Simon Andrews

Publications

• DNA Methylation Changes During Preimplantation Development Reveal Inter-species Differences and Reprogramming Events at Imprinted Genes
  Clinical Epigenetics. May, 2020  |   Pubmed ID: 32393379
• Low Rates of Mutation in Clinical Grade Human Pluripotent Stem Cells Under Different Culture Conditions
  Nature Communications. Mar, 2020  |   Pubmed ID: 32251294
• RNA Proximity Sequencing Data and Analysis Pipeline from a Human Neuroblastoma Nuclear Transcriptome
  Scientific Data. 01, 2020  |   Pubmed ID: 31992717
• A KHDC3L Mutation Resulting in Recurrent Hydatidiform Mole Causes Genome-wide DNA Methylation Loss in Oocytes and Persistent Imprinting Defects Post-fertilisation
  Genome Medicine. 12, 2019  |   Pubmed ID: 31847873
• BNC1 Regulates Cell Heterogeneity in Human Pluripotent Stem Cell-derived Epicardium
  Development (Cambridge, England). Dec, 2019  |   Pubmed ID: 31767620
• Endogenous Retroviral Insertions Drive Non-canonical Imprinting in Extra-embryonic Tissues
  Genome Biology. 10, 2019  |   Pubmed ID: 31665063
• Ageing Affects DNA Methylation Drift and Transcriptional Cell-to-cell Variability in Mouse Muscle Stem Cells
  Nature Communications. 09, 2019  |   Pubmed ID: 31554804
• RNA Proximity Sequencing Reveals the Spatial Organization of the Transcriptome in the Nucleus
  Nature Biotechnology. 07, 2019  |   Pubmed ID: 31267103
• MicroRNA-155 is Essential for the Optimal Proliferation and Survival of Plasmablast B Cells
  Life Science Alliance. 06, 2019  |   Pubmed ID: 31097471
• Correction To: Comparison of Whole-genome Bisulfite Sequencing Library Preparation Strategies Identifies Sources of Biases Affecting DNA Methylation Data
  Genome Biology. 02, 2019  |   Pubmed ID: 30795792
• FastQ Screen: A Tool for Multi-genome Mapping and Quality Control
  F1000Research. 2018  |   Pubmed ID: 30254741
• Publisher Correction: TDP-43 Gains Function Due to Perturbed Autoregulation in a Tardbp Knock-in Mouse Model of ALS-FTD
  Nature Neuroscience. Aug, 2018  |   Pubmed ID: 29872124
• Unbiased Quantification of Immunoglobulin Diversity at the DNA Level with VDJ-seq
  Nature Protocols. 06, 2018  |   Pubmed ID: 29725123
• TDP-43 Gains Function Due to Perturbed Autoregulation in a Tardbp Knock-in Mouse Model of ALS-FTD
  Nature Neuroscience. 04, 2018  |   Pubmed ID: 29556029
• Comparison of Whole-genome Bisulfite Sequencing Library Preparation Strategies Identifies Sources of Biases Affecting DNA Methylation Data
  Genome Biology. 03, 2018  |   Pubmed ID: 29544553
• Capture Hi-C Identifies Putative Target Genes at 33 Breast Cancer Risk Loci
  Nature Communications. 03, 2018  |   Pubmed ID: 29531215
• MLL2 Conveys Transcription-independent H3K4 Trimethylation in Oocytes
  Nature Structural & Molecular Biology. 01, 2018  |   Pubmed ID: 29323282
• Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination
  Frontiers in Immunology. 2017  |   Pubmed ID: 29204143
• An EndosiRNA-Based Repression Mechanism Counteracts Transposon Activation During Global DNA Demethylation in Embryonic Stem Cells
  Cell Stem Cell. Nov, 2017  |   Pubmed ID: 29100015
• Transcription and Chromatin Determinants of De Novo DNA Methylation Timing in Oocytes
  Epigenetics & Chromatin. 2017  |   Pubmed ID: 28507606
• Dietary Restriction Protects from Age-associated DNA Methylation and Induces Epigenetic Reprogramming of Lipid Metabolism
  Genome Biology. 03, 2017  |   Pubmed ID: 28351387
• Gender Differences in Global but Not Targeted Demethylation in IPSC Reprogramming
  Cell Reports. 01, 2017  |   Pubmed ID: 28147265
• DNA Methylation and Gene Expression Changes Derived from Assisted Reproductive Technologies Can Be Decreased by Reproductive Fluids
  ELife. 02, 2017  |   Pubmed ID: 28134613
• Cluster Flow: A User-friendly Bioinformatics Workflow Tool
  F1000Research. 2016  |   Pubmed ID: 28299179
• Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells
  Cell Reports. 12, 2016  |   Pubmed ID: 27926872
• Comparative Principles of DNA Methylation Reprogramming During Human and Mouse In Vitro Primordial Germ Cell Specification
