Journal Article: Trajectories of inflammatory biomarkers over the eighth decade and their associations with immune cell profiles and epigenetic ageing
Stevenson, Anna J., McCartney, Daniel L., Harris, Sarah E., Taylor, Adele M., Redmond, Paul, Starr, John M., Zhang, Qian, McRae, Allan F., Wray, Naomi R., Spires-Jones, Tara L., McColl, Barry W., McIntosh, Andrew M., Deary, Ian J. and Marioni, Riccardo E. (2018) Trajectories of inflammatory biomarkers over the eighth decade and their associations with immune cell profiles and epigenetic ageing. Clinical Epigenetics, 10 1: 159. doi:10.1186/s13148-018-0585-x
Journal Article: Identification of 55,000 replicated DNA methylation QTL
McRae, Allan F., Marioni, Riccardo E., Shah, Sonia, Yang, Jian, Powell, Joseph E., Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Bowdler, Lisa, Painter, Jodie N., Murphy, Lee, Martin, Nicholas G., Starr, John M., Wray, Naomi R., Deary, Ian J., Visscher, Peter M. and Montgomery, Grant W. (2018) Identification of 55,000 replicated DNA methylation QTL. Scientific Reports, 8 1: . doi:10.1038/s41598-018-35871-w
Journal Article: Genotype effects contribute to variation in longitudinal methylome patterns in older people
Zhang, Qian, Marioni, Riccardo E., Robinson, Matthew R., Higham, Jon, Sproul, Duncan, Wray, Naomi R., Deary, Ian J., McRae, Allan F. and Visscher, Peter M. (2018) Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine, 10 1: . doi:10.1186/s13073-018-0585-7
(2018–2020) NHMRC Boosting Dementia Research Grants
Disturbances of DNA regulation in obesity, and their relationships to metabolic health
(2018–2020) NHMRC A*STAR Joint Grants
(2018–2019) University of California, San Francisco
Sexual dimorphism in human gene expression
Doctor Philosophy
Fine-mapping of quantitative trait loci in 'omics data
Doctor Philosophy
(2018) Master Philosophy
Analysis of genome-wide association data
McRae, Allan F. (2017). Analysis of genome-wide association data. In Jonathan M. Keith (Ed.), Bioinformatics. Volume II: structure, function, and applications (pp. 161-173) New York, NY, United States: Humana Press. doi:10.1007/978-1-4939-6613-4_9
Stevenson, Anna J., McCartney, Daniel L., Harris, Sarah E., Taylor, Adele M., Redmond, Paul, Starr, John M., Zhang, Qian, McRae, Allan F., Wray, Naomi R., Spires-Jones, Tara L., McColl, Barry W., McIntosh, Andrew M., Deary, Ian J. and Marioni, Riccardo E. (2018) Trajectories of inflammatory biomarkers over the eighth decade and their associations with immune cell profiles and epigenetic ageing. Clinical Epigenetics, 10 1: 159. doi:10.1186/s13148-018-0585-x
Identification of 55,000 replicated DNA methylation QTL
McRae, Allan F., Marioni, Riccardo E., Shah, Sonia, Yang, Jian, Powell, Joseph E., Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Bowdler, Lisa, Painter, Jodie N., Murphy, Lee, Martin, Nicholas G., Starr, John M., Wray, Naomi R., Deary, Ian J., Visscher, Peter M. and Montgomery, Grant W. (2018) Identification of 55,000 replicated DNA methylation QTL. Scientific Reports, 8 1: . doi:10.1038/s41598-018-35871-w
Genotype effects contribute to variation in longitudinal methylome patterns in older people
Zhang, Qian, Marioni, Riccardo E., Robinson, Matthew R., Higham, Jon, Sproul, Duncan, Wray, Naomi R., Deary, Ian J., McRae, Allan F. and Visscher, Peter M. (2018) Genotype effects contribute to variation in longitudinal methylome patterns in older people. Genome Medicine, 10 1: . doi:10.1186/s13073-018-0585-7
Epigenetic prediction of complex traits and death
McCartney, Daniel L., Hillary, Robert F., Stevenson, Anna J., Ritchie, Stuart J., Walker, Rosie M., Zhang, Qian, Morris, Stewart W., Bermingham, Mairead L., Campbell, Archie, Murray, Alison D., Whalley, Heather C., Gale, Catharine R., Porteous, David J., Haley, Chris S., McRae, Allan F., Wray, Naomi R., Visscher, Peter M., McIntosh, Andrew M., Evans, Kathryn L., Deary, Ian J. and Marioni, Riccardo E. (2018) Epigenetic prediction of complex traits and death. Genome Biology, 19 1: 136. doi:10.1186/s13059-018-1514-1
Fung, Jenny N., Mortlock, Sally, Girling, Jane E., Holdsworth-Carson, Sarah J., Teh, Wan Tinn, Zhu, Zhihong, Lukowski, Samuel W., McKinnon, Brett D., McRae, Allan, Yang, Jian, Healey, Martin, Powell, Joseph E., Rogers, Peter A. W. and Montgomery, Grant W (2018) Genetic regulation of disease risk and endometrial gene expression highlights potential target genes for endometriosis and polycystic ovarian syndrome. Scientific Reports, 8 1: 11424. doi:10.1038/s41598-018-29462-y
Xue, Angli, Wu, Yang, Zhu, Zhihong, Zhang, Futao, Kemper, Kathryn E., Zheng, Zhili, Yengo, Loic, Lloyd-Jones, Luke R., Sidorenko, Julia, Wu, Yeda, eQTLGen Consortium, McRae, Allan F., Visscher, Peter M., Zeng, Jian and Yang, Jian (2018) Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes. Nature Communications, 9 1: 2941. doi:10.1038/s41467-018-04951-w
Story Jovanova, Olivera, Nedeljkovic, Ivana, Derek, Spieler, Walker, Rosie M., Liu, Chunyu, Luciano, Michelle, Bressler, Jan, Brody, Jennifer, Drake, Amanda J., Evans, Kathryn L., Gondalia, Rahul, Kunze, Sonja, Kuhnel, Brigitte, Lahti, Jari, Lemaitre, Rozenn N., Marioni, Riccardo E., Swenson, Brenton, Himali, Jayandra Jung, Wu, Hongsheng, Li, Yun, McRae, Allan F., Russ, Tom C., Stewart, James, Wang, Zhiying, Zhang, Guosheng, Ladwig, Karl-Heinz, Uitterlinden, Andre G., Guo, Xiuqing, Peters, Annette, Räikkönen, Katri, Starr, John M., Waldenberger, Melanie, Wray, Naomi R., Whitsel, Eric A., Sotoodehnia, Nona, Seshadri, Sudha, Porteous, David J., van Meurs, Joyce, Mosley, Thomas H., McIntosh, Andrew M., Mendelson, Michael M., Levy, Daniel, Hou, Lifang, Eriksson, Johan G., Fornage, Myriam, Deary, Ian J., Baccarelli, Andrea, Tiemeier, Henning and Amin, Najaf (2018) DNA methylation signatures of depressive symptoms in middle-aged and elderly persons: meta-analysis of multiethnic epigenome-wide studies. JAMA Psychiatry, . doi:10.1001/jamapsychiatry.2018.1725
Qi, Ting, Wu, Yang, Zeng, Jian, Zhang, Futao, Xue, Angli, Jiang, Longda, Zhu, Zhihong, Kemper, Kathryn, Yengo, Loic, Zheng, Zhili, eQTLGen Consortium, Marioni, Riccardo E., Montgomery, Grant W., Deary, Ian J., Wray, Naomi R., Visscher, Peter M., McRae, Allan F. and Yang, Jian (2018) Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood. Nature Communications, 9 1: 2282. doi:10.1038/s41467-018-04558-1
Cuellar Partida, Gabriel, Laurin, Charles, Ring, Susan M., Gaunt, Tom R., McRae, Allan, Visscher, Peter M., Montgomery, Grant W., Martin, Nicholas G., Hemani, Gibran, Suderman, Matthew, Relton, Caroline L., Davey Smith, George and Evans, David M. (2018) Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans. Human Molecular Genetics, . doi:10.1093/hmg/ddy206
GWAS on family history of Alzheimer's disease
Marioni, Riccardo E., Harris, Sarah E., Zhang, Qian, McRae, Allan F., Hagenaars, Saskia P., Hill, W. David, Davies, Gail, Ritchie, Craig W., Gale, Catharine R., Starr, John M., Goate, Alison M., Porteous, David J., Yang, Jian, Evans, Kathryn L., Deary, Ian J., Wray, Naomi R. and Visscher, Peter M. (2018) GWAS on family history of Alzheimer's disease. Translational Psychiatry, 8 1: 99. doi:10.1038/s41398-018-0150-6
Genome-wide average DNA methylation is determined in utero
