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Items: 25

1.

Simphony: simulating large-scale, rhythmic data.

Singer JM, Fu DY, Hughey JJ.

PeerJ. 2019 May 23;7:e6985. doi: 10.7717/peerj.6985. eCollection 2019.

2.

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

DeFelice MM, Clark HR, Hughey JJ, Maayan I, Kudo T, Gutschow MV, Covert MW, Regot S.

Sci Signal. 2019 Apr 30;12(579). pii: eaau3568. doi: 10.1126/scisignal.aau3568.

PMID:
31040261
3.

LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data.

Singer JM, Hughey JJ.

J Biol Rhythms. 2019 Feb;34(1):5-18. doi: 10.1177/0748730418813785. Epub 2018 Nov 25.

4.

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

Gutschow MV, Mason JC, Lane KM, Maayan I, Hughey JJ, Bajar BT, Amatya DN, Valle SD, Covert MW.

Mol Biol Cell. 2019 Jan 15;30(2):282-292. doi: 10.1091/mbc.E18-07-0423. Epub 2018 Nov 21.

PMID:
30462580
5.

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

Wu G, Ruben MD, Schmidt RE, Francey LJ, Smith DF, Anafi RC, Hughey JJ, Tasseff R, Sherrill JD, Oblong JE, Mills KJ, Hogenesch JB.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12313-12318. doi: 10.1073/pnas.1809442115. Epub 2018 Oct 30.

6.

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

Rhoades SD, Bastarache L, Denny JC, Hughey JJ.

Chronobiol Int. 2018 Nov;35(12):1702-1712. doi: 10.1080/07420528.2018.1508152. Epub 2018 Sep 5.

7.

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

Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, Butte AJ.

Cell Rep. 2018 Jul 31;24(5):1377-1388. doi: 10.1016/j.celrep.2018.07.003.

8.

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

Tackenberg MC, Jones JR, Page TL, Hughey JJ.

J Biol Rhythms. 2018 Jun;33(3):223-232. doi: 10.1177/0748730418768116. Epub 2018 Apr 11.

9.

Phenotype risk scores identify patients with unrecognized Mendelian disease patterns.

Bastarache L, Hughey JJ, Hebbring S, Marlo J, Zhao W, Ho WT, Van Driest SL, McGregor TL, Mosley JD, Wells QS, Temple M, Ramirez AH, Carroll R, Osterman T, Edwards T, Ruderfer D, Velez Edwards DR, Hamid R, Cogan J, Glazer A, Wei WQ, Feng Q, Brilliant M, Zhao ZJ, Cox NJ, Roden DM, Denny JC.

Science. 2018 Mar 16;359(6381):1233-1239. doi: 10.1126/science.aal4043.

10.

Evidence for widespread dysregulation of circadian clock progression in human cancer.

Shilts J, Chen G, Hughey JJ.

PeerJ. 2018 Jan 31;6:e4327. doi: 10.7717/peerj.4327. eCollection 2018.

11.

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

Kudo T, Jeknić S, Macklin DN, Akhter S, Hughey JJ, Regot S, Covert MW.

Nat Protoc. 2018 Jan;13(1):155-169. doi: 10.1038/nprot.2017.128. Epub 2017 Dec 21.

PMID:
29266096
12.

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

Hughey JJ, Ray BK, Lee AR, Voorhees KN, Kelly CP, Schuppan D.

BMC Gastroenterol. 2017 Dec 11;17(1):156. doi: 10.1186/s12876-017-0713-7.

13.

Guidelines for Genome-Scale Analysis of Biological Rhythms.

