Publications by authors named "Jacob Hughey"

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Blood Clock Correlation Distance (BloodCCD) as a novel marker to detect circadian rhythm disruption in cancer survivors with insomnia.
Brian J Altman, Po-Ju Lin, Lindsey J Mattick, Elliot H Outland, Javier Bautista, Jacob J Hughey

BJC Rep· September 2025

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LimoRhyde2: Genomic analysis of biological rhythms based on effect sizes.
Dora Obodo, Elliot H Outland, Jacob J Hughey

PLoS One· December 2023

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The phenotype-genotype reference map: Improving biobank data science through replication.
Lisa Bastarache, Sarah Delozier, Anita Pandit, Jing He, Adam Lewis, Jacob J Hughey

Am J Hum Genet· September 2023

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Sex Inclusion in Transcriptome Studies of Daily Rhythms.
Dora Obodo, Elliot H Outland, Jacob J Hughey

J Biol Rhythms· February 2023

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LimoRhyde2: genomic analysis of biological rhythms based on effect sizes.
Dora Obodo, Elliot H Outland, Jacob J Hughey

bioRxiv· February 2023

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The seeker R package: simplified fetching and processing of transcriptome data.
Joshua L Schoenbachler, Jacob J Hughey

PeerJ· January 2023

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The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants.
Layla Aref, Lisa Bastarache, Jacob J Hughey

Bioinformatics· October 2022

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Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS.
Rebecca Irlmeier, Jacob J Hughey, Lisa Bastarache, Joshua C Denny, Qingxia Chen

Bioinformatics· April 2022

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Analysis of Electronic Health Records Reveals Medication-Related Interference on Point-of-Care Urine Drug Screening Assays.
Nadia Ayala-Lopez, Jennifer M Colby, Jacob J Hughey

J Anal Toxicol· February 2022

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Optogenetic stimulation of VIPergic SCN neurons induces photoperiodic-like changes in the mammalian circadian clock.
Michael C Tackenberg, Jacob J Hughey, Douglas G McMahon

Eur J Neurosci· November 2021

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Automated quality control and cell identification of droplet-based single-cell data using dropkick.
Cody N Heiser, Victoria M Wang, Bob Chen, Jacob J Hughey, Ken S Lau

Genome Res· October 2021

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The Role of Electronic Health Records in Advancing Genomic Medicine.
Jodell E Linder, Lisa Bastarache, Jacob J Hughey, Josh F Peterson

Annu Rev Genomics Hum Genet· August 2021

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A Computational Approach to Identify Interfering Medications on Urine Drug Screening Assays without Data from Confirmatory Testing.
Nadia Ayala-Lopez, Layla Aref, Jennifer M Colby, Jacob J Hughey

J Anal Toxicol· April 2021

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pmparser and PMDB: resources for large-scale, open studies of the biomedical literature.
Joshua L Schoenbachler, Jacob J Hughey

PeerJ· March 2021

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The risks of using the chi-square periodogram to estimate the period of biological rhythms.
Michael C Tackenberg, Jacob J Hughey

PLoS Comput Biol· January 2021

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Distinct Components of Photoperiodic Light Are Differentially Encoded by the Mammalian Circadian Clock.
Michael C Tackenberg, Jacob J Hughey, Douglas G McMahon

J Biol Rhythms· August 2020

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Eating breakfast and avoiding late-evening snacking sustains lipid oxidation.
Kevin Parsons Kelly, Owen P McGuinness, Maciej Buchowski, Jacob J Hughey, Heidi Chen

PLoS Biol· February 2020

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Discovering Cross-Reactivity in Urine Drug Screening Immunoassays through Large-Scale Analysis of Electronic Health Records.
Jacob J Hughey, Jennifer M Colby

Clin Chem· December 2019

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Improving the phenotype risk score as a scalable approach to identifying patients with Mendelian disease.
Lisa Bastarache, Jacob J Hughey, Jeffrey A Goldstein, Julie A Bastraache, Satya Das

J Am Med Inform Assoc· December 2019

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Releasing a preprint is associated with more attention and citations for the peer-reviewed article.
Darwin Y Fu, Jacob J Hughey

Elife· December 2019

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Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record.
Jacob J Hughey, Seth D Rhoades, Darwin Y Fu, Lisa Bastarache, Joshua C Denny

BMC Genomics· November 2019

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Simphony: simulating large-scale, rhythmic data.
Jordan M Singer, Darwin Y Fu, Jacob J Hughey

PeerJ· May 2019

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NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop.
Mialy M DeFelice, Helen R Clark, Jacob J Hughey, Inbal Maayan, Takamasa Kudo

Sci Signal· April 2019

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LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data.
Jordan M Singer, Jacob J Hughey

J Biol Rhythms· February 2019

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Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level.
Miriam V Gutschow, John C Mason, Keara M Lane, Inbal Maayan, Jacob J Hughey

Mol Biol Cell· January 2019

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