Chris Faulk

Mathia L. Colwell, Nicole Flack, Amanda Rezabek, Christopher Faulk Intergenerational arsenic exposure on the mouse epigenome and metabolic physiology. Environmental and Molecular Mutagenesis. 2023 Jan 2. doi: 10.1002/em.22526. PMID: 36593717. (IF 3.2)

Palumbo JM, Thomas BF, Budimirovic D, Siegel S, Tassone F, Hagerman R, Faulk C, O'Quinn S, Sebree T. Role of the endocannabinoid system in fragile X syndrome: potential mechanisms for benefit from cannabidiol treatment. Journal of Neurodevelopmental Disorders. 2023 Jan 9;15(1):1. doi: 10.1186/s11689-023-09475-z. PMID: 36624400; PMCID: PMC9830713. (IF 3.5)

Flack N, Drown M, Walls C, Pratte J, McLain A, Faulk C. Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform. 2023 Apr 4;5(2):lqad033. doi: 10.1093/nargab/lqad033. PMID: 37025970; PMCID: PMC10071556. (IF prediction 5.0)

Melotto G, Jones MW, Bosley K, Flack N, Frank LE, Jacobson E, Kipp EJ, Nelson S, Ramirez M, Walls C, Koch RL, Lindsey ARI, Faulk C. The genome of the soybean gall midge (Resseliella maxima). G3 (Bethesda). 2023 Apr 11;13(4):jkad046. doi: 10.1093/g3journal/jkad046. PMID: 36861345; PMCID: PMC10085792. (IF 2.8)

Kipp EJ, Lindsey LL, Milstein MS, Blanco CM, Baker JP, Faulk C, Oliver JD, Larsen PA. Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects. Parasit Vectors. 2023 Feb 14;16(1):68. doi: 10.1186/s13071-023-05679-3. PMID: 36788607; PMCID: PMC9930342. (IF 3.0)

Faulk C. Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates. Genome Res. 2023 Jun;33(6):948-956. doi: 10.1101/gr.277743.123. Epub 2023 Jul 13. PMID: 37442577. (IF 9.0)

Christopher Faulk. De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing. Nucleic Acids Research June 2022). (IF 16.9) *Awarded “Breakthrough Status” (Top 1-2% of papers)

Melissa K. Drown, Amanda N. DeLiberto, Nicole Flack, Meghan Doyle, Alexander Westover, John Proefrock, Sandra Heilshorn, Evan D’Alessandro, Douglas L. Crawford, Christopher Faulk, and Marjorie F. Oleksiak. Sequencing bait: Nuclear and mitogenome assembly of an abundant coastal subtropical fish, Atherinomorus stipes. Genome Biology and Evolution. (IF 4.07) July 2022.

Soto-Palma, Carolina, Laura J. Niedernhofer, Christopher D. Faulk, and Xiao Dong. “Epigenetics, DNA Damage, and Aging.” The Journal of Clinical Investigation 132, no. 16 (August 15, 2022). https://doi.org/10.1172/JCI158446. (IF 19.5)

Srisomboon, Yotesawee, Koji Iijima, Mathia Colwell, Peter J. Maniak, Marissa Macchietto, Christopher Faulk, Hirohito Kita, and Scott M. O’Grady. Allergen-Induced DNA Release by the Airway Epithelium Amplifies Type 2 Immunity. The Journal of Allergy and Clinical Immunology, October 25, 2022, S0091-6749(22)01416-6. https://doi.org/10.1016/j.jaci.2022.09.034. (IF 14.29)

Rosa-Medina, E. A., Urriola, P. E., Jang, J. C., Faulk, C. D., Johnston, L. J., & Shurson, G. C. (2021). Effect of supplementing lactation and nursery pig diets with capsaicin on growth performance and gene expression of nursery pigs. Translational animal science, 5(4), txab201. PubMed Central ID Number: PMC8562730 doi: 10.1093/tas/txab201

