Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks
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Martin Schäfer | Philip L. De Jager | David A. Bennett | Holger Schwender | Hans-Ulrich Klein | D. Bennett | P. D. Jager | H. Klein | H. Schwender | Martin Schäfer | P. L. Jager | D. Bennett
[1] Peter Davies,et al. Identification of normal and pathological aging in prospectively studied nondemented elderly humans , 1992, Neurobiology of Aging.
[2] J. Barral,et al. Ubiquilin-1 regulates amyloid precursor protein maturation and degradation by stimulating K63-linked polyubiquitination of lysine 688 , 2012, Proceedings of the National Academy of Sciences.
[3] A. Herskovits,et al. The regulation of tau phosphorylation by PCTAIRE 3: Implications for the pathogenesis of Alzheimer's disease , 2006, Neurobiology of Disease.
[4] Manolis Kellis,et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci , 2014 .
[5] Brian L. West,et al. Colony-Stimulating Factor 1 Receptor Signaling Is Necessary for Microglia Viability, Unmasking a Microglia Progenitor Cell in the Adult Brain , 2014, Neuron.
[6] Eric Tardif,et al. Pathological reorganization of NMDA receptors subunits and postsynaptic protein PSD-95 distribution in Alzheimer's disease. , 2014, Current Alzheimer research.
[7] James B. Brown,et al. Modeling gene expression using chromatin features in various cellular contexts , 2012, Genome Biology.
[8] Katja Ickstadt,et al. Toward Integrative Bayesian Analysis in Molecular Biology , 2018 .
[9] M. Hiramatsu,et al. Involvement of GAT2/BGT‐1 in the preventive effects of betaine on cognitive impairment and brain oxidative stress in amyloid &bgr; peptide‐injected mice , 2019, European journal of pharmacology.
[10] Claudia Angelini,et al. Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems , 2014, Front. Cell Dev. Biol..
[11] Seth Love,et al. Overexpression of Kinesin Superfamily Motor Proteins in Alzheimer's Disease. , 2017, Journal of Alzheimer's disease : JAD.
[12] Vladislav A Petyuk,et al. Label-free quantitative LC-MS proteomics of Alzheimer's disease and normally aged human brains. , 2012, Journal of proteome research.
[13] E. Marcotte,et al. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. , 2011, Genome research.
[14] Hans-Ulrich Klein,et al. Uncovering the Role of the Methylome in Dementia and Neurodegeneration. , 2016, Trends in molecular medicine.
[15] Martin Schäfer,et al. Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models , 2014, Bioinform..
[16] Jaakko Nevalainen,et al. Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields , 2017, Bioinform..
[17] Data production leads,et al. An integrated encyclopedia of DNA elements in the human genome , 2012 .
[18] George C Tseng,et al. Statistical Methods in Integrative Genomics. , 2016, Annual review of statistics and its application.
[19] Holger Rosenbrock,et al. Evaluation of Pharmacokinetics and Pharmacodynamics of BI 425809, a Novel GlyT1 Inhibitor: Translational Studies , 2018, Clinical and translational science.
[20] Marina Vannucci,et al. Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data , 2011, Bioinform..
[21] K. Pollard,et al. Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin , 2016, Nature Genetics.
[22] S. Scheff,et al. Alzheimer's disease-related alterations in synaptic density: neocortex and hippocampus. , 2006, Journal of Alzheimer's disease : JAD.
[23] D. Bennett,et al. LONG-TERM FETAL CELL TRANSPLANT IN HUNTINGTON DISEASE: STAYIN’ ALIVE , 2007, Neurology.
[24] J. Hamilton,et al. Colony stimulating factors and myeloid cell biology in health and disease. , 2013, Trends in immunology.
[25] Bin Zhao,et al. Roles of AMP-activated Protein Kinase in Alzheimer’s Disease , 2012, NeuroMolecular Medicine.
[26] Manoj Kumar,et al. INGE GRUNDKE-IQBAL AWARD FOR ALZHEIMER’S RESEARCH: NEUROTOXIC REACTIVE ASTROCYTES ARE INDUCED BY ACTIVATED MICROGLIA , 2019, Alzheimer's & Dementia.
[27] David A. Bennett,et al. Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline , 2018, Front. Genet..
