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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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Chen EP, Markosyan N, Connolly E, Lawson JA, Li X, Grant GR, Grosser T, FitzGerald GA, Smyth EM. Myeloid Cell COX-2 deletion reduces mammary tumor growth through enhanced cytotoxic T-lymphocyte function. Carcinogenesis. 2014 Aug;35(8):1788-97. doi: 10.1093/carcin/bgu053. Epub 2014 Mar 3. PubMed PMID: 24590894; PubMed Central PMCID: PMC4123643.
Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA sequencing. Genome Biol. 2014 Jun 30;15(6):R86. doi: 10.1186/gb-2014-15-6-r86. PubMed PMID: 24981968; PubMed Central PMCID: PMC4197826.
Karamanian VA, Harhay M, Grant GR, Palevsky HI, Grizzle WE, Zamanian RT, Ihida-Stansbury K, Taichman DB, Kawut SM, Jones PL. Erythropoietin upregulation in pulmonary arterial hypertension. Pulm Circ. 2014 Jun;4(2):269-79. doi: 10.1086/675990. PubMed PMID: 25006446; PubMed Central PMCID: PMC4070770.
Chen L, Yang G, Monslow J, Todd L, Cormode DP, Tang J, Grant GR, DeLong JH, Tang SY, Lawson JA, Pure E, Fitzgerald GA. Myeloid cell microsomal prostaglandin E synthase-1 fosters atherogenesis in mice. Proc Natl Acad Sci U S A. 2014 May 6;111(18):6828-33. doi: 10.1073/pnas.1401797111. Epub 2014 Apr 21. PubMed PMID: 24753592; PubMed Central PMCID: PMC4020105.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P. Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3. PubMed PMID: 24185836; PubMed Central PMCID: PMC4018468.
Grosser T, Fries S, Lawson JA, Kapoor SC, Grant GR, Fitzgerald GA. Response to letters regarding article, "Drug resistance and pseudoresistance: an unintended consequence of enteric coating aspirin". Circulation. 2013 Sep 17;128(12):e191. doi: 10.1161/CIRCULATIONAHA.113.004750. PubMed PMID: 24043153.
Farkas MH, Grant GR, White JA, Sousa ME, Consugar MB, Pierce EA. Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. BMC Genomics. 2013 Jul 18;14:486. doi: 10.1186/1471-2164-14-486. PubMed PMID: 23865674; PubMed Central PMCID: PMC3924432.
Grosser T, Fries S, Lawson JA, Kapoor SC, Grant GR, FitzGerald GA. Drug resistance and pseudoresistance: an unintended consequence of enteric coating aspirin. Circulation. 2013 Jan 22;127(3):377-85. doi: 10.1161/CIRCULATIONAHA.112.117283. Epub 2012 Dec 4. PubMed PMID: 23212718; PubMed Central PMCID: PMC3552520.
Chen L, Yang G, Xu X, Grant G, Lawson JA, Bohlooly-Y M, FitzGerald GA. Cell selective cardiovascular biology of microsomal prostaglandin E synthase-1. Circulation. 2013 Jan 15;127(2):233-43. doi: 10.1161/CIRCULATIONAHA.112.119479. Epub 2012 Nov 30. PubMed PMID: 23204105; PubMed Central PMCID: PMC3546279.
Aurrecoechea C, Barreto A, Brestelli J, Brunk BP, Cade S, Doherty R, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Hu S, Iodice J, Kissinger JC, Kraemer ET, Li W, Pinney DF, Pitts B, Roos DS, Srinivasamoorthy G, Stoeckert CJ Jr, Wang H, Warrenfeltz S. EuPathDB: the eukaryotic pathogen database. Nucleic Acids Res. 2013 Jan;41(Database issue):D684-91. doi: 10.1093/nar/gks1113. Epub 2012 Nov 21. PubMed PMID: 23175615; PubMed Central PMCID: PMC3531183.
Paschos GK, Ibrahim S, Song WL, Kunieda T, Grant G, Reyes TM, Bradfield CA, Vaughan CH, Eiden M, Masoodi M, Griffin JL, Wang F, Lawson JA, Fitzgerald GA. Obesity in mice with adipocyte-specific deletion of clock component Arntl. Nat Med. 2012 Dec;18(12):1768-77. doi: 10.1038/nm.2979. Epub 2012 Nov 11. PubMed PMID: 23142819; PubMed Central PMCID: PMC3782286.
Xu J, Grant G, Sabin LR, Gordesky-Gold B, Yasunaga A, Tudor M, Cherry S. Transcriptional pausing controls a rapid antiviral innate immune response in Drosophila. Cell Host Microbe. 2012 Oct 18;12(4):531-43. doi: 10.1016/j.chom.2012.08.011. PubMed PMID: 23084920; PubMed Central PMCID: PMC3479682.
Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN. Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res. 2012 Jul;22(7):1266-81. doi: 10.1101/gr.128876.111. Epub 2012 Apr 3. PubMed PMID: 22472103; PubMed Central PMCID: PMC3396368.
Yu Y, Ricciotti E, Scalia R, Tang SY, Grant G, Yu Z, Landesberg G, Crichton I, Wu W, Puré E, Funk CD, FitzGerald GA. Vascular COX-2 modulates blood pressure and thrombosis in mice. Sci Transl Med. 2012 May 2;4(132):132ra54. doi: 10.1126/scitranslmed.3003787. PubMed PMID: 22553252; PubMed Central PMCID: PMC3882087.
Farkas MH, Grant GR, Pierce EA. Transcriptome analyses to investigate the pathogenesis of RNA splicing factor retinitis pigmentosa. Adv Exp Med Biol. 2012;723:519-25. doi: 10.1007/978-1-4614-0631-0_65. Review. PubMed PMID: 22183372; PubMed Central PMCID: PMC6387625.
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