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Dr Jake Gratten

Honorary Principal Fellow

Mater Research Institute-UQ
Faculty of Medicine
jacob.gratten@mater.uq.edu.au

Overview

Dr Gratten completed his undergraduate studies and PhD at The University of Queensland, before undertaking postdoctoral training in evolutionary and quantitative genetics at the University of Sheffield. He then returned to Australia and shifted research focus to psychiatric and neurological genetics, taking up a position as research fellow at the Queensland Brain Institute. In 2013, he was recruited to UQ's Centre for Neurogenetics and Statistical Genomics, and in 2017 was awarded an NHMRC Career Development Fellowship (Level 2). He established the Cognitive Health Genomics group at Mater Research Institute in 2018, with the goal to improve understanding of the etiology of psychiatric and neurological disorders through analysis and integration of whole genome datasets. He has received >$5M in research funding from the NHMRC, Autism Cooperative Research Centre and both Australian (BICARE) and international (Brain & Behavior Research Foundation) philanthropic funders.

Qualifications

  • Bachelor of Science, The University of Queensland
  • Bachelor of Science Honours Class 1 in Zoology, The University of Queensland
  • Doctor of Philosophy, The University of Queensland

Publications

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Grants

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Supervision

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Available Projects

  • Cellular genomics of Parkinson's disease

    We are seeking a highly motivated PhD candidate with a background and interest in human genomics, statistics and neurodegenerative disease to join the Cognitive Health Genomics group at the Mater Research Institute, UQ. The successful candidate would work on an NHMRC-funded study to identify selectively vulnerable neuronal and/or glial cell types across the spatial and temporal course of Parkinson’s disease using single cell approaches.

    Project description

    Parkinson’s disease (PD) is a complex neurodegenerative condition affecting 1% of Australians aged ≥60-years. There is no cure, and the number of affected individuals is rising steeply as populations age. Understanding the genetic basis of PD is critical to developing new therapeutics to counter the growing disease burden. Large-scale genome-wide association studies (GWAS) of PD have identified nearly 100 risk loci, but interpretation of these findings remains challenging; we do not yet know the identity of most PD risk genes, nor the specific cell types in which they act, nor when they act during the course of disease, which hampers efforts to identify targets for interventions. We will address these challenges by using single nucleus RNA-seq to identify cell types involved in the onset and progression of Lewy body pathology in PD-related brain regions.

    Requirements

    • Bachelor’s degree with first class honours, or Masters, in statistics, mathematics, bioinformatics, human genetics, animal breeding, or an equivalent field.
    • Prior research experience in human genomics or animal breeding, including a familiarity with high-throughput genomic data and working in a high-performance computing environment.
    • Skills in the R statistical computing language and/or python, C++ or an equivalent computing language.
    • High degree of motivation and organisation, and an ability to work both independently and as part of a team.
    • (Co-)authorship on at least one peer-reviewed publication (for International applicants)
    • Excellent written and oral communications skills in English.

    For further information please contact Dr Jake Gratten, jacob.gratten@mater.uq.edu.au, +61-7-34437585.

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Publications

Featured Publications

Journal Article

  • Using brain cell-type-specific protein interactomes to interpret neurodevelopmental genetic signals in schizophrenia

    Hsu, Yu-Han H., Pintacuda, Greta, Liu, Ruize, Nacu, Eugeniu, Kim, April, Tsafou, Kalliopi, Petrossian, Natalie, Crotty, William, Suh, Jung Min, Riseman, Jackson, Martin, Jacqueline M., Biagini, Julia C., Mena, Daya, Ching, Joshua K.T., Malolepsza, Edyta, Li, Taibo, Singh, Tarjinder, Ge, Tian, Egri, Shawn B., Tanenbaum, Benjamin, Stanclift, Caroline R., Apffel, Annie M., Ripke, Stephan, Neale, Benjamin M., Corvin, Aiden, Walters, James T.R., Farh, Kai-How, Holmans, Peter A., Lee, Phil ... Lage, Kasper (2023). Using brain cell-type-specific protein interactomes to interpret neurodevelopmental genetic signals in schizophrenia. iScience, 26 (5) 106701, 106701. doi: 10.1016/j.isci.2023.106701

  • Interactions between the lipidome and genetic and environmental factors in autism

    Yap, Chloe X., Henders, Anjali K., Alvares, Gail A., Giles, Corey, Huynh, Kevin, Nguyen, Anh, Wallace, Leanne, McLaren, Tiana, Yang, Yuanhao, Hernandez, Leanna M., Gandal, Michael J., Hansell, Narelle K., Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P., Leslie, Jodie, Levis Frenk, Mira, Masi, Anne, Mathew, Nisha E., Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L., Nunn, Lorelle, Strike, Lachlan T. ... The Busselton Health Study Investigators (2023). Interactions between the lipidome and genetic and environmental factors in autism. Nature Medicine, 29 (4), 936-949. doi: 10.1038/s41591-023-02271-1

