Intelligent and effective informatic deconvolution of “Big Data” and its future impact on the quantitative nature of neurodegenerative disease therapy
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Viswanath Devanarayan | Hugo Geerts | Stuart Maudsley | Bronwen Martin | Brain Health Modeling Initiative | H. Geerts | V. Devanarayan | Stuart Maudsley | B. Martin
[1] L. Luttrell,et al. Beyond Desensitization: Physiological Relevance of Arrestin-Dependent Signaling , 2010, Pharmacological Reviews.
[2] Jonas Bergquist,et al. MALDI imaging of post‐mortem human spinal cord in amyotrophic lateral sclerosis , 2013, Journal of neurochemistry.
[3] Stuart Maudsley,et al. iTRAQ Analysis of Complex Proteome Alterations in 3xTgAD Alzheimer's Mice: Understanding the Interface between Physiology and Disease , 2008, PloS one.
[4] H. Prokosch,et al. Perspectives for Medical Informatics , 2009, Methods of Information in Medicine.
[5] Noémie Elhadad,et al. Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts , 2013, J. Biomed. Informatics.
[6] Catherine N. Norton,et al. LigerCat: Using "MeSH Clouds" from Journal, Article, or Gene Citations to Facilitate the Identification of Relevant Biomedical Literature , 2009, AMIA.
[7] Olaf Sporns,et al. Complex network measures of brain connectivity: Uses and interpretations , 2010, NeuroImage.
[8] Stuart Maudsley,et al. Bioinformatic approaches to metabolic pathways analysis. , 2011, Methods in molecular biology.
[9] L. Luttrell,et al. Informatic deconvolution of biased GPCR signaling mechanisms from in vivo pharmacological experimentation. , 2016, Methods.
[10] Hugo Geerts,et al. Mechanistic disease modeling as a useful tool for improving CNS drug research and development , 2011 .
[11] Athanasios Gotsopoulos,et al. Proteomic Profiling in the Brain of CLN1 Disease Model Reveals Affected Functional Modules , 2016, NeuroMolecular Medicine.
[12] Robert P. Sheridan,et al. Deep Neural Nets as a Method for Quantitative Structure-Activity Relationships , 2015, J. Chem. Inf. Model..
[13] Nathan A. Yates,et al. High Resolution Discovery Proteomics Reveals Candidate Disease Progression Markers of Alzheimer’s Disease in Human Cerebrospinal Fluid , 2015, PloS one.
[14] Bobbie-Jo M Webb-Robertson. Support vector machines for improved peptide identification from tandem mass spectrometry database search. , 2009, Methods in molecular biology.
[15] Jason Weston,et al. Natural Language Processing (Almost) from Scratch , 2011, J. Mach. Learn. Res..
[16] Fleur Mougin,et al. Reuse of termino-ontological resources and text corpora for building a multilingual domain ontology: An application to Alzheimer's disease , 2014, J. Biomed. Informatics.
[17] Stuart Maudsley,et al. GIT2 Acts as a Systems-Level Coordinator of Neurometabolic Activity and Pathophysiological Aging , 2016, Front. Endocrinol..
[18] C. Jack,et al. Hypothetical model of dynamic biomarkers of the Alzheimer's pathological cascade , 2010, The Lancet Neurology.
[19] Y Uto,et al. Development of Hospital Data Warehouse for Cost Analysis of DPC Based on Medical Costs , 2007, Methods of Information in Medicine.
[20] L. Luttrell,et al. Arrestin pathways as drug targets. , 2013, Progress in molecular biology and translational science.
[21] Vikas Singh,et al. Imaging-based enrichment criteria using deep learning algorithms for efficient clinical trials in mild cognitive impairment , 2015, Alzheimer's & Dementia.
[22] R. Lefkowitz,et al. β-Arrestin 2: A Receptor-Regulated MAPK Scaffold for the Activation of JNK3 , 2000 .
[23] Christophe Lemetre,et al. An introduction to artificial neural networks in bioinformatics - application to complex microarray and mass spectrometry datasets in cancer studies , 2008, Briefings Bioinform..
[24] V. Lobanov,et al. An Improved Model for Disease Progression in Patients From the Alzheimer's Disease Neuroimaging Initiative , 2012, Journal of clinical pharmacology.
[25] Jörg Hanrieder,et al. MALDI Imaging Mass Spectrometry of Neuropeptides in Parkinson's Disease , 2012, Journal of visualized experiments : JoVE.