Li, Shuai, Wong, Ee Ming, Dugué, Pierre-Antoine, McRae, Allan F., Kim, Eunae, Joo, Ji-Hoon Eric, Nguyen, Tuong L, Stone, Jennifer, Dite, Gillian S, Armstrong, Nicola J, Mather, Karen A, Thalamuthu, Anbupalam, Wright, Margaret J., Ames, David, Milne, Roger L, Craig, Jeffrey M, Saffery, Richard, Montgomery, Grant W., Song, Yun-Mi, Sung, Joohon, Spector, Timothy D, Sachdev, Perminder S, Giles, Graham G, Southey, Melissa C and Hopper, John L (2018) Genome-wide average DNA methylation is determined in utero. International Journal of Epidemiology, 47 3: 908-916. doi:10.1093/ije/dyy028
Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits
Wu, Yang, Zeng, Jian, Zhang, Futao, Zhu, Zhihong, Qi, Ting, Zheng, Zhili, Lloyd-Jones, Luke R., Marioni, Riccardo E., Martin, Nicholas G., Montgomery, Grant W., Deary, Ian J., Wray, Naomi R., Visscher, Peter M., McRae, Allan F. and Yang, Jian (2018) Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits. Nature Communications, 9 918: . doi:10.1038/s41467-018-03371-0
GWAS of epigenetic aging rates in blood reveals a critical role for TERT
Lu, Ake T., Xue, Luting, Salfati, Elias L., Chen, Brian H., Ferrucci, Luigi, Levy, Daniel, Joehanes, Roby, Murabito, Joanne M., Kiel, Douglas P., Tsai, Pei-Chien, Yet, Idil, Bell, Jordana T., Mangino, Massimo, Tanaka, Toshiko, McRae, Allan F., Marioni, Riccardo E., Visscher, Peter M., Wray, Naomi R., Deary, Ian J., Levine, Morgan E., Quach, Austin, Assimes, Themistocles, Tsao, Philip S., Absher, Devin, Stewart, James D., Li, Yun, Reiner, Alex P., Hou, Lifang, Baccarelli, Andrea A., Whitsel, Eric A., Aviv, Abraham, Cardona, Alexia, Day, Felix R., Wareham, Nicholas J., Perry, John R. B., Ong, Ken K., Raj, Kenneth, Lunetta, Kathryn L. and Horvath, Steve (2018) GWAS of epigenetic aging rates in blood reveals a critical role for TERT. Nature Communications, 9 1: 387. doi:10.1038/s41467-017-02697-5
Gerring, Zachary F., McRae, Allan F., Montgomery, Grant W. and Nyholt, Dale R. (2018) Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine. BMC Genomics, 19 1: 69. doi:10.1186/s12864-018-4450-2
Meta-analysis of epigenome-wide association studies of cognitive abilities
Marioni, Riccardo E., McRae, Allan F, Bressler, Jan, Colicino, Elena, Hannon, Eilis, Li, Shuo, Prada, Diddier, Smith, Jennifer A, Trevisi, Letizia, Tsai, Pei-Chien, Vojinovic, Dina, Simino, Jeannette, Levy, Daniel, Liu, Chunyu, Mendelson, Michael, Satizabal, Claudia L, Yang, Qiong, Jhun, Min A, Kardia, Sharon L R, Zhao, Wei, Bandinelli, Stefania, Ferrucci, Luigi, Hernandez, Dena G, Singleton, Andrew B, Harris, Sarah E, Starr, John M, Kiel, Douglas P, McLean, Robert R, Just, Allan C, Schwartz, Joel, Spiro, Avron, Vokonas, Pantel, Amin, Najaf, Ikram, M Arfan, Uitterlinden, Andre G, van Meurs, Joyce B J, Spector, Tim D, Steves, Claire, Baccarelli, Andrea A, Bell, Jordana T, van Duijn, Cornelia M, Fornage, Myriam, Hsu, Yi-Hsiang, Mill, Jonathan, Mosley, Thomas H, Seshadri, Sudha and Deary, Ian J (2018) Meta-analysis of epigenome-wide association studies of cognitive abilities. Molecular Psychiatry, . doi:10.1038/s41380-017-0008-y
Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins
Wang, Yunzhang, Karlsson, Robert, Lampa, Erik, Zhang, Qian, Hedman, Åsa K., Almgren, Malin, Almqvist, Catarina, McRae, Allan F., Marioni, Riccardo E., Ingelsson, Erik, Visscher, Peter M., Deary, Ian J., Lind, Lars, Morris, Tiffany, Beck, Stephan, Pedersen, Nancy L. and Hägg, Sara (2018) Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins. Epigenetics, 13 9: 1-13. doi:10.1080/15592294.2018.1526028
DNA methylation analysis identifies loci for blood pressure regulation
Richard, Melissa A., Huan, Tianxiao, Ligthart, Symen, Gondalia, Rahul, Jhun, Min A., Brody, Jennifer A., Irvin, Marguerite R., Marioni, Riccardo, Shen, Jincheng, Tsai, Pei-Chien, Montasser, May E., Jia, Yucheng, Syme, Catriona, Salfati, Elias L., Boerwinkle, Eric, Guan, Weihua, Mosley, Thomas H., Bressler, Jan, Morrison, Alanna C., Liu, Chunyu, Mendelson, Michael M., Uitterlinden, André G., van Meurs, Joyce B., Heijmans, Bastiaan T., ’t Hoen, Peter A.C., van Meurs, Joyce, Isaacs, Aaron, Jansen, Rick, Franke, Lude, Boomsma, Dorret I., Pool, René, van Dongen, Jenny, Hottenga, Jouke J., van Greevenbroek, Marleen M.J., Stehouwer, Coen D.A., van der Kallen, Carla J.H., Schalkwijk, Casper G., Wijmenga, Cisca, Zhernakova, Alexandra, Tigchelaar, Ettje F., Slagboom, P. Eline, Beekman, Marian, Deelen, Joris, van Heemst, Diana, Veldink, Jan H., van den Berg, Leonard H., van Duijn, Cornelia M., Hofman, Albert, Uitterlinden, André G., Jhamai, P. Mila, Verbiest, Michael, Suchiman, H. Eka D., Verkerk, Marijn, van der Breggen, Ruud, van Rooij, Jeroen, Lakenberg, Nico, Mei, Hailiang, van Iterson, Maarten, van Galen, Michiel, Bot, Jan, van ’t Hof, Peter, Deelen, Patrick, Nooren, Irene, Moed, Matthijs, Vermaat, Martijn, Zhernakova, Dasha V., Luijk, René, Bonder, Marc Jan, van Dijk, Freerk, Arindrarto, Wibowo, Kielbasa, Szymon M., Swertz, Morris A., van Zwet, Erik W., Franco, Oscar H., Zhang, Guosheng, Li, Yun, Stewart, James D., Bis, Joshua C., Psaty, Bruce M., Chen, Yii-Der Ida, Kardia, Sharon L.R., Zhao, Wei, Turner, Stephen T., Absher, Devin, Aslibekyan, Stella, Starr, John M., McRae, Allan F., Hou, Lifang, Just, Allan C., Schwartz, Joel D., Vokonas, Pantel S., Menni, Cristina, Spector, Tim D., Shuldiner, Alan, Damcott, Coleen M., Rotter, Jerome I., Palmas, Walter, Liu, Yongmei, Paus, Tomáš, Horvath, Steve, O'Connell, Jeffrey R., Guo, Xiuqing, Pausova, Zdenka, Assimes, Themistocles L., Sotoodehnia, Nona, Smith, Jennifer A., Arnett, Donna K., Deary, Ian J., Baccarelli, Andrea A., Bell, Jordana T., Whitsel, Eric, Dehghan, Abbas, Levy, Daniel and Fornage, Myriam (2017) DNA methylation analysis identifies loci for blood pressure regulation. American Journal of Human Genetics, 101 6: 888-902. doi:10.1016/j.ajhg.2017.09.028
Testing two evolutionary theories of human aging with DNA methylation data
Robins, Chloe, McRae, Allan F., Powell, Joseph E., Wiener, Howard W., Aslibekyan, Stella, Kennedy, Elizabeth M., Absher, Devin M., Arnett, Donna K., Montgomery, Grant W., Visscher, Peter M., Cutler, David J. and Conneely, Karen N. (2017) Testing two evolutionary theories of human aging with DNA methylation data. Genetics, 207 4: 1547-1560. doi:10.1534/genetics.117.300217
An epigenome-wide association study meta-analysis of educational attainment
Karlsson Linnér, R., Marioni, R. E., Rietveld, C. A., Simpkin, A. J., Davies, N. M., Watanabe, K., Armstrong, N. J., Auro, K., Baumbach, C., Bonder, M. J., Buchwald, J., Fiorito, G., Ismail, K., Iurato, S., Joensuu, A., Karell, P., Kasela, S, Lahti, J., McRae, A. F., Mandaviya, P. R., Seppälä, I., Wang, Y., Baglietto, L., Binder, E. B., Harris, S. E., Hodge, A. M., Horvath, S., Hurme, M., Johannesson, M., Latvala, A., Mather, K. A., Medland, S. E., Metspalu, A., Milani, L., Milne, R. L., Pattie, A., Pedersen, N. L., Peters, A., Polidoro, S., Räikkönen, K., Severi, G., Starr, J. M., Stolk, L., Waldenberger, M., BIOS Consortium, Eriksson, J. G., Esko, T., Franke, L., Gieger, C., Giles, G. G., Hägg, S., Jousilahti, P., Kaprio, J., Kähönen, M., Lehtimäki, T., Martin, N. G., van Meurs, J. B. C., Ollikainen, M., Perola, M., Posthuma, D., Raitakari, O. T., Sachdev, P. S., Taskesen, E., Uitterlinden, A. G., Vineis, P., Wijmenga, C., Wright, M. J., Relton, C., Davey Smith, G., Deary, I. J., Koellinger, P. D. and Benjamin, D. J. (2017) An epigenome-wide association study meta-analysis of educational attainment. Molecular Psychiatry, 22 12: 1680-1690. doi:10.1038/mp.2017.210