[28] Rüdiger Schweigreiter,et al. Apolipoprotein D takes center stage in the stress response of the aging and degenerative brain☆ , 2014, Neurobiology of Aging.
[29] Hilkka Soininen,et al. Alzheimer's disease-associated ubiquilin-1 regulates presenilin-1 accumulation and aggresome formation , 2010, Alzheimer's & Dementia.
[30] Bin Li,et al. Disruption of microtubule network by Alzheimer abnormally hyperphosphorylated tau , 2007, Acta Neuropathologica.
[31] Gordon K Smyth,et al. Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .
[32] David S. Greenberg,et al. Alzheimer's brains show inter-related changes in RNA and lipid metabolism , 2017, Neurobiology of Disease.
[33] Bin Zhang,et al. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility , 2018, Nature Genetics.
[34] Teng Jiang,et al. Microglia in Alzheimer's Disease , 2014, BioMed research international.
[35] David A Bennett,et al. Religious Orders Study and Rush Memory and Aging Project. , 2018, Journal of Alzheimer's disease : JAD.
[36] Roberto Montemanni,et al. A divide and conquer matheuristic algorithm for the Prize-collecting Steiner Tree Problem , 2016, Comput. Oper. Res..
[37] Luc Buée,et al. AMP-activated protein kinase modulates tau phosphorylation and tau pathology in vivo , 2016, Scientific Reports.
[38] Ping Xu,et al. The Loss of c-Jun N-Terminal Protein Kinase Activity Prevents the Amyloidogenic Cleavage of Amyloid Precursor Protein and the Formation of Amyloid Plaques In Vivo , 2011, The Journal of Neuroscience.
[39] Hans-Ulrich Klein,et al. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in the aging and Alzheimer human brain , 2018, Nature Neuroscience.
[40] Kevin Y. Yip,et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data , 2012, Genome research.
[41] R. Luján,et al. RGS7/Gβ5/R7BP complex regulates synaptic plasticity and memory by modulating hippocampal GABABR-GIRK signaling , 2014, eLife.
[42] Jing Tian,et al. Amyloid beta-mediated KIF5A deficiency disrupts anterograde axonal mitochondrial movement , 2019, Neurobiology of Disease.
[43] Mariana Vargas-Caballero,et al. Pharmacological targeting of CSF1R inhibits microglial proliferation and prevents the progression of Alzheimer’s-like pathology , 2016, Brain : a journal of neurology.
[44] Julia A. Lasserre,et al. Histone modification levels are predictive for gene expression , 2010, Proceedings of the National Academy of Sciences.
[45] Xiaojiang Xu,et al. Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression , 2010, BMC Bioinformatics.
[46] Ramesh Kandimalla,et al. Multiple faces of dynamin-related protein 1 and its role in Alzheimer's disease pathogenesis. , 2016, Biochimica et biophysica acta.
[47] Christian Borgs,et al. Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem , 2012, J. Comput. Biol..
[48] Y. Moreau,et al. Computational tools for prioritizing candidate genes: boosting disease gene discovery , 2012, Nature Reviews Genetics.
[49] Martin Dugas,et al. Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia , 2012, Nature Medicine.
[50] Diego Sanchez,et al. Apolipoprotein D modulates amyloid pathology in APP/PS1 Alzheimer's disease mice , 2015, Neurobiology of Aging.
[51] Berthold Göttgens,et al. Critical Modulation of Hematopoietic Lineage Fate by Hepatic Leukemia Factor , 2017, Cell reports.
[52] Yi Zhong,et al. Digital sorting of complex tissues for cell type-specific gene expression profiles , 2013, BMC Bioinformatics.
[53] Martin Schäfer,et al. Integrative analysis of multiple genomic variables using a hierarchical Bayesian model , 2017, Bioinform..
[54] C. Jack,et al. NIA-AA Research Framework: Toward a biological definition of Alzheimer’s disease , 2018, Alzheimer's & Dementia.
[55] J. Schneider,et al. Neuropathology of older persons without cognitive impairment from two community-based studies , 2006, Neurology.
[56] Ayellet V. Segrè,et al. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation , 2018, Nature Genetics.
[57] Martin Dugas,et al. Integrative Analyses for Omics Data: A Bayesian Mixture Model to Assess the Concordance of ChIP-chip and ChIP-seq Measurements , 2012, Journal of toxicology and environmental health. Part A.
