Publications

2016

Schiöth, H.B., Boström, A., Murphy, S.K., Erhart, W., Hampe, J., Moylan, C. and J. Mwinyi.  2016. A targeted analysis reveals relevant shifts in the methylation and transcription of genes responsible for bile acid homeostasis and drug metabolism in non-alcoholic fatty liver disease. BMC Genomics 17:462. PMCID: PMC4908840

Yamanoi, K., Matsumura, N., Murphy, S.K., Baba, T., Abiko, K., Hamanishi, J., Yamaguchi, K., Koshiyama, M., Konishi, I. and M. Mandai. 2016. Suppression of ABHD2, identified through a functional genomics screen, causes anoikis resistance, chemoresistance and poor prognosis in ovarian cancer. Oncotarget (in press). PMID: 27323405

Soubry, A.S., Guo, L., Huang, Z., Hoyo, C., Romanus, S., Price, T. and S.K. Murphy. 2016. Obesity-related DNA methylation at imprinted genes in human sperm: Results from the TIEGER study. Clinical Epigenetics 8:51.

Fuemmeler, B.F., Wang, L., Iversen, E.S., Maguire, R., Murphy, S.K. and C. Hoyo. 2016. Association between prepregnancy BMI and gestational weight gain with size, tempo and velocity of infant weight gain: Analysis of the Newborn Epigenetic Study (NEST) cohort. Childhood Obesity (in press). PMID: 27135650

Dewi, F.N., Wood, C.E., Willson, C.J., Register, T.C., Lees, C.J., Howard, T.D., Huang, Z., Murphy, S.K., Tooze, J.A., Chou, J.W., Miller, L.D. and J.M. Cline. 2016. Effects o pubertal exposure to dietary soy on estrogen receptor activity in the breast of cynomolgus macaques. Cancer Prevention Research 9:385-395.

Moylan, C.A. and S.K Murphy. 2016. DNA Methylation: Basic Principles. In: Medical Epigenetics, (Trygve Tollefsbol, ed.), Chapter 2, Elsevier (in press). 

Murakami, R., Matsumura, N., Mandai, M., Yoshihara, K., Tanabe, H., Yamanoi, K., Abiko, K., Yoshioka, Y., Hamanishi, J., Yamaguchi, K., Baba, T., Koshiyama, M., Enomoto, T., Okamoto, A., Murphy, S.K., Mori, S., Mikami, Y., Minamiguchi, S. and I. Konishi. 2016. Establishment of a novel histopathological classification of high-grade serous ovarian carcinoma correlated with prognostically distinct gene expression subtypes. The American Journal of Pathology 186:1103-1113. 

McCullough, L.E., Miller, E.E. Mendez, M.A., Murtha, A.P., Murphy, S.K. and C. Hoyo. 2016. Maternal B-vitamins: Effects on offspring weight and DNA methylation at genomically imprinted domains. Clinical Epigenetics 8:8. PMID: 26807160

Joubert, B.R., Felix, J.F., Yousefi, P., Bakulski, K.M., Just, A.C., Breton, C., Reese, S.E., Markunas, C.A., Richmond, R.C., Xu, C.J., Küpers, L.K., Oh, S.S., Hoyo, C., Gruzieva, O., Söderhäll, C., Salas, L.A., Baïz, N., Zhang, H., Lepeule, J., Ruiz, C., Ligthart, S., Wang, T., Taylor, J.A., Duijts, L., Sharp, G.C., Jankipersadsing, S.A., Nilsen, R.M., Vaez, A., Fallin, M.D., Hu, D., Litonjua, A.A., Fuemmeler, B.F., Huen, K., Kere, J., Kull, I., Munthe-Kaas, M.C., Gehring, U., Bustamante, M., Saurel-Coubizolles, M.J., Quraishi, B.M., Ren, J., Tost, J., Gonzalez, J.R., Peters, M.J., Håberg, S.E., Xu, Z., van Meurs, J.B., Gaunt, T.R., Kerkhof, M., Corpeleijn, E., Feinberg, A.P., Eng, C., Baccarelli, A.A., Benjamin Neelon, S.E., Bradman, A., Merid, S.K., Bergström, A., Herceg, Z., Hernandez-Vargas, H., Brunekreef, B., Pinart, M., Heude, B., Ewart, S., Yao, J., Lemonnier, N., Franco, O.H., Wu, M.C., Hofman, A., McArdle, W., Van der Vlies, P., Falahi, F., Gillman, M.W., Barcellos, L.F., Kumar, A., Wickman, M., Guerra, S., Charles, M.A., Holloway, J., Auffray, C., Tiemeier, H.W., Smith, G.D., Postma, D., Hivert, M.F., Eskenazi, B., Vrijheid, M., Arshad, H., Antó, J.M., Dehghan, A., Karmaus, W., Annesi-Maesano, I., Sunyer, J., Ghantous, A., Pershagen, G., Holland, N., Murphy, S.K., DeMeo, D.L., Burchard, E.G., Ladd-Acosta, C., Snieder, H., Nystad, W., Koppelman, G.H., Relton, C.L., Jaddoe, V.W., Wilcox, A., Melén, E., London, S.J. 2016. DNA methylation in newborns and maternal smoking in pregnancy: Genome-wide consortium meta-analysis. American Journal of Human Genetics 98:680-696. PMID: 27040690

2015

Siddiqui, N., DuBois, L., St. John-Williams, L., Thompson, J.W., Grenier, C., Fraser, M.O., Amundsen, C.L. and S.K. Murphy. 2015. Optimizing urine processing protocols for protein and metabolite detection. Journal of Proteomics and Bioinformatics S14:003.