Garton, Fleur C., Benyamin, Beben, Zhao, Qiongyi, Liu, Zhijun, Gratten, Jacob, Henders, Anjali K., Zhang, Zong-Hong, Edson, Janette, Furlong, Sarah, Morgan, Sarah, Heggie, Susan, Thorpe, Kathryn, Pfluger, Casey, Mather, Karen A., Sachdev, Perminder S., McRae, Allan F., Robinson, Matthew R., Shah, Sonia, Visscher, Peter M., Mangelsdorf, Marie, Henderson, Robert D., Wray, Naomi R. and McCombe, Pamela A. (2017) Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics and Genomic Medicine, 5 4: 418-428. doi:10.1002/mgg3.302
Role of DNA methylation in type 2 diabetes etiology: using genotype as a causal anchor
Elliott, Hannah R., Shihab, Hashem A., Lockett, Gabrielle A., Holloway, John W., McRae, Allan F., Smith, George Davey, Ring, Susan M., Gaunt, Tom R. and Relton, Caroline L. (2017) Role of DNA methylation in type 2 diabetes etiology: using genotype as a causal anchor. Diabetes, 66 6: 1713-1722. doi:10.2337/db16-0874
Hedman, Åsa K., Mendelson, Michael M., Marioni, Riccardo E., Gustafsson, Stefan, Joehanes, Roby, Irvin, Marguerite R., Zhi, Degui, Sandling, Johanna K., Yao, Chen, Liu, Chunyu, Liang, Liming, Huan, Tianxiao, McRae, Allan F., Demissie, Serkalem, Shah, Sonia, Starr, John M., Cupples, L. Adrienne, Deloukas, Panos, Spector, Timothy D., Sundstrom, Johan, Krauss, Ronald M., Arnett, Donna K., Deary, Ian J., Lind, Lars, Levy, Daniel and Ingelsson, Erik (2017) Epigenetic patterns in blood associated with lipid traits predict incident coronary heart disease events and are enriched for results from genome-wide association studies. Circulation: Cardiovascular Genetics, 10 1: . doi:10.1161/CIRCGENETICS.116.001487
The Genetic Architecture of Gene Expression in Peripheral Blood (vol 100, pg 228, 2017)
Lloyd-Jones, Luke R., Holloway, Alexander, McRae, Allan, Yang, Jian, Small, Kerrin, Zhao, Jing, Zeng, Biao, Bakshi, Andrew, Metspalu, Andres, Dermitzakis, Manolis, Gibson, Greg, Spector, Tim, Montgomery, Grant, Esko, Tonu, Visscher, Peter M. and Powell, Joseph E. (2017) The Genetic Architecture of Gene Expression in Peripheral Blood (vol 100, pg 228, 2017). American Journal of Human Genetics, 100 2: 371-371. doi:10.1016/j.ajhg.2017.01.026
The genetic architecture of gene expression in peripheral blood
Lloyd-Jones, Luke R., Holloway, Alexander, McRae, Allan, Yang, Jian, Small, Kerrin, Zeng, Biao, Bakshi, Andrew, Metspalu, Andres, Dermitzakis, Manolis, Gibson, Greg, Spector, Tim, Montgomery, Grant, Esko, Tonu, Visscher, Peter M. and Powell, Joseph E. (2017) The genetic architecture of gene expression in peripheral blood. American Journal of Human Genetics, 100 2: 228-237. doi:10.1016/j.ajhg.2016.12.008
DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases
Ligthart, Symen, Marzi, Carola, Aslibekyan, Stella, Mendelson, Michael M., Conneely, Karen N., Tanaka, Toshiko, Colicino, Elena, Waite, Lindsay L., Joehanes, Roby, Guan, Weihua, Brody, Jennifer A., Elks, Cathy, Marioni, Riccardo, Jhun, Min A., Agha, Golareh, Bressler, Jan, Ward-Caviness, Cavin K., Chen, Brian H., Huan, Tianxiao, Bakulski, Kelly, Salfati, Elias L., Fiorito, Giovanni, Wahl, Simone, Schramm, Katharina, Sha, Jin, Hernandez, Dena G., Just, Allan C., Smith, Jennifer A., Sotoodehnia, Nona, Pilling, Luke C., Pankow, James S., Tsao, Phil S., Liu, Chunyu, Zhao, Wei, Guarrera, Simonetta, Michopoulos, Vasiliki J., Smith, Alicia K., Peters, Marjolein J., Melzer, David, Vokonas, Pantel, Fornage, Myriam, Prokisch, Holger, Bis, Joshua C., Chu, Audrey Y., Herder, Christian, Grallert, Harald, Yao, Chen, Shah, Sonia, McRae, Allan F., Lin, Honghuang, Horvath, Steve, Fallin, Daniele, Hofman, Albert, Wareham, Nicholas J., Wiggins, Kerri L., Feinberg, Andrew P., Starr, John M., Visscher, Peter M., Murabito, Joanne M., Kardia, Sharon L. R., Absher, Devin M., Binder, Elisabeth B., Singleton, Andrew B., Bandinelli, Stefania, Peters, Annette, Waldenberger, Melanie, Matullo, Giuseppe, Schwartz, Joel D., Demerath, Ellen W., Uitterlinden, André G., Van Meurs, Joyce B. J., Franco, Oscar H., Chen, Yii-Der Ida, Levy, Daniel, Turner, Stephen T., Deary, Ian J., Ressler, Kerry J., Dupuis, Josée, Ferrucci, Luigi, Ong, Ken K., Assimes, Themistocles L., Boerwinkle, Eric, Koenig, Wolfgang, Arnett, Donna K., Baccarelli, Andrea A., Benjamin, Emelia J. and Dehghan, Abbas (2016) DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases. Genome Biology, 17 1: 255-255. doi:10.1186/s13059-016-1119-5
Autosomal genetic control of human gene expression does not differ across the sexes
Kassam, Irfahan, Lloyd-Jones, Luke, Holloway, Alexander, Small, Kerrin S., Zeng, Biao, Bakshi, Andrew, Metspalu, Andres, Gibson, Greg, Spector, Tim D., Esko, Tonu, Montgomery, Grant W., Powell, Joseph E., Yang, Jian, Visscher, Peter M. and McRae, Allan F. (2016) Autosomal genetic control of human gene expression does not differ across the sexes. Genome Biology, 17 1: 248.1-248.10. doi:10.1186/s13059-016-1111-0
A DNA methylation biomarker of alcohol consumption
Liu, C., Marioni, R. E., Hedman, K., Pfeiffer, L., Tsai, P. -C., Reynolds, L. M., Just, A. C., Duan, Q., Boer, C. G., Tanaka, T., Elks, C. E., Aslibekyan, S., Brody, J. A., Kuhnel, B., Herder, C., Almli, L. M., Zhi, D., Wang, Y., Huan, T., Yao, C., Mendelson, M. M., Joehanes, R., Liang, L., Love, S. -A., Guan, W., Shah, S., McRae, A. F., Kretschmer, A., Prokisch, H., Strauch, K., Peters, A., Visscher, P. M., Wray, N. R., Guo, X., Wiggins, K. L., Smith, A. K., Binder, E. B., Ressler, K. J., Irvin, M. R., Absher, D. M., Hernandez, D., Ferrucci, L., Bandinelli, S., Lohman, K., Ding, J., Trevisi, L., Gustafsson, S., Sandling, J. H., Stolk, L., Uitterlinden, A. G., Yet, I., Castillo-Fernandez, J. E., Spector, T. D., Schwartz, J. D., Vokonas, P., Lind, L., Li, Y., Fornage, M., Arnett, D. K., Wareham, N. J., Sotoodehnia, N., Ong, K. K., van Meurs, J. B. J., Conneely, K. N., Baccarelli, A. A., Deary, I. J., Bell, J. T., North, K. E., Liu, Y., Waldenberger, M., London, S. J., Ingelsson, E. and Levy, D. (2016) A DNA methylation biomarker of alcohol consumption. Molecular Psychiatry, 23 2: 422-433. doi:10.1038/mp.2016.192
Evidence for mitochondrial genetic control of autosomal gene expression
Kassam, Irfahan, Qi, Tuan, Lloyd-Jones, Luke, Holloway, Alexander, Bonder, Marc Jan, Henders, Anjali K., Martin, Nicholas G., Powell, Joseph E., Franke, Lude, Montgomery, Grant W., Visscher, Peter M. and McRae, Allan F. (2016) Evidence for mitochondrial genetic control of autosomal gene expression. Human Molecular Genetics, 25 24: 5332-5338. doi:10.1093/hmg/ddw347
Epigenetic signatures of cigarette smoking