[58] Sven Laur,et al. Robust rank aggregation for gene list integration and meta-analysis , 2012, Bioinform..
[59] Caleb Webber,et al. CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice , 2019, Brain : a journal of neurology.
[60] Hilkka Soininen,et al. Alzheimer's Disease‐Associated Ubiquilin‐1 Regulates Presenilin‐1 Accumulation and Aggresome Formation , 2011, Traffic.
[61] Katsuya Harada,et al. A novel glycine transporter-1 (GlyT1) inhibitor, ASP2535 (4-[3-isopropyl-5-(6-phenyl-3-pyridyl)-4H-1,2,4-triazol-4-yl]-2,1,3-benzoxadiazole), improves cognition in animal models of cognitive impairment in schizophrenia and Alzheimer's disease. , 2012, European journal of pharmacology.
[62] Masaru Tomita,et al. Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns , 2010, BMC Genomics.
[63] M. Ritchie,et al. Methods of integrating data to uncover genotype–phenotype interactions , 2015, Nature Reviews Genetics.
[64] Michael J. Devine,et al. Mitochondria at the neuronal presynapse in health and disease , 2018, Nature Reviews Neuroscience.
[65] Wei Pan,et al. Network‐Based Penalized Regression With Application to Genomic Data , 2013, Biometrics.
[66] W. Wong,et al. ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells , 2009, Proceedings of the National Academy of Sciences.
[67] Judy H. Cho,et al. Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association Studies , 2011, PLoS genetics.
[68] Márcio Costa,et al. Protein Phosphorylation is a Key Mechanism in Alzheimer's Disease. , 2017, Journal of Alzheimer's disease : JAD.
[69] Wei Pan,et al. Predictor Network in Penalized Regression with Application to Microarray Data” , 2009 .
[70] Andrea L. Rosso,et al. Disruption of glutamate receptors at Shank-postsynaptic platform in Alzheimer's disease , 2009, Brain Research.
[71] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[72] Charles C. White,et al. A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease , 2018, Nature Neuroscience.
[73] F. Ginhoux,et al. Fate Mapping Analysis Reveals That Adult Microglia Derive from Primitive Macrophages , 2010, Science.
[74] E. Chang,et al. Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse , 2016, Neuron.
[75] Manolis Kellis,et al. Single-cell transcriptomic analysis of Alzheimer’s disease , 2019, Nature.
[76] Eva Benito,et al. MicroRNA‐125b induces tau hyperphosphorylation and cognitive deficits in Alzheimer's disease , 2014, The EMBO journal.
[77] Benjamin A. Logsdon,et al. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease , 2018, Scientific Data.
[78] Maria Nikodemova,et al. CSF1 overexpression has pleiotropic effects on microglia in vivo , 2014, Glia.
[79] Maria Balea,et al. The ubiquitin proteasomal system: a potential target for the management of Alzheimer's disease , 2016, Journal of cellular and molecular medicine.
[80] Wei Zhang,et al. Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. , 2018, Cell systems.
[81] Roberto Montemanni,et al. PCSF: An R-package for network-based interpretation of high-throughput data , 2017, PLoS Comput. Biol..
[82] C. Myers,et al. Using networks to measure similarity between genes: association index selection , 2013, Nature Methods.
[83] R. Cowburn,et al. Tau‐Tubulin Kinase 1 Expression, Phosphorylation and Co‐Localization with Phospho‐Ser422 Tau in the Alzheimer's Disease Brain , 2013, Brain pathology.
[84] Ellis Patrick,et al. An xQTL map integrates the genetic architecture of the human brain’s transcriptome and epigenome , 2017, Nature Neuroscience.
[85] ENCODEConsortium,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[86] Jian Huang,et al. The Sparse Laplacian Shrinkage Estimator for High-Dimensional Regression. , 2011, Annals of statistics.
[87] David A. Bennett,et al. TDP-43 pathology in anterior temporal pole cortex in aging and Alzheimer’s disease , 2018, Acta Neuropathologica Communications.
[88] C. Briggs,et al. Emerging pathways driving early synaptic pathology in Alzheimer's disease. , 2017, Biochemical and biophysical research communications.
