Investigating the energy crisis in Alzheimer disease using transcriptome study

[1]  Bin Zhang,et al.  Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility , 2018, Nature Genetics.

[2]  Charlotte Soneson,et al.  Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification , 2018, F1000Research.

[3]  Charlotte Soneson,et al.  Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification , 2018, F1000Research.

[4]  E. Laplantine,et al.  Role of Optineurin in the Mitochondrial Dysfunction: Potential Implications in Neurodegenerative Diseases and Cancer , 2018, Front. Immunol..

[5]  Dipanjan Roy,et al.  Integrative Analysis of Hippocampus Gene Expression Profiles Identifies Network Alterations in Aging and Alzheimer’s Disease , 2018, Front. Aging Neurosci..

[6]  Shijie Zhang,et al.  GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits , 2018, Nucleic Acids Res..

[7]  Jun Wang,et al.  SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine , 2018, Nucleic Acids Res..

[8]  Berislav V. Zlokovic,et al.  Blood–brain barrier breakdown in Alzheimer disease and other neurodegenerative disorders , 2018, Nature Reviews Neurology.

[9]  J. Landers,et al.  Transcription factor Pebbled/RREB1 regulates injury-induced axon degeneration , 2018, Proceedings of the National Academy of Sciences.

[10]  Hyojin Kim,et al.  TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions , 2017, Nucleic Acids Res..

[11]  H. Najafabadi,et al.  Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease , 2017, Nature Communications.

[12]  Shun Liu,et al.  RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data , 2017, Nucleic Acids Res..

[13]  S. Bandyopadhyay,et al.  Biological networks in Parkinson’s disease: an insight into the epigenetic mechanisms associated with this disease , 2017, BMC Genomics.

[14]  Ellis Patrick,et al.  An xQTL map integrates the genetic architecture of the human brain’s transcriptome and epigenome , 2017, Nature Neuroscience.

[15]  K. Hao,et al.  A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease , 2017, Nature Neuroscience.

[16]  C. Gaiteri,et al.  Brain xQTL map: Integrating the genetic architecture of the human brain transcriptome and epigenome , 2017, bioRxiv.

[17]  Ja-Eun Kim,et al.  Mitochondrial CCAR2/DBC1 is required for cell survival against rotenone-induced mitochondrial stress. , 2017, Biochemical and biophysical research communications.

[18]  Rob Patro,et al.  Salmon provides fast and bias-aware quantification of transcript expression , 2017, Nature Methods.

[19]  Sunil Kumar,et al.  SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity , 2016, Nucleic Acids Res..

[20]  K. Nagata,et al.  Essential role of the nuclear isoform of RBFOX1, a candidate gene for autism spectrum disorders, in the brain development , 2016, Scientific Reports.

[21]  V. Tiranti,et al.  New genes and pathomechanisms in mitochondrial disorders unraveled by NGS technologies. , 2016, Biochimica et biophysica acta.

[22]  Y. Mei,et al.  Flotillin-1 downregulates K+ current by directly coupling with Kv2.1 subunit , 2016, Protein & Cell.

[23]  M. Robinson,et al.  Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences , 2015, F1000Research.

[24]  M. Robinson,et al.  Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. , 2015, F1000Research.

[25]  M. Faghihi,et al.  Transcriptomics Profiling of Alzheimer’s Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs , 2015, Journal of Alzheimer's disease : JAD.

[26]  M. Prince,et al.  World Alzheimer Report 2015 - The Global Impact of Dementia: An analysis of prevalence, incidence, cost and trends , 2015 .

[27]  O. Troyanskaya,et al.  Predicting effects of noncoding variants with deep learning–based sequence model , 2015, Nature Methods.

[28]  Daniel S. Himmelstein,et al.  Understanding multicellular function and disease with human tissue-specific networks , 2015, Nature Genetics.

[29]  A. Iriki,et al.  Periostin, a neurite outgrowth‐promoting factor, is expressed at high levels in the primate cerebral cortex , 2015, Development, growth & differentiation.

[30]  F. Carr Neurodegeneration: Selective vulnerability , 2015, Nature Reviews Neuroscience.

[31]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[32]  Guanming Wu,et al.  ReactomeFIViz : a Cytoscape app for pathway and network-based data analysis , 2022 .

[33]  Sergio Contrino,et al.  InterMine: extensive web services for modern biology , 2014, Nucleic Acids Res..

[34]  David A. Bennett,et al.  REST and Stress Resistance in Aging and Alzheimer’s Disease , 2014, Nature.

[35]  W. Min,et al.  AIP1 Mediates Vascular Endothelial Cell Growth Factor Receptor-3–Dependent Angiogenic and Lymphangiogenic Responses , 2014, Arteriosclerosis, thrombosis, and vascular biology.

[36]  Nick C Fox,et al.  Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease , 2013, Nature Genetics.

[37]  A. Prat,et al.  Glial influence on the Blood Brain Barrier , 2013, Glia.