Joehanes, Roby, Just, Allan C., Marioni, Riccardo E., Pilling, Luke C., Reynolds, Lindsay M., Mandaviya, Pooja R., Guan, Weihua, Xu, Tao, Elks, Cathy E., Aslibekyan, Stella, Moreno-Macias, Hortensia, Smith, Jennifer A., Brody, Jennifer A., Dhingra, Radhika, Yousefi, Paul, Pankow, James S., Kunze, Sonja, Shah, Sonia H., McRae, Allan F., Lohman, Kurt, Sha, Jin, Absher, Devin M., Ferrucci, Luigi, Zhao, Wei, Demerath, Ellen W., Bressler, Jan, Grove, Megan L., Huan, Tianxiao, Liu, Chunyu, Mendelson, Michael M., Yao, Chen, Kiel, Douglas P., Peters, Annette, Wang-Sattler, Rui, Visscher, Peter M., Wray, Naomi R., Starr, John M., Ding, Jingzhong, Rodriguez, Carlos J., Wareham, Nicholas J., Irvin, Marguerite R., Zhi, Degui, Barrdahl, Myrto, Vineis, Paolo, Ambatipudi, Srikant, Uitterlinden, André G., Hofman, Albert, Schwartz, Joel, Colicino, Elena, Hou, Lifang, Vokonas, Pantel S., Hernandez, Dena G., Singleton, Andrew B., Bandinelli, Stefania, Turner, Stephen T., Ware, Erin B., Smith, Alicia K., Klengel, Torsten, Binder, Elisabeth B., Psaty, Bruce M., Taylor, Kent D., Gharib, Sina A., Swenson, Brenton R., Liang, Liming, Demeo, Dawn L., O'Connor, George T., Herceg, Zdenko, Ressler, Kerry J., Conneely, Karen N., Sotoodehnia, Nona, Kardia, Sharon L. R., Melzer, David, Baccarelli, Andrea A., Van Meurs, Joyce B. J., Romieu, Isabelle, Arnett, Donna K., Ong, Ken K., Liu, Yongmei, Waldenberger, Melanie, Deary, Ian J., Fornage, Myriam, Levy, Daniel and London, Stephanie J. (2016) Epigenetic signatures of cigarette smoking. Circulation: Cardiovascular Genetics, 9 5: 436-447. doi:10.1161/CIRCGENETICS.116.001506
Bakshi, Andrew, Zhu, Zhihong, Vinkhuyzen, Anna A. E., Hill, W. David, Mcrae, Allan F., Visscher, Peter M. and Yang, Jian (2016) Fast set-based association analysis using summary data from GWAS identifies novel gene loci for human complex traits. Scientific Reports, 6 32894. doi:10.1038/srep32894
Kassam, Irfahan and McRae, Allan F. (2016) The autosomal genetic control of sexually dimorphic traits in humans is largely the same across the sexes. Genome Biology, 17 1: . doi:10.1186/s13059-016-1035-8
Pavlides, Jennifer M. Whitehead, Zhu, Zhihong, Gratten, Jacob, Mcrae, Allan F., Wray, Naomi R. and Yang, Jian (2016) Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits. Genome Medicine, 8 1: 84. doi:10.1186/s13073-016-0338-4
Mbarek, Hamdi, Steinberg, Stacy, Nyholt, Dale R., Gordon, Scott D., Miller, Michael B., McRae, Allan F, Hottenga, Jouke Jan, Day, Felix R., Willemsen, Gonneke, de Geus, Eco J., Davies, Gareth E, Martin, Hilary C, Penninx, Brenda W, Jansen, Rick, McAloney, Kerrie, Vink, Jacqueline M., Kaprio, Jaakko, Plomin, Robert, Spector, Tim D., Magnusson, Patrik K., Reversade, Bruno, Harris, R. Alan, Aagaard, Kjersti, Kristjansson, Ragnar P., Olafsson, Isleifur, Eyjolfsson, Gudmundur Ingi, Sigurdardottir, Olof, Iacono, William G., Lambalk, Cornelis B, Montgomery, Grant W., McGue , Matt, Ong, Ken K., Perry, John R.B., Martin, Nicholas G., Stefansson, Hreinn, Stefansson, Kari and Boomsman, Dorret I. (2016) Identification of common genetic variants influencing spontaneous dizygotic twinning and female fertility. American Journal of Human Genetics, 98 5: 898-908. doi:10.1016/j.ajhg.2016.03.008
Marioni, Riccardo E., Harris, Sarah E., Shah, Sonia, McRae, Allan F., von Zglinicki, Thomas, Martin-Ruiz, Carmen, Wray, Naomi R., Visscher, Peter M. and Deary, Ian J. (2016) Corrigendum: The epigenetic clock and telomere length are independently associated with chronological age and mortality [Int J Epidemiol., 45, 2, (424-432)(2016)] DOI: 10.1093/ije/dyw041. International Journal of Epidemiology, 47 1: 356-356. doi:10.1093/ije/dyx233
Marioni, Riccardo E., Harris, Sarah E., Shah, Sonia, McRae, Allan F., von Zglinicki, Thomas, Martin-Ruiz, Carmen, Wray, Naomi R., Visscher, Peter M. and Deary, Ian J. (2016) The epigenetic clock and telomere length are independently associated with chronological age and mortality. International Journal of Epidemiology, 45 2: 424-432. doi:10.1093/ije/dyw041
Shared genetic control of expression and methylation in peripheral blood
Shakhbazov, Konstantin, Powell, Joseph E., Hemani, Gibran, Henders, Anjali K., Martin, Nicholas G., Visscher, Peter M., Montgomery, Grant W. and McRae, Allan F. (2016) Shared genetic control of expression and methylation in peripheral blood. BMC Genomics, 17 1: . doi:10.1186/s12864-016-2498-4
Tseng, Hsu-Wen, Pitt, Miranda E., Glant, Tibor T., McRae, Allan F., Kenna, Tony J., Brown, Matthew A., Pettit, Allison R. and Thomas, Gethin P. (2016) Inflammation-driven bone formation in a mouse model of ankylosing spondylitis: sequential not parallel processes. Arthritis Research and Therapy, 18 1: . doi:10.1186/s13075-015-0805-0
DNA methylation-based measures of biological age: meta-analysis predicting time to death
Chen, Brian H., Marioni, Riccardo E., Colicino, Elena, Peters, Marjolein J., Ward-Caviness, Cavin K., Tsai, Pei-Chien, Roetker, Nicholas S., Just, Allan C., Demerath, Ellen W., Guan, Weihua, Bressler, Jan, Fornage, Myriam, Studenski, Stephanie, Vandiver, Amy R., Moore, Ann Zenobia, Tanaka, Toshiko, Kiel, Douglas P., Liang, Liming, Vokonas, Pantel, Schwartz, Joel, Lunetta, Kathryn L., Murabito, Joanne M., Bandinelli, Stefania, Hernandez, Dena G., Melzer, David, Nalls, Michael, Pilling, Luke C., Price, Timothy R., Singleton, Andrew B., Gieger, Christian, Holle, Rolf, Kretschmer, Anja, Kronenberg, Florian, Kunze, Sonja, Linseisen, Jakob, Meisinger, Christine, Rathmann, Wolfgang, Waldenberger, Melanie, Visscher, Peter M., Shah, Sonia, Wray, Naomi R., McRae, Allan F., Franco, Oscar H., Hofman, Albert, Uitterlinden, Andre G., Absher, Devin, Assimes, Themistocles, Levine, Morgan E., Lu, Ake T., Tsao, Philip S., Hou, Lifang, Manson, JoAnn E., Carty, Cara L., LaCroix, Andrea Z., Reiner, Alexander P., Spector, Tim D., Feinberg, Andrew P., Levy, Daniel, Baccarelli, Andrea, van Meurs, Joyce, Bell, Jordana T., Peters, Annette, Deary, Ian J., Pankow, James S., Ferrucci, Luigi and Horvath, Steve (2016) DNA methylation-based measures of biological age: meta-analysis predicting time to death. Aging, 8 9: 1844-1865. doi:10.18632/aging.101020
Bui, Masato, Benyamin, Beben, Shah, Sonia, Henders, Anjali K., Martin, Nicholas G., Montgomery, Grant W. and McRae, Allan F. (2015) Sharing a placenta is associated with a greater similarity in DNA methylation in monochorionic versus dichorionic twin pars in blood at age 14. Twin Research and Human Genetics, 18 6: 680-685. doi:10.1017/thg.2015.87
The transcriptional landscape of age in human peripheral blood
Peters, Marjolein J., Joehanes, Roby, Pilling, Luke C., Schurmann, Claudia, Conneely, Karen N., Powell, Joseph, Reinmaa, Eva, Sutphin, George L., Zhernakova, Alexandra, Schramm, Katharina, Wilson, Yana A., Kobes, Sayuko, Tukiainen, Taru, Ramos, Yolande F., Goring, Harald H. H., Fornage, Myriam, Liu, Yongmei, Gharib, Sina A., Stranger, Barbara E., De Jager, Philip L., Aviv, Abraham, Levy, Daniel, Murabito, Joanne M., Munson, Peter J., Huan, Tianxiao, Hofman, Albert, Uitterlinden, Andre G., Rivadeneira, Fernando, Van Rooij, Jeroen, Stolk, Lisette, Broer, Linda, Verbiest, Michael M. P. J., Jhamai, Mila, Arp, Pascal, Metspalu, Andres, Tserel, Liina, Milani, Lili, Samani, Nilesh J., Peterson, Part, Kasela, Silva, Codd, Veryan, Peters, Annette, Ward-Caviness, Cavin K., Herder, Christian, Waldenberger, Melanie, Roden, Michael, Singmann, Paula, Zeilinger, Sonja, Illig, Thomas, Homuth, Georg, Grabe, Hans-Jorgen, Volzke, Henry, Steil, Leif, Kocher, Thomas, Murray, Anna, Melzer, David, Yaghootkar, Hanieh, Bandinelli, Stefania, Moses, Eric K., Kent, Jack W., Curran, Joanne E., Johnson, Matthew P., Williams-Blangero, Sarah, Westra, Harm-Jan, McRae, Allan F., Smith, Jennifer A., Kardia, Sharon