[89] James A. Eddy,et al. Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases , 2016, Scientific Data.
[90] Ernest Fraenkel,et al. Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package , 2016, PLoS Comput. Biol..
[91] Shannon L. Risacher,et al. Neuropathological correlates and genetic architecture of microglial activation in elderly human brain , 2019, Nature Communications.
[92] James C. Hu,et al. The Gene Ontology Resource: 20 years and still GOing strong , 2019 .
[93] A. Lusis,et al. Considerations for the design of omics studies , 2017 .
[94] María J. Ramírez,et al. Decreased rabphilin 3A immunoreactivity in Alzheimer’s disease is associated with Aβ burden , 2014, Neurochemistry International.
[95] Ramesh Kandimalla,et al. Protective effects of reduced dynamin-related protein 1 against amyloid beta-induced mitochondrial dysfunction and synaptic damage in Alzheimer's disease. , 2016, Human molecular genetics.
[96] Nynke Oosterhof,et al. Colony-Stimulating Factor 1 Receptor (CSF1R) Regulates Microglia Density and Distribution, but Not Microglia Differentiation In Vivo. , 2018, Cell reports.
[97] Mathieu Blanchette,et al. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts , 2014, Genome Biology.
[98] Hongmin Wang,et al. Overexpression of Ubiquilin-1 Alleviates Alzheimer's Disease-Caused Cognitive and Motor Deficits and Reduces Amyloid-β Accumulation in Mice. , 2017, Journal of Alzheimer's disease : JAD.
[99] Thomas J. Montine,et al. The Tau Tubulin Kinases TTBK1/2 Promote Accumulation of Pathological TDP-43 , 2014, PLoS genetics.
[100] Chao Zhang,et al. Sustained microglial depletion with CSF1R inhibitor impairs parenchymal plaque development in an Alzheimer’s disease model , 2019, Nature Communications.
[101] James L. Buescher,et al. Tau‐tubulin kinase 1 (TTBK1), a neuron‐specific tau kinase candidate, is involved in tau phosphorylation and aggregation , 2006, Journal of neurochemistry.
[102] Kenta Nakai,et al. A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns , 2011, BMC Bioinformatics.
[103] Hans-Ulrich Klein,et al. Integrative Analysis of Histone ChIP‐seq and RNA‐seq Data , 2016, Current protocols in human genetics.
[104] Michael Q. Zhang,et al. Integrative analysis of 111 reference human epigenomes , 2015, Nature.
[105] Thomas Lengauer,et al. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure , 2006, Bioinform..
[106] Leah Edelstein-Keshet,et al. Analysis of a minimal Rho-GTPase circuit regulating cell shape , 2016, Physical biology.
[107] Lana X. Garmire,et al. More Is Better: Recent Progress in Multi-Omics Data Integration Methods , 2017, Front. Genet..
[108] Li Jin,et al. Application of Causal Inference to Genomic Analysis: Advances in Methodology , 2018, Front. Genet..
[109] Hans-Ulrich Klein,et al. A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research , 2018, Scientific Data.
[110] Dennis W Dickson,et al. Is pathological aging a successful resistance against amyloid-beta or preclinical Alzheimer’s disease? , 2014, Alzheimer's Research & Therapy.
[111] Luciano Milanesi,et al. Methods for the integration of multi-omics data: mathematical aspects , 2016, BMC Bioinformatics.
[112] K. Christensen,et al. Novel screening cascade identifies MKK4 as key kinase regulating Tau phosphorylation at Ser422 , 2011, Molecular and Cellular Biochemistry.
[113] David Carling,et al. AMP-activated protein kinase (AMPK) is a tau kinase, activated in response to amyloid β-peptide exposure. , 2011, The Biochemical journal.
[114] Sara Mostafavi,et al. Targeted brain proteomics uncover multiple pathways to Alzheimer's dementia , 2018, Annals of neurology.
[115] Sumio Sugano,et al. Curved EFC/F-BAR-Domain Dimers Are Joined End to End into a Filament for Membrane Invagination in Endocytosis , 2007, Cell.
[116] Enrique Bernal-Delgado,et al. Shared component modelling as an alternative to assess geographical variations in medical practice: gender inequalities in hospital admissions for chronic diseases , 2011, BMC medical research methodology.