  Developmental Cell. 10, 2016  |   Pubmed ID: 27728778
• MYC Activation and BCL2L11 Silencing by a Tumour Virus Through the Large-scale Reconfiguration of Enhancer-promoter Hubs
  ELife. Aug, 2016  |   Pubmed ID: 27490482
• SNPsplit: Allele-specific Splitting of Alignments Between Genomes with Known SNP Genotypes
  F1000Research. 2016  |   Pubmed ID: 27429743
• Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination
  Cell Reports. 06, 2016  |   Pubmed ID: 27264181
• RNA-binding Proteins ZFP36L1 and ZFP36L2 Promote Cell Quiescence
  Science (New York, N.Y.). Apr, 2016  |   Pubmed ID: 27102483
• Pervasive Polymorphic Imprinted Methylation in the Human Placenta
  Genome Research. 06, 2016  |   Pubmed ID: 26769960
• Ageing is Associated with Molecular Signatures of Inflammation and Type 2 Diabetes in Rat Pancreatic Islets
  Diabetologia. Mar, 2016  |   Pubmed ID: 26699651
• Localizing the Lipid Products of PI3Kγ in Neutrophils
  Advances in Biological Regulation. Jan, 2016  |   Pubmed ID: 26596865
• HiCUP: Pipeline for Mapping and Processing Hi-C Data
  F1000Research. 2015  |   Pubmed ID: 26835000
• Erratum To: Deep Sequencing and De Novo Assembly of the Mouse Occyte Transcriptome Define the Contribution of Transcription to the DNA Methylation Landscape
  Genome Biology. Dec, 2015  |   Pubmed ID: 26635312
• Molecular Signatures of Plastic Phenotypes in Two Eusocial Insect Species with Simple Societies
  Proceedings of the National Academy of Sciences of the United States of America. Nov, 2015  |   Pubmed ID: 26483466
• Deep Sequencing and De Novo Assembly of the Mouse Oocyte Transcriptome Define the Contribution of Transcription to the DNA Methylation Landscape
  Genome Biology. Sep, 2015  |   Pubmed ID: 26408185
• ACF Chromatin-remodeling Complex Mediates Stress-induced Depressive-like Behavior
  Nature Medicine. Oct, 2015  |   Pubmed ID: 26390241
• Polycomb Repressive Complex PRC1 Spatially Constrains the Mouse Embryonic Stem Cell Genome
  Nature Genetics. Oct, 2015  |   Pubmed ID: 26323060
• Mapping Long-range Promoter Contacts in Human Cells with High-resolution Capture Hi-C
  Nature Genetics. Jun, 2015  |   Pubmed ID: 25938943
• The Pluripotent Regulatory Circuitry Connecting Promoters to Their Long-range Interacting Elements
  Genome Research. Apr, 2015  |   Pubmed ID: 25752748
• The RNA-binding Protein HuR is Essential for the B Cell Antibody Response
  Nature Immunology. Apr, 2015  |   Pubmed ID: 25706746
• Global Reorganization of the Nuclear Landscape in Senescent Cells
  Cell Reports. Feb, 2015  |   Pubmed ID: 25640177
• Epigenetic Memory of the First Cell Fate Decision Prevents Complete ES Cell Reprogramming into Trophoblast
  Nature Communications. Nov, 2014  |   Pubmed ID: 25423963
• The MiR-155-PU.1 Axis Acts on Pax5 to Enable Efficient Terminal B Cell Differentiation
  The Journal of Experimental Medicine. Oct, 2014  |   Pubmed ID: 25288398
• Unbiased Analysis of Potential Targets of Breast Cancer Susceptibility Loci by Capture Hi-C
  Genome Research. Nov, 2014  |   Pubmed ID: 25122612
• Single-cell Genome-wide Bisulfite Sequencing for Assessing Epigenetic Heterogeneity
  Nature Methods. Aug, 2014  |   Pubmed ID: 25042786
• A Screen for Hydroxymethylcytosine and Formylcytosine Binding Proteins Suggests Functions in Transcription and Chromatin Regulation
  Genome Biology. 2013  |   Pubmed ID: 24156278
• FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency
  Cell Stem Cell. Jul, 2013  |   Pubmed ID: 23850245
• Deficiency in Spliceosome-associated Factor CTNNBL1 Does Not Affect Ongoing Cell Cycling but Delays Exit from Quiescence and Results in Embryonic Lethality in Mice
  Cell Cycle (Georgetown, Tex.). Mar, 2013  |   Pubmed ID: 23343763
• The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells
  Molecular Cell. Dec, 2012  |   Pubmed ID: 23219530
• Mutual Antagonism Between IP(3)RII and MiRNA-133a Regulates Calcium Signals and Cardiac Hypertrophy
  The Journal of Cell Biology. Nov, 2012  |   Pubmed ID: 23166348
