Publications

Peer-Reviewed Publications

  1. Koza RA, Nikonova L, Hogan J, Rim JS, Mendoza T, Faulk C, Skaf J, and Kozak LP, Changes in gene expression foreshadow diet-induced obesity in genetically identical mice. PLoS Genet, 2006. 2(5): p. e81. PMCID: PMC1464831
  2. Kim JD, Faulk C§, and Kim J, Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1. Nucleic Acids Research, 2007. 35(10): p. 3442-52. PMCID: PMC1904287 Considered equal co-first authors
  3. Faulk C and Kim J, Position-based clustering of microarray expression data. Cold Spring Harbor protocols, 2009.2009(9): p. pdb.prot5280.
  4. Faulk CD and Kim J, YY1’s DNA-binding motifs in mammalian olfactory receptor genes. BMC Genomics, 2009. 10: p. 576. PMCID: PMC2791781
  5. Faulk C and Dolinoy DC, Timing is everything: the when and how of environmentally induced changes in the epigenome of animals. Epigenetics, 2011. 6(7): p. 791-7. PMCID: PMC3230539*
  6. Kasili R, Huang CC, Walker JD, Simmons LA, Zhou J, Faulk C, Hulskamp M, and Larkin JC, BRANCHLESS TRICHOMES links cell shape and cell cycle control in Arabidopsis trichomes. Development, 2011. 138(11): p. 2379-88.
  7. Kim JD, Kim H, Ekram MB, Yu S, Faulk C, and Kim J, Rex1/Zfp42 as an epigenetic regulator for genomic imprinting.Human molecular genetics, 2011. 20(7): p. 1353-62. PMCID: PMC3049358
  8. Meyer TJ, McLain AT, Oldenburg JM, Faulk C, Bourgeois MG, Conlin EM, Mootnick AR, de Jong PJ, Roos C, Carbone L, and Batzer MA, An alu-based phylogeny of gibbons (hylobatidae). Mol Biol Evol, 2012. 29(11): p. 3441-50. PMCID: PMC3472497
  9. McLain AT, Meyer TJ, Faulk C, Herke SW, Oldenburg JM, Bourgeois MG, Abshire CF, Roos C, and Batzer MA, An alu-based phylogeny of lemurs (infraorder: lemuriformes). PLoS One, 2012. 7(8): p. e44035. PMCID: PMC3429421
  10. Anderson OS, Nahar MS, Faulk C, Jones TR, Liao C, Kannan K, Weinhouse C, Rozek LS, and Dolinoy DC, Epigenetic responses following maternal dietary exposure to physiologically relevant levels of bisphenol A. Environmental and molecular mutagenesis, 2012. 53(5): p. 334-42. PMCID: PMC3570056
  11. Dolinoy DC and Faulk C, Introduction: the use of animals models to advance epigenetic science. ILAR journal / National Research Council, Institute of Laboratory Animal Resources, 2012. 53(3-4): p. 227-31. PMCID: PMC3747759*
  12. Faulk C, Barks A, and Dolinoy DC, Phylogenetic and DNA methylation analysis reveal novel regions of variable methylation in the mouse IAP class of transposons. BMC genomics, 2013. 14(1): p. 48. Highly Accessed. PMCID: PMC3556122*
  13. Faulk C, Barks A, Liu K, Goodrich JM, and Dolinoy DC, Early-life lead exposure results in dose- and sex-specific effects on weight and epigenetic gene regulation in weanling mice. Epigenomics, 2013. 5(5): p. 487-500.
  14. McLain AT, Carman GW, Fullerton ML, Beckstrom TO, Gensler W, Meyer TJ, Faulk C, and Batzer MA, Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats. Mob DNA, 2013. 4(1): p. 26. Highly Accessed.
  15. Kim JH, Sartor MA, Rozek LS, Faulk C, Anderson OS, Jones TR, Nahar MS, and Dolinoy DC, Perinatal bisphenol A exposure promotes dose-dependent alterations of the mouse methylome. BMC Genomics, 2014. 15(1): p. 30. PMCID: PMC3902427
  16. Faulk C, Liu K, Barks A, Goodrich JM, and Dolinoy DC, Longitudinal epigenetic drift in mice perinatally exposed to lead. Epigenetics, 2014. 9(7).
  17. Faulk C, Barks AK§, Sanchez BN, Zhang Z, Anderson OS, Peterson KE, Dolinoy DC, Perinatal lead (Pb) exposure results in sex-specific effects on weight, food intake, body fat, and insulin response across the murine life course. PLoS ONE, 2014. DOI:10.1371/journal.pone.0104273.
  18. Kumar N, Harashima H, Shweta K, Bramsiepe J, Wang K, Sizani BL, Bertrand L, Johnson M, Faulk C, Simmons LA, Churchman ML, Sugimoto K, Kato N, Dasanayake M, Beemster G, Schnittger A, Larkin J. Functional Conservation in the SIAMESE-RELATED Family of Plant Cyclin-Dependent Kinase Inhibitors. Plant Cell. 2015 Nov 6. pii: tpc.15.00489.
  19. Faulk C, Kim JH, Jones TR, McEachin RC, Nahar MS, Dolinoy DC, and Sartor M, Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver. Environmental Epigenetics 2015 Oct 6. DOI: http://dx.doi.org/10.1093/eep/dvv006. (PMCID: PMC4922640)