L. R., Hovatta, Iiris, Perola, Markus, Ripatti, Samuli, Salomaa, Veikko, Henders, Anjali K., Martin, Nicholas G., Smith, Alicia K., Mehta, Divya, Binder, Elisabeth B., Nylocks, K. Maria, Kennedy, Elizabeth M., Klengel, Torsten, Ding, Jingzhong, Suchy-Dicey, Astrid M., Enquobahrie, Daniel A., Brody, Jennifer, Rotter, Jerome I., Chen, Yii-Der I., Houwing-Duistermaat, Jeanine, Kloppenburg, Margreet, Slagboom, P. Eline, Helmer, Quinta, Den Hollander, Wouter, Bean, Shannon, Raj, Towfique, Bakhshi, Noman, Wang, Qiao Ping, Oyston, Lisa J., Psaty, Bruce M., Tracy, Russell P., Montgomery, Grant W., Turner, Stephen T., Blangero, John, Meulenbelt, Ingrid, Ressler, Kerry J., Yang, Jian, Franke, Lude, Kettunen, Johannes, Visscher, Peter M., Neely, G. Gregory, Korstanje, Ron, Hanson, Robert L., Prokisch, Holger, Ferrucci, Luigi, Esko, Tonu, Teumer, Alexander, Van Meurs, Joyce B. J., Johnson, Andrew D., Nalls, Michael A., Hernandez, Dena G., Cookson, Mark R., Gibbs, Raphael J., Hardy, John, Ramasamy, Adaikalavan, Zonderman, Alan B., Dillman, Allissa, Traynor, Bryan, Smith, Colin, Longo, Dan L., Trabzuni, Daniah, Troncoso, Juan, Van Der Brug, Marcel, Weale, Michael E., O'Brien, Richard, Johnson, Robert, Walker, Robert, Zielke, Ronald H., Arepalli, Sampath, Ryten, Mina, Singleton, Andrew B. and NABEC/UKBEC Consortium (2015) The transcriptional landscape of age in human peripheral blood. Nature Communications, 6 1: 8570.1-8570.14. doi:10.1038/ncomms9570
Genome-wide autozygosity is associated with lower general cognitive ability
Howrigan, D.P., Simonson, M.A., Davies, G., Harris, S.E., Tenesa, A., Starr, J.M., Liewald, D.C., Deary, I.J., McRae, A., Wright, M.J., Montgomery, G.W., Hansell, N., Martin, N.G., Payton, A., Horan, M., Ollier, W.E., Abdellaoui, A., Boomsma, D.I., DeRosse, P., Knowles, E.E.M., Glahn, D.C., Djurovic, S., Melle, I., Andreassen, O.A., Christoforou, A., Steen, V.M., Hellard, S.L., Sundet, K., Reinvang, I., Espeseth, T., Lundervold, A.J., Giegling, I., Konte, B., Hartmann, A.M., Rujescu, D., Roussos, P., Giakoumaki, S., Burdick, K.E., Bitsios, P., Donohoe, G., Corley, R.P., Visscher, P.M., Pendleton, N., Malhotra, A.K., Neale, B.M., Lencz, T. and Keller, M.C. (2015) Genome-wide autozygosity is associated with lower general cognitive ability. Molecular Psychiatry, 21 6: 837-843. doi:10.1038/mp.2015.120
Marioni, Riccardo E., Shah, Sonia, McRae, Allan F., Ritchie, Stuart J., Muniz-Terrera, Graciela, Harris, Sarah E., Gibson, Jude, Redmond, Paul, Cox, Simon R., Pattie, Alison, Corley, Janie, Taylor, Adele, Murphy, Lee, Starr, John M., Horvath, Steve, Visscher, Peter M., Wray, Naomi R. and Deary, Ian J. (2015) The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936. International Journal of Epidemiology, 44 4: 1388-1396. doi:10.1093/ije/dyu277
Improving phenotypic prediction by combining genetic and epigenetic associations
Shah, Sonia, Bonder, Marc J., Marioni, Riccardo E., Zhu, Zhihong, McRae, Allan F., Zhernakova, Alexandra, Harris, Sarah E., Liewald, Dave, Henders, Anjali K., Mendelson, Michael M., Liu, Chunyu, Joehanes, Roby, Liang, Liming, Levy, Daniel, Martin, Nicholas G., Starr, John M., Wijmenga, Cisca, Wray, Naomi R., Yang, Jian, Montgomery, Grant W., Franke, Luke, Deary, Ian J., Visscher, Peter M. and BIOS Consortium (2015) Improving phenotypic prediction by combining genetic and epigenetic associations. American Journal of Human Genetics, 97 1: 75-85. doi:10.1016/j.ajhg.2015.05.014
Seasonal effects on gene expression
Goldinger, Anita, Shakhbazov, Konstantin, Henders, Anjali K., McRae, Allan F., Montgomery, Grant W. and Powell, Joseph E. (2015) Seasonal effects on gene expression. PLoS ONE, 10 5: 1-16. doi:10.1371/journal.pone.0126995
Large autosomal copy-number differences within unselected monozygotic twin pairs are rare
Mcrae, Allan F., Visscher, Peter M., Montgomery, Grant W. and Martin, Nicholas G. (2015) Large autosomal copy-number differences within unselected monozygotic twin pairs are rare. Twin Research and Human Genetics, 18 1: 13-18. doi:10.1017/thg.2014.85
DNA methylation age of blood predicts all-cause mortality in later life
Marioni, Riccardo E., Shah, Sonia, McRae, Allan F., Chen, Brian H., Colicino, Elena, Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Redmond, Paul, Cox, Simon R., Pattie, Alison, Corley, Janie, Murphy, Lee, Martin, Nicholas G., Montgomery, Grant W., Feinberg, Andrew P., Fallin, M. Daniele, Multhaup, Michael L., Jaffe, Andrew E., Joehanes, Roby, Schwartz, Joel, Just, Allan C., Lunetta, Kathryn L., Murabito, Joanne M., Starr, John M., Horvath, Steve, Baccarelli, Andrea A., Levy, Daniel, Visscher, Peter M., Wray, Naomi R. and Deary, Ian J. (2015) DNA methylation age of blood predicts all-cause mortality in later life. Genome Biology, 16 1: 25.1-25.12. doi:10.1186/s13059-015-0584-6
Genetic and environmental exposures constrain epigenetic drift over the human life course
Shah, Sonia, McRae, Allan F., Marioni, Riccardo E., Harris, Sarah E., Gibson, Jude, Henders, Anjali K., Redmond, Paul, Cox, Simon R., Pattie, Alison, Corley, Janie, Murphy, Lee, Martin, Nicholas G., Montgomery, Grant W., Starr, John M., Wray, Naomi R., Deary, Ian J. and Visscher, Peter M. (2014) Genetic and environmental exposures constrain epigenetic drift over the human life course. Genome Research, 24 11: 1725-1733. doi:10.1101/gr.176933.114
Another explanation for apparent epistasis: reply
Hemani, Gibran, Shakhbazov, Konstantin, Westra, Harm-Jan, Esko, Tonu, Henders, Anjali K., McRae, Allan F., Yang, Jian, Gibson, Greg, Martin, Nicholas G., Metspalu, Andres, Franke, Lude, Montgomery, Grant W., Visscher, Peter M. and Powell, Joseph E. (2014) Another explanation for apparent epistasis: reply. Nature, 514 7520: E5-E6. doi:10.1038/nature13692
Contribution of genetic variation to transgenerational inheritance of DNA methylation
McRae, Allan F., Powell, Joseph E., Henders, Anjali K., Bowdler, Lisa, Hemani, Gibran, Shah, Sonia, Painter, Jodie N., Martin, Nicholas G., Visscher, Peter M. and Montgomery, Grant W. (2014) Contribution of genetic variation to transgenerational inheritance of DNA methylation. Genome Biology, 15 5: 1-10. doi:10.1186/gb-2014-15-5-r73
Detection and replication of epistasis influencing transcription in humans
Hemani, Gibran, Shakhbazov, Konstantin, Westra, Harm-Jan, Esko, Tonu, Henders, Anjali K., McRae, Allan F., Yang, Jian, Gibson, Greg, Martin, Nicholas G., Metspalu, Andres, Franke, Lude, Montgomery, Grant W., Visscher, Peter M. and Powell, Joseph E. (2014) Detection and replication of epistasis influencing transcription in humans. Nature, 508 7495: 249-253. doi:10.1038/nature13005
Derks, Eske M., Ayub, Muhammad, Chambert, Kimberly, Del Favero, Jurgen, Johnstone, Mandy, Macgregor, Stuart, Maclean, Alan, McKechanie, Andrew G., McRae, Allan F., Moran, Jennifer L., Pickard, Benjamin S., Purcell, Shaun, Sklar, Pamela, St Clair, David M., Wray, Naomi R., Visscher, Peter M. and Blackwood, Douglas H. R. (2013) A genome wide survey supports the involvement of large copy number variants in schizophrenia with and without intellectual disability. American Journal of Medical Genetics. Part B: Neuropsychiatric Genetics, 162 8: 847-854. doi:10.1002/ajmg.b.32189