  • The shared genetic landscape of blood cell traits and risk of neurological and psychiatric disorders

    Yang, Yuanhao, Zhou, Yuan, Nyholt, Dale R., Yap, Chloe X., Tannenberg, Rudolph K., Wang, Ying, Wu, Yang, Zhu, Zhihong, Taylor, Bruce V. and Gratten, Jacob (2023). The shared genetic landscape of blood cell traits and risk of neurological and psychiatric disorders. Cell Genomics, 3 (2) 100249. doi: 10.1016/j.xgen.2022.100249

  • Mapping genomic loci implicates genes and synaptic biology in schizophrenia

    Trubetskoy, Vassily, Pardiñas, Antonio F, Qi, Ting, Panagiotaropoulou, Georgia, Awasthi, Swapnil, Bigdeli, Tim B, Bryois, Julien, Chen, Chia-Yen, Dennison, Charlotte A, Hall, Lynsey S, Lam, Max, Watanabe, Kyoko, Frei, Oleksandr, Ge, Tian, Harwood, Janet C, Koopmans, Frank, Magnusson, Sigurdur, Richards, Alexander L, Sidorenko, Julia, Wu, Yang, Zeng, Jian, Grove, Jakob, Kim, Minsoo, Li, Zhiqiang, Voloudakis, Georgios, Zhang, Wen, Adams, Mark, Agartz, Ingrid, Atkinson, Elizabeth G ... Schizophrenia Working Group of the Psychiatric Genomics Consortium (2022). Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Nature, 604 (7906), 502-508. doi: 10.1038/s41586-022-04434-5

  • Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

    Okbay, Aysu, Wu, Yeda, Wang, Nancy, Jayashankar, Hariharan, Bennett, Michael, Nehzati, Seyed Moeen, Sidorenko, Julia, Kweon, Hyeokmoon, Goldman, Grant, Gjorgjieva, Tamara, Jiang, Yunxuan, Hicks, Barry, Tian, Chao, Hinds, David A., Ahlskog, Rafael, Magnusson, Patrik K E, Oskarsson, Sven, Hayward, Caroline, Campbell, Archie, Porteous, David J., Freese, Jeremy, Herd, Pamela, Watson, Chelsea, Jala, Jonathan, Conley, Dalton, Koellinger, Philipp D., Johannesson, Magnus, Laibson, David, Meyer, Michelle N. ... Social Science Genetic Association Consortium (2022). Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals. Nature Genetics, 54 (4), 437-449. doi: 10.1038/s41588-022-01016-z

  • Australian Parkinson’s Genetics Study (APGS): pilot (n=1532)

    Bivol, Svetlana, Mellick, George D., Gratten, Jacob, Parker, Richard, Mulcahy, Aoibhe, Mosley, Philip E., Poortvliet, Peter C., Campos, Adrian I., Mitchell, Brittany L., Garcia-Marin, Luis M., Cross, Simone, Ferguson, Mary, Lind, Penelope A., Loesch, Danuta Z., Visscher, Peter M., Medland, Sarah E., Scherzer, Clemens R., Martin, Nicholas G. and Rentería, Miguel E. (2022). Australian Parkinson’s Genetics Study (APGS): pilot (n=1532). BMJ Open, 12 (2) e052032, e052032. doi: 10.1136/bmjopen-2021-052032

  • Investigating the shared genetic architecture between multiple sclerosis and inflammatory bowel diseases

    Yang, Yuanhao, Musco, Hannah, Simpson-Yap, Steve, Zhu, Zhihong, Wang, Ying, Lin, Xin, Zhang, Jiawei, Taylor, Bruce, Gratten, Jacob and Zhou, Yuan (2021). Investigating the shared genetic architecture between multiple sclerosis and inflammatory bowel diseases. Nature Communications, 12 (1) 5641, 5641. doi: 10.1038/s41467-021-25768-0

  • Autism-related dietary preferences mediate autism-gut microbiome associations

    Yap, Chloe X., Henders, Anjali K., Alvares, Gail A., Wood, David L.A., Krause, Lutz, Tyson, Gene W., Restuadi, Restuadi, Wallace, Leanne, McLaren, Tiana, Hansell, Narelle K., Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P., Leslie, Jodie, Frenk, Mira Levis, Masi, Anne, Mathew, Nisha E., Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L., Nunn, Lorelle, Holtmann, Gerald, Strike, Lachlan T., de Zubicaray, Greig I. ... Gratten, Jacob (2021). Autism-related dietary preferences mediate autism-gut microbiome associations. Cell, 184 (24), 5916-5931.e17. doi: 10.1016/j.cell.2021.10.015

  • Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders

    Nabais, Marta F., Laws, Simon M., Lin, Tian, Vallerga, Costanza L., Armstrong, Nicola J., Blair, Ian P., Kwok, John B., Mather, Karen A., Mellick, George D., Sachdev, Perminder S., Wallace, Leanne, Henders, Anjali K., Zwamborn, Ramona A. J., Hop, Paul J., Lunnon, Katie, Pishva, Ehsan, Roubroeks, Janou A. Y., Soininen, Hilkka, Tsolaki, Magda, Mecocci, Patrizia, Lovestone, Simon, Kloszewska, Iwona, Vellas, Bruno, Furlong, Sarah, Garton, Fleur C., Henderson, Robert D., Mathers, Susan, McCombe, Pamela A., Needham, Merrilee ... McRae, Allan F. (2021). Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders. Genome Biology, 22 (1) 90, 1-30. doi: 10.1186/s13059-021-02275-5

  • Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

    Yap, Chloe X., Alvares, Gail A., Henders, Anjali K., Lin, Tian, Wallace, Leanne, Farrelly, Alaina, McLaren, Tiana, Berry, Jolene, Vinkhuyzen, Anna A. E., Trzaskowski, Maciej, Zeng, Jian, Yang, Yuanhao, Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren, Leslie, Jodie, Levis Frenk, Mira, Masi, Anne, Mathew, Nisha E., Muniandy, Melanie, Nothard, Michaela, Visscher, Peter M., Dawson, Paul A., Dissanayake, Cheryl ... Gratten, Jacob (2021). Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank. Molecular Autism, 12 (1) 12, 12. doi: 10.1186/s13229-020-00407-5

  • Analysis of DNA methylation associates the cystine–glutamate antiporter SLC7A11 with risk of Parkinson’s disease

    Vallerga, Costanza L., Zhang, Futao, Fowdar, Javed, McRae, Allan F., Qi, Ting, Nabais, Marta F., Zhang, Qian, Kassam, Irfahan, Henders, Anjali K., Wallace, Leanne, Montgomery, Grant, Chuang, Yu-Hsuan, Horvath, Steve, Ritz, Beate, Halliday, Glenda, Hickie, Ian, Kwok, John B., Pearson, John, Pitcher, Toni, Kennedy, Martin, Bentley, Steven R., Silburn, Peter A., Yang, Jian, Wray, Naomi R., Lewis, Simon J. G., Anderson, Tim, Dalrymple-Alford, John, Mellick, George D., Visscher, Peter M. and Gratten, Jacob (2020). Analysis of DNA methylation associates the cystine–glutamate antiporter SLC7A11 with risk of Parkinson’s disease. Nature Communications, 11 (1) 1238, 1238. doi: 10.1038/s41467-020-15065-7

  • Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis

    Nabais, Marta F., Lin, Tian, Benyamin, Beben, Williams, Kelly L., Garton, Fleur C., Vinkhuyzen, Anna A. E., Zhang, Futao, Vallerga, Costanza L., Restuadi, Restuadi, Freydenzon, Anna, Zwamborn, Ramona A. J., Hop, Paul J., Robinson, Matthew R., Gratten, Jacob, Visscher, Peter M., Hannon, Eilis, Mill, Jonathan, Brown, Matthew A., Laing, Nigel G., Mather, Karen A., Sachdev, Perminder S., Ngo, Shyuan T., Steyn, Frederik J., Wallace, Leanne, Henders, Anjali K., Needham, Merrilee, Veldink, Jan H., Mathers, Susan, Nicholson, Garth ... Wray, Naomi R. (2020). Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. npj Genomic Medicine, 5 (1) 10, 1-9. doi: 10.1038/s41525-020-0118-3

  • Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

    Nalls, Mike A, Blauwendraat, Cornelis, Vallerga, Costanza L, Heilbron, Karl, Bandres-Ciga, Sara, Chang, Diana, Tan, Manuela, Kia, Demis A, Noyce, Alastair J, Xue, Angli, Bras, Jose, Young, Emily, von Coelln, Rainer, Simón-Sánchez, Javier, Schulte, Claudia, Sharma, Manu, Krohn, Lynne, Pihlstrøm, Lasse, Siitonen, Ari, Iwaki, Hirotaka, Leonard, Hampton, Faghri, Faraz, Gibbs, J Raphael, Hernandez, Dena G, Scholz, Sonja W, Botia, Juan A, Martinez, Maria, Corvol, Jean-Christophe, Lesage, Suzanne ... Zhang, Futao (2019). Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies. The Lancet Neurology, 18 (12), 1091-1102. doi: 10.1016/S1474-4422(19)30320-5

  • Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing

    Zhang, Qian, Vallerga, Costanza L., Walker, Rosie M., Lin, Tian, Henders, Anjali K., Montgomery, Grant W., He, Ji, Fan, Dongsheng, Fowdar, Javed, Kennedy, Martin, Pitcher, Toni, Pearson, John, Halliday, Glenda, Kwok, John B., Hickie, Ian, Lewis, Simon, Anderson, Tim, Silburn, Peter A., Mellick, George D., Harris, Sarah E., Redmond, Paul, Murray, Alison D., Porteous, David J., Haley, Christopher S., Evans, Kathryn L., McIntosh, Andrew M., Yang, Jian, Gratten, Jacob, Marioni, Riccardo E. ... Visscher, Peter M. (2019). Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing. Genome Medicine, 11 (1) 54, 54. doi: 10.1186/s13073-019-0667-1

