Publications

Manuscripts Under Consideration or Revision

  • Xie J, Herr S, Ma D, Zhao H, Ma Z, Chang M, Li K, Huang F, Shi R, Yuan C, Transcriptome and methylome analysis of distal spinal cord location after spinal cord injury, Submitted
  • Sanchez OF, Lin L, Xie J, Freeman JL, Yuan C, Lead exposure induces dysregulation of constitutive heterochromatin hallmarks in live cells, Submitted
  • Zhang N, Zhou Y, Xie J, Yuan C, Zeber J, Zhang M, Ash A. Multimorbidity among nursing home residents with obesity, Submitted
  • Nurse, NP, Yuan C, Transgene delivery, expression and retention assisted by complexes, Submitted
  • Mendonca A, Sanchez O, Zhao H, Lin L, Min, A, Yuan C, Flow cytometric sorting of live mammalian cells based on epigenetic modification levels, under revision
  • Que Z, Olivero-Acosta, MI, Zhang J, Eaton M, Tukker AM, Chen X, Shafer JM, Yunis L, Schaber JA, Rochet JC, Bowman A, Yuan C, Huang Z, Skarnes WC, Yang Y, Hyperexcitability and pharmacological responsivenss of cortical neurons derived from human iPSCs carrying epilepsy-assoicated sodium channel Nav1.2-L1342P variant, under revision

2021

  • Zhao H, Ma D, Xie J, Sanchez O, Huang F, Yuan C., Live cell probe for in-situ single cell monitoring of mitochondrial DNA methylation, ACS Sensor, accepted
  • Zhang, Z.;  Cheng, L.;  Zhang, Q.;  Kong, Y.;  He, D.;  Li, K.;  Rea, M.;  Wang, J.;  Wang, R.;  Liu, J.;  Li, Z.;  Yuan, C.;  Liu, E.;  Fondufe-Mittendorf, Y. N.;  Li, L.;  Han, T.;  Wang, C.; Liu, X., Co-Targeting Plk1 and DNMT3a in Advanced Prostate Cancer. Adv Sci (Weinh) 2021, 8 (13), e2101458.
  • Zhang, J.;  Chen, X.;  Eaton, M.;  Wu, J.;  Ma, Z.;  Lai, S.;  Park, A.;  Ahmad, T. S.;  Que, Z.;  Lee, J. H.;  Xiao, T.;  Li, Y.;  Wang, Y.;  Olivero-Acosta, M. I.;  Schaber, J. A.;  Jayant, K.;  Yuan, C.;  Huang, Z.;  Lanman, N. A.;  Skarnes, W. C.; Yang, Y., Severe deficiency of the voltage-gated sodium channel Na(V)1.2 elevates neuronal excitability in adult mice. Cell Rep 2021, 36 (5), 109495.
  • Mendonca, A.;  Sánchez, O. F.;  Xie, J.;  Carneiro, A.;  Lin, L.; Yuan, C., Identifying distinct heterochromatin regions using combinatorial epigenetic probes in live cells. Biochim Biophys Acta Gene Regul Mech 2021, 1864 (8), 194725.
  • Lin, L. F.;  Xie, J.;  Sánchez, O. F.;  Bryan, C.;  Freeman, J. L.; Yuan, C., Low dose lead exposure induces alterations on heterochromatin hallmarks persisting through SH-SY5Y cell differentiation. Chemosphere 2021, 264 (Pt 1), 128486.
  • Xie, J.;  Lin, L.;  Sánchez, O. F.;  Bryan, C.;  Freeman, J. L.; Yuan, C., Pre-differentiation exposure to low-dose of atrazine results in persistent phenotypic changes in human neuronal cell lines. Environ Pollut 2021, 271, 116379.
  • Horzmann, K. A.;  Lin, L. F.;  Taslakjian, B.;  Yuan, C.; Freeman, J. L., Embryonic atrazine exposure and later in life behavioral and brain transcriptomic, epigenetic, and pathological alterations in adult male zebrafish. Cell Biol Toxicol 2021, 37 (3), 421-439.

