Search Results - "Denny, Joshua C."

Chapter 13: Mining electronic health records in the genomics era by Denny, Joshua C

“…The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical…”
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R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment by Carroll, Robert J, Bastarache, Lisa, Denny, Joshua C

“…Phenome-wide association studies (PheWAS) have been used to replicate known genetic associations and discover new phenotype associations for genetic variants…”
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Extracting research-quality phenotypes from electronic health records to support precision medicine by Wei, Wei-Qi, Denny, Joshua C

“…The convergence of two rapidly developing technologies - high-throughput genotyping and electronic health records (EHRs) - gives scientists an unprecedented…”
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Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies by Zhou, Wei, Nielsen, Jonas B., Fritsche, Lars G., Dey, Rounak, Gabrielsen, Maiken E., Wolford, Brooke N., LeFaive, Jonathon, VandeHaar, Peter, Gagliano, Sarah A., Gifford, Aliya, Bastarache, Lisa A., Wei, Wei-Qi, Denny, Joshua C., Lin, Maoxuan, Hveem, Kristian, Kang, Hyun Min, Abecasis, Goncalo R., Willer, Cristen J., Lee, Seunggeun

“…In genome-wide association studies (GWAS) for thousands of phenotypes in large biobanks, most binary traits have substantially fewer cases than controls. Both…”
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A gene-based association method for mapping traits using reference transcriptome data by Gamazon, Eric R, Wheeler, Heather E, Shah, Kaanan P, Mozaffari, Sahar V, Aquino-Michaels, Keston, Carroll, Robert J, Eyler, Anne E, Denny, Joshua C, Nicolae, Dan L, Cox, Nancy J, Im, Hae Kyung

“…Hae Kyung Im and colleagues report a method for predicting gene expression perturbations from genotype data after training on reference transcriptome data…”
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Electronic health records-driven phenotyping: challenges, recent advances, and perspectives by Pathak, Jyotishman, Kho, Abel N, Denny, Joshua C

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Computational phenotype discovery using unsupervised feature learning over noisy, sparse, and irregular clinical data by Lasko, Thomas A, Denny, Joshua C, Levy, Mia A

“…Inferring precise phenotypic patterns from population-scale clinical data is a core computational task in the development of precision, personalized medicine…”
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Learning from Longitudinal Data in Electronic Health Record and Genetic Data to Improve Cardiovascular Event Prediction by Zhao, Juan, Feng, QiPing, Wu, Patrick, Lupu, Roxana A., Wilke, Russell A., Wells, Quinn S., Denny, Joshua C., Wei, Wei-Qi

“…Current approaches to predicting a cardiovascular disease (CVD) event rely on conventional risk factors and cross-sectional data. In this study, we applied…”
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Use of Genetic Variants Related to Antihypertensive Drugs to Inform on Efficacy and Side Effects by Gill, Dipender, Georgakis, Marios K, Koskeridis, Fotios, Jiang, Lan, Feng, Qiping, Wei, Wei-Qi, Theodoratou, Evropi, Elliott, Paul, Denny, Joshua C, Malik, Rainer, Evangelou, Evangelos, Dehghan, Abbas, Dichgans, Martin, Tzoulaki, Ioanna

“…BACKGROUND:Drug effects can be investigated through natural variation in the genes for their protein targets. The present study aimed to use this approach to…”
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Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record by Wei, Wei-Qi, Bastarache, Lisa A, Carroll, Robert J, Marlo, Joy E, Osterman, Travis J, Gamazon, Eric R, Cox, Nancy J, Roden, Dan M, Denny, Joshua C

“…To compare three groupings of Electronic Health Record (EHR) billing codes for their ability to represent clinically meaningful phenotypes and to replicate…”
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Genetically determined serum urate levels and cardiovascular and other diseases in UK Biobank cohort: A phenome-wide mendelian randomization study by Li, Xue, Meng, Xiangrui, He, Yazhou, Spiliopoulou, Athina, Timofeeva, Maria, Wei, Wei-Qi, Gifford, Aliya, Yang, Tian, Varley, Tim, Tzoulaki, Ioanna, Joshi, Peter, Denny, Joshua C, Mckeigue, Paul, Campbell, Harry, Theodoratou, Evropi

