Jacob Hughey

Publications

• Phenotype risk scores identify patients with unrecognized Mendelian disease patterns
• Self-reported dietary adherence, disease-specific symptoms, and quality of life are associated with healthcare provider follow-up in celiac disease
• Automated quality control and cell identification of droplet-based single-cell data using dropkick.
• The Role of Electronic Health Records in Advancing Genomic Medicine.
• Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease.
• Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level.
• Discovering Cross-Reactivity in Urine Drug Screening Immunoassays through Large-Scale Analysis of Electronic Health Records.
• Simphony: simulating large-scale, rhythmic data.
• MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data.
• Population level rhythms in human skin: implications for circadian medicine
• Guidelines for Genome-Scale Analysis of Biological Rhythms.
• Evidence for widespread dysregulation of circadian clock progression in human cancer.
• Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells
• Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans.
• Single-cell variation leads to population invariance in NF-κB signaling dynamics.
• LimoRhyde: a flexible approach for differential analysis of rhythmic transcriptome data
• Single-cell NF-κB dynamics reveal digital activation and analogue information processing
• Analysis of electronic health records reveals medication-related interference on point-of-care urine drug screening assays
• A computational approach to identify interfering medications on urine drug screening assays without data from confirmatory testing
• Eating breakfast and avoiding the evening snack sustains lipid oxidation
• Machine learning identifies a compact gene set for monitoring the circadian clock in human blood
• Simphony: simulating large-scale, rhythmic data
• Factors Associated with Medicine Timing Effects: A Meta-analysis
• Pulling the covers in electronic health records for an association study with self-reported sleep behaviors
• Tau-independent Phase Analysis: A Novel Method for Accurately Determining Phase Shifts
• Population-level rhythms in human skin with implications for circadian medicine
• The risks of using the chi-square periodogram to estimate the period of biological rhythms
• pmparser and PMDB: resources for large-scale, open studies of the biomedical literature
• Automated quality control and cell identification of droplet-based single-cell data using dropkick
• Live-cell measurements of kinase activity in single cells using translocation reporters
• Eating breakfast and avoiding late-evening snacking sustains lipid oxidation
• Optogenetic stimulation of VIPergic SCN neurons induces photoperiodic changes in the mammalian circadian clock
• Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record
• NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop
• A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide.
• Optogenetic stimulation of VIPergic SCN neurons induces photoperiodic‐like changes in the mammalian circadian clock
• Releasing a preprint is associated with more attention and citations for the peer-reviewed article
• Robust meta-analysis of gene expression using the elastic net
• ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system
• Monitoring the circadian clock in human blood using personalized machine learning
• Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology
• High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells
• Computational modeling of mammalian signaling networks
• Single-Cell and Population NF-κB Dynamic Responses Depend on Lipopolysaccharide Preparation
• Microfluidic platform for real-time signaling analysis of multiple single T cells in parallel
• Intra-microfluidic pinocytic loading of human T cells
• The microfluidic multitrap nanophysiometer for hematologic cancer cell characterization reveals temporal sensitivity of the calcein-AM efflux assay
• Widespread dysregulation of the circadian clock in human cancer
• Distinct components of photoperiodic light are differentially encoded by the mammalian circadian clock
• The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants
• Sex inclusion in transcriptome studies of daily rhythms
• The seeker R package: simplified fetching and processing of transcriptome data
• Sex Inclusion in Transcriptome Studies of Daily Rhythms
• LimoRhyde2: genomic analysis of biological rhythms based on effect sizes
• LimoRhyde2: Genomic analysis of biological rhythms based on effect sizes