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1. Probabilistic Models for the Analysis of Gene Expression Profiles
by Quon, Gerald
06/2012
Gene expression profiles are some of the most abundant sources of data about the cellular state of a collection of cells in an organism. Comparison of the... 
tumor purification | expression deconvolution | expression evolution | topic models | cancer | gene expression profiling | prognosis prediction | 0715 | probabilistic models | tumor heterogeneity
Dissertation
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2. Full Text Probabilistic Models for the Analysis of Gene Expression Profiles
by Quon, Gerald and University of Toronto (Canada)
ISBN 0499222822
Gene expression profiles are some of the most abundant sources of data about the cellular state of a collection of cells in an organism. Comparison of the... 
Computer Science
eBook
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3. Full Text Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease
by Gjoneska, Elizabeta and Pfenning, Andreas R and Mathys, Hansruedi and Quon, Gerald and Kundaje, Anshul and Tsai, Li-Huei and Kellis, Manolis
Nature, ISSN 0028-0836, 02/2015, Volume 518, Issue 7539, pp. 365 - 369
Alzheimer's disease (AD) is a severe(1) age-related neurodegenerative disorder characterized by accumulation of amyloid-beta plaques and neurofibrillary... 
TRANSCRIPTION FACTORS | ELEMENTS | ACTIVATION | DATABASE | MICROGLIA | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | BINDING | DIFFERENTIAL EXPRESSION ANALYSIS | DISCOVERY | ENCODE | Chromatin - metabolism | Humans | Neuronal Plasticity - genetics | Conserved Sequence | Female | Alzheimer Disease - immunology | Disease Models, Animal | Proto-Oncogene Proteins - metabolism | Alzheimer Disease - physiopathology | Genetic Predisposition to Disease - genetics | Genome-Wide Association Study | Epigenomics | Up-Regulation - genetics | Down-Regulation - genetics | Hippocampus - metabolism | Animals | Epigenesis, Genetic - genetics | Models, Biological | Polymorphism, Single Nucleotide - genetics | Trans-Activators - metabolism | Enhancer Elements, Genetic - genetics | Mice | Transcription, Genetic - genetics | Alzheimer Disease - genetics | Chromatin - genetics | Immunity - genetics | Memory - physiology | Genetic research | Epigenetic inheritance | Genetic aspects | Research | Neurological research | Alzheimer's disease | Proteins | Transcription factors | Immunology | Ontology | Neurodegeneration | Cell cycle | Gene loci | Gene expression | Alzheimers disease | Binding sites | Index Medicus
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4. Full Text Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases
by Marbach, Daniel and Lamparter, David and Quon, Gerald and Kellis, Manolis and Kutalik, Zoltán and Bergmann, Sven
Nature Methods, ISSN 1548-7091, 03/2016, Volume 13, Issue 4, pp. 366 - 370
Mapping perturbed molecular circuits that underlie complex diseases remains a great challenge. We developed a comprehensive resource of 394 cell type- and... 
MOTIFS | VARIANTS | BIOCHEMICAL RESEARCH METHODS | RISK | NETWORKS | IDENTIFICATION | ENHANCERS | INFERENCE | TRAITS | CELL-TYPES | GENOME-WIDE ASSOCIATION | Brain Diseases - metabolism | Computational Biology - methods | Genome-Wide Association Study | Epigenomics | Humans | Brain Diseases - genetics | Transcription Factors - genetics | Gene Regulatory Networks | Organ Specificity | Promoter Regions, Genetic - genetics | Transcription Factors - metabolism | Protein Interaction Mapping - methods | Genetic Variation - genetics | Genome, Human | Cell Lineage - genetics | Genome-wide association studies | Genetic aspects | Research | Tissues | Genetic regulation | Health aspects | Diseases | Studies | Tissue | Genetics | Disease | Molecular biology | Index Medicus
Journal Article
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5. Full Text The landscape of false-positive transcription factor binding site predictions in yeast
by Quon, Gerald T
2007, ISBN 0494274336
A major shortcoming of most available methods for transcription factor binding site (TFBS) discovery is that they produce a high rate of false-positive motifs... 
