Items where Author is "Mill, Jonathan"

Article

Devall, Matthew and Soanes, Darren M and Smith, Adam R and Dempster, Emma L and Smith, Rebecca G and Burrage, Joe and Iatrou, Artemis and Hannon, Eilis and Troakes, Claire and Moore, Karen and O’Neill, Paul and Al-Sarraj, Safa and Schalkwyk, Leonard and Mill, Jonathan and Weedon, Michael and Lunnon, Katie (2023) Genome-wide characterization of mitochondrial DNA methylation in human brain. Frontiers in Endocrinology, 13. p. 1059120. DOI https://doi.org/10.3389/fendo.2022.1059120

Vellame, Dorothea Seiler and Shireby, Gemma and MacCalman, Ailsa and Dempster, Emma L and Burrage, Joe and Gorrie-Stone, Tyler and Schalkwyk, Leonard S and Mill, Jonathan and Hannon, Eilis (2022) Uncertainty quantification of reference-based cellular deconvolution algorithms. Epigenetics, 18 (1). p. 2137659. DOI https://doi.org/10.1080/15592294.2022.2137659

Flynn, Robert and Washer, Sam and Jeffries, Aaron R and Andrayas, Alexandria and Shireby, Gemma and Kumari, Meena and Schalkwyk, Leonard C and Mill, Jonathan and Hannon, Eilis (2022) Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays. Human Molecular Genetics, 31 (18). pp. 3181-3190. DOI https://doi.org/10.1093/hmg/ddac112

Leung, Szi Kay and Jeffries, Aaron R and Castanho, Isabel and Jordan, Ben T and Moore, Karen and Davies, Jonathan P and Dempster, Emma L and Bray, Nicholas J and O'Neill, Paul and Tseng, Elizabeth and Ahmed, Zeshan and Collier, David A and Jeffery, Erin D and Prabhakar, Shyam and Schalkwyk, Leonard and Jops, Connor and Gandal, Michael J and Sheynkman, Gloria M and Hannon, Eilis and Mill, Jonathan (2021) Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. Cell Reports, 37 (7). p. 110022. DOI https://doi.org/10.1016/j.celrep.2021.110022

Min, Josine L and Hemani, Gibran and Hannon, Eilis and Dekkers, Koen F and Castillo-Fernandez, Juan and Luijk, René and Carnero-Montoro, Elena and Lawson, Daniel J and Burrows, Kimberley and Suderman, Matthew and Bretherick, Andrew D and Richardson, Tom G and Klughammer, Johanna and Iotchkova, Valentina and Sharp, Gemma and Al Khleifat, Ahmad and Shatunov, Aleksey and Iacoangeli, Alfredo and McArdle, Wendy L and Ho, Karen M and Kumar, Ashish and Söderhäll, Cilla and Soriano-Tárraga, Carolina and Giralt-Steinhauer, Eva and Kazmi, Nabila and Mason, Dan and McRae, Allan F and Corcoran, David L and Sugden, Karen and Kasela, Silva and Cardona, Alexia and Day, Felix R and Cugliari, Giovanni and Viberti, Clara and Guarrera, Simonetta and Lerro, Michael and Gupta, Richa and Bollepalli, Sailalitha and Mandaviya, Pooja and Zeng, Yanni and Clarke, Toni-Kim and Walker, Rosie M and Schmoll, Vanessa and Czamara, Darina and Ruiz-Arenas, Carlos and Rezwan, Faisal I and Marioni, Riccardo E and Lin, Tian and Awaloff, Yvonne and Germain, Marine and Aïssi, Dylan and Zwamborn, Ramona and van Eijk, Kristel and Dekker, Annelot and van Dongen, Jenny and Hottenga, Jouke-Jan and Willemsen, Gonneke and Xu, Cheng-Jian and Barturen, Guillermo and Català-Moll, Francesc and Kerick, Martin and Wang, Carol and Melton, Phillip and Elliott, Hannah R and Shin, Jean and Bernard, Manon and Yet, Idil and Smart, Melissa and Gorrie-Stone, Tyler and Shaw, Chris and Al Chalabi, Ammar and Ring, Susan M and Pershagen, Göran and Melén, Erik and Jiménez-Conde, Jordi and Roquer, Jaume and Lawlor, Deborah A and Wright, John and Martin, Nicholas G and Montgomery, Grant W and Moffitt, Terrie E and Poulton, Richie and Esko, Tõnu and Milani, Lili and Metspalu, Andres and Perry, John RB and Ong, Ken K and Wareham, Nicholas J and Matullo, Giuseppe and Sacerdote, Carlotta and Panico, Salvatore and Caspi, Avshalom and Arseneault, Louise and Gagnon, France and Ollikainen, Miina and Kaprio, Jaakko and Felix, Janine F and Rivadeneira, Fernando and Tiemeier, Henning and van IJzendoorn, Marinus H and Uitterlinden, André G and Jaddoe, Vincent WV and Haley, Chris and McIntosh, Andrew M and Evans, Kathryn L and Murray, Alison and Räikkönen, Katri and Lahti, Jari and Nohr, Ellen A and Sørensen, Thorkild IA and Hansen, Torben and Morgen, Camilla S and Binder, Elisabeth B and Lucae, Susanne and Gonzalez, Juan Ramon and Bustamante, Mariona and Sunyer, Jordi and Holloway, John W and Karmaus, Wilfried and Zhang, Hongmei and Deary, Ian J and Wray, Naomi R and Starr, John M and Beekman, Marian and van Heemst, Diana and Slagboom, P Eline and Morange, Pierre-Emmanuel and Trégouët, David-Alexandre and Veldink, Jan H and Davies, Gareth E and de Geus, Eco JC and Boomsma, Dorret I and Vonk, Judith M and Brunekreef, Bert and Koppelman, Gerard H and Alarcón-Riquelme, Marta E and Huang, Rae-Chi and Pennell, Craig E and van Meurs, Joyce and Ikram, M Arfan and Hughes, Alun D and Tillin, Therese and Chaturvedi, Nish and Pausova, Zdenka and Paus, Tomas and Spector, Timothy D and Kumari, Meena and Schalkwyk, Leonard C and Visscher, Peter M and Davey Smith, George and Bock, Christoph and Gaunt, Tom R and Bell, Jordana T and Heijmans, Bastiaan T and Mill, Jonathan and Relton, Caroline L (2021) Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. Nature Genetics, 53 (9). pp. 1311-1321. DOI https://doi.org/10.1038/s41588-021-00923-x