[26] Valeria Rimoldi,et al. Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes , 2015, International journal of molecular sciences.
[27] João Ricardo Sato,et al. Measuring Abnormal Brains: Building Normative Rules in Neuroimaging Using One-Class Support Vector Machines , 2012, Front. Neurosci..
[28] Neta Zach,et al. Big data to smart data in Alzheimer's disease: Real-world examples of advanced modeling and simulation , 2016, Alzheimer's & Dementia.
[29] Csaba Böde,et al. Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design. , 2008, Current protein & peptide science.
[30] Chih-Jen Lin,et al. LIBSVM: A library for support vector machines , 2011, TIST.
[31] Stuart Maudsley,et al. Nuclear GIT2 Is an ATM Substrate and Promotes DNA Repair , 2015, Molecular and Cellular Biology.
[32] James H Harrison,et al. The development of health care data warehouses to support data mining. , 2008, Clinics in laboratory medicine.
[33] Yoshua Bengio,et al. On Using Very Large Target Vocabulary for Neural Machine Translation , 2014, ACL.
[34] W. M. van der Flier,et al. Functional neural network analysis in frontotemporal dementia and Alzheimer's disease using EEG and graph theory , 2009, BMC Neuroscience.
[35] Stuart Maudsley,et al. Minimal Peroxide Exposure of Neuronal Cells Induces Multifaceted Adaptive Responses , 2010, PloS one.
[36] Andrew D. Rouillard,et al. GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions , 2015, Bioinform..
[37] Geoffrey E. Hinton,et al. ImageNet classification with deep convolutional neural networks , 2012, Commun. ACM.
[38] L. Etheredge,et al. Rapid learning: a breakthrough agenda. , 2014, Health affairs.
[39] Teuvo Kohonen,et al. Self-organized formation of topologically correct feature maps , 2004, Biological Cybernetics.
[40] A. Fagan,et al. Functional connectivity and graph theory in preclinical Alzheimer's disease , 2014, Neurobiology of Aging.
[41] Jonathan Tompson,et al. Joint Training of a Convolutional Network and a Graphical Model for Human Pose Estimation , 2014, NIPS.
[42] Raul Rabadan,et al. Data-driven discovery of seasonally linked diseases from an Electronic Health Records system , 2014, BMC Bioinformatics.
[43] Ke Zhou,et al. Supervised embedding of textual predictors with applications in clinical diagnostics for pediatric cardiology. , 2014, Journal of the American Medical Informatics Association : JAMIA.
[44] Markus Stoeckli,et al. MALDI mass spectrometric imaging of biological tissue sections , 2005, Mechanisms of Ageing and Development.
[45] Stuart Maudsley,et al. Live longer sans the AT1A receptor. , 2009, Cell metabolism.
[46] Stuart Maudsley,et al. GIT2 Acts as a Potential Keystone Protein in Functional Hypothalamic Networks Associated with Age-Related Phenotypic Changes in Rats , 2012, PloS one.
[47] Stuart Maudsley,et al. Delineation of a Conserved Arrestin-Biased Signaling Repertoire In Vivo , 2015, Molecular Pharmacology.
[48] Sean R. Davis,et al. NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..
[49] William Stafford Noble,et al. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. , 2003, Journal of proteome research.
[50] Robert J. Lefkowitz,et al. Activation and targeting of extracellular signal-regulated kinases by β-arrestin scaffolds , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[51] Yan Zhao. Intensity-based protein identification by machine learning from a library of tandem mass spectra , 2010 .
[52] Angus Roberts,et al. Extracting antipsychotic polypharmacy data from electronic health records: developing and evaluating a novel process , 2015, BMC Psychiatry.
[53] Avner Schlessinger,et al. GEN3VA: aggregation and analysis of gene expression signatures from related studies , 2016, BMC Bioinformatics.
[54] Patrick Santens,et al. Investigating the role of filamin C in Belgian patients with frontotemporal dementia linked to GRN deficiency in FTLD-TDP brains , 2015, Acta neuropathologica communications.
[55] B. Frey,et al. The human splicing code reveals new insights into the genetic determinants of disease , 2015, Science.
[56] Satoshi Niijima,et al. GEM-TREND: a web tool for gene expression data mining toward relevant network discovery , 2009, BMC Genomics.
[57] Michael Schroeder,et al. GoPubMed: exploring PubMed with the Gene Ontology , 2005, Nucleic Acids Res..
