome. Nature Biotechnology. 30: 1107-16. PMID 23138310 DOI: 10.1038/Nbt.2398  0.659
2012 Song CX, He C. Balance of DNA methylation and demethylation in cancer development. Genome Biology. 13: 173. PMID 23092522 DOI: 10.1186/Gb-2012-13-10-173  0.547
2012 Li Y, Song CX, He C, Jin P. Selective capture of 5-hydroxymethylcytosine from genomic DNA. Journal of Visualized Experiments : Jove. PMID 23070273 DOI: 10.3791/4441  0.597
2012 Wang T, Pan Q, Lin L, Szulwach KE, Song CX, He C, Wu H, Warren ST, Jin P, Duan R, Li X. Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum. Human Molecular Genetics. 21: 5500-10. PMID 23042784 DOI: 10.1093/Hmg/Dds394  0.57
2012 Kellinger MW, Song CX, Chong J, Lu XY, He C, Wang D. 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription. Nature Structural & Molecular Biology. 19: 831-3. PMID 22820989 DOI: 10.1038/Nsmb.2346  0.512
2012 Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell. 149: 1368-80. PMID 22608086 DOI: 10.1016/J.Cell.2012.04.027  0.453
2012 Yao Q, Song CX, He C, Kumaran D, Dunn JJ. Heterologous expression and purification of Arabidopsis thaliana VIM1 protein: in vitro evidence for its inability to recognize hydroxymethylcytosine, a rare base in Arabidopsis DNA. Protein Expression and Purification. 83: 104-11. PMID 22459921 DOI: 10.1016/J.Pep.2012.03.003  0.578
2012 Song CX, Clark TA, Lu XY, Kislyuk A, Dai Q, Turner SW, He C, Korlach J. Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nature Methods. 9: 75-7. PMID 22101853 DOI: 10.1038/Nmeth.1779  0.552
2011 Song CX, He C. The hunt for 5-hydroxymethylcytosine: the sixth base. Epigenomics. 3: 521-3. PMID 22126239 DOI: 10.2217/Epi.11.74  0.52
2011 Szulwach KE, Li X, Li Y, Song CX, Wu H, Dai Q, Irier H, Upadhyay AK, Gearing M, Levey AI, Vasanthakumar A, Godley LA, Chang Q, Cheng X, He C, et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nature Neuroscience. 14: 1607-16. PMID 22037496 DOI: 10.1038/Nn.2959  0.509
2011 Sun F, Zhou L, Zhao BC, Deng X, Cho H, Yi C, Jian X, Song CX, Luan CH, Bae T, Li Z, He C. Targeting MgrA-mediated virulence regulation in Staphylococcus aureus. Chemistry & Biology. 18: 1032-41. PMID 21867918 DOI: 10.1016/J.Chembiol.2011.05.014  0.728
2011 He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, Sun Y, Li X, Dai Q, Song CX, Zhang K, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science (New York, N.Y.). 333: 1303-7. PMID 21817016 DOI: 10.1126/Science.1210944  0.581
2011 Szulwach KE, Li X, Li Y, Song CX, Han JW, Kim S, Namburi S, Hermetz K, Kim JJ, Rudd MK, Yoon YS, Ren B, He C, Jin P. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. Plos Genetics. 7: e1002154. PMID 21731508 DOI: 10.1371/Journal.Pgen.1002154  0.557
2011 Moran-Crusio K, Reavie L, Shih A, Abdel-Wahab O, Ndiaye-Lobry D, Lobry C, Figueroa ME, Vasanthakumar A, Patel J, Zhao X, Perna F, Pandey S, Madzo J, Song C, Dai Q, et al. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell. 20: 11-24. PMID 21723200 DOI: 10.1016/J.Ccr.2011.06.001  0.403
2011 Song CX, Sun Y, Dai Q, Lu XY, Yu M, Yang CG, He C. Detection of 5-hydroxymethylcytosine in DNA by transferring a keto-glucose by using T4 phage β-glucosyltransferase. Chembiochem : a European Journal of Chemical Biology. 12: 1682-5. PMID 21656634 DOI: 10.1002/Cbic.201100278  0.573
2011 Song CX, He C. Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes. Accounts of Chemical Research. 44: 709-17. PMID 21539303 DOI: 10.1021/Ar2000502  0.604
2011 Song CX, Yu M, Dai Q, He C. Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(α)I. Bioorganic & Medicinal Chemistry Letters. 21: 5075-7. PMID 21524909 DOI: 10.1016/J.Bmcl.2011.03.118  0.538
2011 Dai Q, Song CX, Pan T, He C. Syntheses of two 5-hydroxymethyl-2'-deoxycytidine phosphoramidites with TBDMS as the 5-hydroxymethyl protecting group and their incorporation into DNA. The Journal of Organic Chemistry. 76: 4182-8. PMID 21462947 DOI: 10.1021/Jo200566D  0.546
2011 Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen CH, Zhang W, Jian X, Wang J, Zhang L, Looney TJ, Zhang B, Godley LA, et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nature Biotechnology. 29: 68-72. PMID 21151123 DOI: 10.1038/Nbt.1732  0.733
2009 Song CX, Cai GX, Farrell TR, Jiang ZP, Li H, Gan LB, Shi ZJ. Direct functionalization of benzylic C-Hs with vinyl acetates via Fe-catalysis. Chemical Communications (Cambridge, England). 6002-4. PMID 19809624 DOI: 10.1039/B911031C  0.395
2008 Lin S, Song CX, Cai GX, Wang WH, Shi ZJ. Intra/intermolecular direct allylic alkylation via Pd(II)-catalyzed allylic C-H activation. Journal of the American Chemical Society. 130: 12901-3. PMID 18778061 DOI: 10.1021/Ja803452P  0.394
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