“…The role of urate in cardiovascular diseases (CVDs) has been extensively investigated in observational studies; however, the extent of any causal effect…”
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Diversity and inclusion for the All of Us research program: A scoping review by Mapes, Brandy M, Foster, Christopher S, Kusnoor, Sheila V, Epelbaum, Marcia I, AuYoung, Mona, Jenkins, Gwynne, Lopez-Class, Maria, Richardson-Heron, Dara, Elmi, Ahmed, Surkan, Karl, Cronin, Robert M, Wilkins, Consuelo H, Pérez-Stable, Eliseo J, Dishman, Eric, Denny, Joshua C, Rutter, Joni L

“…The All of Us Research Program (All of Us) is a national effort to accelerate health research by exploring the relationship between lifestyle, environment, and…”
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Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance by Wei, Wei-Qi, Teixeira, Pedro L, Mo, Huan, Cronin, Robert M, Warner, Jeremy L, Denny, Joshua C

“…Objective To evaluate the phenotyping performance of three major electronic health record (EHR) components: International Classification of Disease (ICD)…”
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A study of active learning methods for named entity recognition in clinical text by Chen, Yukun, Lasko, Thomas A., Mei, Qiaozhu, Denny, Joshua C., Xu, Hua

“…[Display omitted] •We developed novel active learning algorithms for clinical named entity recognition.•Equal cost per sample is not a practical annotation…”
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PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations by Denny, Joshua C., Ritchie, Marylyn D., Basford, Melissa A., Pulley, Jill M., Bastarache, Lisa, Brown-Gentry, Kristin, Wang, Deede, Masys, Dan R., Roden, Dan M., Crawford, Dana C.

“…Motivation: Emergence of genetic data coupled to longitudinal electronic medical records (EMRs) offers the possibility of phenome-wide association scans…”
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PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability by Kirby, Jacqueline C, Speltz, Peter, Rasmussen, Luke V, Basford, Melissa, Gottesman, Omri, Peissig, Peggy L, Pacheco, Jennifer A, Tromp, Gerard, Pathak, Jyotishman, Carrell, David S, Ellis, Stephen B, Lingren, Todd, Thompson, Will K, Savova, Guergana, Haines, Jonathan, Roden, Dan M, Harris, Paul A, Denny, Joshua C

“…Objective Health care generated data have become an important source for clinical and genomic research. Often, investigators create and iteratively refine…”
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The phenotypic legacy of admixture between modern humans and Neandertals by Simonti, Corinne N., Vernot, Benjamin, Bastarache, Lisa, Bottinger, Erwin, Carrell, David S., Chisholm, Rex L., Crosslin, David R., Hebbring, Scott J., Jarvik, Gail P., Kullo, Iftikhar J., Li, Rongling, Pathak, Jyotishman, Ritchie, Marylyn D., Roden, Dan M., Verma, Shefali S., Tromp, Gerard, Prato, Jeffrey D., Bush, William S., Akey, Joshua M., Denny, Joshua C., Capra, John A.

“…Many modern human genomes retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence of this admixture on human…”
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Using topic modeling via non-negative matrix factorization to identify relationships between genetic variants and disease phenotypes: A case study of Lipoprotein(a) (LPA) by Zhao, Juan, Feng, QiPing, Wu, Patrick, Warner, Jeremy L, Denny, Joshua C, Wei, Wei-Qi

“…Genome-wide and phenome-wide association studies are commonly used to identify important relationships between genetic variants and phenotypes. Most studies…”
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Benefit of Preemptive Pharmacogenetic Information on Clinical Outcome by Roden, Dan M., Driest, Sara L., Mosley, Jonathan D., Wells, Quinn S., Robinson, Jamie R., Denny, Joshua C., Peterson, Josh F.

“…The development of new knowledge around the genetic determinants of variable drug action has naturally raised the question of how this new knowledge can be…”
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Phenome-wide Mendelian-randomization study of genetically determined vitamin D on multiple health outcomes using the UK Biobank study by Meng, Xiangrui, Li, Xue, Timofeeva, Maria N, He, Yazhou, Spiliopoulou, Athina, Wei, Wei-Qi, Gifford, Aliya, Wu, Hongjiang, Varley, Timothy, Joshi, Peter, Denny, Joshua C, Farrington, Susan M, Zgaga, Lina, Dunlop, Malcolm G, McKeigue, Paul, Campbell, Harry, Theodoratou, Evropi

“…Abstract Background Vitamin D deficiency is highly prevalent across the globe. Existing studies suggest that a low vitamin D level is associated with more than…”
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