My Bibliography

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Tang SY, Lordan R, Meng H, Auerbach BJ, Hennessy EJ, Sengupta A, Das US, Joshi R, Marcos-Contreras OA, McConnell R, Grant GR, Ricciotti E, Muzykantov VR, Grosser T, Weiljie AM, FitzGerald GA. Differential Impact In Vivo of Pf4-ΔCre-Mediated and Gp1ba-ΔCre-Mediated Depletion of Cyclooxygenase-1 in Platelets in Mice. Arterioscler Thromb Vasc Biol. 2024 Jun;44(6):1393-1406. doi: 10.1161/ATVBAHA.123.320295. Epub 2024 Apr 25. PubMed PMID: 38660804; PubMed Central PMCID: PMC11138953.

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Brooks TG, Lahens NF, Mrčela A, Grant GR. Challenges and best practices in omics benchmarking. Nat Rev Genet. 2024 May;25(5):326-339. doi: 10.1038/s41576-023-00679-6. Epub 2024 Jan 12. Review. PubMed PMID: 38216661.

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Brooks TG, Lahens NF, Mrčela A, Sarantopoulou D, Nayak S, Naik A, Sengupta S, Choi PS, Grant GR. BEERS2: RNA-Seq simulation through high fidelity in silico modeling. Brief Bioinform. 2024 Mar 27;25(3). doi: 10.1093/bib/bbae164. PubMed PMID: 38605641; PubMed Central PMCID: PMC11009461.

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Naik A, Forrest KM, Paul O, Issah Y, Valekunja UK, Tang SY, Reddy AB, Hennessy EJ, Brooks TG, Chaudhry F, Babu A, Morley M, Zepp JA, Grant GR, FitzGerald GA, Sehgal A, Worthen GS, Frank DB, Morrisey EE, Sengupta S. Circadian regulation of lung repair and regeneration. JCI Insight. 2024 Mar 8;9(5). doi: 10.1172/jci.insight.179745. PubMed PMID: 38456509; PubMed Central PMCID: PMC10972589.

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Brooks TG, Manjrekar A, Mrcˇela A, Grant GR. Meta-analysis of Diurnal Transcriptomics in Mouse Liver Reveals Low Repeatability of Rhythm Analyses. J Biol Rhythms. 2023 Dec;38(6):556-570. doi: 10.1177/07487304231179600. Epub 2023 Jun 29. PubMed PMID: 37382061; PubMed Central PMCID: PMC10615793.

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Meng H, Sengupta A, Ricciotti E, Mrčela A, Mathew D, Mazaleuskaya LL, Ghosh S, Brooks TG, Turner AP, Schanoski AS, Lahens NF, Tan AW, Woolfork A, Grant G, Susztak K, Letizia AG, Sealfon SC, Wherry EJ, Laudanski K, Weljie AM, Meyer NJ, FitzGerald GA. Deep phenotyping of the lipidomic response in COVID-19 and non-COVID-19 sepsis. Clin Transl Med. 2023 Nov;13(11):e1440. doi: 10.1002/ctm2.1440. PubMed PMID: 37948331; PubMed Central PMCID: PMC10637636.

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Brooks TG, Lahens NF, Grant GR, Sheline YI, FitzGerald GA, Skarke C. Diurnal rhythms of wrist temperature are associated with future disease risk in the UK Biobank. Nat Commun. 2023 Aug 24;14(1):5172. doi: 10.1038/s41467-023-40977-5. PubMed PMID: 37620332; PubMed Central PMCID: PMC10449859.

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Naik A, Forrest KM, Paul O, Issah Y, Valekunja UK, Tang SY, Reddy AB, Hennessy EJ, Brooks TG, Chaudhry F, Babu A, Morley M, Zepp JA, Grant GR, FitzGerald GA, Sehgal A, Worthen GS, Frank DB, Morrisey EE, Sengupta S. Circadian regulation of lung repair and regeneration. JCI Insight. 2023 Aug 22;8(16). doi: 10.1172/jci.insight.164720. PubMed PMID: 37463053; PubMed Central PMCID: PMC10543710.

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Skarke C, Lordan R, Barekat K, Naik A, Mathew D, Ohtani T, Greenplate AR, Grant GR, Lahens NF, Gouma S, Troisi E, Sengupta A, Weljie AM, Meng W, Luning Prak ET, Lundgreen K, Bates P, Meng H, FitzGerald GA. Modulation of the Immune Response to Severe Acute Respiratory Syndrome Coronavirus 2 Vaccination by Nonsteroidal Anti-Inflammatory Drugs. J Pharmacol Exp Ther. 2023 Aug;386(2):198-204. doi: 10.1124/jpet.122.001415. Epub 2023 Apr 27. PubMed PMID: 37105582; PubMed Central PMCID: PMC10353078.