Wanner, N., Larsen, P. A., 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(1), 726. PubMed Central ID Number: PMC8499546 doi: 10.1186/s12864-021-08046-7

Wanner, N. M., & Faulk, C. (2021). Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species. Genes, 12(8). PubMed Central ID Number: PMC8391136 doi: 10.3390/genes12081223

Laubach, Z. M., Greenberg, J. R., Turner, J. W., Montgomery, T. M., Pioon, M. O., Sawdy, M. A., . . . Perng, W. (2021). Early-life social experience affects offspring DNA methylation and later life stress phenotype. Nature communications, 12(1), 4398. PubMed Central ID Number: PMC8292380 doi: 10.1038/s41467-021-24583-x

Wanner, N. M., Colwell, M., Drown, C., & Faulk, C. (2021). Developmental cannabidiol exposure increases anxiety and modifies genome-wide brain DNA methylation in adult female mice. Clinical epigenetics, 13(1), 4. PubMed Central ID Number: PMC7789000 doi: 10.1186/s13148-020-00993-4 

Colwell, M., Wanner, N. M., Drown, C., Drown, M., Dolinoy, D. C., & Faulk, C. (2021). Paradoxical whole genome DNA methylation dynamics of 5'aza-deoxycytidine in chronic low-dose exposure in mice. Epigenetics, 16(2), 209-227. PubMed Central ID Number: PMC7889218 doi: 10.1080/15592294.2020.1790951

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.

Wanner N, Colwell M, Drown C, Faulk C. Subacute cannabidiol alters genome-wide DNA methylation in adult mouse hippocampus. Environmental and Molecular Mutagenesis (2020).  

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.)

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

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)

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

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

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

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

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

Colwell M, Drown M, Showel K, Drown C, Palowski A, and Faulk C. 2018. Evolutionary conservation of DNA methylation in CpG sites within ultraconserved non-coding elements. Epigenet. 2018 Feb 6:1-12. doi: 10.1080/15592294.2017.1411447.

Montrose L, Faulk C, Francis J, and Dolinoy DC. 2017. Perinatal lead (Pb) exposure results in sex and tissue-dependent adult DNA methylation alterations in murine IAP transposons. Environ. and Molecular Mutagenesis (2017). doi:10.1002/em.22119 (Editor’s Choice Article).

Faulk C, Kim JH, Anderson OS, Nahar MS, Jones TR, Sartor MA, and Dolinoy DC. 2016. Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A. Epigenet. 2016 Jul 2;11(7):489-500. doi: 10.1080/15592294.2016.1183856.

Kochmanski J, Marchlewicz EH, Savidge, M, Montrose L, Faulk C, and Dolinoy DC. 2016.  Longitudinal effects of developmental bisphenol A and variable diet exposures on epigenetic drift in mice. Reprod. Toxicol. doi:10.1016/j.reprotox.2016.07.021.

Weinhouse C, Sartor MA, Faulk C, Anderson OS, Sant KE, Harris C, and Dolinoy DC. 2016. 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.

Wu J, Wen X, Faulk C. Boehnke K, Zhang H, Dolinoy DC, and Xi C. 2016. Perinatal lead (Pb) exposure alters gut microbiota composition and results in sex-specific bodyweight increases in adult mice. Toxicol. Sci. 2016; doi: 10.1093/toxsci/kfw046.

Faulk C, Kim JH, Jones TR, McEachin RC, Nahar MS, Dolinoy DC, and Sartor M. 2015. Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver. Environ. Epigenetics 2015 Oct 6. DOI: http://dx.doi.org/10.1093/eep/dvv006.

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, and Larkin J. 2015. Functional conservation in the Siamese-related family of plant cyclin-dependent kinase inhibitors. Plant Cell. 2015 Nov 6. pii: tpc.15.00489.

