A systems biology approach for studying neurodegenerative diseases.

[1]  J. Nielsen,et al.  Improvement in the Current Therapies for Hepatocellular Carcinoma Using a Systems Medicine Approach , 2020, Advanced biosystems.

[2]  D. Berry,et al.  Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA , 2020, Annals of oncology : official journal of the European Society for Medical Oncology.

[3]  Jens Nielsen,et al.  Addressing the heterogeneity in liver diseases using biological networks , 2020, Briefings Bioinform..

[4]  Huanming Yang,et al.  An atlas of the protein-coding genes in the human, pig, and mouse brain , 2020, Science.

[5]  D. Geschwind,et al.  Identification of Conserved Proteomic Networks in Neurodegenerative Dementia , 2019, bioRxiv.

[6]  James G. Bollinger,et al.  High-precision plasma β-amyloid 42/40 predicts current and future brain amyloidosis , 2019, Neurology.

[7]  Shaochang Wu,et al.  Differential proteomic analysis of serum exosomes reveals alterations in progression of Parkinson disease , 2019, Medicine.

[8]  A. West,et al.  Proteomic analysis of urinary extracellular vesicles reveal biomarkers for neurologic disease , 2019, EBioMedicine.

[9]  Manolis Kellis,et al.  Single-cell transcriptomic analysis of Alzheimer’s disease , 2019, Nature.

[10]  Anna S. Monzel,et al.  Modeling Parkinson’s disease in midbrain-like organoids , 2019, npj Parkinson's Disease.

[11]  W. Ray,et al.  The Role of APOE4 in Disrupting the Homeostatic Functions of Astrocytes and Microglia in Aging and Alzheimer’s Disease , 2019, Front. Aging Neurosci..

[12]  I. Ferrer,et al.  Unveiling the olfactory proteostatic disarrangement in Parkinson's disease by proteome-wide profiling , 2019, Neurobiology of Aging.

[13]  Yang Yu,et al.  Proteomic Study of a Parkinson's Disease Model of Undifferentiated SH-SY5Y Cells Induced by a Proteasome Inhibitor , 2019, International journal of medical sciences.

[14]  Kieran R. Campbell,et al.  Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes , 2019, Cell stem cell.

[15]  K. Blennow,et al.  Antibody‐based methods for the measurement of α‐synuclein concentration in human cerebrospinal fluid – method comparison and round robin study , 2018, Journal of neurochemistry.

[16]  Qi Wan,et al.  Repetitive transcranial magnetic stimulation for the treatment of Alzheimer's disease: A systematic review and meta-analysis of randomized controlled trials , 2018, PloS one.

[17]  A. Levey,et al.  Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease , 2018, Molecular Neurodegeneration.

[18]  F. Supandi,et al.  Computational prediction of changes in brain metabolic fluxes during Parkinson’s disease from mRNA expression , 2018, PloS one.

[19]  Chadwick M. Hales,et al.  Quantitative proteomics of acutely-isolated mouse microglia identifies novel immune Alzheimer’s disease-related proteins , 2018, Molecular Neurodegeneration.

[20]  J. Nielsen,et al.  Systems biology in hepatology: approaches and applications , 2018, Nature Reviews Gastroenterology & Hepatology.

[21]  A. Levey,et al.  Global quantitative analysis of the human brain proteome in Alzheimer’s and Parkinson’s Disease , 2018, Scientific Data.

[22]  F. Kametani,et al.  Reconsideration of Amyloid Hypothesis and Tau Hypothesis in Alzheimer's Disease , 2018, Front. Neurosci..

[23]  J. Kordower,et al.  Therapeutic approaches to target alpha-synuclein pathology , 2017, Experimental Neurology.

[24]  Eyal Oren,et al.  Global, regional, and national burden of neurological disorders, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016 , 2017, The Lancet. Neurology.

[25]  Anders Larsson,et al.  Global, regional, and national burden of neurological disorders during 1990–2015: a systematic analysis for the Global Burden of Disease Study 2015 , 2017, The Lancet Neurology.

