Professor Leonard Schalkwyk
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Email
lschal@essex.ac.uk -
Telephone
+44 (0) 1206 873322
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Location
3SW.4.34, Colchester Campus
Profile
Biography
Originally a microbiologist from Canada, Leo studied at the University of Alberta, graduating in 1983. His PhD (Dalhousie University, 1991) was on genome mapping of Haloferax, an archaeon from the Dead Sea. He worked on genomic resources for several species and genome mapping of mouse in Hans Lehrach's laboratory at the Imperial Cancer Research Fund laboratory in London and at the Max-Planck-Institut für molekulare Genetik in Berlin. He was at the Social, Genetic and Developmental Psychiatry Research Centre, Kings College London from 2000-2014, where he worked on functional genomics and epigenomics, identifying genes involved in behaviour in the mouse and in depression, schizophrenia and Alzheimers disease in human. His research programme now includes epigenomics methods and environmental epigenomics as well as psychiatric epigenetics.
Qualifications
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1991 PhD in Biochemistry, Dalhousie University. Studies on the structure of the genome of Haloferax volcanii
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1983 BSc in Microbiology, University of Alberta
Appointments
University of Essex
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Professor of Human Genetics, School of Biological Sciences, University of Essex (1/10/2014 - present)
Other academic
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Visiting Professor, SGDP, Institute of Psychiatry, Psychology and Neuroscience, King's College London (1/10/2014 - 30/9/2020)
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Reader in Functional Genomics, SGDP, Institute of Psychiatry, King's College London (1/1/2004 - 30/9/2014)
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Senior Lecturer in Molecular Genetics, SGDP, Institute of Psychiatry, King's College London (1/4/2000 - 31/12/2018)
Research and professional activities
Research interests
Genomic and epigenomic methods and software
Epigenomics and the environment
Alzheimers disease
Schizophrenia
Current research
DNA methylation profiles in human blood and brain, methods and software for epigenomic studies.
Conferences and presentations
Epigenetics Meets Social Neuroscience of Human Attachment
Keynote presentation, Organised one-day hybrid conference with about 100 participants, Colchester, United Kingdom, 5/7/2022
Functional Genomics and Epigenomics in Alzheimer’s disease
Invited presentation, Keynote presentation, ARUK East Network Scientific Meeting 2019, Cambridge, United Kingdom, 22/11/2019
Teaching and supervision
Previous supervision
Degree subject: Computer Science
Degree type: Doctor of Philosophy
Awarded date: 30/6/2023
Degree subject: Biological Sciences
Degree type: Doctor of Philosophy
Awarded date: 15/5/2023
Degree subject: Biosocial Research
Degree type: Doctor of Philosophy
Awarded date: 22/11/2022
Degree subject: Biochemistry
Degree type: Doctor of Philosophy
Awarded date: 8/10/2019
Degree subject: Biological Sciences
Degree type: Master of Science (by Dissertation)
Awarded date: 5/2/2018
Publications
Publications (2)
Grant, OA., Kumari, M., Schalkwyk, L. and Zabet, NR., (2024). Systematic investigation of interindividual variation of DNA methylation in human whole blood
Wang, Y., Grant, OA., Zhai, X., McDonald-Maier, KD. and Schalkwyk, LC., (2022). Recalibrating the cerebellum DNA methylation clock: implications for ageing rates comparison
Journal articles (179)
Hannon, E., Dempster, EL., Davies, JP., Chioza, B., Blake, GET., Burrage, J., Policicchio, S., Franklin, A., Walker, EM., Bamford, RA., Schalkwyk, LC. and Mill, J., (2024). Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles. BMC Biology. 22 (1), 17-
Devall, M., Soanes, DM., Smith, AR., Dempster, EL., Smith, RG., Burrage, J., Iatrou, A., Hannon, E., Troakes, C., Moore, K., O'Neill, P., Al-Sarraj, S., Schalkwyk, L., Mill, J., Weedon, M. and Lunnon, K., (2023). Genome-wide characterization of mitochondrial DNA methylation in human brain.. Frontiers in Endocrinology. 13, 1059120-
Wang, Y., Grant, O., Zhai, X., McDonald-Maier, K. and Schalkwyk, L., (2023). Insights into ageing rates comparison across tissues from recalibrating cerebellum DNA methylation clock. GeroScience. 46 (1), 39-56
Vellame, DS., Shireby, G., MacCalman, A., Dempster, EL., Burrage, J., Gorrie-Stone, T., Schalkwyk, LS., Mill, J. and Hannon, E., (2023). Uncertainty quantification of reference-based cellular deconvolution algorithms.. Epigenetics. 18 (1), 1217-1254
Flynn, R., Washer, S., Jeffries, AR., Andrayas, A., Shireby, G., Kumari, M., Schalkwyk, LC., Mill, J. and Hannon, E., (2022). Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays. Human Molecular Genetics. 31 (18), 3181-3190
Wang, Y., Gorrie-Stone, TJ., Grant, OA., Andrayas, AD., Zhai, X., McDonald-Maier, KD. and Schalkwyk, LC., (2022). InterpolatedXY: a two-step strategy to normalise DNA methylation microarray data avoiding sex bias. Bioinformatics. 38 (16), 3950-3957
Grant, OA., Wang, Y., Kumari, M., Zabet, NR. and Schalkwyk, L., (2022). Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array.. Clinical Epigenetics. 14 (1), 62-
Bao, Y., Gorrie-Stone, T., Hannon, E., Hughes, A., Andrayas, A., Neilson, G., Burrage, J., Mill, J., Schalkwyk, L. and Kumari, M., (2022). Social mobility across the lifecourse and DNA methylation age acceleration in adults in the UK.. Scientific Reports. 12 (1), 22284-22284
Smith, RG., Pishva, E., Shireby, G., Smith, AR., Roubroeks, JAY., Hannon, E., Wheildon, G., Mastroeni, D., Gasparoni, G., Riemenschneider, M., Giese, A., Sharp, AJ., Schalkwyk, L., Haroutunian, V., Viechtbauer, W., van den Hove, DLA., Weedon, M., Brokaw, D., Francis, PT., Thomas, AJ., Love, S., Morgan, K., Walter, J., Coleman, PD., Bennett, DA., De Jager, PL., Mill, J. and Lunnon, K., (2021). A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex.. Nature Communications. 12 (1), 3517-
Min, JL., Hemani, G., Kumari, M., Schalkwyk, LC. and et al, (2021). Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. Nature Genetics. 53 (9), 1311-1321
Hannon, E., Dempster, EL., Mansell, G., Burrage, J., Bass, N., Bohlken, MM., Corvin, A., Curtis, CJ., Dempster, D., Di Forti, M., Dinan, TG., Donohoe, G., Gaughran, F., Gill, M., Gillespie, A., Gunasinghe, C., Hulshoff, HE., Hultman, CM., Johansson, V., Kahn, RS., Kaprio, J., Kenis, G., Kowalec, K., MacCabe, J., McDonald, C., McQuillin, A., Morris, DW., Murphy, KC., Mustard, CJ., Nenadic, I., O'Donovan, MC., Quattrone, D., Richards, AL., Rutten, BP., St Clair, D., Therman, S., Toulopoulou, T., Van Os, J., Waddington, JL., Wellcome Trust Case Control Consortium (WTCCC), CRESTAR consortium, Sullivan, P., Vassos, E., Breen, G., Collier, DA., Murray, RM., Schalkwyk, LS. and Mill, J., (2021). DNA methylation meta-analysis reveals cellular alterations in psychosis and markers of treatment-resistant schizophrenia.. eLife. 10, 1-53
Wang, Y., Hannon, E., Grant, O., Gorrie-Stone, T., Kumari, M., Mill, J., Zhai, X., McDonald-Maier, K. and Schalkwyk, L., (2021). DNA methylation-based sex classifier to predictsex and identify sex chromosome aneuploidy. BMC Genomics. 22 (1), 484-