Faulk C, Barks AK, Sanchez BN, Zhang Z, Anderson OS, Peterson KE, and Dolinoy DC. 2014. 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 9(8): e104273. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104273

Faulk C, Liu K, Barks A, Goodrich J, and Dolinoy DC. 2014. Longitudinal epigenetic drift in mice perinatally exposed to lead (Pb). Epigenetics 9(7): 934-941. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143408/

Kim JH, Sartor MA, Rozek LS, Faulk C., Anderson OS, Jones TR, Nahar MS, and Dolinoy DC. 2014. Perinatal bisphenol A exposure promotes dose-dependent alterations of the mouse methylome. BMC Genomics 15:30, 1471-2164. pdf

Dolinoy DC and Faulk C. 2013. Introduction: The use of animals models to advance epigenetic science. ILAR Journal, National Research Council, Institute of Laboratory Animal Resources 53(3/4): 227-231. pdf

Faulk C, Barks A, and Dolinoy DC. 2013. Phylogenetic and DNA methylation analysis reveal novel regions of variable methylation in the mouse IAP class of transposons. BMC Genomics 14(1): 48. pdf

Faulk C, Barks A, Liu K, Goodrich JM, and Dolinoy DC. 2013. Early-life lead exposure results in dose- and sex-specific effects on weight and epigenetic gene regulation in weanling mice. Epigenomics 5(5): 487-500. pdf

McLain AT, Carman GW, Fullerton ML, Beckstrom TO, Gensler W, Meyer TJ, Faulk C, and Batzer MA. 2013. Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats. Mobile DNA 4:26. pdf

Anderson OS, Nahar MS, Faulk C, Jones TR, Liao C, Kannan K, Weinhouse C, Rozek LS, and Dolinoy DC. 2012. Epigenetic responses following maternal dietary exposure to physiologically relevant levels of bisphenol A. Environmental and Molecular Mutagenesis 53(5): 334-342. pdf

McLain AT, Meyer TJ, Faulk C, Herke SW, Oldenburg JM, Bourgeois MG, Abshire CF, Roos C, and Batzer MA. 2012. An Alu-based phylogeny of lemurs (infraorder: lemuriformes). PLoS ONE 7(8): e44035. pdf

Meyer TJ, McLain AT, Oldenburg JM, Faulk C, Bourgeois MG, Conlin EM, Mootnick AR, de Jong PJ, Roos C, Carbone L, and Batzer MA. 2012. An Alu-based phylogeny of gibbons (hylobatidae). Mol. Biol. Evol. 29(11): p. 3441-3450. pdf

Faulk C and Dolinoy DC. 2011. Timing is everything: The when and how of environmentally induced changes in the epigenome of animals. Epigenetics 6(7): 791-797. pdf

Kasili R, Huang CC, Walker JD, Simmons LA, Zhou J, Faulk C, Hulskamp M, and Larkin JC. 2011. BRANCHLESS TRICHOMES links cell shape and cell cycle control in Arabidopsis trichomes. Development 138(11): 2379-2388. pdf

Kim JD, Kim H, Ekram MB, Yu S, Faulk C, and Kim J. 2011. Rex1/Zfp42 as an epigenetic regulator for genomic imprinting. Human Mol. Genet. 20(7): 1353-1362. pdf

Faulk C and Kim J. 2009. Position-based clustering of microarray expression data. Cold Spring Harb. Protoc. 4(9); doi:10.1101/pdb.prot5280. pdf

Faulk CD and Kim J. 2009. YY1's DNA-binding motifs in mammalian olfactory receptor genes. BMC Genomics 10: 576. pdf

Kim JD, Faulk C, and Kim J. 2007. Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1. Nucleic Acids Res. 35(10): 3442-3452. pdf

Koza RA, Nikonova L, Hogan J, Rim JS, Mendoza T, Faulk C, Skaf J, and Kozak LP. 2006. Changes in gene expression foreshadow diet-induced obesity in genetically identical mice. PLoS Genet. 2(5): e81. pdf

Berry, Oliver F., Simon N. Jarman, and Clare E. Holleley, eds. Applied Environmental Genomics. CSIRO PUBLISHING, 2023. Chapter 6. Lifespan estimation from genomic analysis, Benjamin Mayne and Christopher Faulk.