Varadaraj, A., Patel, P., Serrao, A., Bandyopadhay, T., Jazaeri, A., Lee, N.Y., Murphy, S.K. and K. Mythreye. 2015. Epigenetic regulation of GDF2 suppresses anoikis in ovarian and breast epithelia. Neoplasia 17:826-838.  PMC4681890

King, K., Kane, J.B., Scarbrough, P., Hoyo C. and S.K. Murphy. 2015. Neighborhood and family environment of expectant mothers may influence prenatal programming of adult cancer risk: Discussion and an illustrative biomarker example. Biodemography and Social Biology 62:87-104. PMID: 27050035

Peng, J., Hamanishi, J., Matsumura, N., Abiko, K., Murat, K., Baba, T., Yamaguchi, K., Horikawa, N., Hosoe, Y., Murphy, S.K., Konishi, I. and M. Mandai. 2015. Chemotherapy induces programmed death-ligand 1 overexpression via the Nuclear Factor kappa beta to foster an immunosuppressive tumor microenvironment in ovarian cancer. Cancer Research 75:5034-5045. PMID: 26573793

King, K., Darrah, T., Money, E., Meentemer, R., Maguire, R., Nye, M., Michener, L., Murtha, A.P., Skaar, D.A., Murphy, S.K., Mendez, M.A., Vengosh, A. and C. Hoyo. Geographic clustering of elevated blood toxic metal levels in pregnant women. 2015. BMC Public Health 15:1035.

Keenan, M.M., Liu, B., Tang, X., Wu, J., Cyr, D., Stevens, R.D., Ilkayeva, O., Huang, Z., Tollini, L.A., Murphy, S.K., Lucas, J., Muoio, D.M., Kim, S.Y. and J.T. Chi. 2015. ACLY and ACC1 regulate hypoxia-induced apoptosis by modulating ETV4 via alpha-ketoglutarate. PLoS Genetics 11:e1005599.  PMC4599891

Hemachandra, P., Shin, D.H., Dier, U., Iuliano, J.N., Engelberth, S.A., Uusitalo, L.M., Murphy, S.K. and N. Hempel. 2015. Mitochondrial superoxide dismutase has a pro-tumorigenic role in ovarian clear cell carcinoma. Cancer Research 75:4973-4984. PMC4651777

Murphy, S.K., Erginer, E., Huang, Z., Visco, Z. and C. Hoyo. 2015. Genotype-epigenotype interaction at the IGF2 DMR. Genes 6:777-789. PMC4584329

Sachdeva, M., Dodd, R.D., Huang, Z., Grenier, C., Ma, Y., Lev, D.C., Cardona, D.M., Murphy, S.K. and D.G. Kirsch. 2015. Epigenetic silencing of Kruppel like factor-3 increases expression of pro-metastatic miR-182. Cancer Letters 369:202-211. PMC4600675

Vidal, A., Semenova, V., Darrah, T., Vengosh, A., Huang, Z., King, K., Nye, M., Fry, R., Skaar, D., Maguire, R., Murtha, A., Schildkraut, J., Murphy, S., and C. Hoyo. 2015. Maternal cadmium, iron and zinc levels, DNA methylation and birth weight. BMC Pharmacology and Toxicology 16:20.

Li, Y., Xie, C., Murphy, S.K., Skaar, D., Nye, M., Vidal, A.C., Cecil, K.M., Dietrich, K.N., Puga, A., Jirtle, R.L. and C. Hoyo. 2015. Lead exposure during early human development and DNA methylation of imprinted gene regulatory elements in adulthood. Environmental Health Perspectives (in press).

Taylor, M. and S.K. Murphy. 2015. Systems biology and the epigenome. In: Systems Biology in Toxicology and Environmental Health (Rebecca Fry, Ed), Elsevier, Academic Press, Amsterdam, pp. 43-56.

Mo, L., Pospichalova, V., Huang, Z., Murphy, S.K., Payne, S., Wang, F., Kennedy, M., Cianciolo, G.J., Bryja, V., Pizzo,, S.V. and R.E. Bachelder. 2015. Ascites increases expression/function of multidrug resistance proteins in ovarian cancer cells. PLoS One 10:e0131579.

Ding, J., Reynolds, L.M., Zeller, T., Muller, C., Mstat, K.L., Nicklas, B.J., Kritchevsky, S.B., Huang, Z., de la Fuente, A., Soranzo, N., Settlage, R.E., Chuang, C., Howard, T., Xu, N., Goodarzi, M.O., Chen, Y.-D., Rotter, J.I., Siscovick, D.S., Parks, J.S., Murphy, S., Jacobs, D.R., Post, W., Tracy, R.P., Wild, P.S., Blankenberg, S., Hoeschele, I., Herrington, D., McCall, C.E. and Y. Liu. 2015. Alterations of a cellular cholesterol metabolism network is a molecular feature of obesity-related type 2 diabetes and cardiovascular disease. Diabetes (in press.)

McCullough, L.E., Mendez, M.A., Miller, E.E., Schildkraut, J., Murtha, A.P., Murphy, S.K. and C. Hoyo. 2015. Associations between prenatal physical activity, birth weight and DNA methylation at genomically imprinted domains in a multiethnic birth cohort. Epigenetics 10:597-606.

Vidal, A.C, Skaar, D., Maguire R., Dodor, S., Musselwhite, L.W., Bartlett, J.A., Oneko, O., Obure, J., Mlay, P., Murphy, S.K. and C. Hoyo. 2015.  IL-10, IL-15, IL-17, and GMCSF levels in cervical cancer tissue of Tanzanian women infected with HPV16/18 vs. non-HPV-16/18 genotypes. Infectious Agents and Cancer 10:10.

Tang, X., Keenan, M.M., Wu, J., Lin, C., Dubois, L., Thompson, W., Freedland, S.J., Murphy, S.K. and J.A. Chi.  2015. Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis. PLoS Genetics 11:e1005158.

Peng, J., Yoshioka, Y., Mandai, M., Matsumura, N., Baba, T., Yamaguchi, K., Hamanishi, J., Kharma, B., Murakami, R., Abiko, K., Murphy, S.K. and I. Konishi. 2015. The BMP signaling pathway leads to enhanced proliferation in serous ovarian cancer - a potential therapeutic target. Molecular Carcinogenesis (in press).

Nye, M.D., Hoyo, C. and S.K. Murphy. 2015. In vitro lead exposure changes DNA methylation and expression of IGF2 and PEG1/MEST. Toxicology in Vitro 29:544-550.