Leung, SK., Jeffries, AR., Castanho, I., Jordan, BT., Moore, K., Davies, JP., Dempster, EL., Bray, NJ., O'Neill, P., Tseng, E., Ahmed, Z., Collier, DA., Jeffery, ED., Prabhakar, S., Schalkwyk, L., Jops, C., Gandal, MJ., Sheynkman, GM., Hannon, E. and Mill, J., (2021). Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing.. Cell Reports. 37 (7), 110022-110022
Åsenius, F., Gorrie-Stone, TJ., Brew, A., Panchbhaya, Y., Williamson, E., Schalkwyk, LC., Rakyan, VK., Holland, ML., Marzi, SJ. and Williams, DJ., (2020). The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations. PLoS Genetics. 16 (10), e1009035-e1009035
Shireby, GL., Davies, JP., Francis, PT., Burrage, J., Walker, EM., Neilson, GWA., Dahir, A., Thomas, AJ., Love, S., Smith, RG., Lunnon, K., Kumari, M., Schalkwyk, LC., Morgan, K., Brookes, K., Hannon, E. and Mill, J., (2020). Recalibrating the epigenetic clock: implications for assessing biological age in the human cortex.. Brain: a journal of neurology. 143 (12), 3763-3775
Åsenius, F., Gorrie-Stone, TJ., Brew, A., Panchbaya, Y., Williamson, E., Schalkwyk, LC., Rakyan, VK., Holland, ML., Marzi, SJ. and Williams, DJ., (2020). DNA methylation covariation in human whole blood and sperm: implications for studies of intergenerational epigenetic effects
Gorrie-Stone, TJ., Smart, MC., Saffari, A., Malki, K., Hannon, E., Burrage, J., Mill, J., Kumari, M. and Schalkwyk, LC., (2019). Bigmelon: tools for analysing large DNA methylation datasets. Bioinformatics. 35 (6), 981-986
Hannon, E., Marzi, SJ., Schalkwyk, LS. and Mill, J., (2019). Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains. Molecular Brain. 12 (1), 7-
Hughes, A., Bao, Y., Smart, M., Gorrie-Stone, T., Hannon, E., Mill, J., Burrage, J., Schalkwyk, L. and Kumari, M., (2019). THE AUTHORS REPLY. American Journal of Epidemiology. 188 (2), 488-489
Mansell, G., Gorrie-Stone, TJ., Bao, Y., Kumari, M., Schalkwyk, LS., Mill, J. and Hannon, E., (2019). Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics. 20 (1), 366-
Wong, CCY., Smith, RG., Hannon, E., Ramaswami, G., Parikshak, NN., Assary, E., Troakes, C., Poschmann, J., Schalkwyk, LC., Sun, W., Prabhakar, S., Geschwind, DH. and Mill, J., (2019). Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue. Human Molecular Genetics. 28 (13), 2201-2211
Bell, CG., Lowe, R., Adams, PD., Baccarelli, AA., Beck, S., Bell, JT., Christensen, BC., Gladyshev, VN., Heijmans, BT., Horvath, S., Ideker, T., Issa, J-PJ., Kelsey, KT., Marioni, RE., Reik, W., Relton, CL., Schalkwyk, LC., Teschendorff, AE., Wagner, W., Zhang, K. and Rakyan, VK., (2019). DNA methylation aging clocks: challenges and recommendations. Genome Biology. 20 (1), 249-
El Khoury, LY., Gorrie-Stone, TJ., Smart, M., Hughes, A., Bao, Y., Andrayas, A., Burrage, J., Hannon, E., Kumari, M., Mill, J. and Schalkwyk, L., (2019). Systematic under-estimation of the epigenetic clock and age acceleration in older subjects. Genome Biology. 20 (1), 283-
Saffari, A., Arno, M., Nasser, E., Ronald, A., Wong, CCY., Schalkwyk, LC., Mill, J., Dudbridge, F. and Meaburn, EL., (2019). RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation.. Molecular Autism. 10 (1), 38-38
Rutten, BPF., Vermetten, E., Vinkers, CH., Ursini, G., Daskalakis, NP., Pishva, E., de Nijs, L., Houtepen, LC., Eijssen, L., Jaffe, AE., Kenis, G., Viechtbauer, W., van den Hove, D., Schraut, KG., Lesch, K-P., Kleinman, JE., Hyde, TM., Weinberger, DR., Schalkwyk, L., Lunnon, K., Mill, J., Cohen, H., Yehuda, R., Baker, DG., Maihofer, AX., Nievergelt, CM., Geuze, E. and Boks, MPM., (2018). Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder. Molecular Psychiatry. 23 (5), 1145-1156
Smith, RG., Hannon, E., De Jager, PL., Chibnik, L., Lott, SJ., Condliffe, D., Smith, AR., Haroutunian, V., Troakes, C., Al-Sarraj, S., Bennett, DA., Powell, J., Lovestone, S., Schalkwyk, L., Mill, J. and Lunnon, K., (2018). Elevated DNA methylation across a 48-kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology. Alzheimer's and Dementia. 14 (12), 1580-1588
Hughes, A., Smart, M., Gorrie-Stone, T., Hannon, E., Mill, J., Bao, Y., Burrage, J., Schalkwyk, L. and Kumari, M., (2018). Socioeconomic Position and DNA Methylation Age Acceleration across the Lifecourse.. American Journal of Epidemiology. 187 (11), 2346-2354
Hannon, E., Gorrie-Stone, TJ., Smart, MC., Burrage, J., Hughes, A., Bao, Y., Kumari, M., Schalkwyk, LC. and Mill, J., (2018). Leveraging DNA-Methylation Quantitative-Trait Loci to Characterize the Relationship between Methylomic Variation, Gene Expression, and Complex Traits. The American Journal of Human Genetics. 103 (5), 654-665
Marzi, SJ., Leung, SK., Ribarska, T., Hannon, E., Smith, AR., Pishva, E., Poschmann, J., Moore, K., Troakes, C., Al-Sarraj, S., Beck, S., Newman, S., Lunnon, K., Schalkwyk, LC. and Mill, J., (2018). A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex. Nature Neuroscience. 21 (11), 1618-1627
O’Brien, HE., Hannon, E., Hill, MJ., Toste, CC., Robertson, MJ., Morgan, JE., McLaughlin, G., Lewis, CM., Schalkwyk, LC., Hall, LS., Pardiñas, AF., Owen, MJ., O’Donovan, MC., Mill, J. and Bray, NJ., (2018). Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders. Genome Biology. 19 (1), 194-
Viana, J., Hannon, E., Dempster, E., Pidsley, R., Macdonald, R., Knox, O., Spiers, H., Troakes, C., Al-Saraj, S., Turecki, G., Schalkwyk, LC. and Mill, J., (2017). Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions. Human Molecular Genetics. 26 (1), 210-225
Malki, K., Tosto, MG., Mouriño‐Talín, H., Rodríguez‐Lorenzo, S., Pain, O., Jumhaboy, I., Liu, T., Parpas, P., Newman, S., Malykh, A., Carboni, L., Uher, R., McGuffin, P., Schalkwyk, LC., Bryson, K. and Herbster, M., (2017). Highly polygenic architecture of antidepressant treatment response: Comparative analysis of SSRI and NRI treatment in an animal model of depression. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 174 (3), 235-250
Janecka, M., Marzi, SJ., Parsons, MJ., Liu, L., Paya-Cano, JL., Smith, RG., Fernandes, C. and Schalkwyk, LC., (2017). Genetic polymorphisms and their association with brain and behavioural measures in heterogeneous stock mice. Scientific Reports. 7 (1), 41204-
Janecka, M., Mill, J., Basson, MA., Goriely, A., Spiers, H., Reichenberg, A., Schalkwyk, LC. and Fernandes, C., (2017). Advanced paternal age effects in neurodevelopmental disorders?review of potential underlying mechanisms. Translational Psychiatry. 7 (1), e1019-e1019
Janecka, M., Haworth, CMA., Ronald, A., Krapohl, E., Happé, F., Mill, J., Schalkwyk, LC., Fernandes, C., Reichenberg, A. and Rijsdijk, F., (2017). Paternal Age Alters Social Development in Offspring. Journal of the American Academy of Child & Adolescent Psychiatry. 56 (5), 383-390
Lunnon, K., Keohane, A., Pidsley, R., Newhouse, S., Riddoch-Contreras, J., Thubron, EB., Devall, M., Soininen, H., Kłoszewska, I., Mecocci, P., Tsolaki, M., Vellas, B., Schalkwyk, L., Dobson, R., Malik, AN., Powell, J., Lovestone, S. and Hodges, A., (2017). Mitochondrial genes are altered in blood early in Alzheimer's disease. Neurobiology of Aging. 53, 36-47
Devall, M., Smith, RG., Jeffries, A., Hannon, E., Davies, MN., Schalkwyk, L., Mill, J., Weedon, M. and Lunnon, K., (2017). Regional differences in mitochondrial DNA methylation in human post-mortem brain tissue. Clinical Epigenetics. 9 (1), 47-
Spiers, H., Hannon, E., Schalkwyk, LC., Bray, NJ. and Mill, J., (2017). 5-hydroxymethylcytosine is highly dynamic across human fetal brain development. BMC Genomics. 18 (1), 738-