Wang, Yucheng and Hannon, Eilis and Grant, Olivia and Gorrie-Stone, Tyler and Kumari, Meena and Mill, Jonathan and Zhai, Xiaojun and McDonald-Maier, Klaus and Schalkwyk, Leonard (2021) DNA methylation-based sex classifier to predictsex and identify sex chromosome aneuploidy. BMC Genomics, 22 (1). 484-. DOI https://doi.org/10.1186/s12864-021-07675-2

Smith, Rebecca G and Pishva, Ehsan and Shireby, Gemma and Smith, Adam R and Roubroeks, Janou AY and Hannon, Eilis and Wheildon, Gregory and Mastroeni, Diego and Gasparoni, Gilles and Riemenschneider, Matthias and Giese, Armin and Sharp, Andrew J and Schalkwyk, Leonard and Haroutunian, Vahram and Viechtbauer, Wolfgang and van den Hove, Daniel LA and Weedon, Michael and Brokaw, Danielle and Francis, Paul T and Thomas, Alan J and Love, Seth and Morgan, Kevin and Walter, Jörn and Coleman, Paul D and Bennett, David A and De Jager, Philip L and Mill, Jonathan and Lunnon, Katie (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-. DOI https://doi.org/10.1038/s41467-021-23243-4

Hannon, Eilis and Dempster, Emma L and Mansell, Georgina and Burrage, Joe and Bass, Nick and Bohlken, Marc M and Corvin, Aiden and Curtis, Charles J and Dempster, David and Di Forti, Marta and Dinan, Timothy G and Donohoe, Gary and Gaughran, Fiona and Gill, Michael and Gillespie, Amy and Gunasinghe, Cerisse and Hulshoff, Hilleke E and Hultman, Christina M and Johansson, Viktoria and Kahn, René S and Kaprio, Jaakko and Kenis, Gunter and Kowalec, Kaarina and MacCabe, James and McDonald, Colm and McQuillin, Andrew and Morris, Derek W and Murphy, Kieran C and Mustard, Colette J and Nenadic, Igor and O'Donovan, Michael C and Quattrone, Diego and Richards, Alexander L and Rutten, Bart Pf and St Clair, David and Therman, Sebastian and Toulopoulou, Timothea and Van Os, Jim and Waddington, John L and Wellcome Trust Case Control Consortium (WTCCC) and CRESTAR consortium and Sullivan, Patrick and Vassos, Evangelos and Breen, Gerome and Collier, David Andrew and Murray, Robin M and Schalkwyk, Leonard S and Mill, Jonathan (2021) DNA methylation meta-analysis reveals cellular alterations in psychosis and markers of treatment-resistant schizophrenia. eLife, 10. pp. 1-53. DOI https://doi.org/10.7554/elife.58430

