Jacob Joseph Hughey, Ph.D.

Assistant Professor

jake.hughey@vanderbilt.edu

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Faculty Appointments
Assistant Professor of Biomedical Informatics Assistant Professor of Biological Sciences
Education
Ph.D., Bioengineering, Stanford University, Stanford, CaliforniaM.S., Bioengineering, Stanford University, Stanford, CaliforniaB.E., Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
Publications
Singer JM, Hughey JJ. LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data. J. Biol. Rhythms [print-electronic]. 2019 Feb; 34(1): 5-18. PMID: 30472909, PMCID: PMC6376636, DOI: 10.1177/0748730418813785, ISSN: 1552-4531.

Gutschow MV, Mason JC, Lane KM, Maayan I, Hughey JJ, Bajar BT, Amatya DN, Valle SD, Covert MW. Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level. Mol. Biol. Cell [print-electronic]. 2019 Jan 1/15/2019; 30(2): 282-92. PMID: 30462580, DOI: 10.1091/mbc.E18-07-0423, ISSN: 1939-4586.

Wu G, Ruben MD, Schmidt RE, Francey LJ, Smith DF, Anafi RC, Hughey JJ, Tasseff R, Sherrill JD, Oblong JE, Mills KJ, Hogenesch JB. Population-level rhythms in human skin with implications for circadian medicine. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2018 Nov 11/27/2018; 115(48): 12313-8. PMID: 30377266, PMCID: PMC6275491, PII: 1809442115, DOI: 10.1073/pnas.1809442115, ISSN: 1091-6490.

Rhoades SD, Bastarache L, Denny JC, Hughey JJ. Pulling the covers in electronic health records for an association study with self-reported sleep behaviors. Chronobiol. Int [print-electronic]. 2018 Nov; 35(12): 1702-12. PMID: 30183400, PMCID: PMC6282811, DOI: 10.1080/07420528.2018.1508152, ISSN: 1525-6073.

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. MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data. Cell Rep. 2018 Jul 7/31/2018; 24(5): 1377-88. PMID: 30067990, PII: S2211-1247(18)31080-5, DOI: 10.1016/j.celrep.2018.07.003, ISSN: 2211-1247.

Tackenberg MC, Jones JR, Page TL, Hughey JJ. Tau-independent Phase Analysis: A Novel Method for Accurately Determining Phase Shifts. J. Biol. Rhythms [print-electronic]. 2018 Jun; 33(3): 223-32. PMID: 29635963, PMCID: PMC5956570, DOI: 10.1177/0748730418768116, ISSN: 1552-4531.

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. Phenotype risk scores identify patients with unrecognized Mendelian disease patterns. Science. 2018 Mar 3/16/2018; 359(6381): 1233-9. PMID: 29590070, PMCID: PMC5959723, PII: 359/6381/1233, DOI: 10.1126/science.aal4043, ISSN: 1095-9203.

Shilts J, Chen G, Hughey JJ. Evidence for widespread dysregulation of circadian clock progression in human cancer. PeerJ. 2018; 6: e4327. PMID: 29404219, PMCID: PMC5797448, PII: 4327, DOI: 10.7717/peerj.4327, ISSN: 2167-8359.

Kudo T, Jeknic S, Macklin DN, Akhter S, Hughey JJ, Regot S, Covert MW. Live-cell measurements of kinase activity in single cells using translocation reporters. Nat Protoc [print-electronic]. 2018 Jan; 13(1): 155-69. PMID: 29266096, PII: nprot.2017.128, DOI: 10.1038/nprot.2017.128, ISSN: 1750-2799.

Hughey JJ, Ray BK, Lee AR, Voorhees KN, Kelly CP, Schuppan D. Self-reported dietary adherence, disease-specific symptoms, and quality of life are associated with healthcare provider follow-up in celiac disease. BMC Gastroenterol. 2017 Dec 12/11/2017; 17(1): 156. PMID: 29228908, PMCID: PMC5725827, PII: 10.1186/s12876-017-0713-7, DOI: 10.1186/s12876-017-0713-7, ISSN: 1471-230X.

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, Ptácek 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. Guidelines for Genome-Scale Analysis of Biological Rhythms. J. Biol. Rhythms [print-electronic]. 2017 Oct; 32(5): 380-93. PMID: 29098954, PMCID: PMC5692188, DOI: 10.1177/0748730417728663.