Hughes ME, Abruzzi KC, Allada R, Anafi R, Arpat AB, Asher G, Baldi P, de Bekker C, Bell-Pedersen D, Blau J, Brown S, Ceriani MF, Chen Z, Chiu JC, Cox J, Crowell AM, DeBruyne JP, Dijk DJ, DiTacchio L, Doyle FJ, Duffield GE, Dunlap JC, Eckel-Mahan K, Esser KA, FitzGerald GA, Forger DB, Francey LJ, Fu YH, Gachon F, Gatfield D, de Goede P, Golden SS, Green C, Harer J, Harmer S, Haspel J, Hastings MH, Herzel H, Herzog ED, Hoffmann C, Hong C, Hughey JJ, Hurley JM, de la Iglesia HO, Johnson C, Kay SA, Koike N, Kornacker K, Kramer A, Lamia K, Leise T, Lewis SA, Li J, Li X, Liu AC, Loros JJ, Martino TA, Menet JS, Merrow M, Millar AJ, Mockler T, Naef F, Nagoshi E, Nitabach MN, Olmedo M, Nusinow DA, Ptáček LJ, Rand D, Reddy AB, Robles MS, Roenneberg T, Rosbash M, Ruben MD, Rund SSC, Sancar A, Sassone-Corsi P, Sehgal A, Sherrill-Mix S, Skene DJ, Storch KF, Takahashi JS, Ueda HR, Wang H, Weitz C, Westermark PO, Wijnen H, Xu Y, Wu G, Yoo SH, Young M, Zhang EE, Zielinski T, Hogenesch JB.

J Biol Rhythms. 2017 Oct;32(5):380-393. doi: 10.1177/0748730417728663. Epub 2017 Nov 3.

14.

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

Hughey JJ.

Genome Med. 2017 Feb 28;9(1):19. doi: 10.1186/s13073-017-0406-4.

15.

Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans.

Hughey JJ, Butte AJ.

J Biol Rhythms. 2016 Dec;31(6):588-597. doi: 10.1177/0748730416668049. Epub 2016 Oct 4.

16.

Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology.

Mortensen JM, Telis N, Hughey JJ, Fan-Minogue H, Van Auken K, Dumontier M, Musen MA.

J Biomed Inform. 2016 Apr;60:199-209. doi: 10.1016/j.jbi.2016.02.005. Epub 2016 Feb 10.

17.

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

Hughey JJ, Hastie T, Butte AJ.

Nucleic Acids Res. 2016 May 5;44(8):e80. doi: 10.1093/nar/gkw030. Epub 2016 Jan 26.

18.

Robust meta-analysis of gene expression using the elastic net.

Hughey JJ, Butte AJ.

Nucleic Acids Res. 2015 Jul 13;43(12):e79. doi: 10.1093/nar/gkv229. Epub 2015 Mar 31.

19.

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

Hughey JJ, Gutschow MV, Bajar BT, Covert MW.

Mol Biol Cell. 2015 Feb 1;26(3):583-90. doi: 10.1091/mbc.E14-08-1267. Epub 2014 Dec 3.

20.

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

Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW.

Cell. 2014 Jun 19;157(7):1724-34. doi: 10.1016/j.cell.2014.04.039.

21.

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

Byrd TF 4th, Hoang LT, Kim EG, Pfister ME, Werner EM, Arndt SE, Chamberlain JW, Hughey JJ, Nguyen BA, Schneibel EJ, Wertz LL, Whitfield JS, Wikswo JP, Seale KT.

Sci Rep. 2014 May 30;4:5117. doi: 10.1038/srep05117.

22.

Single-cell and population NF-κB dynamic responses depend on lipopolysaccharide preparation.

Gutschow MV, Hughey JJ, Ruggero NA, Bajar BT, Valle SD, Covert MW.

PLoS One. 2013;8(1):e53222. doi: 10.1371/journal.pone.0053222. Epub 2013 Jan 3.

23.

Computational modeling of mammalian signaling networks.

Hughey JJ, Lee TK, Covert MW.

Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):194-209. doi: 10.1002/wsbm.52. Review.

24.

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing.

Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW.

Nature. 2010 Jul 8;466(7303):267-71. doi: 10.1038/nature09145. Epub 2010 Jun 27.

25.

A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide.

Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW.

Sci Signal. 2009 Oct 20;2(93):ra65. doi: 10.1126/scisignal.2000599.

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