King, K., Murphy, S.K. and C. Hoyo. 2015. Epigenetic regulation of newborns' imprinted gene related to gestational growth: Patterning by parental race/ethnicity and maternal socioeconomic status. Journal of Epidemiology and Community Health 69:639-647.

Nagura, M., Matsumura, N., Baba, T., Murakami, R., Kharma, B., Hamanishi, J., Yamaguchi, K., Abiko, K., Koshiyama, M., Mandai., M., Murata, T., Murphy, S.K. and I. Konishi. 2015. Invasion of uterine squamous cell carcinoma cells is facilitated by locoregional interaction with cancer-associated fibroblasts via activating transforming growth factor-beta. Gynecologic Oncology 136:104-111.

2014

Kharma, B., Baba, T., Matsumura, N., Kang, H.S., Hamanishi, J., Murakami, R., McConechy, M.M., Leung, S., Yamaguchi, K., Hosoe, Y., Yoshioka, Y., Murphy, S.K., Mandai, M., Huntsman, D.G. and I. Konishi. 2014. STAT1 drives tumor progression in serous papillary endometrial cancer. Cancer Research 74:6519-6530.

Yamaguchi, K., Matsumura, N., Mandai, M., Baba, T., Konishi, I. and S.K. Murphy. Epigenetic and genetic dispositions of ovarian carcinomas. Oncoscience 1:574-579. 

Vidal, A.C., Neelon, S.E.B., Liu, Y., Tuli, A., Fuemmeler, B.F., Hoyo, C., Murtha, A.P., Huang, Z., Schildkraut, J., Overcash, F., Kurtzberg, J., Jirtle, R.L., Iversen, E.S. and S.K. Murphy. 2014. Maternal stress, preterm birth, and DNA methylation at imprint regulatory sequences in humans. Genetics and Epigenetics 6:37-44.  PDF

Baba, T., Kang, H.S., Hosoe, Y., Kharma, B., Abiko, K., Matsumura, N., Hamanishi, J., Yamaguchi, K., Yoshiola, Y., Koshiyama, M., Mandai, M., Murphy, S.K. and I. Konishi. 2014. Menstrual cyclic change of metastin/GPR54 in endometrium. Medical Molecular Morphology (in press).

Davidson, B.A., Rubatt, J., Corcoran, D., Teoh, D., Bernardini, M., Grace, L., Soper, J.W., Berchuck, A., Siamakpour-Reihani, S., Chen, W., Owzar, K., Murphy, S.K. and A.A. Secord. 2014. Differential angiogenic gene expression in TP53 wild-type and mutant ovarian cancer cell lines. Frontiers in Oncology (in press).

Vidal, A.C., Smith, J.S., Iversen, E., Valea, F., Bentley, R. Gradison, M., Yarnall, K., Ford, A., Overcash, F., Grant, K., Murphy, S.K. and C. Hoyo. 2014. HPV genotypes and cervical intraepithelial neoplasia in a multiethnic cohort in the Southeastern United States. Cancer Causes and Control 25:1055-1062.

Smeester, L., Yosim, A.E., Nye, M.D., Hoyo, C. Murphy, S.K. and R.C. Fry. 2014. Imprinted genes and the environment: links to the toxic metals arsenic, cadmium, lead and mercury. Genes 5:477-496.

Hoyo, C., Daltveit, A.K., Iversen, E.S., Neelon, S.E.B., Fuemmeler, B.F., Schildkraut, J.M., Murtha, A.P., Overcash, F., Vidal, A.C., Wang, F., Huang, Z., Kurtzberg, J., Seewaldt, V., Forman, M., Jirtle, R.L. and S.K. Murphy. 2014. Erythrocyte folate concentrations, birth weight, and CpG methylation at genomically imprinted domains in a multiethnic cohort of newborns. Epigenetics 9:1120-1130.

Murphy, S.K. 2014. Paternal obesity–a risk factor for autism? Nature Reviews Endocrinology 10:389-390.

Vidal, A.C., Overcash, F., Murphy, S.K., Murtha, A.P., Schildkraut, J.M., Forman, M.R., Demark-Wahnefried, W., Kurtzberg, J.K., Skaar, D., Jirtle, R.L. and C. Hoyo. 2014. Associations between birth and one year anthropometric measurements and IGF2 and IGF2R genetic variants in African American and Caucasian American infants. Journal of Pediatric Genetics 2:119-127

Vidal, A., Murphy, S.K. and C. Hoyo. 2014. Should we develop a new HPV vaccine for African-American women? Expert Review of Vaccines (in press).

Nye, M.D., Fry, R.C., Hoyo, C. and S.K. Murphy. 2014. Investigating epigenetic effects of prenatal exposure to toxic metals in newborns: challenges and benefits. Medical Epigenetics 2:53-59.

Soubry, A., Hoyo, C, Jirtle, R.L. and S.K. Murphy. 2014. A paternal environmental legacy: evidence for epigenetic inheritance through the male germ line. BioEssays 36:359-371.  PDF

Yamaguchi, K., Huang, Z., Matsumura, N., Mandai, M., Okamoto, T., Baba, T., Konishi, I., Berchuck, A. and S.K. Murphy. Epigenetic determinants of ovarian clear cell carcinoma biology. International Journal of Cancer 135:585-597. PDF

Moylan, C.A., Pang, H., Dellinger, A., Suzuki, A., Garrett, M., Ashley-Koch, A., Murphy, S.K., Guy, C.D., Choi, S.S., Michelotti, G., Hampton, D.D., Chen, Y., Tillmann, H.L., Hauser, M.A., Abdelmalek, M.F. and A.M. Diehl. 2014. Hepatic gene expression profiles differentiate advanced from mild nonalcoholic fatty liver disease. Hepatology 59:471-482. PDF

Alvarez Secord, A., Teoh, D., Jia, J., Nixon, A.B., Grace, L., Adams, D.J. and S.K. Murphy.  2014. Dasatinib (BMS-35482) interacts synergistically with docetaxel, gemcitabine, topotecan and doxorubicin in ovarian cancer cells with high SRC pathway activation and protein expression. International Journal of Gynecological Cancer 24:218-225. 