Thomson, P. A., Parla, J. S., McRae, A. F., Kramer, M., Ramakrushnan, K., Yao, J., Soares, D. C., McCarthy, S., Morris, S. W., Cardone, L., Cass, S., Ghiban, E., Hennah, W., Evans, K. L., Rebolini, D., Millar, J. K., Harris, S. E., Starr, J. M., MacIntyre, J., Generation Scotland, McIntosh, A. M., Watson, J. D., Deary, I. J., Visscher, P. M., Blackwood, D. H., McCombie, W. R. and Porteous, D. J. (2013) 708 common and 2010 rare DISC1 locus variants identified in 1542 subjects: analysis for association with psychiatric disorder and cognitive traits. Molecular Psychiatry, Advance online publication 6: 1-8. doi:10.1038/mp.2013.68
Case-control association testing of common variants from sequencing of DNA pools
McRae, Allan F., Richter, Melinda M. and Lind, Penelope A. (2013) Case-control association testing of common variants from sequencing of DNA pools. PLoS One, 8 6: e65410.1-e65410.4. doi:10.1371/journal.pone.0065410
Byrne, E. M., Carrillo-Roa, T., Henders, A. K., Bowdler, L., McRae, A. F., Heath, A. C., Martin, N. G., Montgomery, G. W., Krause, L. and Wray, N. R. (2013) Monozygotic twins affected with major depressive disorder have greater variance in methylation than their unaffected co-twin. Translational Psychiatry, 3 6: e269.1-e269.6. doi:10.1038/tp.2013.45
Powell, Joseph E., Henders, Anjali K., McRae, Allan F., Kim, Jinhee, Hemani, Gibran, Martin, Nicholas G., Dermitzakis, Emmanouil T., Gibson, Greg, Montgomery, Grant W. and Visscher, Peter M. (2013) Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data. PLoS Genetics, 9 5: e1003502.1-e1003502.10. doi:10.1371/journal.pgen.1003502
No association between general cognitive ability and rare copy number variation
McRae, Allan F., Wright, Margaret J., Hansell, Narelle K., Montgomery, Grant W. and Martin, Nicholas G. (2013) No association between general cognitive ability and rare copy number variation. Behavior Genetics, 43 3: 202-207. doi:10.1007/s10519-013-9587-9
Genetic and nongenetic variation revealed for the principal components of human gene expression
Goldinger, Anita, Henders, Anjali K., McRae, Allan F., Martin, Nicholas G., Gibson, Greg, Montgomery, Grant W., Visscher, Peter M. and Powell, Joseph E. (2013) Genetic and nongenetic variation revealed for the principal components of human gene expression. Genetics, 195 3: 1117-1128. doi:10.1534/genetics.113.153221
Byrne, Enda M., Johnson, Julie, McRae, Allan F., Nyholt, Dale R., Medland, Sarah E., Gehrman, Philip R., Heath, Andrew C., Madden, Pamela A. F., Montgomery, Grant W., Chenevix-Trench, Georgia and Martin, Nicholas G. (2012) A genome-wide association study of caffeine-related sleep disturbance: confirmation of a role for a common variant in the adenosine receptor. Sleep, 35 7: 967-975. doi:10.5665/sleep.1962
The Brisbane systems genetics study: genetical genomics meets complex trait genetics
Powell, Joseph E., Henders, Anjali K., McRae, Allan F., Caracella, Anthony, Smith, Sara, Wright, Margaret J., Whitfield, John B., Dermitzakis, Emmanouil T., Martin, Nicholas G., Visscher, Peter M. and Montgomery, Grant W. (2012) The Brisbane systems genetics study: genetical genomics meets complex trait genetics. PLoS One, 7 4: e35430.1-e35430.9. doi:10.1371/journal.pone.0035430
Powell, Joseph E., Henders, Anjali K., McRae, Allan F., Wright, Margaret J., Martin, Nicholas G., Dermitzakis, Emmanouil T., Montgomery, Grant W. and Visscher, Peter M. (2012) Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Research, 22 3: 456-466. doi:10.1101/gr.126540.111
Mosing, Miriam A., Medland, Sarah E., McRae, Allan, Landers, Joseph George, Wright, Margaret J. and Martin, Nicholas G. (2012) Genetic influences on life span and its relationship to personality: A 16-year follow-up study of a sample of aging twins. Psychosomatic Medicine, 74 1: 16-22. doi:10.1097/PSY.0b013e3182385784
Jablensky, A ., Angelicheva, D ., Donohoe, G. J., Cruickshank, M., Azmanov, D. N., Morris, D. W., McRae, A., Weickert, C. S., Carter, K. W., Chandler, D., Alexandrov, B., Usheva, A., Morar, B., Verbrugghe, P. L., Filipovska, A., Rackham, O., Bishop, A. R., Rasmussen, K. Ø., Dragovic, M., Cooper, M., Phillips, M., Badcock, J., Bramon-Bosch, E., Almeida, O. P., Flicker, L., Gill, M., Corvin, A., MacGregor, S. and Kalaydjieva, L. (2012) Promoter polymorphisms in two overlapping 6p25 genes implicate mitochondrial proteins in cognitive deficit in schizophrenia. Molecular Psychiatry, 17 12: 1328-1339. doi:10.1038/mp.2011.129
Variation in BMPR1B, TGFRB1 and BMPR2 and control of dizygotic twinning
Luong, Hein T. T., Chaplin, Justin, McRae, Allan F., Medland, Sarah E., Willemsen, Gonneke, Nyholt, Dale R., Henders, Anjali K., Hoekstra, Chantal, Duffy, David L., Martin, Nicholas G., Boomsma, Dorret I., Montgomery, Grant W. and Painter, Jodie N. (2011) Variation in BMPR1B, TGFRB1 and BMPR2 and control of dizygotic twinning. Twin Research and Human Genetics, 14 5: 408-416. doi:10.1375/twin.14.5.408
Larsson, Mats, Duffy, David L., Zhu, Gu, Liu, Jimmy Z., Macgregor, Stuart, McRae, Allan F., Wright, Margaret J., Sturm, Richard A., Mackey, David A., Montgomery, Grant W., Martin, Nicholas G. and Medland, Sarah E. (2011) GWAS findings for human iris patterns: Associations with variants in genes that influence normal neuronal pattern development. American Journal of Human Genetics, 89 2: 334-343. doi:10.1016/j.ajhg.2011.07.011
Association between ORMDL3, IL1RL1 and a deletion on chromosome 17q21 with asthma risk in Australia
Ferreira, Manuel A. R., McRae, Allan F., Medland, Sarah E., Nyholt, Dale R., Gordon, Scott D., Wright, Margaret J., Henders, Anjali K., Madden, Pamela A., Visscher, Peter M., Wray, Naomi R., Heath, Andrew C., Montgomery, Grant W., Duffy, David L. and Martin, Nicholas G. (2011) Association between ORMDL3, IL1RL1 and a deletion on chromosome 17q21 with asthma risk in Australia. European Journal of Human Genetics, 19 4: 458-464. doi:10.1038/ejhg.2010.191
Frank, Rene A. W., McRae, Allan F., Pocklington, Andrew J., van de Lagemaat, Louie N., Navarro, Pau, Croning, Mike D. R., Komiyama, Noboru H., Bradley, Sophie J., Challiss, R. A. John, Armstrong, J. Douglas, Finn, Robert D., Malloy, Mary P., MacLean, Alan W., Harris, Sarah E., Starr, John M., Bhaskar, Sanjeev S., Howard, Eleanor K., Hunt, Sarah E., Coffey, Alison J., Ranganath, Venkatesh, Deloukas, Panos, Rogers, Jane, Muir, Walter J., Deary, Ian J., Blackwood, Douglas H., Visscher, Peter M. and Grant, Seth G. N. (2011) Clustered coding variants in the glutamate receptor complexes of individuals with schizophrenia and bipolar disorder. PLoS One, 6 4: e19011.1-e19011.9. doi:10.1371/journal.pone.0019011
Gratten, J., Wilson, A. J., McRae, A. F., Beraldi, D., Visscher, P. M., Pemberton, J. M. and Slate, J. (2010) No evidence for warming climate theory of coat colour change in Soay sheep: A comment on Maloney et al.. Biology Letters, 6 5: 678-679. doi:10.1098/rsbl.2010.0160
Sommerlad, Susan, McRae, Allan F., McDonald, Brenda, Johnstone, Isobel, Cuttell, Leigh, Seddon, Jennifer M. and O'Leary, Caroline A. (2010) Congenital sensorineural deafness in Australian Stumpy-tail Cattle Dogs is an autosomal recessive trait that maps to CFA10. PLoS One, 5 10: e13364. doi:10.1371/journal.pone.0013364
A versatile gene-based test for genome-wide association studies
