The Hurley Laboratory at

RPI

Selected Publications


2021

Could COVID-19 eliminate the alarm clock? Hurley, J.M.
Science Translational Medicine 2021 Jan 20; 13(577)
Post-Transcriptional Circadian Regulation in Macrophages Organizes Temporally Distinct Immunometabolic States. Collins, E.J., Cervantes-Silva, M.P., Timmons, G.A., O’Siorain, J.R., Curtis, A.M., Hurley, J.M.
Genome Research In Press.

2020

Can your diet change your clock? Hurley, J.M.
Science Translational Medicine 2020 Dec 02; 12(572)
Can eating help treat malaria? Hurley, J.M.
Science Translational Medicine 2020 Sept 16; 12(561)
Could gut flora cycles be key to treating diabetes? Hurley, J.M.
Science Translational Medicine 2020 Jul 22; 12(553)
Intrinsic disorder is an essential characteristic of components in the conserved circadian circuit Pelham, JF, Dunlap, JC, and Hurley, JM
Cell Communication and Signaling 2020 Nov 11;18(1):181.
From genetics to molecular oscillations: the circadian clock in Neurospora crassa. Jankowski, M., Chase, Z., and Hurley, J.M.
The Mycota, In press
The tick tock of toxicity. Hurley, J.M.
Science Translational Medicine 2020 Feb 12; 12(530)
ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output. De los Santos H, Collins EJ, Mann C, Sagan AW, Jankowski MS, Bennett KP, Hurley JM.
Bioinformatics. 2020 Feb 1;36(3):773-781.


2019

ENCORE: A Visualization Tool for Insight into Circadian Omics. De los Santos H, Bennett KP, Hurley JM.
ACM BCB. 2019 Sep;2019:5-14.


2018

Characterizing Time-of-Day Conformational Changes in the Intrinsically Disordered Proteins of the Circadian Clock. Pelham JF, Mosier AE, Hurley JM.
Methods Enzymol. 2018;611:503-529.
Circadian Proteomic Analysis Uncovers Mechanisms of Post-Transcriptional Regulation in Metabolic Pathways. Hurley JM, Jankowski MS, De los Santos H, Crowell AM, Fordyce SB, Zucker JD, Kumar N, Purvine SO, Robinson EW, Shukla A, Zink E, Cannon WR, Baker SE, Loros JJ, Dunlap JC.
Cell Syst. 2018 Dec 26;7(6):613-626.e5. doi: 10.1016/j.cels.2018.10.014. Epub 2018 Dec 12.
Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa William R. Cannon, Jeremy D. Zucker, Douglas J. Baxter, Neeraj Kumar, Scott E. Baker, Jennifer M. Hurley and Jay C. Dunlap
Processes 2018, 6(6), 63; https://doi.org/10.3390/pr6060063


2017

Guidelines for Genome-Scale Analysis of Biological Rhythm. 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.
Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations. Hannah De los Santos, Emily J Collins, Jennifer M Hurley, Kristin P Bennett Aug 2017 Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. 2017 August 20; :455-463.
Evolution to environmental contamination ablates the circadian clock of an aquatic sentinel species. Coldsnow KD, Relyea RA, Hurley JM.
Ecol Evol. 2017 Oct 28;7(23):10339-10349. doi: 10.1002/ece3.3490. eCollection 2017 Dec.


2016

The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell-Fusion. Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurely JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D. G3 (Bethesda). 2016 Nov 16. pii: g3.116.034298. doi: 10.1534/g3.116.034298. [Epub ahead of print]
Circadian Oscillators: Around the Transcription-Translation Feedback Loop and on to Output. Hurley JM, Loros JJ, Dunlap JC Trends Biochem Sci. 2016 Aug 3. pii: S0968-0004(16)30096-2. doi: 10.1016/j.tibs.2016.07.009. [Epub ahead of print]
Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock. Conrad KS, Hurley JM, Widom J, Ringelberg CS, Loros JJ, Dunlap JC, Crane BR. EMBO J. 2016 Jun 23. pii: e201694327. [Epub ahead of print]