  • The genetic relationship between female reproductive traits and six psychiatric disorders

    Ni, Guiyan, Amare, Azmeraw T., Zhou, Xuan, Mills, Natalie, Gratten, Jacob and Lee, S. Hong (2019). The genetic relationship between female reproductive traits and six psychiatric disorders. Scientific Reports, 9 (1) 12041, 12041. doi: 10.1038/s41598-019-48403-x

  • Association of schizophrenia risk with disordered niacin metabolism in an Indian genome-wide association study

    Periyasamy, Sathish, John, Sujit, Padmavati, Raman, Rajendren, Preeti, Thirunavukkarasu, Priyadarshini, Gratten, Jacob, Vinkhuyzen, Anna, McRae, Allan, Holliday, Elizabeth G., Nyholt, Dale R., Nancarrow, Derek, Bakshi, Andrew, Hemani, Gibran, Nertney, Deborah, Smith, Heather, Filippich, Cheryl, Patel, Kalpana, Fowdar, Javed, McLean, Duncan, Tirupati, Srinivasan, Nagasundaram, Arunkumar, Gundugurti, Prasad Rao, Selvaraj, Krishnamurthy, Jegadeesan, Jayaprakash, Jorde, Lynn B., Wray, Naomi R., Brown, Matthew A., Suetani, Rachel, Giacomotto, Jean ... Mowry, Bryan J. (2019). Association of schizophrenia risk with disordered niacin metabolism in an Indian genome-wide association study. JAMA Psychiatry, 76 (10), 1026-1034. doi: 10.1001/jamapsychiatry.2019.1335

  • Parkinson's disease age at onset genome-wide association study: defining heritability, genetic loci, and α-synuclein mechanisms

    Blauwendraat, Cornelis, Heilbron, Karl, Vallerga, Costanza L., Bandres-Ciga, Sara, von Coelln, Rainer, Pihlstrøm, Lasse, Simón-Sánchez, Javier, Schulte, Claudia, Sharma, Manu, Krohn, Lynne, Siitonen, Ari, Iwaki, Hirotaka, Leonard, Hampton, Noyce, Alastair J., Tan, Manuela, Gibbs, J. Raphael, Hernandez, Dena G., Scholz, Sonja W., Jankovic, Joseph, Shulman, Lisa M., Lesage, Suzanne, Corvol, Jean-Christophe, Brice, Alexis, van Hilten, Jacobus J., Marinus, Johan, Eerola-Rautio, Johanna, Tienari, Pentti, Majamaa, Kari, Toft, Mathias ... Singleton, Andrew B. (2019). Parkinson's disease age at onset genome-wide association study: defining heritability, genetic loci, and α-synuclein mechanisms. Movement Disorders, 34 (6) mds.27659, 866-875. doi: 10.1002/mds.27659

  • Examining the impact of imputation errors on fine-mapping using DNA methylation QTL as a model trait

    Chundru, V. Kartik, Marioni, Riccardo E., Prendergast, James G. D., Vallerga, Costanza L., Lin, Tian, Berveridge, Allan J., SGPD Consortium, Gratten, Jacob, Hume, David A., Deary, Ian J., Wray, Naomi R., Visscher, Peter M. and McRae, Allan F. (2019). Examining the impact of imputation errors on fine-mapping using DNA methylation QTL as a model trait. Genetics, 212 (3), 577-586. doi: 10.1534/genetics.118.301861

  • Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson's disease heritability

    Reynolds, Regina H., Botia, Juan, Nalls, Mike A., Hardy, John, Taliun, Sarah A. Gagliano, Ryten, Mina, Noyce, Alastair J., Nicolas, Aude, Cookson, Mark R., Bandres-Ciga, Sara, Gibbs, J. Raphael, Hernandez, Dena G., Singleton, Andrew B., Reed, Xylena, Leonard, Hampton, Blauwendraat, Cornelis, Faghri, Faraz, Bras, Jose, Guerreiro, Rita, Tucci, Arianna, Kia, Demis A., Houlden, Henry, Plun-Favreau, Helene, Mok, Kin Y., Wood, Nicholas W., Lovering, Ruth, R'Bibo, Lea, Rizig, Mie, Chelban, Viorica ... Pearson, John (2019). Moving beyond neurons: the role of cell type-specific gene regulation in Parkinson's disease heritability. Npj Parkinsons Disease, 5 (1) 6, 6. doi: 10.1038/s41531-019-0076-6

  • Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences

    Karlsson Linnér, Richard, Biroli, Pietro, Kong, Edward, Meddens, S. Fleur W., Wedow, Robbee, Fontana, Mark Alan, Lebreton, Maël, Tino, Stephen P., Abdellaoui, Abdel, Hammerschlag, Anke R., Nivard, Michel G., Okbay, Aysu, Rietveld, Cornelius A., Timshel, Pascal N., Trzaskowski, Maciej, Vlaming, Ronald de, Zünd, Christian L., Bao, Yanchun, Buzdugan, Laura, Caplin, Ann H., Chen, Chia-Yen, Eibich, Peter, Fontanillas, Pierre, Gonzalez, Juan R., Joshi, Peter K., Karhunen, Ville, Kleinman, Aaron, Levin, Remy Z., Lill, Christina M. ... Beauchamp, Jonathan P. (2019). Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences. Nature Genetics, 51 (2), 245-257. doi: 10.1038/s41588-018-0309-3

  • Imprint of assortative mating on the human genome

    Yengo, Loic, Robinson, Matthew R., Keller, Matthew C., Kemper, Kathryn E., Yang, Yuanhao, Trzaskowski, Maciej, Gratten, Jacob, Turley, Patrick, Cesarini, David, Benjamin, Daniel J., Wray, Naomi R., Goddard, Michael E., Yang, Jian and Visscher, Peter M. (2018). Imprint of assortative mating on the human genome. Nature Human Behaviour, 2 (12), 948-954. doi: 10.1038/s41562-018-0476-3

  • Study protocol for the Australian autism biobank: an international resource to advance autism discovery research

    Alvares, Gail A., Dawson, Paul A., Dissanayake, Cheryl, Eapen, Valsamma, Gratten, Jacob, Grove, Rachel, Henders, Anjali, Heussler, Helen, Lawson, Lauren, Masi, Anne, Raymond, Emma, Rose, Felicity, Wallace, Leanne, Wray, Naomi R. and Whitehouse, Andrew J. O. (2018). Study protocol for the Australian autism biobank: an international resource to advance autism discovery research. BMC Pediatrics, 18 (1) 284, 284. doi: 10.1186/s12887-018-1255-z

  • Age at first birth in women is genetically associated with increased risk of schizophrenia

    Ni, Guiyan, Gratten, Jacob, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Wray, Naomi R. and Lee, Sang Hong (2018). Age at first birth in women is genetically associated with increased risk of schizophrenia. Scientific Reports, 8 (1) 10168, 10168. doi: 10.1038/s41598-018-28160-z

  • Trans-eQTLs identified in whole blood have limited influence on complex disease biology

    Yap, Chloe X., Lloyd-Jones, Luke, Holloway, Alexander, Smartt, Peter, Wray, Naomi R., Gratten, Jacob and Powell, Joseph E. (2018). Trans-eQTLs identified in whole blood have limited influence on complex disease biology. European Journal of Human Genetics, 26 (9), 1-8. doi: 10.1038/s41431-018-0174-7

  • Sizing up whole-genome sequencing studies of common diseases

    Wray, Naomi R. and Gratten, Jacob (2018). Sizing up whole-genome sequencing studies of common diseases. Nature Genetics, 50 (5), 635-637. doi: 10.1038/s41588-018-0113-0

  • Gene networks associated with non-syndromic intellectual disability

    Lee, Soohyun, Rudd, Stephen, Gratten, Jacob, Visscher, Peter M., Prins, Johannes B. and Dawson, Paul A. (2017). Gene networks associated with non-syndromic intellectual disability. Journal of Neurogenetics, 32 (1), 6-14. doi: 10.1080/01677063.2017.1404058

  • Whole-exome sequencing in amyotrophic lateral sclerosis suggests NEK1 is a risk gene in Chinese

    Gratten, Jacob, Zhao, Qiongyi, Benyamin, Beben, Garton, Fleur, He, Ji, Leo, Paul J., Mangelsdorf, Marie, Anderson, Lisa, Zhang, Zong-Hong, Chen, Lu, Chen, Xiang-Ding, Cremin, Katie, Deng, Hong-Weng, Edson, Janette, Han, Ying-Ying, Harris, Jessica, Henders, Anjali K., Jin, Zi-Bing, Li, Zhongshan, Lin, Yong, Liu, Xiaolu, Marshall, Mhairi, Mowry, Bryan J., Ran, Shu, Reutens, David C., Song, Sharon, Tan, Li-Jun, Tang, Lu, Wallace, Robyn H. ... Fan, Dongsheng (2017). Whole-exome sequencing in amyotrophic lateral sclerosis suggests NEK1 is a risk gene in Chinese. Genome Medicine, 9 (97) 97, 97. doi: 10.1186/s13073-017-0487-0

  • Cross-ethnic meta-analysis identifies association of the GPX3-TNIP1 locus with amyotrophic lateral sclerosis

    Benyamin, Beben, He, Ji, Zhao, Qiongyi, Gratten, Jacob, Garton, Fleur, Leo, Paul J., Liu, Zhijun, Mangelsdorf, Marie, Al-Chalabi, Ammar, Anderson, Lisa, Butler, Timothy J., Chen, Lu, Chen, Xiang-Ding, Cremin, Katie, Deng, Hong-Weng, Devine, Matthew, Edson, Janette, Fifita, Jennifer A., Furlong, Sarah, Han, Ying-Ying, Harris, Jessica, Henders, Anjali K., Jeffree, Rosalind L., Jin, Zi-Bing, Li, Zhongshan, Li, Ting, Li, Mengmeng, Lin, Yong, Liu, Xiaolu ... Fan, Dongsheng (2017). Cross-ethnic meta-analysis identifies association of the GPX3-TNIP1 locus with amyotrophic lateral sclerosis. Nature Communications, 8 (1) 611, 611. doi: 10.1038/s41467-017-00471-1

  • Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort

    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

  • Rare variants are common in schizophrenia

    Gratten, Jacob (2016). Rare variants are common in schizophrenia. Nature Neuroscience, 19 (11), 1426-1428. doi: 10.1038/nn.4422

  • Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits

    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, 84. doi: 10.1186/s13073-016-0338-4

  • Genetic pleiotropy in complex traits and diseases: implications for genomic medicine

    Gratten, Jacob and Visscher, Peter M. (2016). Genetic pleiotropy in complex traits and diseases: implications for genomic medicine. Genome Medicine, 8 (78) 78, 1-3. doi: 10.1186/s13073-016-0332-x

  • Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses

    Okbay, Aysu, Baselmans, Bart M. L., De Neve, Jan-Emmanuel, Turley, Patrick, Nivard, Michel G., Fontana, Mark Alan, Meddens, S. Fleur W., Linner, Richard Karlsson, Rietveld, Cornelius A., Derringer, Jaime, Gratten, Jacob, Lee, James J., Liu, Jimmy Z., de Vlaming, Ronald, Ahluwalia, Tarunveer S., Buchwald, Jadwiga, Cavadino, Alana, Frazier-Wood, Alexis C., Furlotte, Nicholas A., Garfield, Victoria, Geisel, Marie Henrike, Gonzalez, Juan R., Haitjema, Saskia, Karlsson, Robert, van der Laan, Sander W., Ladwig, Karl-Heinz, Lahti, Jari, van der Lee, Sven J., Lind, Penelope A. ... Cesarini, David (2016). Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses. Nature Genetics, 48 (6), 624-633. doi: 10.1038/ng.3552

  • Risk of psychiatric illness from advanced paternal age is not predominantly from de novo mutations

    Gratten, Jacob, Wray, Naomi R., Peyrot, Wouter J., McGrath, John J., Visscher, Peter M. and Goddard, Michael E. (2016). Risk of psychiatric illness from advanced paternal age is not predominantly from de novo mutations. Nature Genetics, 48 (7), 718-+. doi: 10.1038/ng.3577

  • Genome-wide association study identifies 74 loci associated with educational attainment

    Okbay, Aysu, Beauchamp, Jonathan P., Fontana, Mark Alan, Lee, James J., Pers, Tune H., Rietveld, Cornelius A., Turley, Patrick, Chen, Guo-Bo, Emilsson, Valur, Meddens, S. Fleur W., Oskarsson, Sven, Pickrell, Joseph K., Thom, Kevin, Timshel, Pascal, de Vlaming, Ronald, Abdellaoui, Abdel, Ahluwalia, Tarunveer S., Bacelis, Jonas, Baumbach, Clemens, Bjornsdottir, Gyda, Brandsma, Johannes H., Concas, Maria Pina, Derringer, Jaime, Furlotte, Nicholas A., Galesloot, Tessel E., Girotto, Giorgia, Gupta, Richa, Hall, Leanne M., Harris, Sarah E. ... Benjamin, Daniel J. (2016). Genome-wide association study identifies 74 loci associated with educational attainment. Nature, 533 (7604), 539-542. doi: 10.1038/nature17671

  • Evidence for genetic overlap between schizophrenia and age at first birth in women

    Mehta, Divya, Tropf, Felix C., Gratten, Jacob, Bakshi, Andrew, Zhu, Zhihong, Bacanu, Silviu-Alin, Hemani, Gibran, Magnusson, Patrik K. E., Barban, Nicola, Esko, Tonu, Metspalu, Andres, Snieder, Harold, Mowry, Bryan J., Kendler, Kenneth S., Yang, Jian, Visscher, Peter M., McGrath, John J., Mills, Melinda C., Wray, Naomi R. and Lee, S. Hong (2016). Evidence for genetic overlap between schizophrenia and age at first birth in women. Jama Psychiatry, 73 (5), 497-505. doi: 10.1001/jamapsychiatry.2016.0129

  • Small non-coding RNA expression from anterior cingulate cortex in schizophrenia shows sex specific regulation

    Ragan, Chikako, Patel, Kalpana, Edson, Janette, Zhang, Zong-Hong, Gratten, Jacob and Mowry, Bryan (2016). Small non-coding RNA expression from anterior cingulate cortex in schizophrenia shows sex specific regulation. Schizophrenia Research, 183, 82-87. doi: 10.1016/j.schres.2016.11.024

  • Mapping and differential expression analysis from short-read RNA-Seq data in model organisms