[58] Michael W. Berry,et al. Functional Cohesion of Gene Sets Determined by Latent Semantic Indexing of PubMed Abstracts , 2011, PloS one.
[59] H Nielsen,et al. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. , 1999, Protein engineering.
[60] Duncan J. Watts,et al. Collective dynamics of ‘small-world’ networks , 1998, Nature.
[61] S. Rombouts,et al. Loss of ‘Small-World’ Networks in Alzheimer's Disease: Graph Analysis of fMRI Resting-State Functional Connectivity , 2010, PloS one.
[62] G Tusch,et al. Data warehouse and data mining in a surgical clinic. , 2000, Studies in health technology and informatics.
[63] Pablo Moscato,et al. Identification of a 5-Protein Biomarker Molecular Signature for Predicting Alzheimer's Disease , 2008, PloS one.
[64] Maneesh Sahani,et al. Models of Neuronal Stimulus-Response Functions: Elaboration, Estimation, and Evaluation , 2017, Front. Syst. Neurosci..
[65] Kengo Kinoshita,et al. VaProS: a database-integration approach for protein/genome information retrieval , 2016, Journal of Structural and Functional Genomics.
[66] Thomas Villmann,et al. Classification of mass-spectrometric data in clinical proteomics using learning vector quantization methods , 2007, Briefings Bioinform..
[67] D. Stekel,et al. A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data , 2015, BMC Genomics.
[68] Sana Siddiqui,et al. Classification of Alzheimer Diagnosis from ADNI Plasma Biomarker Data , 2013, BCB.
[69] Thibault Helleputte,et al. Robust biomarker identification for cancer diagnosis with ensemble feature selection methods , 2010, Bioinform..
[70] Chris Mungall,et al. AmiGO: online access to ontology and annotation data , 2008, Bioinform..
[71] Stephen F. Carter,et al. Prediction of dementia in MCI patients based on core diagnostic markers for Alzheimer disease , 2013, Neurology.
[72] Erik M. van Mulligen,et al. Comparing and combining chunkers of biomedical text , 2011, J. Biomed. Informatics.
[73] Ramin Homayouni,et al. Expression Levels of Obesity-Related Genes Are Associated with Weight Change in Kidney Transplant Recipients , 2013, PloS one.
[74] Stuart Maudsley,et al. MINIREVIEW—EXPLORING THE BIOLOGY OF GPCRS: FROM IN VITRO TO IN VIVO Fulfilling the Promise of "Biased" G Protein–Coupled Receptor Agonism , 2015 .
[75] M. Cercignani,et al. Network functional connectivity and whole-brain functional connectomics to investigate cognitive decline in neurodegenerative conditions. , 2016, Functional neurology.
[76] Jianfeng Feng,et al. A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data , 2008, BMC Bioinformatics.
[77] Taigang He,et al. Integrated genomic approaches identify major pathways and upstream regulators in late onset Alzheimer’s disease , 2015, Scientific Reports.
[78] L. Luttrell,et al. Refining efficacy: exploiting functional selectivity for drug discovery. , 2011, Advances in pharmacology.
[79] R. Mullins,et al. β-Arrestin–Dependent Endocytosis of Proteinase-Activated Receptor 2 Is Required for Intracellular Targeting of Activated Erk1/2 , 2000, The Journal of cell biology.
[80] Bin Chen,et al. Predicting drug target interactions using meta-path-based semantic network analysis , 2016, BMC Bioinformatics.
[81] Radford M. Neal. Pattern Recognition and Machine Learning , 2007, Technometrics.
[82] D. Swanson. Migraine and Magnesium: Eleven Neglected Connections , 2015, Perspectives in biology and medicine.
[83] Colin Campbell,et al. The latent process decomposition of cDNA microarray data sets , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[84] M. Caron,et al. Beta-arrestin-dependent formation of beta2 adrenergic receptor-Src protein kinase complexes. , 1999, Science.
[85] Takashi Yoneya. PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords , 2005, BMC Bioinformatics.
[86] C. Strader,et al. Muscarinic agonists and antagonists in the treatment of Alzheimer's disease. , 2001, Farmaco.
[87] Juri Rappsilber,et al. Nano Random Forests to mine protein complexes and their relationships in quantitative proteomics data , 2017, Molecular biology of the cell.
[88] Chunhua Weng,et al. Methods and dimensions of electronic health record data quality assessment: enabling reuse for clinical research , 2013, J. Am. Medical Informatics Assoc..