Liu, Jimmy Z., McRae, Allan F., Nyholt, Dale R., Medland, Sarah E., Wray, Naomi R., Brown, Kevin M., AMFS Investigators, Hayward, Nicholas K., Montgomery, Grant W., Visscher, Peter M., Martin, Nicholas G. and Macgregor, Stuart (2010) A versatile gene-based test for genome-wide association studies. American Journal of Human Genetics, 87 1: 139-145. doi:10.1016/j.ajhg.2010.06.009
Genome-wide association study of height and body mass index in Australian twin families
Liu, Jimmy Z., Medland, Sarah E., Wright, Margaret J., Henders, Anjali K., Heath, Andrew C., Madden, Pamela A. F., Duncan, Alexis, Montgomery, Grant W., Martin, Nicholas G. and McRae, Allan F. (2010) Genome-wide association study of height and body mass index in Australian twin families. Twin Research And Human Genetics, 13 2: 179-193. doi:10.1375/twin.13.2.179
Horn type and horn length genes map to the same chromosomal region in Soay sheep
Johnston, S. E., Beraldi, D., McRae, A. F., Pemberton, J. M. and Slate, J. (2010) Horn type and horn length genes map to the same chromosomal region in Soay sheep. Heredity, 104 2: 196-205. doi:10.1038/hdy.2009.109
Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans
Medland, S, Nyholt, D, Painter, JN, McEnvoy, BP, Allan McRae, Zhu, G, Gordon, SD, Ferreira, MAR, Wright, MJ, Henders, AK, Campbell MJ, Duffy, D, Hansell, N K, Macgregor, S, Slutske, WS, Heath, AC, Montgomery, GW and Martin, NG (2009) Common Variants in the Trichohyalin Gene Are Associated with Straight Hair in Europeans. American Journal of Human Genetics, 85 5: 750-755. doi:10.1016/j.ajhg.2009.10.009
E. M. Byrne, A. F. McRae, D. L. Duffy, Z. Z. Zhao, N. G. Martin, J. B. Whitfield, P. M. Visscher and G. W. Montgomery (2009) Family-based mitochondrial association study of traits related to type 2 diabetes and the metabolic syndrome in adolescents. Diabetologia, 52 11: 2359-2368. doi:10.1007/s00125-009-1510-9
Association Study of Common Mitochondrial Variants and Cognitive Ability
Byrne, EM, McRae, AF, Duffy, DL, Zhao, ZZ, Martin, NG, Wright, MJ, Montgomery, GW and Visscher, PM (2009) Association Study of Common Mitochondrial Variants and Cognitive Ability. BEHAVIOR GENETICS, 39 5: 504-512. doi:10.1007/s10519-009-9276-x
Non-pathological paternal isodisomy of chromosome 2 detected from a genome-wide SNP scan.
Matthew C. Keller, Allan F. McRae, Julie M. McGaughran, Peter M. Visscher, Nicholas G. Martin and Grant W. Montgomery (2009) Non-pathological paternal isodisomy of chromosome 2 detected from a genome-wide SNP scan.. American Journal of Medical Genetics. Part A, 149A 8: 1823-1826. doi:10.1002/ajmg.a.32973
Geographical structure and differential natural selection among North European populations
Brian P. McEvoy, Grant W. Montgomery, Allan F. McRae, Samuli Ripatti, Markus Perola, Tim D. Spector, Lynn Cherkas, Kourosh R. Ahmadi, Dorret Boomsma, Gonneke Willemsen, Jouke J. Hottenga, Nancy L. Pedersen, Patrik K.E. Magnusson, Kirsten Ohm Kyvik, Kaare Christensen, Jaakko Kaprio, Kauko Heikkilä, Aarno Palotie, Elisabeth Widen, Juha Muilu, Ann-Christine Syvänen, Ulrika Liljedahl, Orla Hardiman, Simon Cronin, Leena Peltonen, Nicholas G. Martin and Peter M. Visscher (2009) Geographical structure and differential natural selection among North European populations. Genome Research, 19 5: 804-814. doi:10.1101/gr.083394.108
Family-based genome-wide association studies
Benyamin, Beben, Visscher, Peter M. and McRae, Allan F. (2009) Family-based genome-wide association studies. Pharmacogenomics, 10 2: 181-190. doi:10.2217/14622416.10.2.181
DNA methylation profiles in monozygotic and dizygotic twins
Zachary A Kaminsky, Thomas Tang, Sun-Chong Wang, Carolyn Ptak, Gabriel H T Oh, Albert H C Wong, Laura A Feldcamp, Carl Virtanen, Jonas Halfvarson, Curt Tysk, Allan F McRae, Peter M Visscher, Grant W Montgomery, Irving I Gottesman, Nicholas G Martin and Art Petronis (2009) DNA methylation profiles in monozygotic and dizygotic twins. Nature Genetics, 41 2: 240-245. doi:10.1038/ng.286
Variants in TF and HFE Explain 40% of Genetic Variation in Serum-Transferrin Levels
Beben Benyamin, Allan F. McRae, Gu Zhu, Scott Gordon, Anjali K. Henders, Aarno Palotie, Leena Peltonen, Nicholas G. Martin, Grant W. Montgomery, John B. Whitfield and Peter M. Visscher (2009) Variants in TF and HFE Explain 40% of Genetic Variation in Serum-Transferrin Levels. American Journal of Human Genetics, 84 1: 60-65. doi:10.1016/j.ajhg.2008.11.011
Knight, Helen M., Pickard, Benjamin S., Maclean, Alan, Malloy, Mary P., Soares, Dinesh C., McRae, Allan F., Condie, Alison, White, Angela, Hawkins, William, McGhee, Kevin, van Beck, Margaret, MacIntyre, Donald J., Starr, John M., Deary, Ian J., Visscher, Peter M., Porteous, David J., Cannon, Ronald E., St Clair, David, Muir, Walter J. and Blackwood, Douglas H. R. (2009) A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder, and depression. American Journal of Human Genetics, 85 6: 833-846. doi:10.1016/j.ajhg.2009.11.003
Divergence between human populations estimated from linkage disequilibrium
Sved, John A., McRae, Allan F. and Visscher, Peter M. (2008) Divergence between human populations estimated from linkage disequilibrium. American Journal of Human Genetics, 83 6: 737-743. doi:10.1016/j.ajhg.2008.10.019
Linkage and Association Analyses of Longitudinally Measured Lipid Phenotypes in Adolescence
Middelberg, Rita P., Gordon, Scott D., Zhu, Gu, McRae, Allan, Montgomery, Grant W., Martin, Nicholas G. and Whitfield, John B. (2008) Linkage and Association Analyses of Longitudinally Measured Lipid Phenotypes in Adolescence. Twin Research and Human Genetics, 11 6: 603-620. doi:10.1375/twin.11.6.603
Byrne, Enda M., Mcrae, Allan F., Zhao, Zhen-Zhen, Martin, Nicholas G., Montgomery, Grant W. and Visscher, Peter M. (2008) The use of common mitochondrial variants to detect and characterise population structure in the Australian population: Implications for genome-wide association studies. European Journal of Human Genetics, 16 11: 1396-1403. doi:10.1038/ejhg.2008.117
Calculation of IBD probabilities with dense SNP or sequence data
Keith, Jonathan M., McRae, Allan, Duffy, David, Mengersen, Kerrie and Visscher, Peter M. (2008) Calculation of IBD probabilities with dense SNP or sequence data. Genetic Epidemiology, 32 6: 513-519. doi:10.1002/gepi.20324
Power and SNP tagging in whole mitochondrial genome association studies
McRae, Allan F., Byrne, Enda M., Zhao, Zhen Zhen, Montgomery, Grant W. and Visscher, Peter M. (2008) Power and SNP tagging in whole mitochondrial genome association studies. Genome Research, 18 6: 911-917. doi:10.1101/gr.074872.107
A localized negative genetic correlation constrains microevolution of coat color in wild sheep
Gratten, J., Wilson, A. J., McRae, A. F., Beraldi, D., Visscher, P. M., Pemberton, J. M. and Slate, J. (2008) A localized negative genetic correlation constrains microevolution of coat color in wild sheep. Science, 319 5861: 318-320. doi:10.1126/science.1151182
Mapping quantitative trait loci underlying fitness-related traits in a free-living sheep population
Beraldi, Dario, McRae, Allan F., Gratten, Jacob, Slate, Jon, Visscher, Peter M. and Pemberton, Josephine M. (2007) Mapping quantitative trait loci underlying fitness-related traits in a free-living sheep population. Evolution, 61 6: 1403-1416. doi:10.1111/j.1558-5646.2007.00106.x