[26]  J. Nielsen,et al.  Improving the economics of NASH/NAFLD treatment through the use of systems biology. , 2017, Drug discovery today.

[27]  I. Hellmann,et al.  Comparative Analysis of Single-Cell RNA Sequencing Methods , 2016, bioRxiv.

[28]  G. Barreto,et al.  Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network , 2017, Front. Aging Neurosci..

[29]  W. Oertel,et al.  Current and experimental treatments of Parkinson disease: A guide for neuroscientists , 2016, Journal of neurochemistry.

[30]  Xiaolong Liu,et al.  The application of proteomics in different aspects of hepatocellular carcinoma research. , 2016, Journal of proteomics.

[31]  Jens Nielsen,et al.  Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance. , 2016, Cell metabolism.

[32]  Jens Nielsen,et al.  Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis , 2016, Nucleic acids research.

[33]  Tunahan Çakır,et al.  Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma , 2016, Front. Neurosci..

[34]  C. Wahlestedt,et al.  Transcriptomic Profiling of Extracellular RNAs Present in Cerebrospinal Fluid Identifies Differentially Expressed Transcripts in Parkinson’s Disease , 2016, Journal of Parkinson's disease.

[35]  Neil Buckholtz,et al.  Accelerating Medicines Partnership: Alzheimer’s Disease (AMP-AD) Knowledge Portal Aids Alzheimer’s Drug Discovery through Open Data Sharing , 2016, Expert opinion on therapeutic targets.

[36]  C. Manzoni,et al.  Is Alpha-Synuclein Loss-of-Function a Contributor to Parkinsonian Pathology? Evidence from Non-human Primates , 2016, Front. Neurosci..

[37]  Achim Kraus,et al.  PROTEOMICS: The first 15 years , 2016, Proteomics. Clinical applications.

[38]  M. Dunn.  PROTEOMICS: The first 15 years , 2016, Proteomics.

[39]  J. Jankovic,et al.  Dopa-responsive dystonia—clinical and genetic heterogeneity , 2015, Nature Reviews Neurology.

[40]  B. Marcos,et al.  Growth factor treatment to overcome Alzheimer's dysfunctional signaling. , 2015, Cellular signalling.

[41]  Gwenn S. Smith,et al.  Deep Brain Stimulation Influences Brain Structure in Alzheimer's Disease , 2015, Brain Stimulation.

[42]  A. Gavai,et al.  Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain , 2015, PloS one.

[43]  G. Tononi,et al.  TMS Enhances Retention of a Motor Skill in Parkinson's Disease , 2015, Brain Stimulation.

[44]  M. Goedert,et al.  Axotrophin/MARCH7 acts as an E3 ubiquitin ligase and ubiquitinates tau protein in vitro impairing microtubule binding , 2014, Biochimica et biophysica acta.

[45]  J. Cummings,et al.  Alzheimer’s disease drug-development pipeline: few candidates, frequent failures , 2014, Alzheimer's Research & Therapy.

[46]  K. Ülgen,et al.  Systematic analysis of transcription-level effects of neurodegenerative diseases on human brain metabolism by a newly reconstructed brain-specific metabolic network , 2014, FEBS open bio.

[47]  D. Galasko,et al.  Targeted Discovery and Validation of Plasma Biomarkers of Parkinson’s Disease , 2014, Journal of proteome research.

[48]  R. Albin,et al.  Modifiable cardiovascular risk factors and axial motor impairments in Parkinson disease , 2014, Neurology.

[49]  Hagai Bergman,et al.  Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing , 2014, PLoS Comput. Biol..

[50]  H. Soares,et al.  Meta-Analysis of Peripheral Blood Apolipoprotein E Levels in Alzheimer’s Disease , 2014, PloS one.

[51]  T. Asada,et al.  Immunohistochemical analysis of ubiquilin‐1 in the human hippocampus: Association with neurofibrillary tangle pathology , 2014, Neuropathology : official journal of the Japanese Society of Neuropathology.