[38]  Andrea Ballabio,et al.  Signals from the lysosome: a control centre for cellular clearance and energy metabolism , 2013, Nature Reviews Molecular Cell Biology.

[39]  F. Polleux,et al.  The CAMKK2-AMPK Kinase Pathway Mediates the Synaptotoxic Effects of Aβ Oligomers through Tau Phosphorylation , 2013, Neuron.

[40]  M. Gill,et al.  Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data , 2013, PloS one.

[41]  Gabriëlle H S Buitendijk,et al.  Seven New Loci Associated with Age-Related Macular Degeneration , 2013, Nature Genetics.

[42]  Peng Jin,et al.  Dynamics of DNA methylation in aging and Alzheimer's disease. , 2012, DNA and cell biology.

[43]  Sergio Contrino,et al.  InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data , 2012, Bioinform..

[44]  Alin Ciobica,et al.  Hippocampal neuronal loss in the CA1 and CA3 areas of Alzheimer's disease patients. , 2012, Psychiatria Danubina.

[45]  Satya vani Guttula,et al.  Analyzing Microarray Data of Alzheimer's Using Cluster Analysis to Identify the Biomarker Genes , 2012, International journal of Alzheimer's disease.

[46]  Pierre J Magistretti,et al.  Brain energy metabolism: focus on astrocyte-neuron metabolic cooperation. , 2011, Cell metabolism.

[47]  Manolis Kellis,et al.  HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants , 2011, Nucleic Acids Res..

[48]  L. Gu,et al.  MDM2 Regulates Vascular Endothelial Growth Factor mRNA Stabilization in Hypoxia , 2011, Molecular and Cellular Biology.

[49]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[50]  Laurent Duret,et al.  Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. , 2011, Human molecular genetics.

[51]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[52]  S. Brandner Nanog, Gli, and p53: a new network of stemness in development and cancer , 2010, The EMBO journal.

[53]  Ning Li,et al.  The Transcription Factor Cux1 Regulates Dendritic Morphology of Cortical Pyramidal Neurons , 2010, PloS one.

[54]  T. Harris,et al.  The Conserved Mitochondrial Twin Cx9C Protein Cmc2 Is a Cmc1 Homologue Essential for Cytochrome c Oxidase Biogenesis* , 2010, The Journal of Biological Chemistry.

[55]  C. Winters,et al.  Differential NMDA receptor-dependent calcium loading and mitochondrial dysfunction in CA1 vs. CA3 hippocampal neurons , 2010, Neurobiology of Disease.

[56]  Xinkun Wang,et al.  Frontiers in Aging Neuroscience Aging Neuroscience Review Article , 2022 .

[57]  K. Frazer,et al.  Human genetic variation and its contribution to complex traits , 2009, Nature Reviews Genetics.

[58]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[59]  Xue-wen Chen,et al.  Genome-wide transcriptome profiling of region-specific vulnerability to oxidative stress in the hippocampus. , 2007, Genomics.

[60]  Ann Marie Craig,et al.  NMDA Receptor Subunits Have Differential Roles in Mediating Excitotoxic Neuronal Death Both In Vitro and In Vivo , 2007, The Journal of Neuroscience.

[61]  Eric A Newman,et al.  Glial Cells Dilate and Constrict Blood Vessels: A Mechanism of Neurovascular Coupling , 2006, The Journal of Neuroscience.

[62]  Xue-wen Chen,et al.  High intrinsic oxidative stress may underlie selective vulnerability of the hippocampal CA1 region. , 2005, Brain research. Molecular brain research.

[63]  Hui Zhang,et al.  Involvement of Retinoblastoma Protein and HBP1 in Histone H10 Gene Expression , 2000, Molecular and Cellular Biology.

[64]  S. Kish,et al.  Ornithine Decarboxylase in Human Brain: Influence of Aging, Regional Distribution, and Alzheimer's Disease , 1998, Journal of neurochemistry.

[65]  M. Aldrich,et al.  Major Histocompatibility Class II Molecules in the CNS: Increased Microglial Expression at the Onset of Narcolepsy in a Canine Model , 1996, The Journal of Neuroscience.

[66]  R. Hamill,et al.  Glucocorticoid receptor mRNA in Alzheimer's diseased hippocampus , 1995, Brain Research.

[67]  J. Nobrega,et al.  Brain Cytochrome Oxidase in Alzheimer's Disease , 1992, Journal of neurochemistry.

[68]  G. Acquaah-Mensah,et al.  A regulatory role for the insulin- and BDNF-linked RORA in the hippocampus: implications for Alzheimer's disease. , 2015, Journal of Alzheimer's disease : JAD.

[69]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[70]  Xiongwei Zhu,et al.  Abnormal mitochondrial dynamics and neurodegenerative diseases. , 2010, Biochimica et biophysica acta.

[71]  J. Coyle,et al.  Oxidative stress in neurodegenerative diseases. , 1996, Annual review of pharmacology and toxicology.