Smith, AR., Smith, RG., Condliffe, D., Hannon, E., Schalkwyk, L., Mill, J. and Lunnon, K., (2016). Increased DNA methylation near TREM2 is consistently seen in the superior temporal gyrus in Alzheimer's disease brain. Neurobiology of Aging. 47, 35-40
Hannon, E., Dempster, E., Viana, J., Burrage, J., Smith, AR., Macdonald, R., St Clair, D., Mustard, C., Breen, G., Therman, S., Kaprio, J., Toulopoulou, T., Pol, HEH., Bohlken, MM., Kahn, RS., Nenadic, I., Hultman, CM., Murray, RM., Collier, DA., Bass, N., Gurling, H., McQuillin, A., Schalkwyk, L. and Mill, J., (2016). An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation. Genome Biology. 17 (1), 176-
Lunnon, K., Hannon, E., Smith, RG., Dempster, E., Wong, C., Burrage, J., Troakes, C., Al-Sarraj, S., Kepa, A., Schalkwyk, L. and Mill, J., (2016). Variation in 5-hydroxymethylcytosine across human cortex and cerebellum. Genome Biology. 17 (1), 27-
Carter, KW., Carter, KW., Francis, RW., Bresnahan, M., Gissler, M., Grønborg, TK., Gross, R., Gunnes, N., Hammond, G., Hornig, M., Hultman, CM., Huttunen, J., Langridge, A., Leonard, H., Newman, S., Parner, ET., Petersson, G., Reichenberg, A., Sandin, S., Schendel, DE., Schalkwyk, L., Sourander, A., Steadman, C., Stoltenberg, C., Suominen, A., Surén, P., Susser, E., Sylvester Vethanayagam, A. and Yusof, Z., (2016). ViPAR: a software platform for the Virtual Pooling and Analysis of Research Data. International Journal of Epidemiology. 45 (2), 408-416
Malki, K., Du Rietz, E., Crusio, WE., Pain, O., Paya‐Cano, J., Karadaghi, RL., Sluyter, F., de Boer, SF., Sandnabba, K., Schalkwyk, LC., Asherson, P. and Tosto, MG., (2016). Transcriptome analysis of genes and gene networks involved in aggressive behavior in mouse and zebrafish. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics. 171 (6), 827-838
Houtepen, LC., Vinkers, CH., Carrillo-Roa, T., Hiemstra, M., Van Lier, PA., Meeus, W., Branje, S., Heim, CM., Nemeroff, CB., Mill, J., Schalkwyk, LC., Creyghton, MP., Kahn, RS., Joëls, M., Binder, EB. and Boks, MPM., (2016). Genome-wide DNA methylation levels and altered cortisol stress reactivity following childhood trauma in humans. Nature Communications. 7 (1), creators-Schalkwyk=3ALeonard_C=3A=3A
Hannon, E., Spiers, H., Viana, J., Pidsley, R., Burrage, J., Murphy, TM., Troakes, C., Turecki, G., O'Donovan, MC., Schalkwyk, LC., Bray, NJ. and Mill, J., (2016). Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. Nature Neuroscience. 19 (1), 48-54
Malki, K., Tosto, MG., Pain, O., Sluyter, F., Mineur, YS., Crusio, WE., de Boer, S., Sandnabba, KN., Kesserwani, J., Robinson, E., Schalkwyk, LC. and Asherson, P., (2016). Comparative mRNA analysis of behavioral and genetic mouse models of aggression. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics. 171 (3), 427-436
Marzi, SJ., Meaburn, EL., Dempster, EL., Lunnon, K., Paya-Cano, JL., Smith, RG., Volta, M., Troakes, C., Schalkwyk, LC. and Mill, J., (2016). Tissue-specific patterns of allelically-skewed DNA methylation. Epigenetics. 11 (1), 24-35
Hannon, E., Lunnon, K., Schalkwyk, L. and Mill, J., (2015). Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. Epigenetics. 10 (11), 1024-1032
Elliott, G., Hong, C., Xing, X., Zhou, X., Li, D., Coarfa, C., Bell, RJA., Maire, CL., Ligon, KL., Sigaroudinia, M., Gascard, P., Tlsty, TD., Harris, RA., Schalkwyk, LC., Bilenky, M., Mill, J., Farnham, PJ., Kellis, M., Marra, MA., Milosavljevic, A., Hirst, M., Stormo, GD., Wang, T. and Costello, JF., (2015). Intermediate DNA methylation is a conserved signature of genome regulation. Nature Communications. 6 (1), creators-Schalkwyk=3ALeonard_C=3A=3A
Janecka, M., Manduca, A., Servadio, M., Trezza, V., Smith, R., Mill, J., Schalkwyk, LC., Reichenberg, A. and Fernandes, C., (2015). Effects of advanced paternal age on trajectories of social behavior in offspring. Genes, Brain and Behavior. 14 (6), 443-453
Malki, K., Pain, O., Tosto, MG., Du Rietz, E., Carboni, L. and Schalkwyk, LC., (2015). Identification of genes and gene pathways associated with major depressive disorder by integrative brain analysis of rat and human prefrontal cortex transcriptomes. Translational Psychiatry. 5 (3), e519-e519
Martin, C., Tansey, KE., Schalkwyk, LC. and Powell, TR., (2015). The inflammatory cytokines: molecular biomarkers for major depressive disorder?. Biomarkers in Medicine. 9 (2), 169-180
Malki, K., Mineur, YS., Tosto, MG., Campbell, J., Karia, P., Jumabhoy, I., Sluyter, F., Crusio, WE. and Schalkwyk, LC., (2015). Pervasive and opposing effects of Unpredictable Chronic Mild Stress (UCMS) on hippocampal gene expression in BALB/cJ and C57BL/6J mouse strains. BMC Genomics. 16 (1), 262-
Spiers, H., Hannon, E., Schalkwyk, LC., Smith, R., Wong, CCY., O’Donovan, MC., Bray, NJ. and Mill, J., (2015). Methylomic trajectories across human fetal brain development. Genome Research. 25 (3), 338-352
Boks, MP., Mierlo, HCV., Rutten, BPF., Radstake, TRDJ., De Witte, L., Geuze, E., Horvath, S., Schalkwyk, LC., Vinkers, CH., Broen, JCA. and Vermetten, E., (2015). Longitudinal changes of telomere length and epigenetic age related to traumatic stress and post-traumatic stress disorder. Psychoneuroendocrinology. 51, 506-512
Ilott, NE., Schneider, T., Mill, J., Schalkwyk, L., Brolese, G., Bizarro, L., Stolerman, IP., Dempster, E. and Asherson, P., (2014). Long-term effects of gestational nicotine exposure and food-restriction on gene expression in the striatum of adolescent rats. PLoS ONE. 9 (2), creators-Schalkwyk=3ALeonard_C=3A=3A
Condliffe, D., Wong, A., Troakes, C., Proitsi, P., Patel, Y., Chouliaras, L., Fernandes, C., Cooper, J., Lovestone, S., Schalkwyk, L., Mill, J. and Lunnon, K., (2014). Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain. Neurobiology of Aging. 35 (8), 1850-1854
Viana, J., Pidsley, R., Troakes, C., Spiers, H., Wong, CCY., Al-Sarraj, S., Craig, I., Schalkwyk, L. and Mill, J., (2014). Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain. Epigenetics. 9 (4), 587-599
Bell, JT., Loomis, AK., Butcher, LM., Gao, F., Zhang, B., Hyde, CL., Sun, J., Wu, H., Ward, K., Harris, J., Scollen, S., Davies, MN., Schalkwyk, LC., Mill, J., Williams, FMK., Li, N., Deloukas, P., Beck, S., McMahon, SB., Wang, J., John, SL. and Spector, TD., (2014). Differential methylation of the TRPA1 promoter in pain sensitivity. Nature Communications. 5 (1), 2978-
Wong, CCY., Meaburn, EL., Ronald, A., Price, TS., Jeffries, AR., Schalkwyk, LC., Plomin, R. and Mill, J., (2014). Methylomic analysis of monozygotic twins discordant for autism spectrum disorder and related behavioural traits. Molecular Psychiatry. 19 (4), 495-503
Pidsley, R., Viana, J., Hannon, E., Spiers, H., Troakes, C., Al-saraj, S., Mechawar, N., Turecki, G., Schalkwyk, LC., Bray, NJ. and Mill, J., (2014). Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia. Genome Biology. 15 (10), creators-Schalkwyk=3ALeonard_C=3A=3A
Malki, K., Pain, O., Du Rietz, E., Tosto, MG., Paya-Cano, J., Sandnabba, KN., de Boer, S., Schalkwyk, LC. and Sluyter, F., (2014). Genes and Gene Networks Implicated in Aggression Related Behaviour. neurogenetics. 15 (4), 255-266
Powell, TR., McGuffin, P., D'Souza, UM., Cohen-Woods, S., Hosang, GM., Martin, C., Matthews, K., Day, RK., Farmer, AE., Tansey, KE. and Schalkwyk, LC., (2014). Putative transcriptomic biomarkers in the inflammatory cytokine pathway differentiate major depressive disorder patients from control subjects and bipolar disorder patients. PLoS ONE. 9 (3), creators-Schalkwyk=3ALeonard_C=3A=3A