Vidal, A., Henry, N.M., Murphy, S.K., Oneko, O., Nye, M., Bartlett, J.A., Overcash, F., Huang, Z., Wang, F., Mlay, P., Obure, J., Smith, J., Vasquez, B., Swai, B., Hernandez, B. and C. Hoyo. 2014. PEG1/MEST and IGF2 DNA methylation in CIN and cervical cancer. Clinical and Translational Oncology 16:266-272.  PDF

2013

Alvarez Secord, A., Bernardini, M.Q., Broadwater, G., Grace, L.A., Huang, Z., Baba, T., Kondoh, E., Sfakianos, G., Havrilesky, L.J. and S.K. Murphy. 2013. TP53 status is associated with Thrombospondin 1 expression in vitro. Frontiers in Oncology 3:269.  PDF

Soubry, A., Murphy, S.K., Wang, F., Huang, Z., Vidal, A.C., Fuemmeler, B.F., Kurtzberg, J., Murtha, A., Jirtle, R.L., Schildkraut, J.M. and C. Hoyo. 2013. Newborns of obese parents have altered DNA methylation patterns at imprinted genes. International Journal of Obesity (in press).  PDF

Murphy, S.K., Yang, H., Moylan, C.A., Pang, H., Dellinger, A. Abdelmalek, M.F., Garrett, M.E., Ashley-Koch, A., Suzuki, A., Tillmann, H.L. Hauser, M.A. and A.M. Diehl. 2013. Relationship between methylome and transcriptome in patients with non-alcoholic fatty liver disease. Gastroenterology 145:1076-1087.  PDF

Okamoto, T., Mandai, M., Matsumura, N., Yamaguchi, K., Kondoh, H., Amano, Y., Baba, T., Hamanishi, J. Abiko, K., Kosaka, K., Murphy, S.K., Mori, S. and I. Konishi. 2013. Hepatocyte nuclear factor-1beta (HNF-1beta) promotes glucose uptake and glycolytic activity in ovarian clear cell carcinoma. Molecular Carcinogenesis (in press). 

Murphy, S.K. 2013. Prenatal sensitization of a postnatal trigger for metabolic disease. Journal of Clinical Investigation 123:2786-2788.  PDF

Huang, Z. and S.K. Murphy. 2013. Increased intragenic IGF2 methylation is associated with repression of insulator activity and elevated expression in serous ovarian carcinoma. Frontiers in Women's Cancer 3:131.  PDF

Liu, Y., Hoyo, C., Murphy, S.K., Huang, Z., Overcash, F., Thompson, J., Brown, H. and A.P. Murtha. 2013. DNA methylation at imprint regulatory regions in preterm birth and infection. American Journal of Obstetrics and Gynecology 208:395.e1-7.  PDF

Vidal, A., Murtha, A.P., Murphy, S.K., Fortner, K., Overcash, F., Henry, N., Schildkraut, J.M., Forman, M.R., Demark-Wahnefried, W., Kurtzberg, J., Jirtle, R. and C. Hoyo. 2013. Maternal BMI, IGF-I levels and birth weight in African American and White infants. International Journal of Pediatrics 191472. PDF

Vidal, A.C., Murphy, S.K., Murtha, A.P., Schildkraut, J.M., Soubry, A., Huang, Z., Neelon, S.E., Fuemmeler, B., Iversen, E., Wang, F., Kurtzberg, J., Jirtle, R.L. and C. Hoyo. 2013 Associations between antibiotic exposure during pregnancy, birth weight and aberrant methylation at imprinted genes among offspring. International Journal of Obesity 37:907-913.  PDF

Murphy, S.K. and J.W. Hollingsworth. 2013. Stress: A possible link between genetics, epigenetics, and childhood asthma. American Journal of Respiratory and Critical Care Medicine 187:563-564.  PDF

Kharma, B., Baba, T., Mandai, M., Matsumura, N., Murphy, S.K., Kang, H.S., Yamanoi, K., Hamanishi, J., Yamaguchi, K., Yoshioka, Y. and I. Konishi. 2013. Utilization of genomic signatures to identify high efficacy candidate drugs for chemorefractory endometrial cancers. International Journal of Cancer 133:2234-2244.  PDF

Nye, M.D., Hoyo, C., Huang, Z., Vidal, A.C., Wang, F., Overcash, F., Smith, J.S., Vasquez, B., Hernandez, B., Swai, B., Oneko, O., Mlay, P., Obure, J. Gammon, M.D., Bartlett, J.A. and S.K. Murphy. 2013. Associations between methylation of Paternally Expressed Gene 3 (PEG3), cervical intraepithelial neoplasia and invasive cervical cancer. PLoS One 8:e56325.  PDF

Sfakianos, G.P., Iversen, E.S., Whitaker, R., Akushevich, L., Schildkraut, J.M., Murphy, S.K., Marks, J.R. and A. Berchuck. 2013. Validation of ovarian cancer gene expression signatures for survival and subtype in formalin fixed paraffin embedded tissues.  Gynecologic Oncology 129:159-164.  PDF

Soubry, A., Schildkraut, J.S., Murtha, A., Wang, F., Huang, Z., Bernal, A., Kurtzberg, J., Jirtle, R.L., Murphy, S.K. and C. Hoyo. 2013. Paternal obesity is associated with IGF2 hypomethylation in newborns: results from a Newbron Epigenetics STudy (NEST) cohort. BMC Medicine 11:29. [HIGHLY ACCESSED]  PDF

Murphy, S.K. and C. Hoyo. 2013. Sculpting our future: Environmental nudging of the imprintome.  In: Environmental Epigenomics in Health and Disease, (Randy Jirtle and Fred Tyson, eds.), pp. 51-73, Springer-Verlag, Berlin Heidelburg. 

