URMC / Labs / Murphy Lab / Publications

Publications

1. Duong P
2. Rodriguez-Parks A
3. Kang J
4. Murphy 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.
1. Duong P
2. Rodriguez-Parks A
3. Kang J
4. Murphy PJ
CUT&Tag Applied to Zebrafish Adult Tail Fins Reveals a Return of Embryonic H3K4me3 Patterns During Regeneration.; Research square. 2024 Apr 03.
1. Alexander WB
2. Wang W
3. Hill MA
4. O'Dell MR
5. Ruffolo LI
6. Guo B
7. Jackson KM
8. Ullman N
9. Friedland SC
10. McCall MN
11. Patel A
12. Figueroa-Guilliani N
13. Georger M
14. Belt BA
15. Whitney-Miller CL
16. Linehan DC
17. Murphy PJ
18. Hezel AF
Smad4 restricts injury-provoked biliary proliferation and carcinogenesis.; Disease models & mechanisms; Vol 17(6). 2024 Feb 28.
1. Reda A
2. Hategan LA
3. McLean TAB
4. Creighton SD
5. Luo JQ
6. Chen SES
7. Hua S
8. Winston S
9. Reeves I
10. Padmanabhan A
11. Dahi TA
12. Ramzan F
13. Brimble MA
14. Murphy PJ
15. Walters BJ
16. Stefanelli G
17. Zovkic 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.
1. Blanc R
2. Shah N
3. Salama N
4. Meng F
5. Mousaei A
6. Chakkalakal J
7. Onukwufor J
8. Murphy P
9. Calvi L
10. Dirksen R
Epigenetic erosion of H4K20me1 induced by inflammation drives aged stem cell ferroptosis.; Research square. 2024 Feb 14.
1. Halblander FN
2. Meng FW
3. Murphy PJ
Anp32e protects against accumulation of H2A.Z at Sox motif containing promoters during zebrafish gastrulation.; Developmental biology. 2023 Dec 28.
1. Meng FW
2. Murphy KE
3. Makowski CE
4. Delatte B
5. Murphy PJ
Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression.; Development (Cambridge, England); Vol 150(21). 2023 Jan 08.
1. Murphy PJ
2. Berger F
The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations.; Development (Cambridge, England); Vol 150(21). 2023 Jan 03.
1. Chen S
2. Rosin LF
3. Pegoraro G
4. Moshkovich N
5. Murphy PJ
6. Yu G
7. Lei EP
NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization.; Nucleic acids research. 2022 Jul 12.
1. Hickey GJ
2. Wike CL
3. Nie X
4. Guo Y
5. Tan M
6. Murphy PJ
7. Cairns BR
Establishment of developmental gene silencing by ordered polycomb complex recruitment in early zebrafish embryos.; eLife; Vol 11. 2022 Jan 04.
1. Ruff GL
2. Murphy KE
3. Smith ZR
4. Vertino PM
5. Murphy PJ
Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation.; BMC cancer; Vol 21(1). 2021 Dec 18.
1. Akdogan-Ozdilek B
2. Duval KL
3. Meng FW
4. Murphy PJ
5. Goll 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.
1. Stefanelli G
2. Makowski CE
3. Brimble MA
4. Hall M
5. Reda A
6. Creighton SD
7. Leonetti AM
8. McLean TAB
9. Zakaria JM
10. Baumbach J
11. Greer CB
12. Davidoff AM
13. Walters BJ
14. Murphy PJ
15. Zovkic 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.
1. Meng FW
2. Murphy PJ
Rolling uphill: in vivo reacquisition of pluripotency during cranial neural crest differentiation.; Communications biology; Vol 4(1). 2021 May 20.
1. Murphy PJ
2. Guo J
3. Jenkins TG
4. James ER
5. Hoidal JR
6. Huecksteadt T
7. Broberg DS
8. Hotaling JM
9. Alonso DF
10. Carrell DT
11. Cairns BR
12. Aston KI
NRF2 loss recapitulates heritable impacts of paternal cigarette smoke exposure.; PLoS genetics; Vol 16(6). 2020 Jun.
1. Murphy KE
2. Meng FW
3. Makowski CE
4. Murphy PJ
Genome-wide chromatin accessibility is restricted by ANP32E.; Nature communications; Vol 11(1). 2020 Jan 08.
1. Rougeot J
2. Chrispijn ND
3. Aben M
4. Elurbe DM
5. Andralojc KM
6. Murphy PJ
7. Jansen PWTC
8. Vermeulen M
9. Cairns BR
10. Kamminga 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.
1. Murphy PJ
2. Wu SF
3. James CR
4. Wike CL
5. Cairns BR
Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming.; Cell; Vol 172(5). 2018 Feb 22.
1. Jenkins TG
2. James ER
3. Alonso DF
4. Hoidal JR
5. Murphy PJ
6. Hotaling JM
7. Cairns BR
8. Carrell DT
9. Aston KI
Cigarette smoking significantly alters sperm DNA methylation patterns.; Andrology; Vol 5(6). 2017 Nov.
1. Guo J
2. Grow EJ
3. Yi C
4. Mlcochova H
5. Maher GJ
6. Lindskog C
7. Murphy PJ
8. Wike CL
9. Carrell DT
10. Goriely A
11. Hotaling JM
12. Cairns 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.
1. Murphy PJ
2. Cairns BR
Genome-wide DNA methylation profiling in zebrafish.; Methods in cell biology; Vol 135. 2016.
1. Murphy PJ
2. Cipriany BR
3. Wallin CB
4. Ju CY
5. Szeto K
6. Hagarman JA
7. Benitez JJ
8. Craighead HG
9. Soloway 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.
1. Benítez JJ
2. Topolancik J
3. Tian HC
4. Wallin CB
5. Latulippe DR
6. Szeto K
7. Murphy PJ
8. Cipriany BR
9. Levy SL
10. Soloway PD
11. Craighead HG
Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells.; Lab on a chip; Vol 12(22). 2012 Nov 21.
1. Cipriany BR
2. Murphy PJ
3. Hagarman JA
4. Cerf A
5. Latulippe D
6. Levy SL
7. Benítez JJ
8. Tan CP
9. Topolancik J
10. Soloway PD
11. Craighead 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.
1. Park YJ
2. Herman H
3. Gao Y
4. Lindroth AM
5. Hu BY
6. Murphy PJ
7. Putnam JR
8. Soloway PD
Sequences sufficient for programming imprinted germline DNA methylation defined.; PloS one; Vol 7(3). 2012.
1. Watanabe T
2. Tomizawa S
3. Mitsuya K
4. Totoki Y
5. Yamamoto Y
6. Kuramochi-Miyagawa S
7. Iida N
8. Hoki Y
9. Murphy PJ
10. Toyoda A
11. Gotoh K
12. Hiura H
13. Arima T
14. Fujiyama A
15. Sado T
16. Shibata T
17. Nakano T
18. Lin H
19. Ichiyanagi K
20. Soloway PD
21. Sasaki 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.
1. Cipriany BR
2. Zhao R
3. Murphy PJ
4. Levy SL
5. Tan CP
6. Craighead HG
7. Soloway PD
Single molecule epigenetic analysis in a nanofluidic channel.; Analytical chemistry; Vol 82(6). 2010 Mar 15.