Tarantino, LM. and Schalkwyk, LC., (2014). Introduction to mammalian genome special issue: genetics of behavior. Mammalian Genome. 25 (1-2), 1-2
Powell, TR., Powell‐Smith, G., Haddley, K., Mcguffin, P., Quinn, J., Schalkwyk, LC., Farmer, AE. and D'Souza, UM., (2014). Mood‐stabilizers differentially affect housekeeping gene expression in human cells. International Journal of Methods in Psychiatric Research. 23 (2), 279-288
Malki, K., Keers, R., Tosto, MG., Lourdusamy, A., Carboni, L., Domenici, E., Uher, R., McGuffin, P. and Schalkwyk, LC., (2014). The endogenous and reactive depression subtypes revisited: integrative animal and human studies implicate multiple distinct molecular mechanisms underlying major depressive disorder. BMC Medicine. 12 (1), 73-
Smith, RG., Fernandes, C., Kember, R., Schalkwyk, LC., Buxbaum, J., Reichenberg, A. and Mill, J., (2014). Transcriptomic changes in the frontal cortex associated with paternal age. Molecular Autism. 5 (1), creators-Schalkwyk=3ALeonard_C=3A=3A
Lunnon, K., Smith, R., Hannon, E., De Jager, PL., Srivastava, G., Volta, M., Troakes, C., Al-Sarraj, S., Burrage, J., Macdonald, R., Condliffe, D., Harries, LW., Katsel, P., Haroutunian, V., Kaminsky, Z., Joachim, C., Powell, J., Lovestone, S., Bennett, DA., Schalkwyk, LC. and Mill, J., (2014). Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease. Nature Neuroscience. 17 (9), 1164-1170
Punapart, M., Eltermaa, M., Oflijan, J., Sütt, S., Must, A., Kõks, S., Schalkwyk, LC., Fernandes, C., Vasar, E., Soomets, U. and Terasmaa, A., (2014). Effect of chronic valproic Acid treatment on hepatic gene expression profile in wfs1 knockout mouse. PPAR Research. 2014, 1-11
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Smith, RG., Reichenberg, A., Kember, RL., Buxbaum, JD., Schalkwyk, LC., Fernandes, C. and Mill, J., (2013). Advanced paternal age is associated with altered DNA methylation at brain-expressed imprinted loci in inbred mice: implications for neuropsychiatric disease. Molecular Psychiatry. 18 (6), 635-636
Powell, TR., Smith, RG., Hackinger, S., Schalkwyk, LC., Uher, R., McGuffin, P., Mill, J. and Tansey, KE., (2013). DNA methylation in interleukin-11 predicts clinical response to antidepressants in GENDEP. Translational Psychiatry. 3 (9), e300-e300
Powell, TR., Tansey, KE., Breen, G., Farmer, AE., Craig, IW., Uher, R., McGuffin, P., D’Souza, UM. and Schalkwyk, LC., (2013). ATP-binding cassette sub-family F member 1 (ABCF1) is identified as a putative therapeutic target of escitalopram in the inflammatory cytokine pathway. Journal of Psychopharmacology. 27 (7), 609-615
Pidsley, R., Wong, CCY., Volta, M., Lunnon, K., Mill, J. and Schalkwyk, LC., (2013). A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics. 14 (1), 293-
Powell, TR., Schalkwyk, LC., Heffernan, AL., Breen, G., Lawrence, T., Price, T., Farmer, AE., Aitchison, KJ., Craig, IW., Danese, A., Lewis, C., McGuffin, P., Uher, R., Tansey, KE. and D'Souza, UM., (2013). Tumor necrosis factor and its targets in the inflammatory cytokine pathway are identified as putative transcriptomic biomarkers for escitalopram response. European Neuropsychopharmacology. 23 (9), 1105-1114
Navarrete, K., Pedroso, I., De Jong, S., Stefansson, H., Steinberg, S., Stefansson, K., Ophoff, RA., Schalkwyk, LC. and Collier, DA., (2013). TCF4 (e2-2; ITF2): a schizophrenia-associated gene with pleiotropic effects on human disease. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics. 162 (1), 1-16
Malki, K., Tosto, MG., Jumabhoy, I., Lourdusamy, A., Sluyter, F., Craig, I., Uher, R., McGuffin, P. and Schalkwyk, LC., (2013). Integrative Mouse and Human mRNA Studies Using WGCNA Nominates Novel Candidate Genes Involved in the Pathogenesis of Major Depressive Disorder. Pharmacogenomics. 14 (16), 1979-1990
Lill, M., Kõks, S., Soomets, U., Schalkwyk, LC., Fernandes, C., Lutsar, I. and Taba, P., (2013). Peripheral blood RNA gene expression profiling in patients with bacterial meningitis. Frontiers in Neuroscience. 7 (7), 33-
Kõks, S., Overall, RW., Ivask, M., Soomets, U., Guha, M., Vasar, E., Fernandes, C. and Schalkwyk, LC., (2013). Silencing of theWFS1gene in HEK cells induces pathways related to neurodegeneration and mitochondrial damage. Physiological Genomics. 45 (5), 182-190
Kember, RL., Dempster, EL., Lee, THA., Schalkwyk, LC., Mill, J. and Fernandes, C., (2012). Maternal separation is associated with strain‐specific responses to stress and epigenetic alterations to Nr3c1, Avp, and Nr4a1 in mouse. Brain and Behavior. 2 (4), 455-467
Pidsley, R., Fernandes, C., Viana, J., Paya-Cano, JL., Liu, L., Smith, RG., Schalkwyk, LC. and Mill, J., (2012). DNA methylation at the Igf2/H19 imprinting control region is associated with cerebellum mass in outbred mice. Molecular Brain. 5 (1), 42-
Davies, MN., Volta, M., Pidsley, R., Lunnon, K., Dixit, A., Lovestone, S., Coarfa, C., Harris, RA., Milosavljevic, A., Troakes, C., Al-Sarraj, S., Dobson, R., Schalkwyk, LC. and Mill, J., (2012). Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood. Genome Biology. 13 (6), R43-
Jeffries, AR., Perfect, LW., Ledderose, J., Schalkwyk, LC., Bray, NJ., Mill, J. and Price, J., (2012). Stochastic Choice of Allelic Expression in Human Neural Stem Cells. Stem Cells. 30 (9), 1938-1947
Parsons, MJ., Grimm, C., Paya-Cano, J., Fernandes, C., Liu, L., Philip, VM., Chesler, EJ., Nietfeld, W., Lehrach, H. and Schalkwyk, LC., (2012). Genetic variation in hippocampal microRNA expression differences in C57BL/6 J X DBA/2 J (BXD) recombinant inbred mouse strains. BMC Genomics. 13 (1), 476-
Keers, R., Pedroso, I., Breen, G., Aitchison, KJ., Nolan, PM., Cichon, S., Nöthen, MM., Rietschel, M., Schalkwyk, LC. and Fernandes, C., (2012). Reduced anxiety and depression-like behaviours in the circadian period mutant mouse afterhours. PLoS ONE. 7 (6), creators-Schalkwyk=3ALeonard_C=3A=3A
Malki, K., Lourdusamy, A., Binder, E., Payá-Cano, J., Sluyter, F., Craig, I., Keers, R., McGuffin, P., Uher, R. and Schalkwyk, LC., (2012). Antidepressant-dependent mRNA changes in mouse associated with hippocampal neurogenesis in a mouse model of depression. Pharmacogenetics and Genomics. 22 (11), 765-776
Malki, K., Campbell, J., Davies, M., Keers, R., Uher, R., Ward, M., Paya‐Cano, J., Aitchinson, KJ., Binder, E., Sluyter, F., Kuhn, K., Selzer, S., Craig, I., McGuffin, P. and Schalkwyk, LC., (2012). Pharmacoproteomic investigation into antidepressant response in two mouse inbred strains. PROTEOMICS. 12 (14), 2355-2365
Dempster, EL., Pidsley, R., Schalkwyk, LC., Owens, S., Georgiades, A., Kane, F., Kalidindi, S., Picchioni, M., Kravariti, E., Toulopoulou, T., Murray, RM. and Mill, J., (2011). Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder. Human Molecular Genetics. 20 (24), 4786-4796
Kõks, S., Soomets, U., Plaas, M., Terasmaa, A., Noormets, K., Tillmann, V., Vasar, E., Fernandes, C. and Schalkwyk, LC., (2011). Hypothalamic gene expression profile indicates a reduction in G protein signaling in the Wfs1 mutant mice. Physiological Genomics. 43 (24), 1351-1358
Binder, E., Malki, K., Paya-Cano, JL., Fernandes, C., Aitchison, KJ., Mathé, AA., Sluyter, F. and Schalkwyk, LC., (2011). Antidepressants and the resilience to early-life stress in inbred mouse strains. Pharmacogenetics and Genomics. 21 (12), 779-789
Malki, K., Uher, R., Paya-Cano, J., Binder, E., Rietschel, M., Zobel, A., Mors, O., Hauser, J., Henigsberg, N., Jerman, B., Souery, D., Placentino, A., Ng, MY., Cohen-Woods, S., Sluyter, F., Farmer, A., Aitchison, KJ., Craig, IW., Lewis, CM., McGuffin, P. and Schalkwyk, LC., (2011). Convergent Animal and Human Evidence Suggests a Role of PPM1A Gene in Response to Antidepressants. Biological Psychiatry. 69 (4), 360-365