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Anderson ST, Meng H, Brooks TG, Tang SY, Lordan R, Sengupta A, Nayak S, Mřela A, Sarantopoulou D, Lahens NF, Weljie A, Grant GR, Bushman FD, FitzGerald GA. Sexual dimorphism in the response to chronic circadian misalignment on a high-fat diet. Sci Transl Med. 2023 May 17;15(696):eabo2022. doi: 10.1126/scitranslmed.abo2022. Epub 2023 May 17. PubMed PMID: 37196066.

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Vaquero-Garcia J, Aicher JK, Jewell S, Gazzara MR, Radens CM, Jha A, Norton SS, Lahens NF, Grant GR, Barash Y. RNA splicing analysis using heterogeneous and large RNA-seq datasets. Nat Commun. 2023 Mar 3;14(1):1230. doi: 10.1038/s41467-023-36585-y. PubMed PMID: 36869033; PubMed Central PMCID: PMC9984406.

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Kelly DE, Ramdas S, Ma R, Rawlings-Goss RA, Grant GR, Ranciaro A, Hirbo JB, Beggs W, Yeager M, Chanock S, Nyambo TB, Omar SA, Woldemeskel D, Belay G, Li H, Brown CD, Tishkoff SA. The genetic and evolutionary basis of gene expression variation in East Africans. Genome Biol. 2023 Feb 24;24(1):35. doi: 10.1186/s13059-023-02874-4. PubMed PMID: 36829244; PubMed Central PMCID: PMC9951478.

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Lahens NF, Rahman M, Cohen JB, Cohen DL, Chen J, Weir MR, Feldman HI, Grant GR, Townsend RR, Skarke C, Study Investigators ATC. Time-specific associations of wearable sensor-based cardiovascular and behavioral readouts with disease phenotypes in the outpatient setting of the Chronic Renal Insufficiency Cohort. Digit Health. 2022 Jan-Dec;8:20552076221107903. doi: 10.1177/20552076221107903. eCollection 2022 Jan-Dec. PubMed PMID: 35746950; PubMed Central PMCID: PMC9210076.

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Brooks TG, Mrčela A, Lahens NF, Paschos GK, Grosser T, Skarke C, FitzGerald GA, Grant GR. Nitecap: An Exploratory Circadian Analysis Web Application. J Biol Rhythms. 2022 Feb;37(1):43-52. doi: 10.1177/07487304211054408. Epub 2021 Nov 2. PubMed PMID: 34724846; PubMed Central PMCID: PMC9003665.

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Lordan R, Prior S, Hennessy E, Naik A, Ghosh S, Paschos GK, Skarke C, Barekat K, Hollingsworth T, Juska S, Mazaleuskaya LL, Teegarden S, Glascock AL, Anderson S, Meng H, Tang SY, Weljie A, Bottalico L, Ricciotti E, Cherfane P, Mrcela A, Grant G, Poole K, Mayer N, Waring M, Adang L, Becker J, Fries S, FitzGerald GA, Grosser T. Considerations for the Safe Operation of Schools During the Coronavirus Pandemic. Front Public Health. 2021;9:751451. doi: 10.3389/fpubh.2021.751451. eCollection 2021. Review. PubMed PMID: 34976917; PubMed Central PMCID: PMC8716382.

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Lahens NF, Brooks TG, Sarantopoulou D, Nayak S, Lawrence C, Mrčela A, Srinivasan A, Schug J, Hogenesch JB, Barash Y, Grant GR. CAMPAREE: a robust and configurable RNA expression simulator. BMC Genomics. 2021 Sep 25;22(1):692. doi: 10.1186/s12864-021-07934-2. PubMed PMID: 34563123; PubMed Central PMCID: PMC8467241.

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Tang SY, Meng H, Anderson ST, Sarantopoulou D, Ghosh S, Lahens NF, Theken KN, Ricciotti E, Hennessy EJ, Tu V, Bittinger K, Weiljie AM, Grant GR, FitzGerald GA. Sex-dependent compensatory mechanisms preserve blood pressure homeostasis in prostacyclin receptor-deficient mice. J Clin Invest. 2021 Jul 15;131(14). doi: 10.1172/JCI136310. PubMed PMID: 34101620; PubMed Central PMCID: PMC8279587.