Hughey JJ. Machine learning identifies a compact gene set for monitoring the circadian clock in human blood. Genome Med. 2017 Feb 2/28/2017; 9(1): 19. PMID: 28241858, PMCID: PMC5329904, PII: 10.1186/s13073-017-0406-4, DOI: 10.1186/s13073-017-0406-4, ISSN: 1756-994X.

Hughey JJ, Butte AJ. Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans. J. Biol. Rhythms [print-electronic]. 2016 Dec; 31(6): 588-97. PMID: 27702781, PMCID: PMC5105327, PII: 0748730416668049, DOI: 10.1177/0748730416668049, ISSN: 1552-4531.

Hughey JJ, Hastie T, Butte AJ. ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system. Nucleic Acids Res [print-electronic]. 2016 May 5/5/2016; 44(8): e80. PMID: 26819407, PMCID: PMC4856978, PII: gkw030, DOI: 10.1093/nar/gkw030, ISSN: 1362-4962.

Mortensen JM, Telis N, Hughey JJ, Fan-Minogue H, Van Auken K, Dumontier M, Musen MA. Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology. J Biomed Inform [print-electronic]. 2016 Apr; 60: 199-209. PMID: 26873781, PMCID: PMC4836980, PII: S1532-0464(16)00027-7, DOI: 10.1016/j.jbi.2016.02.005, ISSN: 1532-0480.

Hughey JJ, Butte AJ. Robust meta-analysis of gene expression using the elastic net. Nucleic Acids Res [print-electronic]. 2015 Jul 7/13/2015; 43(12): e79. PMID: 25829177, PMCID: PMC4499117, PII: gkv229, DOI: 10.1093/nar/gkv229, ISSN: 1362-4962.

Hughey JJ, Gutschow MV, Bajar BT, Covert MW. Single-cell variation leads to population invariance in NF-¿B signaling dynamics. Mol. Biol. Cell [print-electronic]. 2015 Feb 2/1/2015; 26(3): 583-90. PMID: 25473117, PMCID: PMC4310747, PII: mbc.E14-08-1267, DOI: 10.1091/mbc.E14-08-1267, ISSN: 1939-4586.

Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW. High-sensitivity measurements of multiple kinase activities in live single cells. Cell. 2014 Jun 6/19/2014; 157(7): 1724-34. PMID: 24949979, PMCID: PMC4097317, PII: S0092-8674(14)00655-2, DOI: 10.1016/j.cell.2014.04.039, ISSN: 1097-4172.

Byrd TF, 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. The microfluidic multitrap nanophysiometer for hematologic cancer cell characterization reveals temporal sensitivity of the calcein-AM efflux assay. Sci Rep. 2014 May 5/30/2014; 4: 5117. PMID: 24873950, PMCID: PMC4038811, PII: srep05117, DOI: 10.1038/srep05117, ISSN: 2045-2322.

Gutschow MV, Hughey JJ, Ruggero NA, Bajar BT, Valle SD, Covert MW. Single-cell and population NF-¿B dynamic responses depend on lipopolysaccharide preparation. PLoS ONE [print-electronic]. 2013; 8(1): e53222. PMID: 23301045, PMCID: PMC3536753, PII: PONE-D-12-18757, DOI: 10.1371/journal.pone.0053222, ISSN: 1932-6203.

Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature [print-electronic]. 2010 Jul 7/8/2010; 466(7303): 267-71. PMID: 20581820, PMCID: PMC3105528, PII: nature09145, DOI: 10.1038/nature09145, ISSN: 1476-4687.

Hughey JJ, Lee TK, Covert MW. Computational modeling of mammalian signaling networks. Wiley Interdiscip Rev Syst Biol Med. 2010 Mar; 2(2): 194-209. PMID: 20836022, PMCID: PMC3105527, DOI: 10.1002/wsbm.52, ISSN: 1939-005X.

Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW. A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide. Sci Signal. 2009 Oct 10/20/2009; 2(93): ra65. PMID: 19843957, PMCID: PMC2778577, PII: 2/93/ra65, DOI: 10.1126/scisignal.2000599, ISSN: 1937-9145.

Faley S, Seale K, Hughey J, Schaffer DK, VanCompernolle S, McKinney B, Baudenbacher F, Unutmaz D, Wikswo JP. Microfluidic platform for real-time signaling analysis of multiple single T cells in parallel. Lab Chip [print-electronic]. 2008 Oct; 8(10): 1700-12. PMID: 18813394, PMCID: PMC4160168, DOI: 10.1039/b719799c, ISSN: 1473-0197.