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Kember, RL., Fernandes, C., Tunbridge, EM., Liu, L., Payá‐Cano, JL., Parsons, MJ. and Schalkwyk, LC., (2010). A B2 SINE insertion in the Comt1 gene (Comt1B2i) results in an overexpressing, behavior modifying allele present in classical inbred mouse strains. Genes, Brain and Behavior. 9 (8), 925-932
Docherty, SJ., Davis, OSP., Kovas, Y., Meaburn, EL., Dale, PS., Petrill, SA., Schalkwyk, LC. and Plomin, R., (2010). A genome‐wide association study identifies multiple loci associated with mathematics ability and disability. Genes, Brain and Behavior. 9 (2), 234-247
Kõks, S., Velthut, A., Sarapik, A., Altmäe, S., Reinmaa, E., Schalkwyk, LC., Fernandes, C., Lad, HV., Soomets, U., Jaakma, Ü. and Salumets, A., (2010). The differential transcriptome and ontology profiles of floating and cumulus granulosa cells in stimulated human antral follicles. MHR: Basic science of reproductive medicine. 16 (4), 229-240
Meaburn, EL., Schalkwyk, LC. and Mill, J., (2010). Allele-specific methylation in the human genome. Epigenetics. 5 (7), 578-582
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Davis, OSP., Butcher, LM., Docherty, SJ., Meaburn, EL., Curtis, CJC., Simpson, MA., Schalkwyk, LC. and Plomin, R., (2010). A Three-Stage Genome-Wide Association Study of General Cognitive Ability: Hunting the Small Effects. Behavior Genetics. 40 (6), 759-767
Lad, HV., Liu, L., Paya-Cano, JL., Parsons, MJ., Kember, R., Fernandes, C. and Schalkwyk, LC., (2010). Behavioural battery testing: Evaluation and behavioural outcomes in 8 inbred mouse strains. Physiology & Behavior. 99 (3), 301-316
Schosser, A., Pirlo, K., Gaysina, D., Cohen-Woods, S., Schalkwyk, LC., Elkin, A., Korszun, A., Gunasinghe, C., Gray, J., Jones, L., Meaburn, E., Farmer, AE., Craig, IW. and McGuffin, P., (2010). Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays. BMC Research Notes. 3 (1), 274-
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Kõks, S., Soomets, U., Paya-Cano, JL., Fernandes, C., Luuk, H., Plaas, M., Terasmaa, A., Tillmann, V., Noormets, K., Vasar, E. and Schalkwyk, LC., (2009). Wfs1 gene deletion causes growth retardation in mice and interferes with the growth hormone pathway. Physiological Genomics. 37 (3), 249-259
Meaburn, EL., Fernandes, C., Craig, IW., Plomin, R. and Schalkwyk, LC., (2009). Assessing Individual Differences in Genome-Wide Gene Expression in Human Whole Blood: Reliability Over Four Hours and Stability Over 10 Months. Twin Research and Human Genetics. 12 (4), 372-380
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Smith, RG., Kember, RL., Mill, J., Fernandes, C., Schalkwyk, LC., Buxbaum, JD. and Reichenberg, A., (2009). Advancing Paternal Age Is Associated with Deficits in Social and Exploratory Behaviors in the Offspring: A Mouse Model. PLoS ONE. 4 (12), e8456-e8456
Kas, MJH., Gelegen, C., Schalkwyk, LC. and Collier, DA., (2009). Interspecies Comparisons of Functional Genetic Variations and Their Implications in Neuropsychiatry. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics. 150B (3), 309-317
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Parsons, MJ., Grimm, CH., Paya-Cano, JL., Sugden, K., Nietfeld, W., Lehrach, H. and Schalkwyk, LC., (2008). Using hippocampal microRNA expression differences between mouse inbred strains to characterise miRNA function. Mammalian Genome. 19 (7-8), 552-560
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Caspi, A., Williams, B., Kim-Cohen, J., Craig, IW., Milne, BJ., Poulton, R., Schalkwyk, LC., Taylor, A., Werts, H. and Moffitt, TE., (2007). Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism. Proceedings of the National Academy of Sciences. 104 (47), 18860-18865
Docherty, SJ., Butcher, LM., Schalkwyk, LC. and Plomin, R., (2007). Applicability of DNA pools on 500 KSNP microarrays for cost-effective initial screens in genomewide association studies. BMC Genomics. 8 (1), 214-214
Sugden, K., D'Souza, UM., Aitchison, KJ., Schalkwyk, LC., McGuffin, P., Byers, H., Campbell, J., Hye, A. and Pariante, CM., (2007). P.1.31 Gene expression analyses of mouse fibroblast cell line L929 after antidepressant treatment. European Neuropsychopharmacology. 17, S27-S28
Fernandes, C., Hoyle, E., Dempster, E., Schalkwyk, LC. and Collier, DA., (2006). Performance deficit of α7 nicotinic receptor knockout mice in a delayed matching‐to‐place task suggests a mild impairment of working/episodic‐like memory. Genes, Brain and Behavior. 5 (6), 433-440
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Galsworthy, MJ., Paya-Cano, JL., Liu, L., Monleón, S., Gregoryan, G., Fernandes, C., Schalkwyk, LC. and Plomin, R., (2005). Assessing Reliability, Heritability and General Cognitive Ability in a Battery of Cognitive Tasks for Laboratory Mice. Behavior Genetics. 35 (5), 675-692
Butcher, LM., Meaburn, E., Knight, J., Sham, PC., Schalkwyk, LC., Craig, IW. and Plomin, R., (2005). SNPs, microarrays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children. Human Molecular Genetics. 14 (10), 1315-1325
Butcher, LM., Meaburn, E., Dale, PS., Sham, P., Schalkwyk, LC., Craig, IW. and Plomin, R., (2005). Association analysis of mild mental impairment using DNA pooling to screen 432 brain-expressed single-nucleotide polymorphisms. Molecular Psychiatry. 10 (4), 384-392
Simpson, CL., Knight, J., Butcher, LM., Hansen, VK., Meaburn, EL., Schalkwyk, LC., Craig, IW., Powell, JF., Sham, PC. and Al-Chalabi, A., (2005). A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. Nucleic Acids Research. 33 (3), e25-e25
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Nyberg, J., Sandnabba, K., Schalkwyk, L. and Sluyter, F., (2004). Genetic and environmental (inter)actions in male mouse lines selected for aggressive and nonaggressive behavior. Genes, Brain and Behavior. 3 (2), 101-109
Fernandes, C., Liu, L., Paya-Cano, JL., Gregorov�, SA., Forejt, J. and Schalkwyk, LC., (2004). Behavioral Characterization of Wild Derived Male Mice (Mus musculus musculus) of the PWD/Ph Inbred Strain: High Exploration Compared to C57BL/6J. Behavior Genetics. 34 (6), 621-630
Fernandes, C., Paya‐Cano, JL., Sluyter, F., D'Souza, U., Plomin, R. and Schalkwyk, LC., (2004). Hippocampal gene expression profiling across eight mouse inbred strains: towards understanding the molecular basis for behaviour. European Journal of Neuroscience. 19 (9), 2576-2582
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Ben Abdelkhalek, H., Beckers, A., Schuster-Gossler, K., Pavlova, MN., Burkhardt, H., Lickert, H., Rossant, J., Reinhardt, R., Schalkwyk, LC., Müller, I., Herrmann, BG., Ceolin, M., Rivera-Pomar, R. and Gossler, A., (2004). The mouse homeobox gene Not is required for caudal notochord development and affected by the truncate mutation. Genes & Development. 18 (14), 1725-1736
Craig, IW., Mill, J., Craig, GM., Loat, C. and Schalkwyk, LC., (2004). Application of microarrays to the analysis of the inactivation status of human X-linked genes expressed in lymphocytes. European Journal of Human Genetics. 12 (8), 639-646
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Mill, J., Galsworthy, MJ., Paya‐Cano, JL., Sluyter, F., Schalkwyk, LC., Plomin, R. and Asherson, P., (2002). Home‐cage activity in heterogeneous stock (HS) mice as a model of baseline activity. Genes, Brain and Behavior. 1 (3), 166-173