Prior years

  • Xie, J.;  Wettschurack, K.; Yuan, C., Review: In vitro Cell Platform for Understanding Developmental Toxicity. Frontiers in genetics 2020, 11, 623117.
  • Sánchez, O. F.;  Lin, L.;  Bryan, C. J.;  Xie, J.;  Freeman, J. L.; Yuan, C., Profiling epigenetic changes in human cell line induced by atrazine exposure. Environ Pollut 2020, 258, 113712.
  • Wettschurack K, Xie J, Sánchez OF, Yuan C. Review: Engineering in situ biosensors for tracking cellular events. Current Opinion in Chemical Engineering. 2020;30:34-41.
  • Sanchez OF, Mendonca A, Min A, Liu J, Yuan C. Monitoring Histone Methylation (H3K9me3) Changes in Live Cells. ACS omega. 2019;4(8):13250-9.
  • Yuan, C., Lin, L., Carneiro, A., Xie, J., Single-cell epigenomic technology and applications, Chemical Engineering Progress, 2018
  • Wirbisky-Hershberger, S. E.;  Sanchez, O. F.;  Horzmann, K. A.;  Thanki, D.;  Yuan, C.; Freeman, J. L., Atrazine exposure decreases the activity of DNMTs, global DNA methylation levels, and dnmt expression. Food Chem Toxicol 2017, 109 (Pt 1), 727-734.
  • Sanchez, O. F.;  Mendonca, A.;  Carneiro, A. D.; Yuan, C., Engineering Recombinant Protein Sensors for Quantifying Histone Acetylation. ACS Sens 2017, 2 (3), 426-435.
  • Sanchez, O. F.;  Lee, J.;  Yu King Hing, N.;  Kim, S. E.;  Freeman, J. L.; Yuan, C., Lead (Pb) exposure reduces global DNA methylation level by non-competitive inhibition and alteration of dnmt expression. Metallomics : integrated biometal science 2017, 9 (2), 149-160.
  • Mendonca, A.;  Sanchez, O. F.;  Liu, W.;  Li, Z.; Yuan, C., CpG dinucleotide positioning patterns determine the binding affinity of methyl-binding domain to nucleosomes. Biochim Biophys Acta Gene Regul Mech 2017, 1860 (6), 713-720.
  • Tang, T.;  Yuan, C.;  Hwang, H. T.;  Zhao, X.;  Ramkrishna, D.;  Liu, D.; Varma, A., Engineering surface hydrophobicity improves activity of Bacillus thermocatenulatus lipase 2 enzyme. Biotechnol J 2015, 10 (11), 1762-9.
  • Sanchez, O. F.;  Williamson, D.;  Cai, L.; Yuan, C., A sensitive protein-based sensor for quantifying histone acetylation levels. Talanta 2015, 140, 212-218.
  • Nurse, N. P.; Yuan, C., Cis and trans internucleosomal interactions of H3 and H4 tails in tetranucleosomes. Biopolymers 2015, 103 (1), 33-40.
  • Zhao, X., Qi, F., Yuan, C., Du, W., Liu, D., Lipase-catalyzed process for biodiesel production: enzyme immobilization, process simulation and optimization, Renewable and Sustainable Energy Reviews, 2015, 44:182
  • Jimenez-Useche, I.;  Nurse, N. P.;  Tian, Y.;  Kansara, B. S.;  Shim, D.; Yuan, C., DNA methylation effects on tetra-nucleosome compaction and aggregation. Biophysical journal 2014, 107 (7), 1629-36.
  • Jimenez-Useche, I.;  Shim, D.;  Yu, J.; Yuan, C., Unmethylated and methylated CpG dinucleotides distinctively regulate the physical properties of DNA. Biopolymers 2014, 101 (5), 517-24.
  • Kim, S. E.;  Chang, M.; Yuan, C., One-pot approach for examining the DNA methylation patterns using an engineered methyl-probe. Biosens Bioelectron 2014, 58, 333-7.
  • Hwang, H. T.;  Qi, F.;  Yuan, C.;  Zhao, X.;  Ramkrishna, D.;  Liu, D.; Varma, A., Lipase-catalyzed process for biodiesel production: protein engineering and lipase production. Biotechnol Bioeng 2014, 111 (4), 639-53.