Murphy, S.K. Bassil, C.F. and Z. Huang. 2013. Main principles and outcomes of DNA methylation analysis.  In: Methods in Molecular Biology, (Anastasia Malek, ed.), Humana Press (Springer) 1049:67-74.  PDF

Huang, Z., Bassil, C.F. and S.K. Murphy. 2013. Methylation-specific PCR. In: Methods in Molecular Biology, (Anastasia Malek, ed.), Humana Press (Springer) 1049:75-82. PDF

Huang, Z., Bassil, C.F. and S.K. Murphy. 2013. Bisulfite sequencing of cloned alleles. In: Methods in Molecular Biology, (Anastasia Malek, ed.), Humana Press (Springer) 1049:83-94.  PDF

Bassil, C.F., Huang, Z. and S.K. Murphy. 2013. Bisulfite pyrosequencing. In: Methods in Molecular Biology, (Anastasia Malek, ed.), Humana Press (Springer) 1049:95-107.  PDF

2012

Das, R., Anderson, N, Koran, M.I., Weidman, J.R., Mikkelsen, T.S., Kamal, M., Murphy, S.K., Linblad-Toh, K., Greally, J.M. and R.L. Jirtle. 2012. Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica. BMC Genomics 13:394.   PDF

Joubert, B.R. Haberg, S.E., Nilsen, R.M., Wang, X., Vollset, S.E., Murphy, S.K., Huang, Z., Hoyo, C., Midttun, O., Cupul-Uicab, L.A., Ueland, P.M., Wu, M.C., Nystad, W., Bell, D.A., Peddada, S.D. and S.J. London. 2012. 450k Epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy. Environmental Health Perspectives 120:1425-1431. [EHP Paper of the Year]  PDF

Murphy, S.K., Huang, Z. and C. Hoyo. 2012. Differentially methylated regions of imprinted genes in prenatal, perinatal and postnatal human tissues. PLoS One 7:e40924.  PDF

Korch, C. Spillman, M.A., Jackson, T.A., Jacobsen, B.M. Murphy, S.K., Lessey, B.A., Jordan, V.C. Bradford, A.P. 2012. DNA profiling analysis of endometrial and ovarian cell lines reveals misidentification, redundancy and contamination. Gynecologic Oncology 127:241-248.  PDF

Liu, Y., Murphy, S.K., Murtha, A.P., Fuemmeler, B.F., Schildkraut, J., Huang, Z., Overcash, F., Kurtzberg, J., Jirtle, R., Iversen, E.S., Forman, M.R. and C. Hoyo. 2012. Depression in pregnancy, infant birth weight and DNA methylation of imprint regulatory elements. Epigenetics 7:735-746.  PDF

Skaar, D.A., Li, Y., Bernal, A.J., Hoyo, C., Murphy, S.K. and R.L. Jirtle. 2012. The human imprintome and its role in disease susceptibility. ILAR Journal 53:337-354.   PDF

Hoyo, C., Fortner, K., Murtha, A.P., Schildkraut, J.M., Soubry, A., Demark-Wahnefried, W., Jirtle, R.L., Kurtzberg, J., Forman, M.R., Overcash, F., Huang, Z. and S.K. Murphy. 2012. Association of cord blood methylation fractions at imprinted insulin-like growth factor 2 (IGF2), plasma IGF2 and birth weight. Cancer Causes Control 23:635-645.  PDF

Hoyo, C., Murphy, S.K., Schildkraut, J.M., Vidal, A.C., Skaar, D., Millikan, R.C., Galanko, J., Sandler, R.S., Jirtle, R. and T. Keku. 2012. IGF2R genetic variants, circulating IGF2 concentrations and colon cancer risk in African Americans and Whites. Disease Markers 32:133-141.  PDF

Perkins, E., Murphy, S.K., Murtha, A.P., Schildkraut, J., Jirtle, R.L., Demark-Wahnefried, W., Forman, M.R., Kurtzberg, J., Overcash, F., Huang, Z., and C. Hoyo. 2012. Insulin-like growth factor 2/H19 methylation at birth and risk of overweight and obesity in children. Journal of Pediatrics 161:31-39.  PDF

Murphy, S.K. Targeting the epigenome in ovarian cancer. 2012. Future Oncology 8:151-164.  PDF

Murphy, S.K., Adigun, A., Huang, Z., Overcash, F., Wang, F., Jirtle, R.L., Schildkraut, J.S., Murtha, A.P., Iversen, E.S. and C. Hoyo. 2012. Gender-specific methylation differences in relation to prenatal exposure to cigarette smoke. Gene 494:36-43.  PDF

Yamamura, S., Matsumura, N., Mandai, M., Huang, Z., Oura, T., Baba, T., Hamanishi, J., Yamaguchi, K., Sook, K., Okamoto, T., Abiko, K., Mori, S., Murphy, S.K. and I. Konishi. 2012. The activated TGF-beta signaling pathway in peritoneal metastases is a potential therapeutic target in ovarian cancer. International Journal of Cancer 130:20-28. PDF

2011

Soubry, A., Murphy, S.K., Huang, Z., Murtha, A., Schildkraut, J. M., Jirtle, R. L., Wang, F., Kurtzberg, J., Deamrk-Wahnefried, W., Forman, M. R. and C. Hoyo. 2011. The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of IGF2 imprint control regions in the offspring. Clinical Epigenetics 3:2.  PDF

Secord, A.A., Darcy, K.M., Hutson, A., Huang, Z., Lee, P.S., Jewell, E.L., Havrilesky, L.J., Markman, M.,  Muggia, F. and S.K. Murphy. 2011. The regulation of MASPIN expression in epithelial ovarian cancer: Association with p53 status, and MASPIN promoter methylation: A Gynecologic Oncology Group study. Gynecologic Oncology 123:314-319.  PDF

BonDurant, A. E., Huang, Z., Whitaker, R. S., Simel, L. R., Berchuck, A. and S. K. Murphy. 2011. Quantitative detection of RASSF1A DNA promoter methylation in tumors and serum of patients with serous epithelial ovarian cancer. Gynecologic Oncology 123:581-587.  PDF

Vidal, A.C., Murphy, S.K., Hernandez, B.Y., Vasquez, B., Bartlett, J.A., Oneko, O., Mlay, P., Obure, J., Overcash, F., Smith, J.S., van der Kolk, M. and C. Hoyo. 2011. Distribution of HPV genotypes in cervical intraepithelial lesions and cervical cancer in Tanzanian women. Infectious Agents and Cancer 6:20. [HIGHLY ACCESSED] PDF