Biology, Molecular
eBook
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6. Full Text FTO Obesity Variant Circuitry and Adipocyte Browning in Humans
by Claussnitzer, Melina and Dankel, Simon N and Kim, Kyoung-Han and Quon, Gerald and Meuleman, Wouter and Haugen, Christine and Glunk, Viktoria and Sousa, Isabel S and Beaudry, Jacqueline L and Puviindran, Vijitha and Abdennur, Nezar A and Liu, Jannel and Svensson, Per-Arne and Hsu, Yi-Hsiang and Drucker, Daniel J and Mellgren, Gunnar and Hui, Chi-Chung and Hauner, Hans and Kellis, Manolis and Sahlgrenska akademin and Institute of Medicine, Department of Molecular and Clinical Medicine and Institutionen för medicin, avdelningen för molekylär och klinisk medicin and Göteborgs universitet and Gothenburg University and Sahlgrenska Academy
The New England Journal of Medicine, ISSN 0028-4793, 09/2015, Volume 373, Issue 10, pp. 895 - 907
In this study, the authors used epigenetics, allelic activity, motif conservation, and other techniques to dissect the regulatory circuitry and mechanistic... 
MEDICINE, GENERAL & INTERNAL | IRX3 | GENE-EXPRESSION | BODY-MASS INDEX | RISK | ADULT OBESITY | CHILDHOOD | LOCUS | ADIPOSE-TISSUE | Thermogenesis - genetics | Gene Expression | Epigenomics | RNA Editing | Humans | Molecular Sequence Data | Alpha-Ketoglutarate-Dependent Dioxygenase FTO | Risk | Mitochondria - metabolism | Obesity - genetics | Obesity - metabolism | Proteins - genetics | Thermogenesis - physiology | Phenotype | Animals | Genetic Engineering | Adipocytes - metabolism | Base Sequence | Alleles | Clustered Regularly Interspaced Short Palindromic Repeats | Mice | Haplotypes | Obesity | Care and treatment | Research | Gene expression | Appetite | CRISPR | Adipose tissue | Physical activity | Body fat | Genomics | Genes | Body weight | Genomes | Adipocytes | Weight control | Conserved sequence | Mitochondria | Thermogenesis | Derepression | Gastrointestinal surgery | Index Medicus | Abridged Index Medicus | Cell and Molecular Biology | Cell- och molekylärbiologi
Journal Article
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7. Full Text Commentary: Optimizing Postoperative Surveillance of Pediatric Low-Grade Glioma Using Tumor Behavior Patterns
by Quon, Jennifer L and Grant, Gerald A
Neurosurgery, ISSN 0148-396X, 04/2019
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8. Full Text Commentary: Limited Dorsal Myeloschisis: Reconsideration of its Embryological Origin
by Quon, Jennifer L and Grant, Gerald A
Neurosurgery, ISSN 0148-396X, 02/2019
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9. Full Text Integrative analysis of 111 reference human epigenomes
by Roadmap Epigenomics Consortium, Epigenomics Consortium and Kundaje, Anshul and Meuleman, Wouter and Ernst, Jason and Bilenky, Misha and Yen, Angela and Heravi-Moussavi, Alireza and Kheradpour, Pouya and Zhang, Zhizhuo and Wang, Jianrong and Ziller, Michael J and Amin, Viren and Whitaker, John W and Schultz, Matthew D and Ward, Lucas D and Sarkar, Abhishek and Quon, Gerald and Sandstrom, Richard S and Eaton, Matthew L and Wu, Yi-Chieh and Pfenning, Andreas R and Wang, Xinchen and Claussnitzer, Melina and Liu, Yaping and Coarfa, Cristian and Harris, R. Alan and Shoresh, Noam and Epstein, Charles B and Gjoneska, Elizabeta and Leung, Danny and Xie, Wei and Hawkins, R. David and Lister, Ryan and Hong, Chibo and Gascard, Philippe and Mungall, Andrew J and Moore, Richard and Chuah, Eric and Tam, Angela and Canfield, Theresa K and Hansen, R. Scott and Kaul, Rajinder and Sabo, Peter J and Bansal, Mukul S and Carles, Annaick and Dixon, Jesse R and Farh, Kai-How and Feizi, Soheil and Karlic, Rosa and Kim, Ah-Ram and Kulkarni, Ashwinikumar and Li, Daofeng and Lowdon, Rebecca and Elliott, Ginell and Mercer, Tim R and Neph, Shane J and Onuchic, Vitor and Polak, Paz and Rajagopal, Nisha and Ray, Pradipta and Sallari, Richard C and Siebenthall, Kyle T and Sinnott-Armstrong, Nicholas A and Stevens, Michael and Thurman, Robert E and Wu, Jie and Zhang, Bo and Zhou, Xin and Beaudet, Arthur E and Boyer, Laurie A and De Jager, Philip L and Farnham, Peggy J and Fisher, Susan J and Haussler, David and Jones, Steven J. M and Li, Wei and Marra, Marco A and McManus, Michael T and Sunyaev, Shamil and Thomson, James A and Tlsty, Thea D and Tsai, Li-Huei and Wang, Wei and Waterland, Robert A and Zhang, Michael Q and Chadwick, Lisa H and Bernstein, Bradley E and Costello, Joseph F and Ecker, Joseph R and Hirst, Martin and Meissner, Alexander and Milosavljevic, Aleksandar and Ren, Bing and Stamatoyannopoulos, John A and Wang, Ting and Kellis, Manolis and Roadmap Epigenomics Consortium
Nature, ISSN 0028-0836, 02/2015, Volume 518, Issue 7539, pp. 317 - 329
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a... 