  • Mendonca, A., Chang, E., Yuan, C., Hydroxymethylation of DNA influences nucleosomal conformation and stability, Biochimica et Biophysica Acta – Gene Regulatory Mechanisms, 2014, 1839, 1323
  • Nurse, N. P.;  Jimenez-Useche, I.;  Smith, I. T.; Yuan, C., Clipping of flexible tails of histones H3 and H4 affects the structure and dynamics of the nucleosome. Biophysical journal 2013, 104 (5), 1081-8.
  • Jimenez-Useche, I.;  Ke, J.;  Tian, Y.;  Shim, D.;  Howell, S. C.;  Qiu, X.; Yuan, C., DNA methylation regulated nucleosome dynamics. Sci Rep 2013, 3, 2121.
  • Howell, S.C., Andreson K., Jimenez-Useche, I., Yuan, C., Qiu, X., Measuring the interactions between nucleosomes and the roles of histone tails, Biophysical Journal, 2013, 105:194-199
  • Andresen, K., Jimenez-Useche, I., Howell, S., Yuan, C., Qiu, X., Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tails, PLoS ONE, 2013 8(11): e78587
  • Jimenez-Useche, I.; Yuan, C., The effect of DNA CpG methylation on the dynamic conformation of a nucleosome. Biophysical journal 2012, 103 (12), 2502-12.
  • Ding, S., Zhu, T., Chen, J.S., Wang, Z., Yuan, C., Lou, X.W., Controlled synthesis of hierarchical NiO nanosheet hollow spheres with enhanced supercapacitvie performance, Journal of Material Chemistry, 2011, 21:6602-6606
  • Yuan, C., Chen, H., Lou, X.W., Archer, L.A., DNA bending stiffness on small length scales, Physical Review Letters, 2008, 100, 018102
  • Lou, X.W., Yuan, C., Archer, L.A., Double-walled SnO2 nano-cocoons with movable magnetic cores, Advanced Materials, 2007, 19, 3328-3332
  • Yuan, C., Lou, X.W., Rhoades, E., Chen, H., Archer, L.A., T4 DNA ligase is more than an effective trap of cyclized product, Nucleic Acids Research, 2007, 35, 5294-5302
  • Lou, X.W., Yuan, C., Zhang, Q., Archer, L.A., Platinum-Functionalized octahedral silica nanocages: synthesis and characterization, Angew.Chem. Int. Ed., 2006, 45, 3825-3829
  • Yuan, C., Rhoades, E., Heuer, D.M., Saha, S., Lou, X.W., Archer, L.A., Comprehensive interpretation of gel electrophoresis data, Analytical Chemistry, 2006, 78, 6179-6186
  • Yuan, C., Rhoades, E., Lou, X.W., Archer, L.A., Spontaneous sharp bending of DNA: role of melting bubbles”, Nucleic Acids Research, 2006, 16, 4554-4560
  • Lou, X.W., Yuan, C., Rhoades, E., Zhang, Q., Archer, L.A., Encapsulation and Ostwald ripening of Au and Au-Cl complex nanostructures in silica shells, Advanced Functional Materials, 2006, 16, 1679-1684
  • Lou, X.W., Wang, Y., Yuan, C., Lee, J.Y., Archer, L.A., Template-free synthesis of SnO2 hollow nanostructures with high lithium storage capacity, Advanced Materials, 2006, 18, 2325-2329
  • Lou, X.W., Yuan, C., Archer, L.A., An unusual example of hyperbranched metal nano-crystals and their shape evolution, Chemistry of Materials, 2006, 18, 3921-3923
  • Yuan, C., Rhoades, E., Heuer, D.M., Archer, L.A., Mismatch induced DNA “unbending” upon duplex opening, Biophysical Journal, 2005, 89, 2564-2573
  • Heuer, D.M., Yuan, C., Saha, S., Archer, L.A., Effect of topological asymmetry on the electrophoretic mobility of branched DNA structures with and without single-base mismatches, Electrophoresis, 2005, 26, 64-70