Faulk C. 2018. Implications of DNA methylation in toxicology. In: ToxicoEpigenetics: Core Principles and Applications. Dolinoy DC and McCullough S, Eds., Springer.

Laubach Z, Faulk C, Cardenas A, and Perng W. 2017. Nutrition, DNA methylation, and developmental origins of cardiometabolic disease: A signal systems approach. Handbook of Nutrition, Diet, and Epigenetics. Preedy VR and Patel VB, Eds., Springer. doi:10.1007/978-3-319-31143-2_107-1.

Faulk C and Dolinoy DC. 2013. Complex phenotypes: Epigenetic manifestation of enivironmental exposures in environmental epigenomics. In: Health and Disease. RL Jirtle and F Tyson (Eds.), Springer.

C Faulk. CpG Density Mutagenesis in Evolution and Lifespan Estimation. Environmental Mutagenesis and Genomics Society, Chicago, IL. September 15, 2023. (Invited Speaker)

C Faulk. Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates. Environmental Mutagenesis and Genomics Society, Chicago, IL. September 12, 2023. (Invited Speaker)

C Faulk. Adaptive Sampling for Epigenetics, Disease Surveillance, and Conservation. Nanopore Day, Chicago, IL. April 12, 2023. (Invited Speaker)

Colwell ML, Drown M, Drown C, Borchers A, Showel K, and Faulk C. 2017. Ultraconserved noncoding element DNA methylation in vertebrates, mice, and human populations. Environ. Mutagenesis and Genom. Soc. (Poster) Sep. 9.

Faulk C. 2017. Bisphenol A and transposon methylation in mice and men. FASEB Mobile DNA. Big Sky, MT. (Invited Lightning Talk) June 18.

Faulk C. 2017. DNA methylation in ultra-conserved elements: From generations to species. Integrated Toxicol. and Environ. Health Prog. Seminar, Duke University, Chapel Hill, NC. (Invited Talk). Feb. 10.

Faulk C. 2017. Weaving together nutrition, genomics, and epigenetics. Dept of Animal Science Seminar, Univ. of MN. May 19.

Faulk C. 2017. Western diet and early life nutritional modifications: Programming obesity epidemics? 2nd Internatl. Conf. on Obesity and Chronic Diseases, San Francisco, CA. (Invited Talk) July 6-8.

McLain A, and Faulk C. 2017. The evolution of lifespan and the epigenome assessed by CpG frequency in conserved primate and vertebrate promoters. Genome Informatics CSHL Mtg., Cold Spring Harbor, NY. (Platform Talk) Nov. 1-4.

Colwell ML, Drown M, Showel K, Esparza J, Borchers A, and Faulk C. 2016. DNA methylation of ultra-conserved non-coding elements in mouse tissues. Environ. Mutagenesis and Genom. Soc., Kansas City, MO. Sep. 24. (Poster)

Colwell ML and Faulk C. 2016. Expression of PIWIL proteins in mouse somatic tissue. Midwest Chromatin Mtg., Grand Rapids, MI. June 6. (Poster)

Drown M, Crooker B, and Faulk C. 2016. Epigenetic profiling of selected and nonselected bovine populations. Undergraduate Research Opportunity (UROP) Symp., Minneapolis MN. April 29. (Poster)

Faulk C. 2016. Differential methylation discovery with epigenomic data. Environmental Mutagenesis and Genom. Soc., Kansas City, MO. Sep. 24. (Invited Workshop Talk)

