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Patrick J. Murphy

  • Assistant Professor


2-9619 KMRB
(585) 275-0113

Office Hours: By appointment


Research Overview

Our lab investigates the mechanisms that activate or silence genes. As cells divide during development, changes in gene expression provide each cell type with a specific identity and function. In a similar sense, when the gene expression patterns of normal adult cells change inappropriately, the cell identity also changes, and this can lead to carcinogenesis. We utilize the zebrafish model in combination with mammalian cell lines to investigate how epigenetic marks control gene expression patterns to drive cell state transitions. This work relies on classic genetics and developmental biology methods, new DNA sequencing technologies, and bioinformatics applications.

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Zebrafish Genomics

The zebrafish model has emerged as incredibly valuable when combined with genomics for understanding mechanisms of vertebrate developmental processes in vivo. Zebrafish fertilization and early organismal development occur ex utero, and each breeding pair can produce over 200 offspring in precisely timed matings. Therefore, many thousands of cells can be harvested at specific developmental stages for complex genomics studies.

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The Murphy Lab – Fanju Meng, Claire Makowski, Kristin Murphy (left to right)



** indicates mentee

Selected Publications

  • Murphy P.J., Guo J.**, Jenkins T.G., James E.R., Hoidal J.R., Huecksteadt T., Hotaling J.M., Carrell D.T., Cairns B.R., Aston K.I. 2019. Oxidative Stress Underlies Cigarette Smoke Induced Epigenetic Inheritance. (under review at eLife) - BioRxiv 750638 [Preprint]
  • Rougeot, J., Chrispijn, N.D., Aben, M., Elurbe, D.M., Andralojc, K.M., Murphy, P.J., Jansen, P.W.T.C., Vermeulen, M., Cairns, B.R., and Kamminga, L.M. 2019. Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan. Development. (In Press) - BioRxiv 468769 [Preprint]
  • Murphy P.J., Wu S.F., James C.R.**, Wike C.L., Cairns B.R. 2018. Placeholder Nucleosomes Underlie Germline to Embryo DNA Methylation Reprogramming. Cell. 172: 993-1006.e13. PMID:29456083
  • Jenkins T.G., James E.R., Alonso D.F., Hoidal J.R., Murphy P.J., Hotaling J.M., Cairns B.R., Carrell D.T., Aston K.I. 2017. Cigarette smoking significantly alters sperm DNA methylation patterns. Andrology. 5: 1089-1099. PMCID: PMC5679018
  • Guo J.**, Grow E.J., Yi C., Mlcochova H., Maher G.J., Lindskog C., Murphy P.J., Wike C.L., Carrell D.T., Goriely A., Hotaling J.M., Cairns B.R. 2017. Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development. Cell Stem Cell. 21533-546.e6. PMCID: PMC5832720
  • Murphy P.J., Cairns B.R. 2016. Genome-Wide DNA Methylation Profiling in Zebrafish. Methods CellBiol. 135: 345-59. PMID:27443935
  • Murphy, K.E., Murphy, P.J., and Carrell, D.T. 2014.Epigenetic Changes in the Paternal Germline. In Transgenerational Epigenetics, T. Tollefsbol, ed. (Oxford: Academic Press), pp. 43–55.
  • Murphy P.J., Cipriany B.R., Wallin C., Ju C.Y.**, Benítez J.J., Szeto K., Craighead H.G., Soloway P.D. 2013. Single‐molecule Analysis of Combinatorial Epigenomic States in Normal and Tumor Cells. Proc Natl Acad SciU S A. 110: 7772-7. PMCID: PMC3651511
  • Benítez J.J., Topolancik J., Wallin C., Tian H.C., Latulippe D., Cipriany B.R., Murphy P.J., Soloway P.D., Craighead H.G. 2012. Microfluidic Extraction, Elongation, and Hybridization of Human Chromosomal DNA from Single Cells. Lab on a Chip. 12: 4848‐4854.c. PMCID: PMC3954578
  • Cipriany B.R., Murphy P.J., Hagarman J.A., Cerf A., Latulippe D., Levy S.L., Benítez J.J., Tan C.P., Topolancik J., Soloway P.D., Craighead H.G. 2012. Real‐Time Analysis and Selection of Methylated DNA by Fluorescence‐Activated Single Molecule Sorting in a Nanofluidic Channel. Proc Natl Acad Sci U S A. 109: 8477‐8482. PMCID: PMC3365150
  • Park Y.J., Herman H., Gao Y., Lindroth A.M., Hu B.Y., Murphy P.J., Putnam J.R.**, Soloway P.D. 2012. Sequences sufficient for programming imprinted germline DNA methylation defined. PLoS One. 7: e33024. PMCID: PMC3293921
  • Watanabe T., Tomizawa S., Mitsuya K., Totoki Y., Yamamoto Y., Kuramochi‐Miyagawa S., Iida N., Hoki Y., Murphy P.J., Toyoda A., Gotoh K., Hiura H., Arima T., Fujiyama A., Sado T., Shibata T., Nakano T., Lin H., Ichiyanagi K., Soloway P.D., Sasaki H. 2011. Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus. Science. 332: 848‐852. PMCID: PMC3368507
  • Cipriany B.R., Zhao R., Murphy P.J., Levy S.L., Tan C.P., Craighead H.G., Soloway P.D. 2010. Single-molecule epigenetic analysis in a nanofluidic channel. Anal Chem. 82: 2480‐2487. PMCID: PMC2839087