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Leong, WL., Dobson, MJ., Logsdon, Jr., JM., Abdel-Majid, RM., Schalkwyk, LC., Guernsey, DL. and Neumann, PE., (2000). ETn insertion in the mouse Adcy1 gene: transcriptional and phylogenetic analyses. Mammalian Genome. 11 (2), 97-103
Gösele, C., Hong, L., Kreitler, T., Rossmann, M., Hieke, B., Groß, U., Kramer, M., Himmelbauer, H., Bihoreau, M-T., Kwitek-Black, AE., Twigger, S., Tonellato, PJ., Jacob, HJ., Schalkwyk, LC., Lindpaintner, K., Ganten, D., Lehrach, H. and Knoblauch, M., (2000). High-Throughput Scanning of the Rat Genome Using Interspersed Repetitive Sequence-PCR Markers. Genomics. 69 (3), 287-294
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Zhu, B., Smith, JA., Tracey, SM., Konfortov, BA., Welzel, K., Schalkwyk, LC., Lehrach, H., Kollers, S., Masabanda, J., Buitkamp, J., Fries, R., Williams, JL. and Miller, JR., (1999). A 5× genome coverage bovine BAC library: production, characterization, and distribution. Mammalian Genome. 10 (7), 706-709
Hills, D., Tracey, S., Masabanda, J., Fries, R., Schalkwyk, LC., Lehrach, H., Miller, JR. and Williams, JL., (1999). A bovine YAC library containing four- to five-fold genome equivalents. Mammalian Genome. 10 (8), 837-838
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Himmelbauer, H., Wedemeyer, N., Haaf, T., Wanker, EE., Schalkwyk, LC. and Lehrach, H., (1998). IRS-PCR-based genetic mapping of the huntingtin interacting protein gene (HIP1) on mouse Chromosome 5. Mammalian Genome. 9 (1), 26-31
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Toye, AA., Schalkwyk, L., Lehrach, H. and Bumstead, N., (1997). A yeast artificial chromosome (YAC) library containing 10 haploid chicken genome equivalents. Mammalian Genome. 8 (4), 274-276
Crnogorac-Jurcevic, T., Brown, JR., Lehrach, H. and Schalkwyk, LC., (1997). Tetraodon fluviatilis,a New Puffer Fish Model for Genome Studies. Genomics. 41 (2), 177-184
Cai, L., Schalkwyk, LC., Schoeberlein-Stehli, A., Zee, RYL., Smith, A., Haaf, T., Georges, M., Lehrach, H. and Lindpaintner, K., (1997). Construction and Characterization of a 10-Genome Equivalent Yeast Artificial Chromosome Library for the Laboratory Rat,Rattus norvegicus. Genomics. 39 (3), 385-392
Hunter, KW., Riba, L., Schalkwyk, L., Clark, M., Resenchuk, S., Beeghly, A., Su, J., Tinkov, F., Lee, P., Ramu, E., Lehrach, H. and Housman, D., (1996). Toward the construction of integrated physical and genetic maps of the mouse genome using interspersed repetitive sequence PCR (IRS-PCR) genomics.. Genome Research. 6 (4), 290-299
McCarthy, L., Hunter, K., Schalkwyk, L., Riba, L., Anson, S., Mott, R., Newell, W., Bruley, C., Bar, I. and Ramu, E., (1995). Efficient high-resolution genetic mapping of mouse interspersed repetitive sequence PCR products, toward integrated genetic and physical mapping of the mouse genome.. Proceedings of the National Academy of Sciences. 92 (12), 5302-5306
Schalkwyk, LC., Francis, F. and Lehrach, H., (1995). Techniques in mammalian genome mapping. Current Opinion in Biotechnology. 6 (1), 37-43
Breen, M., Deakin, L., Macdonald, B., Miller, S., Sibson, R., Tarttelin, E., Avner, P., Bourgade, F., Guenet, JL., Montagutelli, X., Poirier, C., Simon, D., Tailor, D., Bishop, M., Kelly, M., Rysavy, F., Rastan, S., Norris, D., Shepherd, D., Abbott, C., Pilz, A., Hodge, S., Jackson, I., Boyd, Y., Blair, H., Maslen, G., Todd, JA., Reed, PW., Stoye, J., Ashworth, A., McCarthy, L., Cox, R., Schalkwyk, LC., Lehrach, H., Klose, J., Gangadharan, U. and Brown, S., (1994). Towards high resolution maps of the mouse and human genomes?a facility for ordering markers to 0.1 cM resolution. Human Molecular Genetics. 3 (4), 621-627
A.Jones, K., M.Black, D., A.Brown, M., L.Griffiths, B., M.Nicolai, H., A.Chambers, J., Bonjardim, M., Xu, C-F., Boyd, M., MeFariane, R., Korn, B., Poustka, A., A.North, M., Schalkwyk, L., Lehrach, H. and Solomon, E., (1994). The detailed characterisation of a 400 kb cosmid walk in the BRCA1 region: identification and localisation of 10 genes including a dual-specificity phosphatase. Human Molecular Genetics. 3 (11), 1927-1934
Jones, JE., Huckaby, CS., Stafford, MD. and Linnoila, RI., (1994). An MspI RFLP of the human AHR gene.. Human molecular genetics. 3 (11), 2083-
(1994). CORRIGENDUM. Human Molecular Genetics. 3 (5), 852-852
Hoheisel, J., (1993). High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe. Cell. 73 (1), 109-120
Schalkwyk, LC., Charlebois, RL. and Doolittle, WF., (1993). Insertion sequences on plasmid pHV1 of Haloferax volcanii. Canadian Journal of Microbiology. 39 (2), 201-206
Schalkwyk, LC., (1993). Chapter 15 Halobacterial genes and genomes. New Comprehensive Biochemistry. 26 (C), 467-496
Cohen, A., Lam, WL., Charlebois, RL., Doolittle, WF. and Schalkwyk, LC., (1992). Localizing genes on the map of the genome of Haloferax volcanii, one of the Archaea.. Proceedings of the National Academy of Sciences. 89 (5), 1602-1606
Doolittle, WF., Lam, WL., Schalkwyk, LC., Charlebois, RL., Cline, SW. and Cohen, A., (1992). Progress in developing the genetics of the halobacteria.. Biochemical Society symposium. 58 (58), 73-78
Charlebois, RL., Schalkwyk, LC., Hofman, JD. and Doolittle, WF., (1991). Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2. Journal of Molecular Biology. 222 (3), 509-524
Charlebois, RL., Hofman, JD., Schalkwyk, LC., Lam, WL. and Doolittle, WF., (1989). Genome mapping in halobacteria. Canadian Journal of Microbiology. 35 (1), 21-29
Cline, SW., Schalkwyk, LC. and Doolittle, WF., (1989). Transformation of the archaebacterium Halobacterium volcanii with genomic DNA. Journal of Bacteriology. 171 (9), 4987-4991
Cline, SW., Lam, WL., Charlebois, RL., Schalkwyk, LC. and Doolittle, WF., (1989). Transformation methods for halophilic archaebacteria. Canadian Journal of Microbiology. 35 (1), 148-152
Hofman, JD., Schalkwyk, LC. and Doolittle, WF., (1986). ISH51: a large, degenerate family of insertion sequence-like elements in the genome of the archaehacterium,Halobacterium volcanii. Nucleic Acids Research. 14 (17), 6983-7000
Book chapters (1)
Nock, C., Gauss, C., Schalkwyk, LC., Klose, J., Lehrach, H. and Himmelbauer, H., (1999). Technology development at the interface of proteome research and genomics: Mapping nonpolymorphic proteins on the physical map of mouse chromosomes. In: From Genome to Proteome: Advances in the Practice & Application of Proteomics. Wiley. 447- 452. 9783527301546
Conferences (42)
Mill, J., Hannon, E., Dempster, E., Franklin, A., Burrage, J., Davies, J., Chioza, B., Commin, G., Jeffries, AR., Bamford, RA. and Schalkwyk, L., (2023). W76. CELL-SPECIFIC METHYLOMIC VARIATION IN NEURODEVELOPMENT AND SCHIZOPHRENIA
Hannon, E., Davies, J., Chioza, B., Policicchio, S., Burrage, J., Commin, G., Jeffries, AR., Schalkwyk, L., Dempster, E. and Mill, J., (2022). 89. IDENTIFYING CELL-TYPE-SPECIFIC EPIGENETIC VARIATION IN THE CORTEX ASSOCIATED WITH SCHIZOPHRENIA
Shireby, G., Hannon, E., Commin, G., Burrage, J., Davies, J., Policicchio, S., Schalkwyk, L., Dempster, E. and Mill, J., (2021). TH44. LEVERAGING DNA METHYLATION QUANTITATIVE-TRAIT LOCI TO CHARACTERIZE THE RELATIONSHIP BETWEEN METHYLOMIC VARIATION, GENE EXPRESSION, AND PSYCHIATRIC DISEASE
Asenius, F., Marzi, SJ., Gorrie-Stone, TJ., Brew, A., Panchbaya, Y., Williamson, E., Schalkwyk, L., Rakyan, V. and Williams, DJ., (2020). A lack of DNA methylation covariation between human blood and sperm make it unlikely to mediate intergenerational inheritance of acquired traits