[89] Guigang Zhang,et al. Deep Learning , 2016, Int. J. Semantic Comput..
[90] Daniel H. Geschwind,et al. Alzheimer's disease: From big data to mechanism , 2013, Nature.
[91] Kok Long Ang,et al. Targeting of cyclic AMP degradation to beta 2-adrenergic receptors by beta-arrestins. , 2002, Science.
[92] Norbert Schuff,et al. Early role of vascular dysregulation on late-onset Alzheimer's disease based on multifactorial data-driven analysis , 2016, Nature Communications.
[93] Timo Minssen,et al. Intellectual property rights, standards and data exchange in systems biology , 2016, Biotechnology journal.
[94] Michael I. Jordan,et al. Latent Dirichlet Allocation , 2001, J. Mach. Learn. Res..
[95] Kathryn Lunetta,et al. Identification of Gene-Gene Interactions in Alzheimer Disease Using Co-Operative Game Theory , 2011, Alzheimer's & Dementia.
[96] Abdel G. Elkahloun,et al. An integrative genome-wide transcriptome reveals that candesartan is neuroprotective and a candidate therapeutic for Alzheimer’s disease , 2016, Alzheimer's Research & Therapy.
[97] Wenyaw Chan,et al. Predicting progression of Alzheimer's disease , 2010, Alzheimer's Research & Therapy.
[98] P. Bork,et al. Literature mining for the biologist: from information retrieval to biological discovery , 2006, Nature Reviews Genetics.
[99] Stuart Maudsley,et al. Systems-Level G Protein-Coupled Receptor Therapy Across a Neurodegenerative Continuum by the GLP-1 Receptor System , 2014, Front. Endocrinol..
[100] Heng Tao Shen,et al. Principal Component Analysis , 2009, Encyclopedia of Biometrics.
[101] Leonid Peshkin,et al. Resveratrol prevents high fat/sucrose diet-induced central arterial wall inflammation and stiffening in nonhuman primates. , 2014, Cell metabolism.
[102] Hugo Geerts,et al. A Humanized Clinically Calibrated Quantitative Systems Pharmacology Model for Hypokinetic Motor Symptoms in Parkinson’s Disease , 2016, Front. Pharmacol..
[103] Dinggang Shen,et al. Deep ensemble learning of sparse regression models for brain disease diagnosis , 2017, Medical Image Anal..
[104] Srinivas C. Turaga,et al. Connectomic reconstruction of the inner plexiform layer in the mouse retina , 2013, Nature.
[105] Camille Couprie,et al. Learning Hierarchical Features for Scene Labeling , 2013, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[106] Garrett M. Dancik,et al. shinyGEO: a web-based application for analyzing gene expression omnibus datasets , 2016, Bioinform..
[107] P. Embí,et al. Toward Reuse of Clinical Data for Research and Quality Improvement: The End of the Beginning? , 2009, Annals of Internal Medicine.
[108] Stuart Maudsley,et al. Repetitive Peroxide Exposure Reveals Pleiotropic Mitogen-Activated Protein Kinase Signaling Mechanisms , 2010, Journal of signal transduction.
[109] R. Tibshirani,et al. Classification and prediction of clinical Alzheimer's diagnosis based on plasma signaling proteins , 2007, Nature Medicine.
[110] Hongyu Chen,et al. Effective use of latent semantic indexing and computational linguistics in biological and biomedical applications , 2012, Front. Physio..
[111] C. Stam,et al. Alzheimer's disease: connecting findings from graph theoretical studies of brain networks , 2013, Neurobiology of Aging.
[112] Thomas G. Dietterich. An Experimental Comparison of Three Methods for Constructing Ensembles of Decision Trees: Bagging, Boosting, and Randomization , 2000, Machine Learning.
[113] Ruth Williams,et al. Biomarkers: Warning signs , 2011, Nature.
[114] Alcione de Paiva Oliveira,et al. MUMAL2: Improving sensitivity in shotgun proteomics using cost sensitive artificial neural networks and a threshold selector algorithm , 2016, BMC Bioinformatics.
[115] Hans-Michael Müller,et al. Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature , 2004, PLoS biology.
[116] Murray Grossman,et al. Plasma multianalyte profiling in mild cognitive impairment and Alzheimer disease , 2012, Neurology.
[117] Hans-Michael Müller,et al. Textpresso for Neuroscience: Searching the Full Text of Thousands of Neuroscience Research Papers , 2008, Neuroinformatics.