  20. Wu J, Wen X, Faulk C, Boehnke K, Zhang H, Dolinoy DC, Xi C, Perinatal lead (Pb) exposure alters gut microbiota composition and results in sex-specific bodyweight increases in adult mice. Toxicological Sciences 2016; doi: 10.1093/toxsci/kfw046
  21. Faulk C, Kim JH, Anderson OS, Nahar MS, Jones TR, Sartor MA, Dolinoy DC, Detection of Differential DNA Methylation in Repetitive DNA of Mice and Humans Perinatally Exposed to Bisphenol A. Epigenetics. 2016.
  22. Weinhouse C, Sartor MA, Faulk C, Anderson OS, Sant KE, Harris C, Dolinoy DC. Epigenome-wide DNA methylation analysis implicates neuronal and inflammatory signaling pathways in adult murine hepatic tumorigenesis following perinatal exposure to bisphenol A. Environ. Mol. Mutagen. 57, 435–46 (2016).
  23. Kochmanski J, Marchlewicz EH, Savidge, M, Montrose L, Faulk C, Dolinoy DC Longitudinal effects of developmental bisphenol A and variable diet exposures on epigenetic drift in mice. Reprod. Toxicol. (2016). doi:10.1016/j.reprotox.2016.07.021
  24. Montrose L, Faulk C, Francis J, Dolinoy DC Perinatal lead (Pb) exposure results in sex and tissue-dependent adult DNA methylation alterations in murine IAP transposons. Environmental and Molecular Mutagenesis (2017). doi:10.1002/em.22119 Editor’s Choice article
  25. Colwell, M, Drown M, Showel K, Drown C, Palowski A, Faulk C. Evolutionary Conservation of DNA Methylation in CpG Sites within Ultraconserved Non-Coding Elements. Epigenetics. (2017). http://dx.doi.org/10.1080/15592294.2017.1411447 
  26. Laubach, ZM, Perng, W, Dolinoy, DC, Faulk, CD, Holekamp, KE & Getty, T. Epigenetics and the maintenance of developmental plasticity: Extending the signaling theory framework. Biol. Rev. (2018). doi:10.1111/brv.12396
  27. McLain AT, Faulk C. The evolution of CpG density and lifespan in conserved primate and mammalian promoters. Aging. 2018; 10:561-572. https://doi.org/10.18632/aging.101413
  28. Perera BPU, Tsai ZY, Colwell ML, Jones TR, Goodrich JM, Wang K, Sartor MA, Faulk C & Dolinoy DC. Somatic expression of piRNA and associated machinery in the mouse identifies short, tissue-specific piRNA.Epigenetics. (2019). doi:10.1080/15592294.2019.1600389
  29. Dou, JF, Farooqui, Z, Faulk, CD, Barks, AK, Jones, T, Dolinoy, DC, & Bakulski KM. Perinatal Lead (Pb) Exposure and Cortical Neuron-Specific DNA Methylation in Male Mice. Genes. (2019) http://doi.org/10.3390/genes10040274
  30. Perera BPU., Faulk C, Svoboda LK, Goodrich, JM, & Dolinoy, DC. The Role of Environmental Exposures and the Epigenome in Health and Disease. Environmental and Molecular Mutagenesis, em.22311. (2019). http://doi.org/10.1002/em.22311 (PMID: 31177562)
  31. Laubach ZM, Faulk CD, Dolinoy DC, Montrose L, Jones TR, Ray D, Pioon MO & Holekamp KE. Early life social and ecological determinants of global DNA methylation in wild spotted hyenas. Mol. Ecol. (2019). doi:10.1111/mec.15174
  32. Wanner N, Colwell M, Faulk C. The epigenetic legacy of illicit drugs: developmental exposures and late-life phenotypes. (2019) Environmental Epigenetics. Nov 13;5(4):dvz022. http://doi.org/10.1093/eep/dvz022
  33. Faulk C*, Mueller KR*, Cheishvili D, Colwell M, Pepin AS, Syzf M, Hering BJ & Burlak C. Epigenetic biomarkers indicate islet cell death in xenotransplantation. Xenotransplantation (2020). doi:10.1111/xen.12570 *Indicates equal author contributions.
  34. Seiler, C. L., Song, J. ung M., Kotandeniya, D., Chen, J., Kono, T. J. Y., Han, Q., Colwell, M., Auch, B., Sarver, A. L., Upadhyaya, P., Ren, Y., Faulk, C., De Flora, S., La Maestra, S., Chen, Y., Kassie, F. & Tretyakova, N. Y. Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung. Scientific Reports (2020). doi:10.1038/s41598-020-67502-8
  35. Wanner N, Colwell M, Drown C, Faulk C. Subacute cannabidiol alters genome-wide DNA methylation in adult mouse hippocampus. Environmental and Molecular Mutagenesis (2020).  
  36. Colwell M, Wanner N, Drown C, Drown M, Dolinoy D, Faulk C. Paradoxical whole genome DNA methylation dynamics of 5’aza-deoxycytidine in chronic low-dose exposure in mice. Epigenetics. (2020.)