Hoyo, C., Murtha, A.P., Schildkraut, J.M., Jirtle, R.L., Demark-Wahnefried, W., Forman, M.R. Iversen, E.S., Kurtzberg, J., Overcash, F., Huang, Z. and S.K. Murphy. 2011. Methylation variation at IGF2 differentially methylated regions and maternal folic acid use before and during pregnancy. Epigenetics 6:928-936. PDF

Matsumura, N., Huang, Z., Baba, T., Mori, S. Fujii, S., Konishi, I., Berchuck, A. and S.K. Murphy. 2011. Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer. Genome Research 21:74-82. [Genome Research Press Release] [Duke Press Release]  PDF

Hoyo, C., Murtha, A., Schildkraut, J., Forman, M.R., Calingaert, B., Demark-Wahnefried, W., Kurtzberg, J., Jirtle, R.L. and S.K. Murphy. 2011. Folic acid supplementation before and during pregnancy in the Newborn Epigenetics Study (NEST). BMC Public Health 11:46. [HIGHLY ACCESSED] PDF

Teoh, D., Ayeni, T.A., Rubatt, J.M., Adams, D.J., Grace, L., Starr, M.D., Barry, W.T., Berchuck, A., Murphy, S.K. and A.A. Secord. 2011. Dasatinib (BMS-35482) has synergistic activity with paclitaxel and carboplatin in ovarian cancer cells. Gynecologic Oncology 121:187-192.  PDF

Kang, H.S., Baba, T., Matsumura, N., Hamanishi, J., Kharma, B., Kondoh, E., Yoshioka, Y., Oishi, S., Fujii, N., Murphy, S.K. and I. Konishi. 2011. GPR54 is a target for suppression of metastasis in endometrial cancer. Molecular Cancer Therapeutics 10:580-590.  PDF

Zhang, A., Skaar, D., Li, Y., Huang, D., Price, T., Murphy, S.K. and R.L. Jirtle. 2011. Novel retrotransposed imprinted locus identified at human 6p25. Nucleic Acids Research 39:5388-5400. PDF 

Murphy, S.K. and A. Berchuck.  2011. Ovarian cancer progenitor/stem cells; therapeutic potential. In: Emerging Therapeutic Targets in Ovarian Cancer, (Stan Kaye, ed.), pp. 223-244, Springer, New York. 

2010

Lee, P.S., Teaberry, V.S., Bland, A.E., Huang, Z., Whitaker, R.S., Baba, T., Fujii, S., Secord, A.A., Berchuck, A. and S.K. Murphy. 2010. Elevated MAL expression is accompanied by promoter hypomethylation and platinum resistance in epithelial ovarian cancer. International Journal of Cancer 126:1378-1389. PDF

Kondoh, E., Mori, S., Yamaguchi, K., Baba, T., Matsumura, N., Barnett, J. C., Whitaker, R.S., Konishi, I., Fujii, S., Berchuck, A. and S.K. Murphy.  2010. Targeting slow proliferating ovarian cancer cells. International Journal of Cancer 126:2448-2456.  PDF

Yamaguchi, K. Mandai, M., Oura, T., Matsumura, N., Hamanishi, J., Baba, T., Matsui, S., Murphy, S.K., and I. Konishi. 2010. Identification of an ovarian clear cell carcinoma gene signature that reflects inherent disease biology and the carcinogenic process. Oncogene 29:1741-1752.  PDF

Barnett, J.C., Bean, S.M., Nakayama, J.M., Kondoh, E., Murphy, S.K. and A. Berchuck. 2010. High Poly (Adenosine Disphosphate-Ribose) polymerase expression and poor survival in advanced-stage serous ovarian cancer. Obstetrics and Gynecology 115:49-54.  PDF

Barnett, J.C., Bean, S.M., Whitaker, R.S., Kondoh, E., Baba, T., Fujii, S., Marks, J.R., Dressman, H.K., Murphy, S.K. and A. Berchuck.  2010. Ovarian cancer tumor infiltrating T-regulatory (Treg) cells are associated with a metastatic phenotype. Gynecologic Oncology 116:556-562. PDF

Bernardini, M. Q., Baba, T., Lee, P. S., Barnett, J. C., Sfakianos, G. P., Secord, A. A., Murphy, S. K., Iversen, E., Marks, J. R. and A. Berchuck. 2010. Expression signatures of TP53 mutations in serous ovarian cancers. BMC Cancer 10:237. PDF

Matsumura, N., Mandai, M., Okamoto, T., Yamaguchi, K., Yamamura, S., Oura, T., Baba, T., Hamanishi, J., Kang, H.S., Matsui, S., Mori, S., Murphy, S.K. and I. Konishi. 2010. Sorafenib efficacy in ovarian clear cell carcinoma revealed by transcriptome profiling. Cancer Science 101:2658-2663.  PDF

Murphy, S. K.  2010. Targeting ovarian cancer-initiating cells. Anticancer Agents in Medicinal Chemistry 10:157-163.  PDF

Bernal, A., Murphy, S.K. and R.L. Jirtle. 2010.  Mouse models of epigenetic inheritance.  In: Handbook of Epigenetics: The New Molecular and Medical Genetics, (Trygve Tollefsbol, ed.), pp. 233-249, Elsevier, London.

