URMC / Labs / Murphy Lab / Publications Publications Duong PRodriguez-Parks AKang JMurphy PJ CUT&Tag applied to zebrafish adult tail fins reveals a return of embryonic H3K4me3 patterns during regeneration.; Epigenetics & chromatin; Vol 17(1), pp. 22. 2024 Jul 20. Duong PRodriguez-Parks AKang JMurphy PJ CUT&Tag Applied to Zebrafish Adult Tail Fins Reveals a Return of Embryonic H3K4me3 Patterns During Regeneration.; Research square. 2024 Apr 03. Alexander WBWang WHill MAO'Dell MRRuffolo LIGuo BJackson KMUllman NFriedland SCMcCall MNPatel AFigueroa-Guilliani NGeorger MBelt BAWhitney-Miller CLLinehan DCMurphy PJHezel AF Smad4 restricts injury-provoked biliary proliferation and carcinogenesis.; Disease models & mechanisms; Vol 17(6). 2024 Feb 28. Reda AHategan LAMcLean TABCreighton SDLuo JQChen SESHua SWinston SReeves IPadmanabhan ADahi TARamzan FBrimble MAMurphy PJWalters BJStefanelli GZovkic IB Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification.; Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology. 2024 Feb 16. Blanc RShah NSalama NMeng FMousaei AChakkalakal JOnukwufor JMurphy PCalvi LDirksen R Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis.; Research square. 2024 Feb 14. Halblander FNMeng FWMurphy PJ Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation.; Developmental biology. 2023 Dec 28. Meng FWMurphy KEMakowski CEDelatte BMurphy PJ Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression.; Development (Cambridge, England); Vol 150(21). 2023 Jan 08. Murphy PJBerger F The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations.; Development (Cambridge, England); Vol 150(21). 2023 Jan 03. Chen SRosin LFPegoraro GMoshkovich NMurphy PJYu GLei EP NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization.; Nucleic acids research. 2022 Jul 12. Hickey GJWike CLNie XGuo YTan MMurphy PJCairns BR Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos.; eLife; Vol 11. 2022 Jan 04. Ruff GLMurphy KESmith ZRVertino PMMurphy PJ Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation.; BMC cancer; Vol 21(1). 2021 Dec 18. Akdogan-Ozdilek BDuval KLMeng FWMurphy PJGoll MG Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag.; Developmental dynamics : an official publication of the American Association of Anatomists. 2021 Oct 14. Stefanelli GMakowski CEBrimble MAHall MReda ACreighton SDLeonetti AMMcLean TABZakaria JMBaumbach JGreer CBDavidoff AMWalters BJMurphy PJZovkic IB The histone chaperone Anp32e regulates memory formation, transcription, and dendritic morphology by regulating steady-state H2A.Z binding in neurons.; Cell reports; Vol 36(7). 2021 Aug 17. Meng FWMurphy PJ Rolling uphill: in vivo reacquisition of pluripotency during cranial neural crest differentiation.; Communications biology; Vol 4(1). 2021 May 20. Murphy PJGuo JJenkins TGJames ERHoidal JRHuecksteadt TBroberg DSHotaling JMAlonso DFCarrell DTCairns BRAston KI NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure.; PLoS genetics; Vol 16(6). 2020 Jun. Murphy KEMeng FWMakowski CEMurphy PJ Genome-wide chromatin accessibility is restricted by ANP32E.; Nature communications; Vol 11(1). 2020 Jan 08. Rougeot JChrispijn NDAben MElurbe DMAndralojc KMMurphy PJJansen PWTCVermeulen MCairns BRKamminga LM Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan.; Development (Cambridge, England); Vol 146(19). 2019 Sep 30. Murphy PJWu SFJames CRWike CLCairns BR Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming.; Cell; Vol 172(5). 2018 Feb 22. Jenkins TGJames ERAlonso DFHoidal JRMurphy PJHotaling JMCairns BRCarrell DTAston KI Cigarette smoking significantly alters sperm DNA methylation patterns.; Andrology; Vol 5(6). 2017 Nov. Guo JGrow EJYi CMlcochova HMaher GJLindskog CMurphy PJWike CLCarrell DTGoriely AHotaling JMCairns BR Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.; Cell stem cell; Vol 21(4). 2017 Jan 05. Murphy PJCairns BR Genome-wide DNA methylation profiling in zebrafish.; Methods in cell biology; Vol 135. 2016. Murphy PJCipriany BRWallin CBJu CYSzeto KHagarman JABenitez JJCraighead HGSoloway PD Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells.; Proceedings of the National Academy of Sciences of the United States of America; Vol 110(19). 2013 May 07. Benítez JJTopolancik JTian HCWallin CBLatulippe DRSzeto KMurphy PJCipriany BRLevy SLSoloway PDCraighead HG Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells.; Lab on a chip; Vol 12(22). 2012 Nov 21. Cipriany BRMurphy PJHagarman JACerf ALatulippe DLevy SLBenítez JJTan CPTopolancik JSoloway PDCraighead HG Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel.; Proceedings of the National Academy of Sciences of the United States of America; Vol 109(22). 2012 May 29. Park YJHerman HGao YLindroth AMHu BYMurphy PJPutnam JRSoloway PD Sequences sufficient for programming imprinted germline DNA methylation defined.; PloS one; Vol 7(3). 2012. Watanabe TTomizawa SMitsuya KTotoki YYamamoto YKuramochi-Miyagawa SIida NHoki YMurphy PJToyoda AGotoh KHiura HArima TFujiyama ASado TShibata TNakano TLin HIchiyanagi KSoloway PDSasaki H Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus.; Science (New York, N.Y.); Vol 332(6031). 2011 May 13. Cipriany BRZhao RMurphy PJLevy SLTan CPCraighead HGSoloway PD Single molecule epigenetic analysis in a nanofluidic channel.; Analytical chemistry; Vol 82(6). 2010 Mar 15.