Hannon, E., Dempster, E., Burrage, J., Curtis, C., Gillespie, A., Dempster, D., Gunasinghe, C., Schalkwyk, L., Gaughran, F., Murray, R., Di Forti, M., Collier, D., Breen, G. and Mill, J., (2017). AN EPIGENOME-WIDE ASSOCIATION STUDY OF CLOZAPINE USE IN TREATMENT-RESISTANT SCHIZOPHRENIA
Rutten, B., Vermetten, E., Vinkers, C., Pishva, E., Kenis, G., de Nijs, L., Eijssen, L., Viechtbauer, W., van den Hove, D., Schraut, K., Lesch, K-P., Daskalakis, N., Yehuda, R., Schalkwyk, L., Lunnon, K., Mill, J., Nievergelt, C., Baker, DS., Geuze, E. and Boks, MPM., (2015). Blood-based DNA Methylation Signatures of Susceptibility to Traumatic Stress; Results From A Dutch Prospective Military Cohort Study
Spiers, H., Bray, NJ., Hannon, E., Schalkwyk, LC., Wong, CC., Pidsley, R., Smith, RG. and Mill, J., (2015). ISDN2014_0171: Dynamic and sex‐specific changes in DNA methylation during human fetal brain development
Boks, MPM., van Mierlo, H., Rutten, BPF., Radstake, TRDJ., De Witte, LD., Geuze, E., Horvath, S., Schalkwyk, LC., Vinkers, CH., Broen, JCA. and Vermetten, E., (2015). Longitudinal Changes of Telomere Length and Epigenetic Age Related to Traumatic Stress and Post-traumatic Stress Disorder
Powell, TR., Schalkwyk, LC., Breen, G., Lawrence, T., Pariante, C., McGuffin, P., Tansey, K., Uher, R. and D'Souza, UM., (2012). Identifying transcriptomic biomarkers for response to escitalopram in the inflammatory cytokine pathway
Kõks, S., Velthut, A., Sarapik, A., Altmäe, S., Reinmaa, E., Schalkwyk, LC., Fernandes, C., Lad, H., Soomets, U., Jaakma, ÜW. and Salumets, A., (2011). 166 THE DIFFERENTIAL TRANSCRIPTOME AND ONTOLOGY PROFILES OF MURAL AND CUMULUS GRANULOSA CELLS IN STIMULATED HUMAN ANTRAL FOLLICLES
Sikk, K., Koks, S., Soomets, U., Schalkwyk, LC., Fernandes, C., Haldre, S., Aquilonius, S-M. and Taba, P., (2010). Peripheral blood RNA gene expression profiling in illicit methcathinone users reveals effect on immune system
Amos-Landgraf, J. and Schalkwyk, LC., (2008). The 21st International Mammalian Genome Conference Meeting Report
Meaburn, E., Harlaar, N., Craig, IW., Schalkwyk, LC. and Plomin, R., (2007). Genomewide gene expression profiles as a biological basis for non-shared environment: MZ twins discordant for reading ability
Binder, E., Paya-Cano, JL., Sluyter, F. and Schalkwyk, LC., (2006). P.1.d.016 The effects of a selective serotonin reuptake inhibitor and a tricyclic antidepressant on the behaviour of chronically stressed 129SvemJ and C57BL/6J mice in the hole board and forced swim test
Paya-Cano, JL., Sluyter, F., Mineur, YS., Fernandes, C., Crusio, WE. and Schalkwyk, LC., (2006). P.1.a.015 Strain differences in susceptibility to unpredictable chronic mild stress as assessed by hippocampal gene expression profiling
Meaburn, E., Butcher, LM., Harlaar, N., Curtis, C., Craig, IW., Schalkwyk, LC. and Plomin, R., (2006). An association scan using pooled DNA and 100k SNPS identifies a 'SNP set' for early reading
Huezo-Diaz, P., Williamson, R., Nash, MW., Sim, SC., Alhberg, S., Hoda, F., Rietschel, M., Schmal, C., Farmer, A., Schulze, T., Hauser, J., Henigsberg, N., Maier, W., Zobel, A., Larsen, ER., Mors, O., Mendelewicz, J., Marusic, A., Perez, J., Schalkwyk, L., McGuffin, P., Craig, I., Ingelman-Sundberg, M. and Aitchison, KJ., (2006). CYP2D6 and CYP2C19 association data from GENDEP, a multicentre European study
D'Souza, UM., Sugden, K., Pariante, CM., Byers, H., Ward, M., Schalkwyk, LC., McGuffin, P. and Aitchison, KJ., (2006). Effects of antidepressant treatment on gene expression in mouse cultured cells
Butcher, LM., Meaburn, EL., Craig, IW., Schalkwyk, LC. and Plomin, R., (2006). A genomewide association scan for GE interplay in childhood
D'Souza, UM., Sugden, K., Pariante, CM., Byers, H., Ward, M., Schalkwyk, LC., McGuffin, P. and Aitchison, KJ., (2006). Effects of antidepressant treatment on gene expression in mouse cultured cells
Liu, L., Fernandes, C., Brookes, K., Paya-Capo, J., Asherson, P. and Schalkwyk, LC., (2005). P.2.07 Selecting over-active extremes in outbred heterogeneous stock (HS) mice for gene expression profiling: nominating novel candidate genes for over-activity
Meaburn, EL., Butcher, LM., Knight, J., Craig, I., Schalkwyk, LC. and Plomin, R., (2005). QTLs for reading disability at 7 years: Genotyping pooled DNA on 100K SNP microarrays
Butcher, LM., Meaburn, E., Knight, J., Sham, PC., Schalkwyk, LC., Craig, IW. and Plomin, R., (2005). SNPs, microarrays, and pooled DNA: Identification of four loci associated with mild mental impairment in a sample of 6000 children
Butcher, LM., Meaburn, E., Knight, J., Sham, PC., Schalkwyk, LC., Craig, IW. and Plomin, R., (2005). Allelotyping over 10,000 SNPs using DNA pools and microarrays nominates four SNPs associated with mild mental impairment
Sugden, K., D'Souza, UM., McGuffin, P., Schalkwyk, LC., Aitchison, KJ. and Pariante, CM., (2005). Gene expression analyses of a mouse fibroblast cell line after antidepressant treatment
Fernandes, C., Liu, L., Paya-Cano, JL., Whatley, SA. and Schalkwyk, LC., (2004). Correlating behaviour with gene expression: Identifying genes for anxiety and cognition in the mouse.
Meaburn, EL., Butcher, ML., Liu, L., Fernandes, C., Sham, P., Plomin, R., Craig, I. and Schalkwyk, L., (2004). DNA pools on 10K genechips: Solving the QTL problem of large samples and large numbers of SNPS
Chamberlain, S., Bizarro, L., Fernandes, C., Schalkwyk, L. and Stolerman, IP., (2003). Nicotinic receptors containing the alpha7 subunit do not contribute to nicotine discrimination
Sluyter, F. and Schalkwyk, LC., (2003). Symposium: Using microarrays in the analysis of behavior
Fernandes, C., Paya-Cano, J., Sluyter, F., D'Souza, U., Plomin, R. and Schalkwyk, LC., (2003). The power of gene expression profiling and mouse models to unravel behavior.
Meaburn, E., Schalkwyk, L., Criag, I. and Plomin, R., (2003). A genome wide scan using 400 non-synonymous SNP markers in DNA pools identifies genes associated with language impairment in children
Meaburn, EK., Butcher, LM., Schalkwyk, L., Craig, I. and Plomin, R., (2002). Localisation of quantitative trait loci responsible for the heritability of language impairment using DNA pooling
Hill, L., Meaburn, E., Butcher, LM., Schalkwyk, L., Craig, IW. and Plomin, R., (2002). A genome scan using non-synonymous SNPs in coding regions and general cognitive ability
Galsworthy, MJ., Paya-Cano, JL., Liu, L., Fernandes, C., Schalkwyk, L. and Plomin, R., (2002). The reliabilities, interrelationships and quantitative genetics of cognitive tasks in mus musculus: A study of 250 heterogeneous stock mice
Tandon, K., Schalkwyk, L., Patel, M., Kinirons, M., Kerwin, R., McGuffin, P. and Aitchison, KJ., (2002). An amino acid substitution (IIe109Val) in CYP2D6
Tandon, K., Schalkwyk, LC., Checkley, S., Patel, M., Kinirons, M., Kerwin, RW., McGuffin, P. and Aitchison, KJ., (2002). CYP2D6 genotype and treatment with tricyclic antidepressants
Butcher, LM., Meaburn, EL., Hill, L., Plomin, R. and Schalkwyk, L., (2002). How many non-synonymous SNPS are available on public databases?
Tandon, K., Schalkwyk, L., Checkley, S., Patel, M., Kinirons, M., Kerwin, RW., McGuffin, P. and Aitchison, KJ., (2002). CYP2D6 genotype and treatment with tricyclic antidepressants
Meaburn, EL., Plomin, R. and Schalkwyk, L., (2001). Single nucleotide polymorphism genotyping in DNA pools.