2009

Baba, T., Convery, P., Matsumura, N., Whitaker, R. S., Kondoh, E., Perry, T., Huang, Z., Bentley, R. C., Mori, S., Fujii, S., Marks, J. R., Berchuck, A. and S. K. Murphy.  2009. Epigenetic regulation of CD133 and tumorigenicity of CD133(+) ovarian cancer cells. Oncogene 28:209-218.  PDF

Horne, H., Lee, P. S., Murphy, S. K., Alonso, M. A., Olson, J. A. Jr. and J. R. Marks. 2009. Inactivation of the MAL gene in breast cancer is a common event and predicts benefit from adjuvant chemotherapy. Molecular Cancer Research 7:199-209.  PDF

Kondoh, E., Okamoto, T., Higuchi, T., Tatsumi, K., Baba, T., Murphy, S. K., Horiuchi, Y., Kang, H. S., Takakura, K., Konishi, I. and S. Fujii. 2009. Stress affects uterine receptivity through ovarian-independent pathway. Human Reproduction 24:945-953.  PDF

Berchuck, A., Iversen, E. S., Luo, J., Clarke, J. P., Horne, H., Levine, D., Boyd, J., Alonso, M. A., Secord, A. A., Bernardini, M. Q., Barnett, J. C., Boren, T., Murphy, S. K., Nevins, J. R., Marks, J. R., Dressman, H. K. and J. M. Lancaster.  2009.  Microarray analysis of early stage serous ovarian cancers demonstrates profiles predictive of favorable outcome. Clinical Cancer Research 15:2448-2455. 

Hoyo, C., Schildkraut, J. S., Murphy, S.K., Chow, W.-H., Vaughn, T. L., Risch, H., Marks, J. R., Jirtle, R. L., Calingaert, B., Mayne, S., Fraumeni, J. Jr., and M. D. Gammon.  2009. IGF2R polymorphisms and risk of esophageal and gastric adenocarcinoma. International Journal of Cancer 125:2673-2678.  PDF

Gregory, S. G., Connelly, J. J., Biscocho, D., Johnson, J., Lintas, C., Donnelly, S., Abramson, R., Wright, H., Ellis, P., Langford, C. F., Worley, G., Delong, G. R., Murphy, S. K., Cuccaro, M., Persico, A. and M. A. Pericak-Vance. 2009. Identification of OXTR as candidate gene within autism spectrum disorders by whole genome microarray and epigenetic analysis. BMC Medicine 7:62. [HIGHLY ACCESSED]   PDF

Mori, S., Chang, J. T., Andrechek, E. R., Matsumura, N., Baba, T., Yao, G., Murphy, S. K. and J. R. Nevins.  2009. Anchorage-independent cell growth signature identifies tumors with metastatic potential. Oncogene 28:2796-2805.  PDF

Ding, X., Mohd, A. B., Huang, Z., Baba, T., Bernardini, M., Lyerly, H. K., Berchuck, A., Murphy, S. K., Buermeyer, A., and G. R. Devi.  2009.  MLH1 expression sensitizes ovarian cancer cells to cell death mediated by XIAP inhibition. British Journal of Cancer 101:269-277.  PDF

Matsumura, N., Huang, Z., Baba, T., Lee, P. S., Mori, S., Chang, J., Kuo, W., Gusberg, A. H., Whitaker, R. S., Gray, J. W., Fujii, S., Berchuck, A. and S. K. Murphy.  2009. Yin yang 1 modulates taxane response in epithelial ovarian cancer.  Molecular Cancer Research 7:210-220. PDF

Hoyo, C., Murphy, S. K. and R. L. Jirtle.  2009. Imprint regulatory elements as epigenetic biosensors of exposure in epidemiological studies.  Journal of Epidemiology and Community Health 63:683-684. PDF

2007

Baba, T., Mori, S., Matsumura, N., Kariya, M., Murphy S. K., Kondoh, E., Kusakari, T., Kuroda, H., Mandai, M., Higuchi, T., Takakura, K., Fukuda, M. N. and S. Fujii. 2007. Trophonin is a potent prognostic marker of ovarian cancer involved in platinum sensitivity.  Biochemical and Biophysical Research Communications 360:363-369.  PDF

O’Sullivan, F., Murphy, S. K., Simel, L. R., McCann, A., Callanan, J. J. and C. M. Nolan. 2007. Imprinted expression of the canine IGF2R, in the absence of an anti-sense transcript or promoter methylation. Evolution and Development 9:579-589.  PDF

Price, T., Murphy, S. K. and E. Younglai. 2007. The possible influence of assisted reproductive technologies on transgenerational reproductive effects of environmental endocrine disruptors. Toxicological Sciences 96:218-226.  PDF

Weidman, J. R., Dolinoy, D. C., Murphy, S. K., and R. L. Jirtle.  2007. Cancer susceptibility: epigenetic manifestation of environmental exposures. The Cancer Journal 13:9-16. PDF

Hempel, N., How, T., Murphy, S. K., Fields, T. A. and G. C. Blobe.  2007.  Loss of Betaglycan expression in ovarian cancer: role in motility and invasion. Cancer Research 67:5231-5238. PDF

Spillman, M. A., Lacy, J., Murphy, S. K., Whitaker, R. S., Grace, L., Teaberry, V., Marks, J. R., and A. Berchuck. 2007. Regulation of the metastasis suppressor gene MKK4 in ovarian cancer. Gynecologic Oncology 105:312-320. PDF

Goh, L., Murphy, S. K., Mukherjee, S. and T. S. Furey.  2007.  Genomic sweeping for hypermethylated genes in unlabeled and imbalanced data using sequence features. Bioinformatics 23:281-288.  PDF

Schildkraut, J. S., Murphy, S. K., Palmeri, R. Huang, Z., Iversen, E., Halabi, S., Calingaert, B, Gusberg, A. H., Marks, J., Moorman, P. and A. Berchuck.  2007. Trinucleotide repeat polymorphisms in the androgen receptor gene and risk of ovarian cancer.  Cancer Epidemiology Biomarkers and Prevention 16:473-480. PDF

Risinger, J. I., Custer, M., Pack, S., Loukinov, D., Maxwell, G. L., Chandramouli, G., Aprelikova, O., Litzi, T., Murphy, S. K., Berchuck, A., Lobanenkov, V., and J.C. Barrett. 2007. Expression analysis of cancer testis antigens in uterine cancers details a high incidence of BORIS expression. Clinical Cancer Research 13:1713-1719. PDF

2006

Huang, Z., Wen, Y., Shandilya, R., Marks, J.R., Berchuck, A. and S. K. Murphy. 2006. High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer. Nucleic Acids Research 34:555-563. PDF