[52]  D. Hwang,et al.  Both Targeted Mass Spectrometry and Flow Sorting Analysis Methods Detected the Decreased Serum Apolipoprotein E Level in Alzheimer's Disease Patients. , 2014, Molecular & Cellular Proteomics.

[53]  D. Peng,et al.  Hyperphosphorylation of Tau Protein in Hippocampus of Central Insulin-Resistant Rats is Associated with Cognitive Impairment , 2013, Cellular Physiology and Biochemistry.

[54]  J. Blusztajn,et al.  BMP9 ameliorates amyloidosis and the cholinergic defect in a mouse model of Alzheimer’s disease , 2013, Proceedings of the National Academy of Sciences.

[55]  Madeline A. Lancaster,et al.  Cerebral organoids model human brain development and microcephaly , 2013, Nature.

[56]  H. Kitano,et al.  Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map , 2013, Molecular Neurobiology.

[57]  J. D. Mills,et al.  RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism , 2013, Neuroscience Letters.

[58]  Nick C Fox,et al.  Clinical and biomarker changes in dominantly inherited Alzheimer's disease. , 2012, The New England journal of medicine.

[59]  Junxia Xie,et al.  Curcumin protects nigral dopaminergic neurons by iron-chelation in the 6-hydroxydopamine rat model of Parkinson’s disease , 2012, Neuroscience Bulletin.

[60]  Sudha Seshadri,et al.  Inverse association between cancer and Alzheimer’s disease: results from the Framingham Heart Study , 2012, BMJ : British Medical Journal.

[61]  D. Geschwind,et al.  Proteomic changes in cerebrospinal fluid of presymptomatic and affected persons carrying familial Alzheimer disease mutations. , 2012, Archives of neurology.

[62]  M. Kabani,et al.  Hsc70 Protein Interaction with Soluble and Fibrillar α-Synuclein* , 2011, The Journal of Biological Chemistry.

[63]  M. Wilkins,et al.  Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease , 2011, PloS one.

[64]  B. Palsson,et al.  Supplement to: Formulating multi-cellular models of metabolism in tissues: application to energy metabolism in the human brain , 2010 .

[65]  Angelo Antonini,et al.  Levodopa in the treatment of Parkinson’s disease: an old drug still going strong , 2010, Clinical interventions in aging.

[66]  S. Duty,et al.  Symptomatic and neuroprotective effects following activation of nigral group III metabotropic glutamate receptors in rodent models of Parkinson's disease , 2010, British journal of pharmacology.

[67]  M. Wollmer.  Cholesterol-related genes in Alzheimer's disease. , 2010, Biochimica et biophysica acta.

[68]  Hideyuki Okano,et al.  New Neurons Clear the Path of Astrocytic Processes for Their Rapid Migration in the Adult Brain , 2010, Neuron.

[69]  B. Jin,et al.  Paroxetine Prevents Loss of Nigrostriatal Dopaminergic Neurons by Inhibiting Brain Inflammation and Oxidative Stress in an Experimental Model of Parkinson’s Disease , 2010, The Journal of Immunology.

[70]  E. Schernhammer,et al.  Parkinson’s disease and cancer risk: a systematic review and meta-analysis , 2010, Cancer Causes & Control.

[71]  I. McKeith,et al.  Single‐cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene , 2009, Annals of neurology.

[72]  B. Engelhardt,et al.  The blood–brain and the blood–cerebrospinal fluid barriers: function and dysfunction , 2009, Seminars in Immunopathology.

[73]  D. Butterfield,et al.  Proteomics-determined differences in the concanavalin-A-fractionated proteome of hippocampus and inferior parietal lobule in subjects with Alzheimer's disease and mild cognitive impairment: implications for progression of AD. , 2009, Journal of proteome research.

[74]  J. Wands,et al.  Alzheimer's Disease is Type 3 Diabetes—Evidence Reviewed , 2008, Journal of diabetes science and technology.

[75]  K. Ülgen,et al.  Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia , 2007, Theoretical Biology and Medical Modelling.

[76]  Mark D'Ascenzo,et al.  8‐Plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease , 2007, Proteomics.