2015

The circadian system as an organizer of metabolism. Hurley JM, Loros JJ, Dunlap JC. Fungal Genet Biol. 2015 Oct 20. pii: S1087-1845(15)30035-9. doi: 10.1016/j.fgb.2015.10.002. [Epub ahead of print] PubMed PMID: 26498192.
A Tool Set for the Genome Wide Analysis of Neurospora crassa by RT-PCR. Hurley JM, Dasgupta A, Andrews P, Crowell AM, Ringelberg C, Loros JJ Dunlap JC. G3 (Bethesda). 2015 Aug 6. pii: g3.115.019141. doi: 10.1534/g3.115.019141. [Epub ahead of print] PMID: 26248984


2014

Dissecting the mechanisms of the clock in Neurospora. Hurley J, Loros JJ, Dunlap JC. Methods Enzymol. 2015;551:29-52. doi: 10.1016/bs.mie.2014.10.009. Epub 2014 Dec 26. PMID: 25662450
Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. Hurley JM, Dasgupta A, Emerson JM, Zhou X, Ringelberg CS, Knabe N, Lipzen AM, Lindquist EA, Daum CG, Barry KW, Grigoriev IV, Smith KM, Galagan JE, Bell-Pedersen D, Freitag M, Cheng C, Loros JJ, Dunlap JC. Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):16995-7002. doi: 10.1073/pnas.1418963111. Epub 2014 Oct 31. PMID: 25362047


2013

Conserved RNA helicase FRH acts nonenzymatically to support the intrinsically disordered neurospora clock protein FRQ. Hurley JM, Larrondo LF, Loros JJ, Dunlap JC. Mol Cell. 2013 Dec 26;52(6):832-43. doi: 10.1016/j.molcel.2013.11.005. Epub 2013 Dec 5. PMID: 24316221
Cell biology: A fable of too much too fast. Hurley JM, Dunlap JC. Nature. 2013 Mar 7;495(7439):57-8. doi: 10.1038/nature11952. Epub 2013 Feb 17. No abstract available. PMID: 23417066


2012

Light-inducible system for tunable protein expression in Neurospora crassa. Hurley JM, Chen CH, Loros JJ, Dunlap JC. G3 (Bethesda). 2012 Oct;2(10):1207-12. doi: 10.1534/g3.112.003939. Epub 2012 Oct 1. PMID: 23050231
Clostridium difficile MazF toxin exhibits selective, not global, mRNA cleavage. Rothenbacher FP, Suzuki M, Hurley JM, Montville TJ, Kirn TJ, Ouyang M, Woychik NA. J Bacteriol. 2012 Jul;194(13):3464-74. doi: 10.1128/JB.00217-12. Epub 2012 Apr 27. PMID: 22544268


2011

Bacterial toxin RelE mediates frequent codon-independent mRNA cleavage from the 5' end of coding regions in vivo. Hurley JM, Cruz JW, Ouyang M, Woychik NA. J Biol Chem. 2011 Apr 29;286(17):14770-8. doi: 10.1074/jbc.M110.108969. Epub 2011 Feb 15. PMID: 21324908


2010

Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems. Arbing MA, Handelman SK, Kuzin AP, Verdon G, Wang C, Su M, Rothenbacher FP, Abashidze M, Liu M, Hurley JM, Xiao R, Acton T, Inouye M, Montelione GT, Woychik NA, Hunt JF. Structure. 2010 Aug 11;18(8):996-1010. doi: 10.1016/j.str.2010.04.018. PMID:20696400


2009

Bacterial toxin HigB associates with ribosomes and mediates translation-dependent mRNA cleavage at A-rich sites. Hurley JM, Woychik NA. J Biol Chem. 2009 Jul 10;284(28):18605-13. doi: 10.1074/jbc.M109.008763. Epub 2009 May 7. PMID: 19423702


2008


A birth-to-death view of mRNA from the RNA recognition motif perspective. Kinzy TG, De Stefano LA, Esposito AM, Hurley JM, Roy R, Valentin-Acevedo AJ, Chang KH, Davila J, Defren JM, Donovan J, Irizarry-Barreto P, Soto A, Ysla RM, Copeland HL, Copeland PR. Biochem Mol Biol Educ. 2008 Jan;36(1):1-8. doi: 10.1002/bmb.20149. PMID: 21591152