Vettakkorumakankav, NN., Stevenson, KJ., Schalkwyk, LC. and Doolittle, WF., (1994). Disruption of the gene coding for dihydrolipoamide dehydrogenase in Haloferax volcanii by homologous recombination.
ROSS, MT., KNIGHTS, CJ., ROEST CROLLIUS, H., LABELLA, T., HOLLOWAY, E., MIFSUD, J., LI, K., LAM, V., VATCHEVA, R., KUMLEIN, J., FRANCIS, F., MOTT, R., SCHALKWYK, L., BHOGAL, R., ZEHETNER, G. and LEHRACH, H., (1993). BUILDING AN INTEGRATED PHYSICAL AND GENETIC-MAP OF THE HUMAN X-CHROMOSOME
DOOLITTLE, WF., CHARLEBOIS, RL., SCHALKWYK, LC., LAM, WL., CONOVER, RK., TSOULUHAS, D., CLINE, SW., HOFMAN, JD. and COHEN, A., (1991). PHYSICAL MAPPING AND GENE-TRANSFER METHODS FOR HALOBACTERIUM (HALOFERAX) VOLCANII
Reports and Papers (3)
Wang, Y., Gorrie-Stone, TJ., Grant, OA., Andrayas, AD., Zhai, X., McDonald-Maier, KD. and Schalkwyk, LC., (2021). interpolatedXY: a two-step strategy to normalise DNA methylation microarray data avoiding sex bias
Wang, Y., Hannon, E., Grant, OA., Gorrie-Stone, TJ., Kumari, M., Mill, J., Zhai, X., McDonald-Maier, KD. and Schalkwyk, LC., (2020). DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy
Hannon, E., Gorrie-Stone, T., Smart, M., Burrage, J., Hughes, A., Bao, Y., Kumari, M., Schalkwyk, L. and Mill, J., (2018). Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits
Other (15)
Hannon, E., Bray, N., Weedon, M., Gorrie-Stone, T., Smart, M., Kumari, M., Schalkwyk, L., O'Donovan, M. and Mill, J., (2019).PLEIOTROPIC EFFECTS OF GENETIC VARIATION ASSOCIATED WITH PSYCHIATRIC DISORDERS ON DNA METHYLATION. European Neuropsychopharmacology. 29,Elsevier BV
Hannon, E., Dempster, E., Burrage, J., McQuillin, A., Clair, DS., Morris, D., Di Forti, M., Gaughran, F., MacCabe, J., Breen, G., Collier, D., Murray, R., Schalkwyk, L. and Mill, J., (2019).AN INTEGRATED GENETIC-EPIGENETIC ANALYSIS OF SCHIZOPHRENIA: EVIDENCE FOR CO-LOCALIZATION OF GENETIC ASSOCIATIONS AND DIFFERENTIAL DNA METHYLATION FROM A LARGE META-ANALYSIS OF WHOLE BLOOD DNA. European Neuropsychopharmacology. 29,Elsevier BV
Mill, J., Hannon, E., Spiers, H., Wong, CCY., Viana, J., O'Donovan, M., Schalkwyk, L. and Bray, N., (2019).Regulatory Genomic Variation In The Developing Brain: Relevance To Neuropsychiatric Phenotypes. European Neuropsychopharmacology. 29,Elsevier BV
Hannon, E., Marzi, S., Schalkwyk, L. and Mill, J., (2019).F61GENETIC RISK VARIANTS FOR BRAIN DISORDERS ARE SIGNIFICANTLY ENRICHED IN ACTIVE ENHANCERS IN THE CORTEX. European Neuropsychopharmacology. 29,Elsevier BV
Hannon, E., Dempster, E., Mansell, G., Schalkwyk, L., Murray, R., McQuillin, A., Kowalec, K., Clair, DS., Morris, D., Sullivan, P., O'Donovan, M., MacCabe, J., Collier, D. and Mill, J., (2019).57METHYLOMIC BIOMARKERS OF SCHIZOPHRENIA AND ANTIPSYCHOTIC MEDICATION EXPOSURE. European Neuropsychopharmacology. 29,Elsevier BV
O'Brien, H., Hannon, E., Hill, M., Toste, C., Robertson, M., Morgan, J., McLaughlin, G., Lewis, C., Schalkwyk, L., Pardinas, A., Owen, M., O'Donovan, M., Mill, J. and Bray, N., (2019).55EXPRESSION QUANTITATIVE TRAIT LOCI IN THE DEVELOPING HUMAN BRAIN AND THEIR ENRICHMENT IN NEUROPSYCHIATRIC DISORDERS. European Neuropsychopharmacology. 29,Elsevier BV
Richmond, RC., Bao, Y., Smart, M., Gorrie-Stone, T., Schalkwyk, L., Mill, J., Davey Smith, G., Benzeval, M., Relton, C. and Kumari, M., (2018).P8 Investigating epigenetic differences in response to shift work: findings fromunderstanding society(UK longitudinal household survey). Poster presentations. 72,BMJ Publishing Group Ltd
Hannon, E., Lunnon, K., Schalkwyk, L. and Mill, J., (2017).CHARACTERIZING INTER-INDIVIDUAL VARIATION IN DNA METHYLATION BETWEEN BLOOD AND BRAIN: IMPLICATIONS FOR EPIGENETIC STUDIES OF PSYCHIATRIC PHENOTYPES. EUROPEAN NEUROPSYCHOPHARMACOLOGY. 27
Hannon, E., Spiers, H., Viana, J., Pidsley, R., Burrage, J., Murphy, T., Troakes, C., Turecki, G., O'Donovan, M., Schalkwyk, L., Bray, NJ. and Mill, J., (2017).METHYLATION QUANTITATIVE TRAIT LOCI (MQTL) IN THE DEVELOPING HUMAN BRAIN AND THEIR ENRICHMENT IN GENOMIC REGIONS ASSOCIATED WITH SCHIZOPHRENIA. EUROPEAN NEUROPSYCHOPHARMACOLOGY. 27
Viana, J., Pidsley, R., Hannon, E., Spiers, H., Troakes, C., Al-Saraj, S., Mechawar, N., Turecki, G., Schalkwyk, L., Bray, NJ. and Mill, J., (2017).INVESTIGATING EPIGENOMIC REGULATION IN SCHIZOPHRENIA. EUROPEAN NEUROPSYCHOPHARMACOLOGY. 27
Xia, B., Kepa, A., Colvert, E., Mea-burn, E., Ronald, A., Schalkwyk, L., Mill, J., Plomin, R., Happe, F. and Wong, CCY., (2017).AN INVESTIGATION OF X-CHROMOSOME INACTIVATION PROFILES USING A GENETICALLY SENSITIVE DISCORDANT TWIN DESIGN. EUROPEAN NEUROPSYCHOPHARMACOLOGY. 27
Hannon, E., Dempster, E., Burrage, J., Smith, A., Gurling, H., Basso, N., McQuillin, A., Schalkwyk, L. and Mill, J., (2017).AN INTEGRATED GENETIC-EPIGENETIC ANALYSIS OF SCHIZOPHRENIA. EUROPEAN NEUROPSYCHOPHARMACOLOGY. 27
Dempster, E., Hannon, E., Schalkwyk, L., Bohlken, M., Kaprio, J., Toulopoulou, T., Spector, T., Hulshoffpol, H., Nenadic, I., Cannon, T., Hultman, C., Murray, R. and Mill, J., (2017).GENOME-WIDE METHYLOMIC ANALYSIS OF MONOZYGOTIC TWINS DISCORDANT FOR SCHIZOPHRENIA. EUROPEAN NEUROPSYCHOPHARMACOLOGY. 27
Wong, CCY., Parikshak, N., Spiers, H., Brays, NJ., Lysenko, L., Troakes, C., Viana, J., Hannon, E., Schalkwyk, L., Geschwind, D. and Mill, J., (2017).METHYLOMIC ANALYSIS OF AUTISM BRAIN: DISEASE ASSOCIATED VARIATION AND SUPPORT FOR A NEURODEVELOPMENTAL COMPONENT TO ETIOLOGY. EUROPEAN NEUROPSYCHOPHARMACOLOGY. 27
Spiers, H., Hannon, E., Schalkwyk, L., Bray, N. and Mill, J., (2017).DNA HYDROXYMETHYLATION ASSOCIATED WITH HUMAN FETAL BRAIN DEVELOPMENT. EUROPEAN NEUROPSYCHOPHARMACOLOGY. 27
Grants and funding
2022
Mapping cell-type-specific regulatory genomic variation in Alzheimer's disease pathology.
Medical Research Council
2020
Building an Autism Research Network in Vietnam
University of Essex (GCRF)
2017
Regulatory genomic profiling in schizophrenia
Medical Research Council
2014
Methylomic Profiling in Schizophrenia: Towards an Integrated Genetic-Epigenetic Approach
Medical Research Council