Preprints
Releasing a preprint is associated with more attention and citations for the peer-reviewed article

Fu and Hughey, bioRxiv

Postprints
Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record

Hughey et al., BMC Genomics 2019

Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease

Bastarache et al., J Am Med Inform Assoc 2019

Discovering Cross-Reactivity in Urine Drug Screening Immunoassays through Large-Scale Analysis of Electronic Health Records

Hughey and Colby, Clin Chem 2019

Simphony: simulating large-scale, rhythmic data

Singer et al., PeerJ 2019

NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop

DeFelice / Clark / Hughey et al., Sci Signal 2019

LimoRhyde: a flexible approach for differential analysis of rhythmic transcriptome data

Singer and Hughey, J Biol Rhythms 2018

Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level

Gutschow et al., Mol Biol Cell 2018

Population-level rhythms in human skin with implications for circadian medicine

Wu et al., PNAS 2018

Pulling the covers in electronic health records for an association study with self-reported sleep behaviors

Rhoades et al., Chronobiol Int 2018

MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data

Hu et al., Cell Rep 2018

Tau-independent Phase Analysis: A Novel Method for Accurately Determining Phase Shifts

Tackenberg et al., J Biol Rhythms 2018

Phenotype risk scores identify patients with unrecognized Mendelian disease patterns

Bastarache et al., Science 2018

Evidence for widespread dysregulation of circadian clock progression in human cancer

Shilts et al., PeerJ 2018

Live-cell measurements of kinase activity in single cells using translocation reporters

Kudo et al., Nat Protoc 2018

Self-reported dietary adherence, disease-specific symptoms, and quality of life are associated with healthcare provider follow-up in celiac disease

Hughey et al., BMC Gastroenterol 2017

Guidelines for Genome-Scale Analysis of Biological Rhythms

Hughes et al., J Biol Rhythms 2017

Machine learning identifies a compact gene set for monitoring the circadian clock in human blood

Hughey, Genome Med 2017

Differential phasing between circadian clocks in the brain and peripheral organs in humans

Hughey and Butte, J Biol Rhythms 2016

Is the Crowd Better as an Assistant or a Replacement in Ontology Engineering? An Exploration Through the Lens of the Gene Ontology

Mortensen et al., J Biomed Inform 2016

ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system

Hughey et al., Nucleic Acids Res 2016

Robust meta-analysis of gene expression using the elastic net

Hughey and Butte, Nucleic Acids Res 2015

Single-cell variation leads to population invariance in NF-κB signaling dynamics

Hughey / Gutschow et al., Mol Biol Cell 2015

High-sensitivity measurements of multiple kinase activities in live single cells

Regot et al., Cell 2014

The microfluidic multi-trap nanophysiometer for hematologic cancer cell characterization reveals temporal sensitivity of the calcein-AM efflux assay

Byrd et al., Sci Rep 2014

Single-cell and Population NF-κB Dynamic Responses Depend on Lipopolysaccharide Preparation

Gutschow / Hughey et al., PLOS One 2013

Single-cell NF-κB dynamics reveal digital activation and analog information processing

Tay / Hughey et al., Nature 2010

Computational modeling of mammalian signaling networks

Hughey et al., Wiley Interdiscip Rev Syst Biol Med 2010

A Noisy Paracrine Signal Determines the Cellular NF-κB Response to Lipopolysaccharide

Lee et al., Sci Signal 2009

Microfluidic platform for real-time signaling analysis of multiple single T cells in parallel

Faley et al., Lab Chip 2008