Faulk C, Colwell ML, Jones TR, Perera B, Sartor MA, and Dolinoy DC. 2016. Development of piRNAs for target-specific DNA methylation. NIH High Risk, High Reward Symp., Bethesda, MD. Dec. 5. (Poster)

Faulk C, Kim JH, Sartor MA, and Dolinoy DC. 2016. Prenatal bisphenol A exposure induces changes in global and individual transposon DNA methylation in both mice and humans. Soc. of Toxicology, New Orleans, LA. March 13-17. (Poster)

Mueller K, Colwell ML, Bybee A, Faulk C, and Burlak C. 2016. Epigenetic biomarkers in Type I diabetes. Midwest Chromatin Mtg., Grand Rapids, MI. June 6. ( Poster)

Faulk C. 2015. Epigenetics: The technology, applications, results, and rewards. Michigan State Univ. BEACON Center. Oct. 9. (Invited Talk)

Faulk C. 2015. Epigenetics and evolution. Michigan State Univ. (Sponsor, Kay Holekamp). Oct. 7. (Invited Talk)

Faulk C. 2015. Finding environmentally sensitive transposons with next-gen sequencing: BPA exposure in mice and humans. SOT Workshop on Toxicological Epigenomics, Soc. of Toxicology. April 23. (Invited Talk)

Faulk C, Kim JH, Sartor MA, and Dolinoy DC. 2015. The epigenetic landscape of repetitive elements in mice and humans prenatally exposed to Bisphenol A. Soc. of Toxicology. March 22-26. (Poster)

Faulk C, Barks A, Liu K., Anderson OS, Goodrich J., Zhang Z, Sànchez B, Peterson K, and Dolinoy DC. 2014. Murine perinatal Pb exposure: Effects on physiology and epigenetic drift over the life course. Environmental Mutagens and Genomics Soc. Sep. 14. (Poster)

Faulk C, Barks AK, Sánchez BN, Zhang Z, Anderson OS, Peterson KE, and Dolinoy DC. 2014. Physiological effects of developmental lead (Pb) exposure on weight, food intake, body fat, and insulin in mice. Soc. of Toxicology. March 27. (Poster)

Faulk C, Barks AK, and Dolinoy DC. 2013. Phylogenetic identification of variably methylated transposons as biomarkers for early environmental exposures. Soc. of Toxicology, San Antonio, TX. March 10. (Poster)

Faulk C, Barks AK, Liu K, Goodrich J, and Dolinoy DC. 2013. Mice and perinatal exposures: Epigenetic effects on imprinted genes and repetitive elements. 8th Annual Michigan Metabolomics and Obesity Center Symp., Ann Arbor, MI. Oct 16. (Poster)

Faulk C, Barks AK, Anderson OS, and Dolinoy DC. 2012. Repeat driven metastability of DNA methylation in response to environmental exposures. Soc. of Toxicology, San Francisco, CA. March 11-14. (Poster)

Faulk C, Barks AK, and Dolinoy DC. 2012. Phylogenetic approach for the identification of DNA biomarkers of early environmental exposures. Developmental Origins of Metabolic Disease Symp., Ann Arbor, MI. Oct. 5. (Poster)

Faulk C, and Kim J. 2009. YY1's DNA-binding motifs in mammalian olfactory receptor genes. Evolution: The Molecular Landscape - 74th Annual Cold Spring Harbor Symp. on Quantitatie Biol., Cold Spring Harbor, NY. (Poster)

Faulk C, and Kim J. YY1-mediated regulation of olfactory receptor genes through DNA binding sites within ORFs. LSU Graduate Symposium. (Poster)

Faulk C, Kim JD, and Kim J. 2006. Retrotransposition and evolution of the DNA binding motifs of YY1, YY2, and Rex1. CBM2 Colloquium, Baton Rouge, LA. (Poster)

Faulk C. 2010. Evolution of YY1, YY2, REX1 and DNA-binding motifs in vertebrate genomes. LSU. pdf