  37.  Wanner NM, Colwell M, Drown C, Faulk C. Developmental cannabidiol exposure increases anxiety and modifies genome-wide brain DNA methylation in adult female mice. Clinical Epigenetics. 2021 Jan 6;13(1):4. doi: 10.1186/s13148-020-00993-4. PMID: 33407853.

  38. Laubach ZM, Greenberg JR, Turner JW, Montgomery TM, Pioon MO, Sawdy MA, Smale L, Cavalcante RG, Padmanabhan KR, Lalancette C, et al. 2021. Early-life social experience affects offspring DNA methylation and later life stress phenotype. Nat Commun 12.

  39. Wanner N, Larsen PA, McLain A, Faulk C. 2021. The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing. BMC Genomics 22: 726. https://doi.org/10.1186/s12864-021-08046-7.

Book Chapters (Peer Reviewed)

  1. Faulk C and Dolinoy DC, Complex Phenotypes: Epigenetic Manifestation of Enivironmental Exposures, in Environmental Epigenomics in Health and Disease, R.L. Jirtle and F. Tyson, Editors. 2013, Springer.
  2. Laubach Z., Faulk C., Cardenas A., and Perng W. Nutrition, DNA Methylation, and Developmental Origins of Cardiometabolic Disease: A Signal Systems Approach. Handbook of Nutrition, Diet, and Epigenetics. Preedy VR and Patel VB, Editors. 2017 Springer.  doi:10.1007/978-3-319-31143-2_107-1

  3. Faulk C. Implications of DNA Methylation in Toxicology, in ToxicoEpigenetics: Core Principles and Applications, Dolinoy DC and McCullough S, Editors. 2018 Springer.