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Slaff B, Radens CM, Jewell P, Jha A, Lahens NF, Grant GR, Thomas-Tikhonenko A, Lynch KW, Barash Y. MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis. Nat Commun. 2021 Jun 7;12(1):3353. doi: 10.1038/s41467-021-23608-9. PubMed PMID: 34099673; PubMed Central PMCID: PMC8184769.

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Sarantopoulou D, Brooks TG, Nayak S, Mrčela A, Lahens NF, Grant GR. Comparative evaluation of full-length isoform quantification from RNA-Seq. BMC Bioinformatics. 2021 May 25;22(1):266. doi: 10.1186/s12859-021-04198-1. Review. PubMed PMID: 34034652; PubMed Central PMCID: PMC8145802.

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Sengupta S, Brooks TG, Grant GR, FitzGerald GA. Accounting for Time: Circadian Rhythms in the Time of COVID-19. J Biol Rhythms. 2021 Feb;36(1):4-8. doi: 10.1177/0748730420953335. Epub 2020 Sep 2. Review. PubMed PMID: 32875944; PubMed Central PMCID: PMC8685580.

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Guo X, Gao X, Keenan BT, Zhu J, Sarantopoulou D, Lian J, Galante RJ, Grant GR, Pack AI. RNA-seq analysis of galaninergic neurons from ventrolateral preoptic nucleus identifies expression changes between sleep and wake. BMC Genomics. 2020 Sep 14;21(1):633. doi: 10.1186/s12864-020-07050-7. PubMed PMID: 32928100; PubMed Central PMCID: PMC7491139.

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Guo X, Keenan BT, Sarantopoulou D, Lim DC, Lian J, Grant GR, Pack AI. Age attenuates the transcriptional changes that occur with sleep in the medial prefrontal cortex. Aging Cell. 2019 Dec;18(6):e13021. doi: 10.1111/acel.13021. Epub 2019 Sep 24. PubMed PMID: 31549781; PubMed Central PMCID: PMC6826131.

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Sun Y, Kim EJ, Felt SA, Taylor LJ, Agarwal D, Grant GR, López CB. Correction: A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes. PLoS Pathog. 2019 Oct;15(10):e1008099. doi: 10.1371/journal.ppat.1008099. eCollection 2019 Oct. PubMed PMID: 31581268; PubMed Central PMCID: PMC6776294.

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Sarantopoulou D, Tang SY, Ricciotti E, Lahens NF, Lekkas D, Schug J, Guo XS, Paschos GK, FitzGerald GA, Pack AI, Grant GR. Comparative evaluation of RNA-Seq library preparation methods for strand-specificity and low input. Sci Rep. 2019 Sep 17;9(1):13477. doi: 10.1038/s41598-019-49889-1. PubMed PMID: 31530843; PubMed Central PMCID: PMC6748930.

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Sengupta S, Tang SY, Devine JC, Anderson ST, Nayak S, Zhang SL, Valenzuela A, Fisher DG, Grant GR, López CB, FitzGerald GA. Circadian control of lung inflammation in influenza infection. Nat Commun. 2019 Sep 11;10(1):4107. doi: 10.1038/s41467-019-11400-9. PubMed PMID: 31511530; PubMed Central PMCID: PMC6739310.

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Manners MT, Yohn NL, Lahens NF, Grant GR, Bartolomei MS, Blendy JA. Transgenerational inheritance of chronic adolescent stress: Effects of stress response and the amygdala transcriptome. Genes Brain Behav. 2019 Sep;18(7):e12493. doi: 10.1111/gbb.12493. Epub 2018 Jul 4. PubMed PMID: 29896789; PubMed Central PMCID: PMC6292780.

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Theken KN, Hersh EV, Lahens NF, Lee HM, Li X, Granquist EJ, Giannakopoulos HE, Levin LM, Secreto SA, Grant GR, Detre JA, FitzGerald GA, Grosser T, Farrar JT. Variability in the Analgesic Response to Ibuprofen Is Associated With Cyclooxygenase Activation in Inflammatory Pain. Clin Pharmacol Ther. 2019 Sep;106(3):632-641. doi: 10.1002/cpt.1446. Epub 2019 Apr 29. PubMed PMID: 30929268; PubMed Central PMCID: PMC6753944.

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Sun Y, Kim EJ, Felt SA, Taylor LJ, Agarwal D, Grant GR, López CB. A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes. PLoS Pathog. 2019 Apr;15(4):e1007707. doi: 10.1371/journal.ppat.1007707. eCollection 2019 Apr. PubMed PMID: 30995283; PubMed Central PMCID: PMC6504078.

