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1. Full Text Multiscale Analysis of Independent Alzheimer’s Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus
by Readhead, Ben and Haure-Mirande, Jean-Vianney and Funk, Cory C and Richards, Matthew A and Shannon, Paul and Haroutunian, Vahram and Sano, Mary and Liang, Winnie S and Beckmann, Noam D and Price, Nathan D and Reiman, Eric M and Schadt, Eric E and Ehrlich, Michelle E and Gandy, Sam and Dudley, Joel T
Neuron (Cambridge, Mass.), ISSN 0896-6273, 07/2018, Volume 99, Issue 1, pp. 64 - 82.e7
systems biology | Roseolovirus | integrative genomics | human herpesvirus | multiscale networks | HHV-6B | HHV-7 | HHV-6A | network biology | Alzheimer's disease | Neurosciences | Neurosciences & Neurology | Life Sciences & Biomedicine | Science & Technology | Amyloid Precursor Protein Secretases - genetics | Encephalitis, Viral - genetics | Encephalitis, Viral - virology | Genomics | Humans | Brain - virology | Gene Expression Profiling | Aspartic Acid Endopeptidases - genetics | Gene Regulatory Networks | Herpesvirus 7, Human | Case-Control Studies | Herpesvirus 6, Human | Viral Load | Alzheimer Disease - pathology | Brain - metabolism | Microbiota | Monomeric Clathrin Assembly Proteins - genetics | Tumor Suppressor Proteins - genetics | Amyloid beta-Protein Precursor - metabolism | Encephalitis, Viral - metabolism | Nuclear Proteins - genetics | Roseolovirus Infections - pathology | Clusterin - genetics | Roseolovirus Infections - genetics | Presenilin-1 - genetics | Mice, Transgenic | Roseolovirus Infections - metabolism | Mice, Knockout | Alzheimer Disease - virology | Animals | Adaptor Proteins, Signal Transducing - genetics | Alzheimer Disease - metabolism | Proteomics | Brain - pathology | Roseolovirus Infections - virology | Encephalitis, Viral - pathology | Mice | MicroRNAs - genetics | Alzheimer Disease - genetics | Cohort Studies | Brain | Medical colleges | Medical research | Genetic research | Medicine, Experimental | Development and progression | b-Site APP cleaving enzyme 1 | Neuropathology | Herpes simplex | Viruses | Gene expression | Neuromodulation | Protein turnover | Proteins | Brain research | Neurodegeneration | Autopsy | Data collection
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2. Full Text Detecting epigenetic motifs in low coverage and metagenomics settings
by Beckmann, Noam D and Beckmann, Noam D and Karri, Sashank and Karri, Sashank and Fang, Gang and Fang, Gang and Bashir, Ali and Bashir, Ali
BMC bioinformatics, ISSN 1471-2105, 2014, Volume 15, Issue Suppl 9, pp. S16 - S16
Genome, Bacterial | Algorithms | Nucleotide Motifs | Base Sequence | Computer Simulation | Epigenesis, Genetic | Metagenomics - methods | Models, Genetic | Bacteria - genetics | Studies | E coli | Pipelines | DNA methylation | Epigenetics | Statistical methods | Genomes | Gene expression | Deoxyribonucleic acid--DNA | Index Medicus | Availability | Strands | Likelihood ratio | Bacteria | Inserts | Bioinformatics | Monitoring
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3. Full Text An integrative multiomic network model links lipid metabolism to glucose regulation in coronary artery disease
by Cohain, Ariella T and Barrington, William T and Jordan, Daniel M and Beckmann, Noam D and Argmann, Carmen A and Houten, Sander M and Charney, Alexander W and Ermel, Raili and Sukhavasi, Katyayani and Franzen, Oscar and Koplev, Simon and Whatling, Carl and Belbin, Gillian M and Yang, Jialiang and Hao, Ke and Kenny, Eimear E and Tu, Zhidong and Zhu, Jun and Gan, Li-Ming and Do, Ron and Giannarelli, Chiara and Kovacic, Jason C and Ruusalepp, Arno and Lusis, Aldons J and Bjorkegren, Johan L. M and Schadt, Eric E
Nature communications, ISSN 2041-1723, 01/2021, Volume 12, Issue 1, pp. 547 - 547