[118] Gabriele M. T. D'Eleuterio,et al. Synthesis of recurrent neural networks for dynamical system simulation , 2015, Neural Networks.
[119] Martin Hofmann-Apitius,et al. ‘HypothesisFinder:’ A Strategy for the Detection of Speculative Statements in Scientific Text , 2013, PLoS Comput. Biol..
[120] Yong He,et al. Mapping the Alzheimer’s Brain with Connectomics , 2012, Front. Psychiatry.
[121] Itamar Simon,et al. MILANO – custom annotation of microarray results using automatic literature searches , 2005, BMC Bioinformatics.
[122] Guilherme Del Fiol,et al. Automatically Extracting Sentences from Medline Citations to Support Clinicians' Information Needs , 2012, 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology.
[123] Jeffrey M Weinberg,et al. Warning signs. , 2003, Cutis.
[124] Carlo Vittorio Cannistraci,et al. Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data. , 2016, Methods in molecular biology.
[125] L. Luttrell,et al. Functional signaling biases in G protein-coupled receptors: Game Theory and receptor dynamics. , 2012, Mini reviews in medicinal chemistry.
[126] T. Kohonen. Self-organized formation of topographically correct feature maps , 1982 .
[127] Brendan J. Frey,et al. Deep learning of the tissue-regulated splicing code , 2014, Bioinform..
[128] Linda Douw,et al. The Connectome Visualization Utility: Software for Visualization of Human Brain Networks , 2014, PloS one.
[129] Hongyu Chen,et al. Textrous!: Extracting Semantic Textual Meaning from Gene Sets , 2013, PloS one.
[130] Guangtao Ge,et al. Classification of premalignant pancreatic cancer mass-spectrometry data using decision tree ensembles , 2008, BMC Bioinformatics.
[131] Hongyu Chen,et al. Plurigon: three dimensional visualization and classification of high-dimensionality data , 2013, Front. Physiol..
[132] Fuhai Song,et al. Alzheimer's Disease: Genomics and Beyond. , 2015, International review of neurobiology.
[133] Guilherme Del Fiol,et al. Automatically Extracting Sentences from Medline Citations to Support Clinicians' Information Needs , 2012, HISB.
[134] HONG YUE,et al. Co-expression network-based analysis of hippocampal expression data associated with Alzheimer's disease using a novel algorithm , 2016, Experimental and therapeutic medicine.
[135] Regina Berretta,et al. Multivariate Protein Signatures of Pre-Clinical Alzheimer's Disease in the Alzheimer's Disease Neuroimaging Initiative (ADNI) Plasma Proteome Dataset , 2012, PloS one.
[136] Kathleen M Jagodnik,et al. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd , 2016, Nature Communications.
[137] Avi Ma'ayan,et al. Genes2WordCloud: a quick way to identify biological themes from gene lists and free text , 2011, Source Code for Biology and Medicine.
[138] Majnu John,et al. Graph analysis of structural brain networks in Alzheimer’s disease: beyond small world properties , 2016, Brain Structure and Function.
[139] A. Azmi,et al. Development of Precision Small-Molecule Proneurotrophic Therapies for Neurodegenerative Diseases. , 2017, Vitamins and hormones.
[140] Li M Fu,et al. Analysis of Parkinson's disease pathophysiology using an integrated genomics-bioinformatics approach. , 2015, Pathophysiology : the official journal of the International Society for Pathophysiology.
[141] Jimeng Sun,et al. Building bridges across electronic health record systems through inferred phenotypic topics , 2015, J. Biomed. Informatics.
[142] Christos Davatzikos,et al. Individualized statistical learning from medical image databases: Application to identification of brain lesions , 2014, Medical Image Anal..
[143] Andrés Ortiz,et al. Ensembles of Deep Learning Architectures for the Early Diagnosis of the Alzheimer's Disease , 2016, Int. J. Neural Syst..
[144] Quoc V. Le,et al. Sequence to Sequence Learning with Neural Networks , 2014, NIPS.
[145] Marek Ostaszewski,et al. Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases , 2016, Big Data.
[146] Concha Bielza,et al. Machine Learning in Bioinformatics , 2008, Encyclopedia of Database Systems.
[147] Albert Y. Zomaya,et al. A Review of Ensemble Methods in Bioinformatics , 2010, Current Bioinformatics.
[148] Stuart Maudsley,et al. β-arrestin-selective G protein-coupled receptor agonists engender unique biological efficacy in vivo. , 2013, Molecular endocrinology.