[77]  J. Cummings,et al.  Effective pharmacologic management of Alzheimer's disease. , 2007, The American journal of medicine.

[78]  M. Stampfer,et al.  Cardiovascular disease and Alzheimer's disease: common links , 2006, Journal of internal medicine.

[79]  G. Deuschl,et al.  A randomized trial of deep-brain stimulation for Parkinson's disease. , 2006, The New England journal of medicine.

[80]  H. Cai,et al.  BACE1, a Major Determinant of Selective Vulnerability of the Brain to Amyloid-β Amyloidogenesis, is Essential for Cognitive, Emotional, and Synaptic Functions , 2005, The Journal of Neuroscience.

[81]  D. Nyholm,et al.  Duodenal levodopa infusion monotherapy vs oral polypharmacy in advanced Parkinson disease , 2005, Neurology.

[82]  Michel Goedert,et al.  GSK3 inhibitors: development and therapeutic potential , 2004, Nature Reviews Drug Discovery.

[83]  Allan I. Levey,et al.  Oxidative Modifications and Down-regulation of Ubiquitin Carboxyl-terminal Hydrolase L1 Associated with Idiopathic Parkinson's and Alzheimer's Diseases* , 2004, Journal of Biological Chemistry.

[84]  Rina Bandopadhyay,et al.  The expression of DJ-1 (PARK7) in normal human CNS and idiopathic Parkinson's disease. , 2004, Brain : a journal of neurology.

[85]  S. Mandel,et al.  Early and Late Gene Changes in MPTP Mice Model of Parkinson's Disease Employing cDNA Microarray , 2002, Neurochemical Research.

[86]  S. Mandel,et al.  Gene expression analysis in N‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridine mice model of Parkinson's disease using cDNA microarray: effect of R‐apomorphine , 2001, Journal of neurochemistry.

[87]  K Kosaka,et al.  Up-regulation of calcineurin Abeta mRNA in the Alzheimer's disease brain: assessment by cDNA microarray. , 2001, Biochemical and biophysical research communications.

[88]  A. Czernik,et al.  Altered expression of a-type but not b-type synapsin isoform in the brain of patients at high risk for Alzheimer's disease assessed by DNA microarray technique , 2001, Neuroscience Letters.

[89]  Nancy Andrews,et al.  Transferrin receptor is necessary for development of erythrocytes and the nervous system , 1999, Nature Genetics.

[90]  M. Memo,et al.  Lewy-body dementia and responsiveness to cholinesterase inhibitors: a paradigm for heterogeneity of Alzheimer's disease? , 1996, Trends in pharmacological sciences.

[91]  A. Hirano.  Amyotrophic lateral sclerosis and parkinsonism-dementia complex on Guam: immunohistochemical studies. , 1992, The Keio journal of medicine.

[92]  E. Mufson,et al.  Cortical neurons express nerve growth factor receptors in advanced age and Alzheimer disease. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[93]  R. Nixon,et al.  Enzymatically active lysosomal proteases are associated with amyloid deposits in Alzheimer brain. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[94]  B. Frangione,et al.  Brain amyloid in normal aging and cerebral amyloid angiopathy is antigenically related to Alzheimer's disease beta-protein. , 1987, The American journal of pathology.

[95]  L. Dayon,et al.  Analyzing Cerebrospinal Fluid Proteomes to Characterize Central Nervous System Disorders: A Highly Automated Mass Spectrometry-Based Pipeline for Biomarker Discovery. , 2019, Methods in molecular biology.

[96]  E. Marcotte,et al.  Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data , 2008, Nature Protocols.

[97]  E. Wassermann.  Risk and safety of repetitive transcranial magnetic stimulation: report and suggested guidelines from the International Workshop on the Safety of Repetitive Transcranial Magnetic Stimulation, June 5-7, 1996. , 1998, Electroencephalography and clinical neurophysiology.

[98]  R. Sandyk.  The Relationship Between Diabetes Mellitus and Parkinson'S Disease , 1993 .