Shireby, Gemma L and Davies, Jonathan P and Francis, Paul T and Burrage, Joe and Walker, Emma M and Neilson, Grant WA and Dahir, Aisha and Thomas, Alan J and Love, Seth and Smith, Rebecca G and Lunnon, Katie and Kumari, Meena and Schalkwyk, Leonard C and Morgan, Kevin and Brookes, Keeley and Hannon, Eilis and Mill, Jonathan (2020) Recalibrating the epigenetic clock: implications for assessing biological age in the human cortex. Brain: a journal of neurology, 143 (12). pp. 3763-3775. DOI https://doi.org/10.1093/brain/awaa334

El Khoury, Louis Y and Gorrie-Stone, Tyler J and Smart, Melissa and Hughes, Amanda and Bao, Yanchun and Andrayas, Alexandria and Burrage, Joe and Hannon, Eilis and Kumari, Meena and Mill, Jonathan and Schalkwyk, Leonard (2019) Systematic under-estimation of the epigenetic clock and age acceleration in older subjects. Genome Biology, 20 (1). 283-. DOI https://doi.org/10.1186/s13059-019-1810-4

Saffari, Ayden and Arno, Matt and Nasser, Eric and Ronald, Angelica and Wong, Chloe CY and Schalkwyk, Leonard C and Mill, Jonathan and Dudbridge, Frank and Meaburn, Emma L (2019) RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation. Molecular Autism, 10 (1). p. 38. DOI https://doi.org/10.1186/s13229-019-0285-1

Mansell, Georgina and Gorrie-Stone, Tyler J and Bao, Yanchun and Kumari, Meena and Schalkwyk, Leonard S and Mill, Jonathan and Hannon, Eilis (2019) Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics, 20 (1). 366-. DOI https://doi.org/10.1186/s12864-019-5761-7

Hannon, Eilis and Marzi, Sarah J and Schalkwyk, Leonard S and Mill, Jonathan (2019) Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains. Molecular Brain, 12 (1). 7-. DOI https://doi.org/10.1186/s13041-019-0429-4

O’Brien, Heath E and Hannon, Eilis and Hill, Matthew J and Toste, Carolina C and Robertson, Matthew J and Morgan, Joanne E and McLaughlin, Gemma and Lewis, Cathryn M and Schalkwyk, Leonard C and Hall, Lynsey S and Pardiñas, Antonio F and Owen, Michael J and O’Donovan, Michael C and Mill, Jonathan and Bray, Nicholas J (2018) Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders. Genome Biology, 19 (1). 194-. DOI https://doi.org/10.1186/s13059-018-1567-1

Hannon, Ellis and Gorrie-Stone, Tyler J and Smart, Melissa C and Burrage, Joe and Hughes, Amanda and Bao, Yanchun and Kumari, Meena and Schalkwyk, Leonard C and Mill, Jonathan (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). pp. 654-665. DOI https://doi.org/10.1016/j.ajhg.2018.09.007

Hughes, Amanda and Smart, Melissa and Gorrie-Stone, Tyler and Hannon, Eilis and Mill, Jonathan and Bao, Yanchun and Burrage, Joe and Schalkwyk, Leo and Kumari, Meena (2018) Socioeconomic Position and DNA Methylation Age Acceleration across the Lifecourse. American Journal of Epidemiology, 187 (11). pp. 2346-2354. DOI https://doi.org/10.1093/aje/kwy155

Marzi, Sarah J and Leung, Szi Kay and Ribarska, Teodora and Hannon, Eilis and Smith, Adam R and Pishva, Ehsan and Poschmann, Jeremie and Moore, Karen and Troakes, Claire and Al-Sarraj, Safa and Beck, Stephan and Newman, Stuart and Lunnon, Katie and Schalkwyk, Leonard C and Mill, Jonathan (2018) A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex. Nature Neuroscience, 21 (11). pp. 1618-1627. DOI https://doi.org/10.1038/s41593-018-0253-7