    Zhao, Qiong-Yi, Gratten, Jacob, Restaudi, Restuadi and Li, Xuan (2016). Mapping and differential expression analysis from short-read RNA-Seq data in model organisms. Quantitative Biology, 4 (1), 22-35. doi: 10.1007/s40484-016-0060-7

  • Heterogeneity of genetic architecture of body size traits in a free-living population

    Berenos, Camillo, Ellis, Philip A., Pilkington, Jill G., Lee, S. Hong, Gratten, Jake and Pemberton, Josephine M. (2015). Heterogeneity of genetic architecture of body size traits in a free-living population. Molecular Ecology, 24 (8), 1810-1830. doi: 10.1111/mec.13146

  • Biological insights from 108 schizophrenia-associated genetic loci

    Schizophrenia Working Group of the Psychiatric Genomics Consortium, Catts, Stanley V., Gratten, Jacob, Lee, S. Hong, Wray, Naomi R., Visscher, Peter M., Mowry, Bryan J., Nertney, Deborah A., Psychosis Endophenotypes International Consortium and Wellcome Trust Case-Control Consortium 2 (2014). Biological insights from 108 schizophrenia-associated genetic loci. Nature, 511 (7510), 421-427. doi: 10.1038/nature13595

  • Large-scale genomics unveils the genetic architecture of psychiatric disorders

    Gratten, Jacob, Wray, Naomi R., Keller, Matthew C. and Visscher, Peter M. (2014). Large-scale genomics unveils the genetic architecture of psychiatric disorders. Nature Neuroscience, 17 (6), 782-790. doi: 10.1038/nn.3708

  • Life history trade-offs at a single locus maintain sexually selected genetic variation

    Johnston, Susan E., Gratten, Jacob, Berenos, Camillo, Pilkington, Jill G., Clutton-Brock, Tim H., Pemberton, Josephine M. and Slate, Jon (2013). Life history trade-offs at a single locus maintain sexually selected genetic variation. Nature, 502 (7469), 93-95. doi: 10.1038/nature12489

  • Comparing schizophrenia symptoms in the Iban of Sarawak with other populations to elucidate clinical heterogeneity

    McLean, Duncan, Barrett, Robert, Loa, Peter, Thara, Rangaswamy, John, Sujit, McGrath, John, Gratten, Jake and Mowry, Bryan (2013). Comparing schizophrenia symptoms in the Iban of Sarawak with other populations to elucidate clinical heterogeneity. Asia-Pacific Psychiatry, 7 (1), 36-44. doi: 10.1111/appy.12093

  • Introgression and the fate of domesticated genes in a wild mammal population

    Feulner, Philine G. D., Gratten, Jacob, Kijas, James W., Visscher, Peter M., Pemberton, Josephine M. and Slate, Jon (2013). Introgression and the fate of domesticated genes in a wild mammal population. Molecular Ecology, 22 (16), 4210-4221. doi: 10.1111/mec.12378

  • Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease

    Gratten, Jacob, Visscher, Peter M., Mowry, Bryan J. and Wray, Naomi R. (2013). Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease. Nature Genetics, 45 (3), 234-238. doi: 10.1038/ng.2555

  • Selection and microevolution of coat pattern are cryptic in a wild population of sheep

    Gratten, J., Pilkington, J. G., Brown, E. A., Clutton-Brock, T. H., Pemberton, J. M. and Slate, J. (2012). Selection and microevolution of coat pattern are cryptic in a wild population of sheep. Molecular Ecology, 21 (12), 2977-2990. doi: 10.1111/j.1365-294X.2012.05536.x

  • The emerging spectrum of allelic variation in schizophrenia: current evidence and strategies for the identification and functional characterization of common and rare variants

    Mowry, B. J. and Gratten, J. (2012). The emerging spectrum of allelic variation in schizophrenia: current evidence and strategies for the identification and functional characterization of common and rare variants. Molecular Psychiatry, 18 (1), 38-52. doi: 10.1038/mp.2012.34

  • Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

    Santure, Anna W., Gratten, Jake, Mossman, Jim A., Sheldon, Ben C. and Slate, Jon (2011). Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics, 12 (15) 283, 283.1-283.18. doi: 10.1186/1471-2164-12-283

  • No evidence for warming climate theory of coat colour change in Soay sheep: A comment on Maloney et al.

