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

Jacob Hughey's public data