Publications

Francisco Rodriguez-Algarra, Robert AE Seaborne, Amy F Danson, Selin Yildizoglu, Harunori Yoshikawa, Pui Pik Law, Zakaryya Ahmad, Victoria A Maudsley, Ama Brew, Nadine Holmes, others

CUT&Tag recovers up to half of ENCODE ChIP-seq peaks

Di Hu, Leyla Abbasova, Brian Schilder, Alexi Nott, Nathan Skene, Sarah Marzi

A balanced measure shows superior performance of pseudobulk methods over mixed models and pseudoreplication approaches in single-cell RNA-sequencing analysis

Alan Murphy, Nathan Skene

The histone modification H3K4me3 is altered at the ANK1 locus in Alzheimer's disease brain

Adam R Smith, Rebecca G Smith, Ruby Macdonald, Sarah Marzi, Joe Burrage, Claire Troakes, Safa Al-Sarraj, Jonathan Mill, Katie Lunnon

ScFlow: A scalable and reproducible analysis pipeline for single-cell RNA sequencing data

Combiz Khozoie, Nurun Fancy, Mahdi M Marjaneh, Alan Murphy, Paul M Matthews, Nathan Skene

MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics

Alan Murphy, Brian Schilder, Nathan Skene

Conditional GWAS analysis to identify disorder-specific SNPs for psychiatric disorders

Enda M Byrne, Zhihong Zhu, Ting Qi, Nathan Skene, Julien Bryois, Antonio F Pardinas, Eli Stahl, Jordan W Smoller, Marcella Rietschel, Michael J Owen, others

Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression

Andrea Cerase, Alexander N Young, Nerea Blanes Ruiz, Andreas Buness, Gabrielle M Sant, Mirjam Arnold, Monica Di Giacomo, Michela Ascolani, Manish Kumar, Andreas Hierholzer, others

CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders

Kitty Murphy, Alexi Nott, Sarah Marzi

Altered perivascular fibroblast activity precedes ALS disease onset

Anna Månberg, Nathan Skene, Folkert Sanders, Marta Trusohamn, Julia Remnestål, Anna Szczepinska, Inci Sevval Aksoylu, Peter Lönnerberg, Lwaki Ebarasi, Stefan Wouters, others

Single nucleus sequencing fails to detect microglial activation in human tissue

N Thrupp, C Sala Frigerio, L Wolfs, NG Skene, S Poovathingal, Y Fourne, PM Matthews, T Theys, R Mancuso, B de Strooper, others

Probabilistic cell typing enables fine mapping of closely related cell types in situ

Xiaoyan Qian, Kenneth D Harris, Thomas Hauling, Dimitris Nicoloutsopoulos, Ana B Muñoz-Manchado, Nathan Skene, Jens Hjerling-Leffler, Mats Nilsson

Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson’s disease

Julien Bryois, Nathan Skene, Thomas Folkmann Hansen, Lisette JA Kogelman, Hunna J Watson, Zijing Liu, Leo Brueggeman, Gerome Breen, Cynthia M Bulik, Ernest Arenas, others

DNA methylation covariation in human whole blood and sperm: implications for studies of intergenerational epigenetic effects

Fredrika Åsenius, Tyler J Gorrie-Stone, Ama Brew, Yasmin Panchbaya, Elizabeth Williamson, Leonard C Schalkwyk, Vardhman K Rakyan, Michelle L Holland, Sarah Marzi, David J Williams

A lack of DNA methylation covariation between human blood and sperm make it unlikely to mediate intergenerational inheritance of acquired traits

F Asenius, SJ Marzi, TJ Gorrie-Stone, A Brew, Y Panchbaya, E Williamson, L Schalkwyk, V Rakyan, DJ Williams

Genome-wide analysis of insomnia in 1,331,010 individuals identifies new risk loci and functional pathways

Philip R Jansen, Kyoko Watanabe, Sven Stringer, Nathan Skene, Julien Bryois, Anke R Hammerschlag, Christiaan A de Leeuw, Jeroen S Benjamins, Ana B Muñoz-Manchado, Mats Nagel, others

Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains

Eilis Hannon, Sarah Marzi, Leonard S Schalkwyk, Jonathan Mill

Epigenetics in eating disorders: a systematic review

Christopher Hübel, Sarah Marzi, Gerome Breen, Cynthia M Bulik

Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals

Jonathan RI Coleman, Julien Bryois, Héléna A Gaspar, Philip R Jansen, Jeanne E Savage, Nathan Skene, Robert Plomin, Ana B Muñoz-Manchado, Sten Linnarsson, Greg Crawford, others

Proteomic analysis of postsynaptic proteins in regions of the human neocortex

Marcia Roy, Oksana Sorokina, Nathan Skene, Clemence Simonnet, Francesca Mazzo, Ruud Zwart, Emanuele Sher, Colin Smith, J Douglas Armstrong, Seth GN Grant

Integrative analysis of rare variants and pathway information shows convergent results between immune pathways, drug targets and epilepsy genes

Hoang T Nguyen, Amanda Dobbyn, Alexander W Charney, Julien Bryois, April Kim, Whitney Mcfadden, Nathan Skene, Laura M Huckins, Weiqing Wang, Douglas M Ruderfer, others