Murphy, S. K., Huang, Z., Wen, Y., Spillman, M. A., Whitaker, R. S., Nichols, T. B., Marks, J., and A. Berchuck. 2006. Frequent IGF2/H19 domain epigenetic alterations and elevated IGF2 expression in epithelial ovarian cancer. Molecular Cancer Research 4:283-292. PDF

Murphy, S. K., Nolan, C. M., Huang, Z. Kucera, K. S., Freking, B. A., Smith, T. P. L., Leymaster, K. A., Weidman, J. R., and R. L. Jirtle. 2006. Callipyge mutation affects gene expression in cis: A potential role for chromatin structure. Genome Research 16:340-346. PDF

2005

Murphy, S. K., Freking, B. A., Smith, T. P. L., Leymaster, K., Nolan, C. M., Wylie, A. A., Evans, H. K., and R. L. Jirtle. 2005. Abnormal postnatal maintenance of elevated DLK1 levels in callipyge sheep. Mammalian Genome 16:171-183. PDF

Berchuck, A., Iversen, E. S., Lancaster, J. M., Pittman, J., Luo, J., Lee, P., Murphy, S. K., Dressman, H. K., Febbo, P. G., West, M., Nevins, J. R., and Marks, J. R. 2005.  Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers. Clinical Cancer Research 11:3686-3696. PD

Spillman, M. A., Schildkraut, J. M., Halabi, S., Moorman, P., Calingaert, B., Bentley, R.C., Marks, J.R., Murphy, S. K., and A. Berchuck. 2005. Transforming Growth Factor ß Receptor I polyalanine repeat polymorphism does not increase ovarian cancer risk. Gynecologic Oncology 97:543-549. PDF

Wang, W., Huper, G., Guo, L. Murphy, S. K., Olson, J. A., and J. R. Marks. 2005. Analysis of methylation sensitive transcriptome identifies GADD45 alpha as a frequently methylated gene in breast cancer. Oncogene 24:2705-2714. PDF

Pre-2005

Weidman, J. R., Murphy, S. K., Nolan, C. M., and R. L. Jirtle. 2004. Phylogenetic footprint analysis of IGF2 in mammals. Genome Research 14:1726-1732. [Featured on Cover] PDF

Murphy, S. K., and R. L. Jirtle.  2003.  Imprinting evolution and the price of silence.  BioEssays 25(6):577-588. [Featured on Cover] PDF

Dietz, L. G., Wylie, A. A., Rauen, K. A., Murphy, S. K., Jirtle, R. L., and P. D. Cotter.  2003. Exclusion of maternal uniparental disomy of chromosome 14 in patients referred for Prader-Willi syndrome using a multiplex methylation polymerase chain reaction assay. Journal of Medical Genetics 40:e46. PDF

Murphy, S.K., Wylie, A.A., Coveler, K.J., Cotter, P.D., Papenhausen, P.R., Sutton, V.R., Shaffer, L.G., and R.L. Jirtle. 2003. Epigenetic detection of human chromosome 14 uniparental disomy. Human Mutation 22:92-97. PDF

Freking, B.A., Murphy, S.K., Wylie, A.A., Rhodes, S., Leymaster, K.A., Keele, J.W., Jirtle. R.L., and T.P.L. Smith.  2002.  Identification of the single base change causing the callipyge muscle hypertrophy phenotype in sheep, the only known example of polar overdominance in mammals. Genome Research 12(10):1496-1506. [Featured on Cover] [Press Release] PDF

Li, T., Vu, T.H., Lee, K.O., Bui, H.Q., Zeng, Z., Nguyen, B.T., Hu, J., Jirtle, R.L., Murphy, S.K., Nguyen, C. V., and A.R. Hoffman.  2002.  An imprinted PEG1/MEST antisense expressed predominantly in testis and in mature spermatozoa.  Journal of Biological Chemistry 277:13518-13527. PDF

Evans, H.K., Wylie, A.A., Murphy, S.K., and R.L. Jirtle.  2001.  The neuronatin gene resides in a “micro-imprinted” domain on human chromosome 20q11.2.  Genomics 77:99-104. PDF

Keller, M.A., Murphy, S.K., and G.D. Parks.  2001.  RNA replication from the Simian Virus 5 antigenomic promoter requires three sequence-dependent elements separated by sequence-independent spacer regions. Journal of Virology 75:3993-3998. PDF

Murphy, S.K., Wylie, A.A., and R.L. Jirtle.  2001.  Imprinting of PEG3, the human homolog of a mouse gene involved in nurturing behavior.  Genomics 71(1):110-117. [Featured on Cover] [Press Release] PDF

Murphy, S.K., and R.L. Jirtle. 2001.  Non-genotoxic causes of cancer.  In: The Cancer Handbook, (Alison M.R., and Gooderham, N. G., eds.), pp. 317-333, Nature Publishing Group Reference, London.  

Murphy, S.K., and R.L. Jirtle.  2000.  Imprinted genes as potential genetic and epigenetic toxicological targets. Environmental Health Perspectives 108(suppl):5-11. PDF

Wylie, A.A., Murphy, S.K., Orton, T.C., and R.L. Jirtle.  2000.  Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation.  Genome Research 10:1711-1718. PDF

Murphy, S.K., and G.D. Parks.  1999.  RNA replication for the Paramyxovirus simian virus 5 requires an internal repeated (CGNNNN) sequence motif.  Journal of Virology 73:805-809. PDF

Murphy, S.K., Ito, Y., and G.D. Parks.  1998.  A functional antigenomic promoter for the Paramyxovirus simian virus 5 requires proper spacing between an essential internal segment and the 3' terminus.  Journal of Virology 72:10-19. PDF

Murphy, S.K., and G.D. Parks.  1997.  Genome nucleotide lengths divisible by six are not essential but enhance replication of defective interfering RNAs of the Paramyxovirus simian virus 5.  Virology 232:145-157. PDF

Murphy, S.K., and J.D. Oliver.  1992.  Effects of temperature abuse on survival of  Vibrio vulnificus in oysters.  Applied and Environmental Microbiology 58:2771-2775. P


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