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Genetic Predisposition to Disease - genetics | Hypercholesterolemia - blood | Cholesterol - blood | Coronary Artery Disease - metabolism | Diabetes Mellitus, Type 2 - genetics | Humans | Mice, Inbred C57BL | Gene Expression Regulation | Lipid Metabolism | Diabetes Mellitus, Type 2 - metabolism | Gene Regulatory Networks | Coronary Artery Disease - blood | Diabetes Mellitus, Type 2 - blood | Animals | Models, Biological | Coronary Artery Disease - genetics | Glucose - metabolism | Female | Polymorphism, Single Nucleotide | Hypercholesterolemia - genetics | Blood Glucose - metabolism | Genome-Wide Association Study - methods | Hypercholesterolemia - metabolism | Lanosterol | Diabetes mellitus | Coronary artery | Health risks | Lipids | Risk | Cardiovascular disease | Glucose | Metabolism | Gene expression | Coronary artery disease | Cholesterol | Glucose metabolism | Hypercholesterolemia | Coronary vessels | Surgery | Diabetes | Lipid metabolism | Lanosterol synthase | Diabetes mellitus (non-insulin dependent) | Heart diseases | Statins | Genotypes | Index Medicus
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4. Full Text Population-Based Genome-wide Association Studies Reveal Six Loci Influencing Plasma Levels of Liver Enzymes
by Yuan, Xin and Waterworth, Dawn and Perry, John R.B and Lim, Noha and Song, Kijoung and Chambers, John C and Zhang, Weihua and Vollenweider, Peter and Stirnadel, Heide and Johnson, Toby and Bergmann, Sven and Beckmann, Noam D and Li, Yun and Ferrucci, Luigi and Melzer, David and Hernandez, Dena and Singleton, Andrew and Scott, James and Elliott, Paul and Waeber, Gerard and Cardon, Lon and Frayling, Timothy M and Kooner, Jaspal S and Mooser, Vincent
American journal of human genetics, ISSN 0002-9297, 2008, Volume 83, Issue 4, pp. 520 - 528
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Fundamental and applied biological sciences. Psychology | General aspects. Genetic counseling | Medical genetics | Biological and medical sciences | Molecular and cellular biology | Genetics of eukaryotes. Biological and molecular evolution | Medical sciences | Genetics, Population | Liver - enzymology | gamma-Glutamyltransferase - blood | Humans | Middle Aged | Genotype | Male | Alanine Transaminase - blood | Adult | Female | Aged | Enzymes - blood | Genome, Human | Alkaline Phosphatase - blood | Cohort Studies | Liver diseases | Analysis | Physiological aspects | Genetic aspects | Research | Genetic transcription | Population genetics | Blood plasma | Plasma | Enzymes | Genomics | Liver | Genetic diversity | Ribonucleic acid--RNA | Chromosomes | Index Medicus | Report
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5. Full Text An inflammatory cytokine signature predicts COVID-19 severity and survival
by Del Valle, Diane Marie and Kim-Schulze, Seunghee and Huang, Hsin-Hui and Beckmann, Noam D and Nirenberg, Sharon and Wang, Bo and Lavin, Yonit and Swartz, Talia H and Madduri, Deepu and Stock, Aryeh and Marron, Thomas U and Xie, Hui and Patel, Manishkumar and Tuballes, Kevin and Van Oekelen, Oliver and Rahman, Adeeb and Kovatch, Patricia and Aberg, Judith A and Schadt, Eric and Jagannath, Sundar and Mazumdar, Madhu and Charney, Alexander W and Firpo-Betancourt, Adolfo and Mendu, Damodara Rao and Jhang, Jeffrey and Reich, David and Sigel, Keith and Cordon-Cardo, Carlos and Feldmann, Marc and Parekh, Samir and Merad, Miriam and Gnjatic, Sacha
Nature medicine, ISSN 1078-8956, 10/2020, Volume 26, Issue 10, pp. 1636 - 1643
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Medicine, Research & Experimental | Science & Technology | Cell Biology | Research & Experimental Medicine | Pandemics | Humans | Middle Aged | Coronavirus Infections - physiopathology | Male | Coronavirus Infections - mortality | COVID-19 | SARS-CoV-2 | Tumor Necrosis Factor-alpha - immunology | Betacoronavirus | Female | Cytokines - immunology | Severity of Illness Index | Pneumonia, Viral - therapy | Interleukin-1beta - immunology | Survival Rate | Hospitalization | Coronavirus Infections - immunology | Pneumonia, Viral - immunology | Pneumonia, Viral - physiopathology | Coronavirus Infections - therapy | Interleukin-6 - immunology | Aged | Pneumonia, Viral - mortality | Interleukin-8 - immunology | Cytokines | Physiological aspects | Medical research | Medical colleges | Hospital patients | Prognosis | Interleukins | Comorbidity | Tumor necrosis factor | Severe acute respiratory syndrome | Medicine, Experimental | Inflammation | Coronaviruses | Health aspects | Index Medicus
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6. Full Text The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease
by Wang, Minghui and Beckmann, Noam D and Roussos, Panos and Wang, Erming and Zhou, Xianxiao and Wang, Qian and Ming, Chen and Neff, Ryan and Ma, Weiping and Fullard, John F and Hauberg, Mads E and Bendl, Jaroslav and Peters, Mette A and Logsdon, Ben and Wang, Pei and Mahajan, Milind and Mangravite, Lara M and Dammer, Eric B and Duong, Duc M and Lah, James J and Seyfried, Nicholas T and Levey, Allan I and Buxbaum, Joseph D and Ehrlich, Michelle and Gandy, Sam and Katsel, Pavel and Haroutunian, Vahram and Schadt, Eric and Zhang, Bin
Scientific data, ISSN 2052-4463, 09/2018, Volume 5, Issue 1, pp. 180185 - 180185
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Alzheimer Disease - physiopathology | Genetic Predisposition to Disease | Genome-Wide Association Study | Genomics | Humans | Transcriptome | Proteome | Alzheimer Disease - metabolism | Proteomics | Aged, 80 and over | Cognitive Dysfunction - genetics | Alzheimer Disease - genetics | Cohort Studies | Neurodegenerative diseases | Autopsy | Cognitive ability | Quality control | Genomes | Proteomes | Gene expression | Alzheimers disease | Alzheimer's disease | Index Medicus
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7. Full Text Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity
by Carcamo-Orive, Ivan and Hoffman, Gabriel E and Cundiff, Paige and Beckmann, Noam D and D’Souza, Sunita L and Knowles, Joshua W and Patel, Achchhe and Papatsenko, Dimitri and Abbasi, Fahim and Reaven, Gerald M and Whalen, Sean and Lee, Philip and Shahbazi, Mohammad and Henrion, Marc Y.R and Zhu, Kuixi and Wang, Sven and Roussos, Panos and Schadt, Eric E and Pandey, Gaurav and Chang, Rui and Quertermous, Thomas and Lemischka, Ihor
Cell stem cell, ISSN 1934-5909, 04/2017, Volume 20, Issue 4, pp. 518 - 532.e9
variance partition | differentiation variability | iPSC library | network analysis | eQTL | key drivers | Polycomb targets | allelic imbalance | transcriptional variability | Cell & Tissue Engineering | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Cell Line | Reproducibility of Results | Genetic Association Studies | Humans | Polycomb-Group Proteins - metabolism | Gene Regulatory Networks | Genetic Heterogeneity | Cell Differentiation - genetics | Gene Expression Regulation, Developmental | Alleles | Bayes Theorem | Transcription, Genetic | Induced Pluripotent Stem Cells - metabolism | Quantitative Trait Loci - genetics | Index Medicus
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8. Full Text Multiscale causal networks identify VGF as a key regulator of Alzheimer's disease
by Beckmann, Noam D and Lin, Wei-Jye and Wang, Minghui and Cohain, Ariella T and Charney, Alexander W and Wang, Pei and Ma, Weiping and Wang, Ying-Chih and Jiang, Cheng and Audrain, Mickael and Comella, Phillip H and Fakira, Amanda K and Hariharan, Siddharth P and Belbin, Gillian M and Girdhar, Kiran and Levey, Allan and Seyfried, Nicholas T and Dammer, Eric B and Duong, Duc and Lah, James J and Haure-Mirande, Jean-Vianney and Shackleton, Ben and Fanutza, Tomas and Blitzer, Robert and Kenny, Eimear and Zhu, Jun and Haroutunian, Vahram and Katsel, Pavel and Gandy, Sam and Tu, Zhidong and Ehrlich, Michelle E and Zhang, Bin and Salton, Stephen R and Schadt, Eric E
Nature communications, ISSN 2041-1723, 08/2020, Volume 11, Issue 1, pp. 3942 - 3942
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Networks | Animal models | Neurodegenerative diseases | Pathogenesis | Data sets | β-Amyloid | Homology | Gene expression | Alzheimer's disease | Deoxyribonucleic acid--DNA | Multiscale methods | Index Medicus
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