Devall, Matthew and Smith, Rebecca G and Jeffries, Aaron and Hannon, Eilis and Davies, Matthew N and Schalkwyk, Leonard and Mill, Jonathan and Weedon, Michael and Lunnon, Katie (2017) Regional differences in mitochondrial DNA methylation in human post-mortem brain tissue. Clinical Epigenetics, 9 (1). 47-. DOI https://doi.org/10.1186/s13148-017-0337-3

Janecka, Magdalena and Haworth, Claire MA and Ronald, Angelica and Krapohl, Eva and Happé, Francesca and Mill, Jonathan and Schalkwyk, Leonard C and Fernandes, Cathy and Reichenberg, Abraham and Rijsdijk, Frühling (2017) Paternal Age Alters Social Development in Offspring. Journal of the American Academy of Child & Adolescent Psychiatry, 56 (5). pp. 383-390. DOI https://doi.org/10.1016/j.jaac.2017.02.006

Lunnon, Katie and Hannon, Eilis and Smith, Rebecca G and Dempster, Emma and Wong, Chloe and Burrage, Joe and Troakes, Claire and Al-Sarraj, Safa and Kepa, Agnieszka and Schalkwyk, Leonard and Mill, Jonathan (2016) Variation in 5-hydroxymethylcytosine across human cortex and cerebellum. Genome Biology, 17 (1). 27-. DOI https://doi.org/10.1186/s13059-016-0871-x

Hannon, Eilis and Dempster, Emma and Viana, Joana and Burrage, Joe and Smith, Adam R and Macdonald, Ruby and St Clair, David and Mustard, Colette and Breen, Gerome and Therman, Sebastian and Kaprio, Jaakko and Toulopoulou, Timothea and Pol, Hilleke E Hulshoff and Bohlken, Marc M and Kahn, Rene S and Nenadic, Igor and Hultman, Christina M and Murray, Robin M and Collier, David A and Bass, Nick and Gurling, Hugh and McQuillin, Andrew and Schalkwyk, Leonard and Mill, Jonathan (2016) An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation. Genome Biology, 17 (1). 176-. DOI https://doi.org/10.1186/s13059-016-1041-x

Smith, Adam R and Smith, Rebecca G and Condliffe, Daniel and Hannon, Eilis and Schalkwyk, Leonard and Mill, Jonathan and Lunnon, Katie (2016) Increased DNA methylation near TREM2 is consistently seen in the superior temporal gyrus in Alzheimer's disease brain. Neurobiology of Aging, 47. pp. 35-40. DOI https://doi.org/10.1016/j.neurobiolaging.2016.07.008

Marzi, Sarah J and Meaburn, Emma L and Dempster, Emma L and Lunnon, Katie and Paya-Cano, Jose L and Smith, Rebecca G and Volta, Manuela and Troakes, Claire and Schalkwyk, Leonard C and Mill, Jonathan (2016) Tissue-specific patterns of allelically-skewed DNA methylation. Epigenetics, 11 (1). pp. 24-35. DOI https://doi.org/10.1080/15592294.2015.1127479

Hannon, Eilis and Spiers, Helen and Viana, Joana and Pidsley, Ruth and Burrage, Joe and Murphy, Therese M and Troakes, Claire and Turecki, Gustavo and O'Donovan, Michael C and Schalkwyk, Leonard C and Bray, Nicholas J and Mill, Jonathan (2016) Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. Nature Neuroscience, 19 (1). pp. 48-54. DOI https://doi.org/10.1038/nn.4182

Hannon, Eilis and Lunnon, Katie and Schalkwyk, Leonard and Mill, Jonathan (2015) Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. Epigenetics, 10 (11). pp. 1024-1032. DOI https://doi.org/10.1080/15592294.2015.1100786

Spiers, Helen and Hannon, Eilis and Schalkwyk, Leonard C and Smith, Rebecca and Wong, Chloe CY and O’Donovan, Michael C and Bray, Nicholas J and Mill, Jonathan (2015) Methylomic trajectories across human fetal brain development. Genome Research, 25 (3). pp. 338-352. DOI https://doi.org/10.1101/gr.180273.114