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Ricciotti E, Sarantopoulou D, Grant GR, Sanzari JK, Krigsfeld GS, Kiliti AJ, Kennedy AR, Grosser T. Distinct vascular genomic response of proton and gamma radiation-A pilot investigation. PLoS One. 2019;14(2):e0207503. doi: 10.1371/journal.pone.0207503. eCollection 2019. PubMed PMID: 30742630; PubMed Central PMCID: PMC6370185.

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Shakhmantsir I, Nayak S, Grant GR, Sehgal A. Spliceosome factors target timeless (tim) mRNA to control clock protein accumulation and circadian behavior in Drosophila. Elife. 2018 Dec 5;7. doi: 10.7554/eLife.39821. PubMed PMID: 30516472; PubMed Central PMCID: PMC6281371.

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Song WL, Ricciotti E, Liang X, Grosser T, Grant GR, FitzGerald GA. Lipocalin-Like Prostaglandin D Synthase but Not Hemopoietic Prostaglandin D Synthase Deletion Causes Hypertension and Accelerates Thrombogenesis in Mice. J Pharmacol Exp Ther. 2018 Dec;367(3):425-432. doi: 10.1124/jpet.118.250936. Epub 2018 Oct 10. PubMed PMID: 30305427; PubMed Central PMCID: PMC6226547.

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Gupta P, Uner OE, Nayak S, Grant GR, Kalb RG. SAP97 regulates behavior and expression of schizophrenia risk enriched gene sets in mouse hippocampus. PLoS One. 2018;13(7):e0200477. doi: 10.1371/journal.pone.0200477. eCollection 2018. PubMed PMID: 29995933; PubMed Central PMCID: PMC6040763.

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Guo X, Riobo-Del Galdo NA, Kim EJ, Grant GR, Manning DR. Overlap in signaling between Smoothened and the α subunit of the heterotrimeric G protein G13. PLoS One. 2018;13(5):e0197442. doi: 10.1371/journal.pone.0197442. eCollection 2018. PubMed PMID: 29763457; PubMed Central PMCID: PMC5953476.

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Norton SS, Vaquero-Garcia J, Lahens NF, Grant GR, Barash Y. Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates. Bioinformatics. 2018 May 1;34(9):1488-1497. doi: 10.1093/bioinformatics/btx790. PubMed PMID: 29236961; PubMed Central PMCID: PMC6454425.

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Kim EJ, Grant GR, Bowman AS, Haider N, Gudiseva HV, Chavali VRM. Complete Transcriptome Profiling of Normal and Age-Related Macular Degeneration Eye Tissues Reveals Dysregulation of Anti-Sense Transcription. Sci Rep. 2018 Feb 14;8(1):3040. doi: 10.1038/s41598-018-21104-7. PubMed PMID: 29445097; PubMed Central PMCID: PMC5813239.

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Skarke C, Lahens NF, Rhoades SD, Campbell A, Bittinger K, Bailey A, Hoffmann C, Olson RS, Chen L, Yang G, Price TS, Moore JH, Bushman FD, Greene CS, Grant GR, Weljie AM, FitzGerald GA. A Pilot Characterization of the Human Chronobiome. Sci Rep. 2017 Dec 7;7(1):17141. doi: 10.1038/s41598-017-17362-6. PubMed PMID: 29215023; PubMed Central PMCID: PMC5719427.

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Sengupta A, Rhoades SD, Kim EJ, Nayak S, Grant GR, Meerlo P, Weljie AM. Sleep restriction induced energy, methylation and lipogenesis metabolic switches in rat liver. Int J Biochem Cell Biol. 2017 Dec;93:129-135. doi: 10.1016/j.biocel.2017.08.014. Epub 2017 Aug 30. PubMed PMID: 28860003.

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Palozola KC, Donahue G, Liu H, Grant GR, Becker JS, Cote A, Yu H, Raj A, Zaret KS. Mitotic transcription and waves of gene reactivation during mitotic exit. Science. 2017 Oct 6;358(6359):119-122. doi: 10.1126/science.aal4671. Epub 2017 Sep 14. PubMed PMID: 28912132; PubMed Central PMCID: PMC5727891.

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Lahens NF, Ricciotti E, Smirnova O, Toorens E, Kim EJ, Baruzzo G, Hayer KE, Ganguly T, Schug J, Grant GR. A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression. BMC Genomics. 2017 Aug 10;18(1):602. doi: 10.1186/s12864-017-4011-0. PubMed PMID: 28797240; PubMed Central PMCID: PMC5553782.