Genetic identification of brain cell types underlying schizophrenia

Nathan Skene, Julien Bryois, Trygve E Bakken, Gerome Breen, James J Crowley, Héléna A Gaspar, Paola Giusti-Rodriguez, Rebecca D Hodge, Jeremy A Miller, Ana B Muñoz-Manchado, others

Early life diet conditions the molecular response to post-weaning protein restriction in the mouse

Amy F Danson, Sarah Marzi, Robert Lowe, Michelle L Holland, Vardhman K Rakyan

Diversity of interneurons in the dorsal striatum revealed by single-cell RNA sequencing and PatchSeq

Ana B Muñoz-Manchado, Carolina Bengtsson Gonzales, Amit Zeisel, Hermany Munguba, Bo Bekkouche, Nathan Skene, Peter Lönnerberg, Jesper Ryge, Kenneth D Harris, Sten Linnarsson, others

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics

Kenneth D Harris, Hannah Hochgerner, Nathan Skene, Lorenza Magno, Linda Katona, Carolina Bengtsson Gonzales, Peter Somogyi, Nicoletta Kessaris, Sten Linnarsson, Jens Hjerling-Leffler

Architecture of the mouse brain synaptome

Fei Zhu, Mélissa Cizeron, Zhen Qiu, Ruth Benavides-Piccione, Maksym V Kopanitsa, Nathan Skene, Babis Koniaris, Javier DeFelipe, Erik Fransén, Noboru H Komiyama, others

Analysis of DNA methylation in young people: limited evidence for an association between victimization stress and epigenetic variation in blood

Sarah Marzi, Karen Sugden, Louise Arseneault, Daniel W Belsky, Joe Burrage, David L Corcoran, Andrea Danese, Helen L Fisher, Eilis Hannon, Terrie E Moffitt, others

A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex

Sarah Marzi, Szi Kay Leung, Teodora Ribarska, Eilis Hannon, Adam R Smith, Ehsan Pishva, Jeremie Poschmann, Karen Moore, Claire Troakes, Safa Al-Sarraj, others

16.1 EPIGENETIC SIGNATURES OF CHILDHOOD AND ADOLESCENT VICTIMISATION USING A GENETICALLY SENSITIVE LONGITUDINAL COHORT STUDY.

Helen Fisher, Sarah Marzi, Louise Arseneault, Chloe Wong, Radhika Kandaswamy, Terrie Moffitt, Susanna Roberts, Jonathan Mill, Avshalom Caspi

GWAS Meta-analysis of neuroticism (N= 449,484) identifies novel genetic loci and pathways

Mats Nagel, Philip R Jansen, Sven Stringer, Kyoko Watanabe, Christiaan A de Leeuw, Julien Bryois, Jeanne E Savage, Anke R Hammerschlag, Nathan Skene, Ana B Muñoz-Manchado, others

GWAS meta-analysis (N= 279,930) identifies new genes and functional links to intelligence

Jeanne E Savage, Philip R Jansen, Sven Stringer, Kyoko Watanabe, Julien Bryois, Christiaan A de Leeuw, Mats Nagel, Swapnil Awasthi, Peter B Barr, Jonathan RI Coleman, others

Genetic polymorphisms and their association with brain and behavioural measures in heterogeneous stock mice

Magdalena Janecka, Sarah Marzi, Michael J Parsons, Lin Liu, Jose L Paya-Cano, Rebecca G Smith, Cathy Fernandes, Leonard C Schalkwyk

A genomic lifespan program that reorganises the young adult brain is targeted in schizophrenia

Nathan Skene, Marcia Roy, Seth GN Grant

Tissue-specific patterns of allelically-skewed DNA methylation

Sarah Marzi, Emma L Meaburn, Emma L Dempster, Katie Lunnon, Jose L Paya-Cano, Rebecca G Smith, Manuela Volta, Claire Troakes, Leonard C Schalkwyk, Jonathan Mill

Severe psychosocial deprivation in early childhood is associated with increased DNA methylation across a region spanning the transcription start site of CYP2E1

Robert Kumsta, Sarah Marzi, Joana Viana, EL Dempster, Bethany Crawford, Michael Rutter, Jonathan Mill, Edmund JS Sonuga-Barke

Iterative fragmentation improves the detection of ChIP-seq peaks for inactive histone marks

Miklós Laczik, Jan Hendrickx, Anne-Clémence Veillard, Mustafa Tammoh, Sarah Marzi, Dominique Poncelet

Identification of vulnerable cell types in major brain disorders using single cell transcriptomes and expression weighted cell type enrichment

Nathan Skene, Seth GN Grant

Stress-induced lipocalin-2 controls dendritic spine formation and neuronal activity in the amygdala

Anna E Skrzypiec, Rahul S Shah, Emanuele Schiavon, Eva Baker, Nathan Skene, Robert Pawlak, Mariusz Mucha

TNiK is required for postsynaptic and nuclear signaling pathways and cognitive function

Marcelo P Coba, Noboru H Komiyama, Jess Nithianantharajah, Maksym V Kopanitsa, Tim Indersmitten, Nathan Skene, Ellie J Tuck, David G Fricker, Kathryn A Elsegood, Lianne E Stanford, others