Gratten, J., Beraldi, D., Lowder, B. V., McRae, A. F., Visscher, P. M., Pemberton, J. M. and Slate, J. (2007) Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep. Proceedings of the Royal Society of London: Biological Sciences, 274 1610: 619-626. doi:10.1098/rspb.2006.3762
Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines
McRae, A. F., Matigian, N. A., Vadlamudi, L., Mulley, J. C., Mowry, B., Martin, N. G., Berkovic, S. F., Hayward, N. K. and Visscher, P. M. (2007) Replicated effects of sex and genotype on gene expression in human lymphoblastoid cell lines. Human Molecular Genetics, 16 4: 364-373. doi:10.1093/hmg/ddl456
Beraldi, Dario, McRae, Allan F., Gratten, Jacob, Slate, Jon, Visscher, Peter M., Pemberton, Josephine M. and Pilkington, Jill G. (2007) Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries). Journal of Parasitology, 37 1: 121-129. doi:10.1016/j.ijpara.2006.09.007
Anderson, Carl A., McRae, Allan F. and Visscher, Peter M. (2006) A simple linear regression method for quantitative trait loci linkage analysis with censored observations. Genetics, 173 3: 1735-1745. doi:10.1534/genetics.106.055921
Beraldi, Dario, McRae, Allan F., Gratten, Jacob, Slate, Jon, Visscher, Peter M. and Pemberton, Josephine M. (2006) Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries). Genetics, 173 3: 1521-1537. doi:10.1534/genetics.106.057141
Examination of a region showing linkage map discrepancies across sheep breeds
McRae, AF and Beraldi, D (2006) Examination of a region showing linkage map discrepancies across sheep breeds. Mammalian Genome, 17 4: 346-353. doi:10.1007/s00335-005-0087-y
McRae, AF, Pemberton, JM and Visscher, PM (2005) Modeling linkage disequilibrium in natural populations: The example of the Soay sheep population of St. Kilda, Scotland. Genetics, 171 1: 251-258. doi:10.1534/genetics.105.040972
McRae, AF, Bishop, SC, Walling, GA, Wilson, AD and Visscher, PM (2005) Mapping of multiple quantitative trait loci for growth and carcass traits in a complex commercial sheep pedigree. Animal Science, 80 8: 135-141.
Bone density in sheep: genetic variation and quantitative trait loci localisation
Campbell, AW, Bain, WE, McRae, AF, Broad, TE, Johnstone, PD, Dodds, KG, Veenvliet, BA, Greer, GJ, Glass, BC, Beattie, AE, Jopson, NB and McEwan, JC (2003) Bone density in sheep: genetic variation and quantitative trait loci localisation. Bone, 33 4: 540-548. doi:10.1016/S8756-3282(03)00228-X
Linkage disequilibrium in domestic sheep
McRae, AF, McEwan, JC, Dodds, KG, Wilson, T, Crawford, AM and Slate, J (2002) Linkage disequilibrium in domestic sheep. Genetics, 160 3: 1113-1122.
Signatures of negative selection in the genetic architecture of human complex traits
Zeng, Jian, de Vlaming, Ronald, Wu, Yang, Robinson, Matthew R., Lloyd-Jones, Luke R., Yengo, Loic, Yap, Chloe X., Xue, Angli, Sidorenko, Julia, Mcrae, Allan F., Powell, Joseph E., Montgomery, Grant W., Metspalu, Andres, Esko, Tonu, Gibson, Greg, Wray, Naomi R., Visscher, Peter M. and Yang, Jian (2018). Signatures of negative selection in the genetic architecture of human complex traits. In: 48th Annual Meeting of the Behavior-Genetics-Association (BGA), Boston MA, United States, (525-525). 20-23 June 2018.
Comparison of Faecal Microbe Diversity Between Motor Neurone Disease (Mnd) and Control Participants
Steyn, Frederik J., Restuadi, Restuadi, Ioannides, Zara, Ngo, Shyuan T., McRae, Allan, Wray, Naomi R., Henderson, Robert and McCombe, Pamela (2017). Comparison of Faecal Microbe Diversity Between Motor Neurone Disease (Mnd) and Control Participants. In: Annual Scientific Meeting of the Australian-and-New-Zealand-Association-of-Neurologists (ANZAN), Gold Coast, Australia, (). 9-12 May 2017. doi:10.1136/jnnp-2017-316074.81
Comparison of faecal microbe diversity between motor neurone disease (MND) and control participants
Steyn, Frederik J., Restuadi, Restuadi, Ioannides, Zara, Ngo, Shyuan T., McRae, Allan, Wray, Naomi R., Henderson, Robert and McCombe, Pamela (2017). Comparison of faecal microbe diversity between motor neurone disease (MND) and control participants. In: Annual Scientific Meeting of the Australian and New Zealand Association of Neurologists (ANZAN), Gold Coast Australia, (). May 9-12, 2017. doi:10.1136/jnnp-2017-316074.81
Kwok, J., Coupland, K., Mellick, G., Mather, K., Thalamuthu, A., Armstrong, N., Sachdev, P., Brodaty, H., Wright, M., Ames, D., Allen, M., Ertekin-Taner, N., McRae, A., Bennett, D., Jager, P. D., Kim, W., Halliday, G. and Dobson-Stone, C. (2015). Genome-wide association study identifies the SLC2A14 gene on chromosome 12P13 as a trans-acting locus for methylation of MAPT gene. In: Special Issue: 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society. 25th Biennial Meeting of the International Society for Neurochemistry Jointly with the 13th Meeting of the Asian Pacific Society for Neurochemistry in Conjunction with the 35th Meeting of the Australasian Neuroscience Society, Cairns, QLD Australia, (113-114). 23-27 August 2015. doi:10.1111/jnc.13188
Thomas, Gethin P., Tseng, Hsu-Wen, Pettit, Allison, Glant, Tibor T., McRae, Allan and Brown, Matthew A. (2013). Endochondral Bone Formation and Advanced Enthesitis Are Key Features Of Proteoglycan Induced Spondylitis Mouse Model Of Ankylosing Spondylitis. In: Abstract Supplement 2013 Annual Meeting. 77th Annual Meeting of the American College of Rheumatology / 48th Annual Meeting of the Association of Rheumatology Health Professionals, San Diego CA, United States, (S231-S231). 25-30 October 2013. doi:10.1002/art.38216
Medland, S. E., Nyholt, D. R., Painter, J. N., McEvoy, B. P., McRae, A. F., Montgomery, G. W. and Martin, N. G. (2010). Common variants in the Trichohyalin gene are associated with straight hair in Europeans genetics and genodermatoses. In: 6th World Congress for Hair Research, Cairns, QLD, Australia, (563-563). 16-19 June 2010. doi:10.1111/j.1600-0625.2010.01097.x
(2018–2020) NHMRC Boosting Dementia Research Grants
Disturbances of DNA regulation in obesity, and their relationships to metabolic health
(2018–2020) NHMRC A*STAR Joint Grants
(2018–2019) University of California, San Francisco
Methods and software tool for complex trait analyses using multi-omics data
(2016–2019) NHMRC Project Grant
Genetics of DNA Methylation and Its Role in Disease Susecptibility
(2015–2018) NHMRC Career Development Fellowship
(2015–2018) University of New South Wales
Inheritance of DNA methylation state in humans
(2012–2014) NHMRC Project Grant
Sexual dimorphism in human gene expression
Doctor Philosophy — Principal Advisor
Other advisors:
Fine-mapping of quantitative trait loci in 'omics data
Doctor Philosophy — Principal Advisor
Other advisors:
Investigation of the shared aetiology between disorders of the brain
Doctor Philosophy — Associate Advisor
Other advisors:
Developing novel methods for complex trait analyses using multi-omics data
Doctor Philosophy — Associate Advisor
Other advisors:
Statistical properties of sequence based relationship matrices and implications for estimating genetic variation for neurological disease
Doctor Philosophy — Associate Advisor
Other advisors:
(2018) Master Philosophy — Associate Advisor
Other advisors:
Mitochondrial and autosomal genetic analyses in the Australian population
(2010) Doctor Philosophy — Associate Advisor
Other advisors: