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Prevalence and impact of baseline resistance-associated substitutions on the efficacy of ledipasvir/sofosbuvir or simeprevir/sofosbuvir against GT1 HCV infection.

Wang GP, Terrault N, Reeves JD, Liu L, Li E, Zhao L, Lim JK, Morelli G, Kuo A, Levitsky J, Sherman KE, Frazier LM, Ramani A, Peter J, Akuskevich L, Fried MW, Nelson DR.

Sci Rep. 2018 Feb 16;8(1):3199. doi: 10.1038/s41598-018-21303-2.


Safety and Effectiveness of Ledipasvir and Sofosbuvir, With or Without Ribavirin, in Treatment-Experienced Patients With Genotype 1 Hepatitis C Virus Infection and Cirrhosis.

Lim JK, Liapakis AM, Shiffman ML, Lok AS, Zeuzem S, Terrault NA, Park JS, Landis CS, Hassan M, Gallant J, Kuo A, Pockros PJ, Vainorius M, Akushevich L, Michael L, Fried MW, Nelson DR, Ben-Ari Z; HCV-TARGET Study Group.

Clin Gastroenterol Hepatol. 2018 Jan 3. pii: S1542-3565(17)31535-5. doi: 10.1016/j.cgh.2017.12.037. [Epub ahead of print]


Genetic drift and selection in many-allele range expansions.

Weinstein BT, Lavrentovich MO, Möbius W, Murray AW, Nelson DR.

PLoS Comput Biol. 2017 Dec 1;13(12):e1005866. doi: 10.1371/journal.pcbi.1005866. eCollection 2017 Dec.


Isocitrate dehydrogenase mutation in Vibrio anguillarum results in virulence attenuation and immunoprotection in rainbow trout (Oncorhynchus mykiss).

Mou X, Spinard EJ, Hillman SL, Nelson DR.

BMC Microbiol. 2017 Nov 14;17(1):217. doi: 10.1186/s12866-017-1124-1.


Thermal crumpling of perforated two-dimensional sheets.

Yllanes D, Bhabesh SS, Nelson DR, Bowick MJ.

Nat Commun. 2017 Nov 9;8(1):1381. doi: 10.1038/s41467-017-01551-y.


Multisite Investigation of Outcomes With Implementation of CYP2C19 Genotype-Guided Antiplatelet Therapy After Percutaneous Coronary Intervention.

Cavallari LH, Lee CR, Beitelshees AL, Cooper-DeHoff RM, Duarte JD, Voora D, Kimmel SE, McDonough CW, Gong Y, Dave CV, Pratt VM, Alestock TD, Anderson RD, Alsip J, Ardati AK, Brott BC, Brown L, Chumnumwat S, Clare-Salzler MJ, Coons JC, Denny JC, Dillon C, Elsey AR, Hamadeh IS, Harada S, Hillegass WB, Hines L, Horenstein RB, Howell LA, Jeng LJB, Kelemen MD, Lee YM, Magvanjav O, Montasser M, Nelson DR, Nutescu EA, Nwaba DC, Pakyz RE, Palmer K, Peterson JF, Pollin TI, Quinn AH, Robinson SW, Schub J, Skaar TC, Smith DM, Sriramoju VB, Starostik P, Stys TP, Stevenson JM, Varunok N, Vesely MR, Wake DT, Weck KE, Weitzel KW, Wilke RA, Willig J, Zhao RY, Kreutz RP, Stouffer GA, Empey PE, Limdi NA, Shuldiner AR, Winterstein AG, Johnson JA; IGNITE Network.

JACC Cardiovasc Interv. 2018 Jan 22;11(2):181-191. doi: 10.1016/j.jcin.2017.07.022. Epub 2017 Nov 1.


Correction to: CYP79 P450 monooxygenases in gymnosperms: CYP79A118 is associated with the formation of taxiphyllin in Taxus baccata.