TRANSCRIPTION FACTORS | RISK LOCI | DYNAMIC DNA METHYLATION | ALZHEIMERS-DISEASE | MULTIDISCIPLINARY SCIENCES | EMBRYONIC STEM-CELLS | HISTONE MODIFICATIONS | CHROMATIN-STATE | REGULATORY REGIONS | GENOME-WIDE ASSOCIATION | MAMMALIAN GENOMES | Chromatin - metabolism | Humans | Reference Values | RNA - genetics | Organ Specificity - genetics | DNA Methylation | Base Sequence | Cell Lineage - genetics | Chromatin - chemistry | Genome-Wide Association Study | Datasets as Topic | Epigenomics | Chromosomes, Human - genetics | Cells, Cultured | Chromosomes, Human - metabolism | DNA - metabolism | Genome, Human - genetics | Chromosomes, Human - chemistry | DNA - genetics | DNA - chemistry | Epigenesis, Genetic - genetics | Enhancer Elements, Genetic - genetics | Genetic Variation - genetics | Histones - metabolism | Chromatin - genetics | Genetic research | Epigenetic inheritance | Research | Human genome | DNA methylation | Enzymes | Genomes | Gene expression | Genomics | Deoxyribonucleic acid--DNA | Index Medicus
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10. Full Text 136 Long-term Supratentorial Radiographic Effects of Surgery and Local Radiation in Children with Infratenorial Ependymoma
by Yecies, Derek W and Esparza, Rogelio and Azad, Tej Deepak and Quon, Jennifer L and Forkert, Nils and Maceachern, Sarah and Cheshier, Samuel Henry and Edwards, Michael S B and Grant, Gerald A and Yeom, Kristen
Neurosurgery, ISSN 0148-396X, 09/2017, Volume 64, Issue CN_suppl_1, pp. 231 - 232
Abstract INTRODUCTION Current standard of care for children with an infratentorial ependymoma includes maximal safe resection with local radiation of 54–59gy.... 
Datasets | Surgery
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11. Full Text scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
by Johansen, N and Quon, G
GENOME BIOLOGY, ISSN 1474-760X, 08/2019, Volume 20, Issue 1, pp. 166 - 166
scRNA-seq dataset integration occurs in different contexts, such as the identification of cell type-specific differences in gene expression across conditions... 
RECONSTRUCTION | Data harmonization | NOISE | FATE | Deep learning | CIRCUITS | ATLAS | scRNA-seq | Alignment | Neural networks | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | Data integration | GENETICS & HEREDITY | Domain adaptation | Response to stimulus | EXPRESSION | Batch effects | RNA-SEQUENCING DATA | REVEALS | Index Medicus
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12. Full Text PLAY project home consultation intervention program for young children with autism spectrum disorders: A randomized controlled trial
by Solomon, Richard and Van Egeren, Laurie A and Mahoney, Gerald and Huber, Melissa S. Quon and Zimmerman, Perri
Journal of Developmental and Behavioral Pediatrics, ISSN 0196-206X, 10/2014, Volume 35, Issue 8, pp. 475 - 485
Objective: To evaluate the effectiveness of the Play and Language for Autistic Youngsters (PLAY) Project Home Consultation model, in combination with usual... 
Parent-mediated intervention | Early intervention | Developmental outcomes | early intervention | BEHAVIOR | PSYCHOLOGY, DEVELOPMENTAL | PARENTS | MODEL | PERVASIVE DEVELOPMENTAL DISORDERS | TODDLERS | PRESCHOOL-CHILDREN | developmental outcomes | BEHAVIORAL SCIENCES | PEDIATRICS | JOINT ATTENTION | HEALTH | parent-mediated intervention | Child Development Disorders, Pervasive - therapy | Humans | Child, Preschool | Male | Treatment Outcome | Child Health Services - methods | Caregivers - education | Child Development Disorders, Pervasive - psychology | Feedback | Child Development Disorders, Pervasive - diagnosis | Video Recording | Female | Referral and Consultation | Parent-Child Relations | Care and treatment | Wellness programs | Usage | Parent and child | Pervasive developmental disorders | Autistic children | Health aspects | Intervention | Clinical trials | Autism | Pediatrics | Social interaction | Children & youth | Index Medicus | Original
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13. Full Text Probabilistic Modeling of Imaging, Genetics and Diagnosis
by Batmanghelich, Nematollah K and Dalca, Adrian and Quon, Gerald and Sabuncu, Mert and Golland, Polina and Alzheimer's Dis Neuroimaging Initi
IEEE Transactions on Medical Imaging, ISSN 0278-0062, 07/2016, Volume 35, Issue 7, pp. 1765 - 1779
We propose a unified Bayesian framework for detecting genetic variants associated with disease by exploiting image-based features as an intermediate phenotype.... 
Bayesian models | imaging genetics | Imaging | Genetics | Brain models | Inference algorithms | variational inference | Alzheimer's disease | probabilistic graphical model | SURFACE-BASED ANALYSIS | LINEAR-REGRESSION | BAYESIAN VARIABLE SELECTION | HUMAN BRAIN | APPROXIMATION | ENGINEERING, BIOMEDICAL | ALZHEIMERS-DISEASE | IMAGING SCIENCE & PHOTOGRAPHIC TECHNOLOGY | PHENOTYPES | ENGINEERING, ELECTRICAL & ELECTRONIC | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | HUMAN CEREBRAL-CORTEX | SEGMENTATION | RADIOLOGY, NUCLEAR MEDICINE & MEDICAL IMAGING | GENOME-WIDE ASSOCIATION | Neuroimaging | Phenotype | Algorithms | Humans | Bayes Theorem | Models, Statistical | Alzheimer Disease | Bayesian statistical decision theory | Usage | Risk factors | Alzheimers disease | Index Medicus
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14. Full Text PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions
by Qiao, Wenlian and Quon, Gerald and Csaszar, Elizabeth and Yu, Mei and Morris, Quaid and Zandstra, Peter W
PLoS Computational Biology, ISSN 1553-734X, 12/2012, Volume 8, Issue 12, pp. e1002838 - e1002838
The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles... 
CELLS | PATTERNS | NORMALIZATION | GENE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Likelihood Functions | Algorithms | Flow Cytometry | Oligonucleotide Array Sequence Analysis | Humans | Least-Squares Analysis | Gene Expression Profiling - methods | Fetal Blood - metabolism | Physiological aspects | Genetic aspects | Research | Gene expression | Health aspects | Population genetics | Blood | Flow cytometry | Cell culture | Ontology | Stem cells | Cell cycle | Population | Experiments | Methods | Index Medicus
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15. Full Text A Plug-and-Play, Drug-on-Pillar Platform for Combination Drug Screening Implemented by Microfluidic Adaptive Printing
by Li, Jiannan and Tan, Wen and Xiao, Wenwu and Carney, Randy P and Men, Yongfan and Li, Yuanpei and Quon, Gerald and Ajena, Yousif and Lam, Kit S and Pan, Tingrui
Analytical Chemistry, ISSN 0003-2700, 12/2018, Volume 90, Issue 23, pp. 13969 - 13977
Traditional high-throughput drug combination screening requires automatic pipetting of drugs into high-density microtiter plates. Here, a drug-on-pillar... 
CHEMISTRY, ANALYTICAL | THERAPY | ARRAY | MICROARRAY | CELL-CULTURE | INHIBITORS | ALGINATE HYDROGELS | CANCER | CHEMOTHERAPY | Microfluidic Analytical Techniques | Cell Survival - drug effects |