• DNA Methylation Profiles Define Stem Cell Identity and Reveal a Tight Embryonic-extraembryonic Lineage Boundary
  Stem Cells (Dayton, Ohio). Dec, 2012  |   Pubmed ID: 23034951
• An Unbiased Assessment of the Role of Imprinted Genes in an Intergenerational Model of Developmental Programming
  PLoS Genetics. 2012  |   Pubmed ID: 22511876
• DNA Methylome Analysis Using Short Bisulfite Sequencing Data
  Nature Methods. Jan, 2012  |   Pubmed ID: 22290186
• Age-dependent Axonal Transport and Locomotor Changes and Tau Hypophosphorylation in a "P301L" Tau Knockin Mouse
  Neurobiology of Aging. Mar, 2012  |   Pubmed ID: 21492964
• High-throughput Analysis of Calcium Signalling Kinetics in Astrocytes Stimulated with Different Neurotransmitters
  PloS One. 2011  |   Pubmed ID: 22046396
• Dynamic CpG Island Methylation Landscape in Oocytes and Preimplantation Embryos
  Nature Genetics. Jun, 2011  |   Pubmed ID: 21706000
• Bismark: a Flexible Aligner and Methylation Caller for Bisulfite-Seq Applications
  Bioinformatics (Oxford, England). Jun, 2011  |   Pubmed ID: 21493656
• Dynamic Regulation of 5-hydroxymethylcytosine in Mouse ES Cells and During Differentiation
  Nature. May, 2011  |   Pubmed ID: 21460836
• Large Scale Loss of Data in Low-diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling
  PloS One. Jan, 2011  |   Pubmed ID: 21305042
• Dynamic Stage-specific Changes in Imprinted Differentially Methylated Regions During Early Mammalian Development and Prevalence of Non-CpG Methylation in Oocytes
  Development (Cambridge, England). Mar, 2011  |   Pubmed ID: 21247965
• What is the Advantage of a Transient Precursor in Autophagosome Biogenesis?
  Autophagy. Jan, 2011  |   Pubmed ID: 20935487
• PI3K Signaling Through the Dual GTPase-activating Protein ARAP3 is Essential for Developmental Angiogenesis
  Science Signaling. Oct, 2010  |   Pubmed ID: 20978237
• Difference Tracker: ImageJ Plugins for Fully Automated Analysis of Multiple Axonal Transport Parameters
  Journal of Neuroscience Methods. Nov, 2010  |   Pubmed ID: 20869987
• Deletion of the RNA-binding Proteins ZFP36L1 and ZFP36L2 Leads to Perturbed Thymic Development and T Lymphoblastic Leukemia
  Nature Immunology. Aug, 2010  |   Pubmed ID: 20622884
• Genome-wide Erasure of DNA Methylation in Mouse Primordial Germ Cells is Affected by AID Deficiency
  Nature. Feb, 2010  |   Pubmed ID: 20098412
• Preferential Associations Between Co-regulated Genes Reveal a Transcriptional Interactome in Erythroid Cells
  Nature Genetics. Jan, 2010  |   Pubmed ID: 20010836
• Global Mapping of DNA Methylation in Mouse Promoters Reveals Epigenetic Reprogramming of Pluripotency Genes
  PLoS Genetics. Jun, 2008  |   Pubmed ID: 18584034
• P-Rex2 Regulates Purkinje Cell Dendrite Morphology and Motor Coordination
  Proceedings of the National Academy of Sciences of the United States of America. Mar, 2008  |   Pubmed ID: 18334636
• PI3K Class IB Pathway in Neutrophils
  Science's STKE : Signal Transduction Knowledge Environment. Oct, 2007  |   Pubmed ID: 17925574
• PI3K Class IB Pathway
  Science's STKE : Signal Transduction Knowledge Environment. Oct, 2007  |   Pubmed ID: 17925573
• PI(3)Kgamma Has an Important Context-dependent Role in Neutrophil Chemokinesis
  Nature Cell Biology. Jan, 2007  |   Pubmed ID: 17173040
• ARAP3 is Essential for Formation of Lamellipodia After Growth Factor Stimulation
  Journal of Cell Science. Feb, 2006  |   Pubmed ID: 16418224
• P-Rex1 Regulates Neutrophil Function
  Current Biology : CB. Oct, 2005  |   Pubmed ID: 16243035
• Regulation of P-Rex1 by Phosphatidylinositol (3,4,5)-trisphosphate and Gbetagamma Subunits
  The Journal of Biological Chemistry. Feb, 2005  |   Pubmed ID: 15545267
• TRP Channels at a Glance
  Journal of Cell Science. Nov, 2004  |   Pubmed ID: 15537828
• P-Rex2, a New Guanine-nucleotide Exchange Factor for Rac
  FEBS Letters. Aug, 2004  |   Pubmed ID: 15304343
• The PX Domain: a New Phosphoinositide-binding Module
  Journal of Cell Science. Mar, 2002  |   Pubmed ID: 11884510