    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

  • Mapping quantitative trait loci in a wild population using linkage and linkage disequilibrium analyses

    Hernandez-Sanchez, J., Chatzipli, A., Beraldi, D., Gratten, J., Pilkington, J. G. and Pemberton, J. M. (2010). Mapping quantitative trait loci in a wild population using linkage and linkage disequilibrium analyses. Genetics Research, 92 (4), 273-281. doi: 10.1017/S0016672310000340

  • Genome mapping in intensively studied wild vertebrate populations

    Slate, Jon, Santure, Anna W., Feulner, Philine G. D., Brown, Emily A., Ball, Alex D., Johnston, Susan E. and Gratten, Jake (2010). Genome mapping in intensively studied wild vertebrate populations. Trends in Genetics, 26 (6), 275-284. doi: 10.1016/j.tig.2010.03.005

  • Erratum to: Gene mapping in the wild with SNPs: Guidelines and future directions (Genetica, (2009), 136, (97-107), 10.1007/s10709-008-9317-z)

    Slate, Jon, Gratten, Jake, Beraldi, Dario, Stapley, Jessica, Hale, Matt and Pemberton, Josephine M. (2010). Erratum to: Gene mapping in the wild with SNPs: Guidelines and future directions (Genetica, (2009), 136, (97-107), 10.1007/s10709-008-9317-z). Genetica, 138 (4), 467-467. doi: 10.1007/s10709-010-9445-0

  • The genetic basis of recessive self colour pattern in a wild sheep population

    Gratten, J., Pilkington, J. G., Brown, E. A., Beraldi, D., Pemberton, J. M. and Slate, J. (2010). The genetic basis of recessive self colour pattern in a wild sheep population. Heredity, 104 (2), 206-214. doi: 10.1038/hdy.2009.105

  • Gene mapping in the wild with SNPs: Guidelines and future directions

    Slate, Jon, Gratten, Jake, Beraldi, Dario, Stapley, Jessica, Hale, Matt and Pemberton, Josephine M. (2009). Gene mapping in the wild with SNPs: Guidelines and future directions. Genetica, 136 (1), 97-107. doi: 10.1007/s10709-008-9317-z

  • Multiplex SNP-SCALE: A cost-effective medium-throughput SNP genotyping method

    Kenta, T., Gratten, J., Haigh, N. S., Hinten, G. N., Slate, J., Butlin, R. K. and Burke, T. (2008). Multiplex SNP-SCALE: A cost-effective medium-throughput SNP genotyping method. Molecular Ecology Resources, 8 (6), 1230-1238. doi: 10.1111/j.1755-0998.2008.02190.x

  • 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

  • Molecular assessment of the genetic integrity, distinctiveness and phylogeographic context of the Saltwater crocodile (Crocodylus porosus) on Palau

    Russello, M. A., Brazaitis, P., Gratten, J., Watkins-Colwell, G. J. and Caccone, A. (2007). Molecular assessment of the genetic integrity, distinctiveness and phylogeographic context of the Saltwater crocodile (Crocodylus porosus) on Palau. Conservation Genetics, 8 (4), 777-787. doi: 10.1007/s10592-006-9225-7

  • 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

  • SNP-SCALE: SNP scoring by colour and length exclusion

    Hinten, G. N., Hale, M. C., Gratten, J., Mossman, J. A., Lowder, B. V., Mann, M. K. and Slate, J. (2007). SNP-SCALE: SNP scoring by colour and length exclusion. Molecular Ecology Notes, 7 (3), 377-388. doi: 10.1111/j.1471-8286.2006.01648.x

  • Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour polymorphism in a free-living population of Soay sheep

    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

  • Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries)

    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

  • Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries)

    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

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Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • Cellular genomics of Parkinson's disease

    We are seeking a highly motivated PhD candidate with a background and interest in human genomics, statistics and neurodegenerative disease to join the Cognitive Health Genomics group at the Mater Research Institute, UQ. The successful candidate would work on an NHMRC-funded study to identify selectively vulnerable neuronal and/or glial cell types across the spatial and temporal course of Parkinson’s disease using single cell approaches.

    Project description

    Parkinson’s disease (PD) is a complex neurodegenerative condition affecting 1% of Australians aged ≥60-years. There is no cure, and the number of affected individuals is rising steeply as populations age. Understanding the genetic basis of PD is critical to developing new therapeutics to counter the growing disease burden. Large-scale genome-wide association studies (GWAS) of PD have identified nearly 100 risk loci, but interpretation of these findings remains challenging; we do not yet know the identity of most PD risk genes, nor the specific cell types in which they act, nor when they act during the course of disease, which hampers efforts to identify targets for interventions. We will address these challenges by using single nucleus RNA-seq to identify cell types involved in the onset and progression of Lewy body pathology in PD-related brain regions.

    Requirements

    • Bachelor’s degree with first class honours, or Masters, in statistics, mathematics, bioinformatics, human genetics, animal breeding, or an equivalent field.
    • Prior research experience in human genomics or animal breeding, including a familiarity with high-throughput genomic data and working in a high-performance computing environment.
    • Skills in the R statistical computing language and/or python, C++ or an equivalent computing language.
    • High degree of motivation and organisation, and an ability to work both independently and as part of a team.
    • (Co-)authorship on at least one peer-reviewed publication (for International applicants)
    • Excellent written and oral communications skills in English.

    For further information please contact Dr Jake Gratten, jacob.gratten@mater.uq.edu.au, +61-7-34437585.

For Media assistance please contact The Office of Marketing and Communications, (07) 3365 1120

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ResearcherID: G-1485-2011

ORCID: 0000-0003-1293-409X

Scopus ID: 16063667500

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