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Hu Q, Kim EJ, Feng J, Grant GR, Heller EA. Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain. PLoS Comput Biol. 2017 Jun;13(6):e1005602. doi: 10.1371/journal.pcbi.1005602. eCollection 2017 Jun. PubMed PMID: 28609483; PubMed Central PMCID: PMC5487056.

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Danford ID, Verkuil LD, Choi DJ, Collins DW, Gudiseva HV, Uyhazi KE, Lau MK, Kanu LN, Grant GR, Chavali VRM, O'Brien JM. Characterizing the "POAGome": A bioinformatics-driven approach to primary open-angle glaucoma. Prog Retin Eye Res. 2017 May;58:89-114. doi: 10.1016/j.preteyeres.2017.02.001. Epub 2017 Feb 20. Review. PubMed PMID: 28223208; PubMed Central PMCID: PMC5464971.

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Shan X, Roberts C, Kim EJ, Brenner A, Grant G, Percec I. Transcriptional and Cell Cycle Alterations Mark Aging of Primary Human Adipose-Derived Stem Cells. Stem Cells. 2017 May;35(5):1392-1401. doi: 10.1002/stem.2592. Epub 2017 Mar 5. PubMed PMID: 28211118; PubMed Central PMCID: PMC5404948.

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Baruzzo G, Hayer KE, Kim EJ, Di Camillo B, FitzGerald GA, Grant GR. Simulation-based comprehensive benchmarking of RNA-seq aligners. Nat Methods. 2017 Feb;14(2):135-139. doi: 10.1038/nmeth.4106. Epub 2016 Dec 12. PubMed PMID: 27941783; PubMed Central PMCID: PMC5792058.

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Benakanakere MR, Finoti LS, Tanaka U, Grant GR, Scarel-Caminaga RM, Kinane DF. Investigation of the functional role of human Interleukin-8 gene haplotypes by CRISPR/Cas9 mediated genome editing. Sci Rep. 2016 Aug 8;6:31180. doi: 10.1038/srep31180. PubMed PMID: 27499075; PubMed Central PMCID: PMC4976357.

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Mazaleuskaya LL, Lawson JA, Li X, Grant G, Mesaros C, Grosser T, Blair IA, Ricciotti E, FitzGerald GA. A broad-spectrum lipidomics screen of antiinflammatory drug combinations in human blood. JCI Insight. 2016 Aug 4;1(12). doi: 10.1172/jci.insight.87031. PubMed PMID: 27547824; PubMed Central PMCID: PMC4990354.

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Tang SY, Monslow J, R Grant G, Todd L, Pawelzik SC, Chen L, Lawson J, Puré E, FitzGerald GA. Cardiovascular Consequences of Prostanoid I Receptor Deletion in Microsomal Prostaglandin E Synthase-1-Deficient Hyperlipidemic Mice. Circulation. 2016 Jul 26;134(4):328-38. doi: 10.1161/CIRCULATIONAHA.116.022308. PubMed PMID: 27440004; PubMed Central PMCID: PMC4963279.

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Yang G, Chen L, Grant GR, Paschos G, Song WL, Musiek ES, Lee V, McLoughlin SC, Grosser T, Cotsarelis G, FitzGerald GA. Timing of expression of the core clock gene Bmal1 influences its effects on aging and survival. Sci Transl Med. 2016 Feb 3;8(324):324ra16. doi: 10.1126/scitranslmed.aad3305. Epub 2016 Feb 3. PubMed PMID: 26843191; PubMed Central PMCID: PMC4870001.

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Hayer KE, Pizarro A, Lahens NF, Hogenesch JB, Grant GR. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data. Bioinformatics. 2015 Dec 15;31(24):3938-45. doi: 10.1093/bioinformatics/btv488. Epub 2015 Sep 3. PubMed PMID: 26338770; PubMed Central PMCID: PMC4673975.

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Li J, Grant GR, Hogenesch JB, Hughes ME. Considerations for RNA-seq analysis of circadian rhythms. Methods Enzymol. 2015;551:349-67. doi: 10.1016/bs.mie.2014.10.020. Epub 2014 Dec 26. PubMed PMID: 25662464.

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Toung JM, Lahens N, Hogenesch JB, Grant G. Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. PLoS One. 2014;9(11):e112040. doi: 10.1371/journal.pone.0112040. eCollection 2014. PubMed PMID: 25396741; PubMed Central PMCID: PMC4232354.