Jacob J Hughey (Atul J Butte)

Publication Activity (10 Years)

Years Active: 2015-2023
Publications (10 Years): 23

Top Topics

Electronic Health Record

Top Venues

Journal of biological rhythms

bioRxiv : the preprint server for biology

Nucleic acids research

This page only lists publications with an associated author ORCID identifier.

Publications

Dora Obodo, Elliot H Outland, Jacob J Hughey
LimoRhyde2: genomic analysis of biological rhythms based on effect sizes. bioRxiv : the preprint server for biology (2023)
Dora Obodo, Elliot H Outland, Jacob J Hughey
LimoRhyde2: genomic analysis of biological rhythms based on effect sizes. bioRxiv : the preprint server for biology (2023)
Dora Obodo, Elliot H Outland, Jacob J Hughey
LimoRhyde2: genomic analysis of biological rhythms based on effect sizes. bioRxiv : the preprint server for biology (2023)
Dora Obodo, Elliot H Outland, Jacob J Hughey
LimoRhyde2: Genomic analysis of biological rhythms based on effect sizes. PloS one 18 (12) (2023)
Joshua L Schoenbachler, Jacob J Hughey
The seeker R package: simplified fetching and processing of transcriptome data. PeerJ 10 (2022)
Layla Aref, Lisa Bastarache, Jacob J Hughey
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants. Bioinformatics (Oxford, England) 38 (21) (2022)
Dora Obodo, Elliot H Outland, Jacob J Hughey
Sex Inclusion in Transcriptome Studies of Daily Rhythms. Journal of biological rhythms (2022)
Joshua L Schoenbachler, Jacob J Hughey
pmparser and PMDB: resources for large-scale, open studies of the biomedical literature. PeerJ 9 (2021)
Michael C Tackenberg, Jacob J Hughey
The risks of using the chi-square periodogram to estimate the period of biological rhythms. PLoS computational biology 17 (1) (2021)
Michael C Tackenberg, Jacob J Hughey, Douglas G McMahon
Optogenetic stimulation of VIPergic SCN neurons induces photoperiodic-like changes in the mammalian circadian clock. The European journal of neuroscience 54 (9) (2021)
Michael C Tackenberg, Jacob J Hughey, Douglas G McMahon
Distinct Components of Photoperiodic Light Are Differentially Encoded by the Mammalian Circadian Clock. Journal of biological rhythms 35 (4) (2020)
Kevin Parsons Kelly, Owen P McGuinness, Maciej Buchowski, Jacob J Hughey, Heidi Chen, James Powers, Terry Page, Carl Hirschie Johnson
Eating breakfast and avoiding late-evening snacking sustains lipid oxidation. PLoS biology 18 (2) (2020)
Mialy M DeFelice, Helen R Clark, Jacob J Hughey, Inbal Maayan, Takamasa Kudo, Miriam V Gutschow, Markus W Covert, Sergi Regot
NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop. Science signaling 12 (579) (2019)
Darwin Y Fu, Jacob J Hughey
Releasing a preprint is associated with more attention and citations for the peer-reviewed article. eLife 8 (2019)
Jacob J Hughey, Seth D Rhoades, Darwin Y Fu, Lisa Bastarache, Joshua C Denny, Qingxia Chen
Cox regression increases power to detect genotype-phenotype associations in genomic studies using the electronic health record. BMC genomics 20 (1) (2019)
Seth D Rhoades, Lisa Bastarache, Joshua C Denny, Jacob J Hughey
Pulling the covers in electronic health records for an association study with self-reported sleep behaviors. Chronobiology international 35 (12) (2018)
Gang Wu, Marc D Ruben, Robert E Schmidt, Lauren J Francey, David F Smith, Ron C Anafi, Jacob J Hughey, Ryan Tasseff, Joseph D Sherrill, John E Oblong, Kevin J Mills, John B Hogenesch
Population-level rhythms in human skin with implications for circadian medicine. Proceedings of the National Academy of Sciences of the United States of America 115 (48) (2018)
Lisa Bastarache, Jacob J Hughey, Scott Hebbring, Joy Marlo, Wanke Zhao, Wanting T Ho, Sara L Van Driest, Tracy L McGregor, Jonathan D Mosley, Quinn S Wells, Michael Temple, Andrea H Ramirez, Robert J Carrol, Travis Osterman, Todd L Edwards, Douglas M Ruderfer, Digna R Velez Edwards, Rizwan Hamid, Joy D Cogan, Andrew M Glazer, Wei-Qi Wei, QiPing Feng, Murray Brilliant, Zhizhuang J Zhao, Nancy J Cox, Dan M Roden, Joshua C Denny
Phenotype risk scores identify patients with unrecognized Mendelian disease patterns. Science (New York, N.Y.) 359 (6381) (2018)
Michael C Tackenberg, Jeff R Jones, Terry L Page, Jacob J Hughey
Tau-independent Phase Analysis: A Novel Method for Accurately Determining Phase Shifts. Journal of biological rhythms 33 (3) (2018)
Jordan M Singer, Jacob J Hughey
LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data. Journal of biological rhythms 34 (1) (2018)
Jacob J Hughey, Bonnie K Ray, Anne R Lee, Kristin N Voorhees, Ciaran P Kelly, Detlef Schuppan
Self-reported dietary adherence, disease-specific symptoms, and quality of life are associated with healthcare provider follow-up in celiac disease. BMC gastroenterology 17 (1) (2017)
Takamasa Kudo, Stevan Jeknić, Derek N Macklin, Sajia Akhter, Jacob J Hughey, Sergi Regot, Markus W Covert
Live-cell measurements of kinase activity in single cells using translocation reporters. Nature protocols 13 (1) (2017)
Jacob J Hughey, Trevor Hastie, Atul J Butte
ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Nucleic acids research 44 (8) (2016)
Jacob J Hughey, Jacob J Hughey
Robust meta-analysis of gene expression using the elastic net. Nucleic acids research 43 (12) (2015)