De Jager, Philip L and Srivastava, Gyan and Lunnon, Katie and Burgess, Jeremy and Schalkwyk, Leonard C and Yu, Lei and Eaton, Matthew L and Keenan, Brendan T and Ernst, Jason and McCabe, Cristin and Tang, Anna and Raj, Towfique and Replogle, Joseph and Brodeur, Wendy and Gabriel, Stacey and Chai, High S and Younkin, Curtis and Younkin, Steven G and Zou, Fanggeng and Szyf, Moshe and Epstein, Charles B and Schneider, Julie A and Bernstein, Bradley E and Meissner, Alex and Ertekin-Taner, Nilufer and Chibnik, Lori B and Kellis, Manolis and Mill, Jonathan and Bennett, David A (2014) Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nature Neuroscience, 17 (9). pp. 1156-1163. DOI https://doi.org/10.1038/nn.3786

Lunnon, Katie and Smith, Rebecca and Hannon, Eilis and De Jager, Philip L and Srivastava, Gyan and Volta, Manuela and Troakes, Claire and Al-Sarraj, Safa and Burrage, Joe and Macdonald, Ruby and Condliffe, Daniel and Harries, Lorna W and Katsel, Pavel and Haroutunian, Vahram and Kaminsky, Zachary and Joachim, Catharine and Powell, John and Lovestone, Simon and Bennett, David A and Schalkwyk, Leonard C and Mill, Jonathan (2014) Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease. Nature Neuroscience, 17 (9). pp. 1164-1170. DOI https://doi.org/10.1038/nn.3782

Condliffe, Daniel and Wong, Andrew and Troakes, Claire and Proitsi, Petroula and Patel, Yogen and Chouliaras, Leonidas and Fernandes, Cathy and Cooper, Jonathan and Lovestone, Simon and Schalkwyk, Leonard and Mill, Jonathan and Lunnon, Katie (2014) Cross-region reduction in 5-hydroxymethylcytosine in Alzheimer's disease brain. Neurobiology of Aging, 35 (8). pp. 1850-1854. DOI https://doi.org/10.1016/j.neurobiolaging.2014.02.002

Viana, Joana and Pidsley, Ruth and Troakes, Claire and Spiers, Helen and Wong, Chloe CY and Al-Sarraj, Safa and Craig, Ian and Schalkwyk, Leonard and Mill, Jonathan (2014) Epigenomic and transcriptomic signatures of a Klinefelter syndrome (47,XXY) karyotype in the brain. Epigenetics, 9 (4). pp. 587-599. DOI https://doi.org/10.4161/epi.27806

Jeffries, Aaron R and Perfect, Leo W and Ledderose, Julia and Schalkwyk, Leonard C and Bray, Nicholas J and Mill, Jonathan and Price, Jack (2012) Stochastic Choice of Allelic Expression in Human Neural Stem Cells. Stem Cells, 30 (9). pp. 1938-1947. DOI https://doi.org/10.1002/stem.1155

Dempster, Emma L and Pidsley, Ruth and Schalkwyk, Leonard C and Owens, Sheena and Georgiades, Anna and Kane, Fergus and Kalidindi, Sridevi and Picchioni, Marco and Kravariti, Eugenia and Toulopoulou, Timothea and Murray, Robin M and Mill, Jonathan (2011) Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder. Human Molecular Genetics, 20 (24). pp. 4786-4796. DOI https://doi.org/10.1093/hmg/ddr416

Meaburn, Emma L and Schalkwyk, Leonard C and Mill, Jonathan (2010) Allele-specific methylation in the human genome. Epigenetics, 5 (7). pp. 578-582. DOI https://doi.org/10.4161/epi.5.7.12960

Schalkwyk, Leonard C and Meaburn, Emma L and Smith, Rebecca and Dempster, Emma L and Jeffries, Aaron R and Davies, Matthew N and Plomin, Robert and Mill, Jonathan (2010) Allelic Skewing of DNA Methylation Is Widespread across the Genome. The American Journal of Human Genetics, 86 (2). pp. 196-212. DOI https://doi.org/10.1016/j.ajhg.2010.01.014

Smith, Rebecca G and Kember, Rachel L and Mill, Jonathan and Fernandes, Cathy and Schalkwyk, Leonard C and Buxbaum, Joseph D and Reichenberg, Abraham (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. DOI https://doi.org/10.1371/journal.pone.0008456

Craig, Ian W and Mill, Jonathan and Craig, Gavin M and Loat, Caroline and Schalkwyk, Leonard C (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). pp. 639-646. DOI https://doi.org/10.1038/sj.ejhg.5201212