Luck K, Jia Q, Huber M, Handrick V, Wong GK, Nelson DR, Chen F, Gershenzon J, Köllner TG.

Plant Mol Biol. 2017 Dec;95(6):647. doi: 10.1007/s11103-017-0674-9.


Factors associated with stroke, myocardial infarction, ischemic heart disease, unstable angina, or mortality in patients from real world clinical practice with newly-diagnosed type 2 diabetes and early glycemic control.

Alatorre CI, Hoogwerf BJ, Deeg MA, Nelson DR, Hunter TM, Ng WT, Rekhter MD.

Curr Med Res Opin. 2018 Feb;34(2):337-343. doi: 10.1080/03007995.2017.1396969. Epub 2017 Nov 24.


Glecaprevir and Pibrentasvir in Patients with HCV and Severe Renal Impairment.

Gane E, Lawitz E, Pugatch D, Papatheodoridis G, Bräu N, Brown A, Pol S, Leroy V, Persico M, Moreno C, Colombo M, Yoshida EM, Nelson DR, Collins C, Lei Y, Kosloski M, Mensa FJ.

N Engl J Med. 2017 Oct 12;377(15):1448-1455. doi: 10.1056/NEJMoa1704053.


Methylene Blue for Bronchopleural Fistula Localization.

Sakata KK, Nasim F, Schiavo DN, Nelson DR, Kern RM, Mullon JJ.

J Bronchology Interv Pulmonol. 2018 Jan;25(1):63-66. doi: 10.1097/LBR.0000000000000423.


Intracellular spectral recompositioning of light enhances algal photosynthetic efficiency.

Fu W, Chaiboonchoe A, Khraiwesh B, Sultana M, Jaiswal A, Jijakli K, Nelson DR, Al-Hrout A, Baig B, Amin A, Salehi-Ashtiani K.

Sci Adv. 2017 Sep 1;3(9):e1603096. doi: 10.1126/sciadv.1603096. eCollection 2017 Sep.


Chronic hepatitis C virus (HCV) increases the risk of chronic kidney disease (CKD) while effective HCV treatment decreases the incidence of CKD.

Park H, Chen C, Wang W, Henry L, Cook RL, Nelson DR.

Hepatology. 2017 Sep 5. doi: 10.1002/hep.29505. [Epub ahead of print]


A Novel Vaccine Targeting Glypican-3 as a Treatment for Hepatocellular Carcinoma.

Wu Q, Pi L, Le Trinh T, Zuo C, Xia M, Jiao Y, Hou Z, Jo S, Puszyk W, Pham K, Nelson DR, Robertson K, Ostrov D, Rameshwar P, Xia CQ, Liu C.

Mol Ther. 2017 Oct 4;25(10):2299-2308. doi: 10.1016/j.ymthe.2017.08.005. Epub 2017 Aug 10.


Glecaprevir plus pibrentasvir for chronic hepatitis C virus genotype 1, 2, 4, 5, or 6 infection in adults with compensated cirrhosis (EXPEDITION-1): a single-arm, open-label, multicentre phase 3 trial.

Forns X, Lee SS, Valdes J, Lens S, Ghalib R, Aguilar H, Felizarta F, Hassanein T, Hinrichsen H, Rincon D, Morillas R, Zeuzem S, Horsmans Y, Nelson DR, Yu Y, Krishnan P, Lin CW, Kort JJ, Mensa FJ.

Lancet Infect Dis. 2017 Oct;17(10):1062-1068. doi: 10.1016/S1473-3099(17)30496-6. Epub 2017 Aug 14.


CYP79 P450 monooxygenases in gymnosperms: CYP79A118 is associated with the formation of taxiphyllin in Taxus baccata.

Luck K, Jia Q, Huber M, Handrick V, Wong GK, Nelson DR, Chen F, Gershenzon J, Köllner TG.

Plant Mol Biol. 2017 Sep;95(1-2):169-180. doi: 10.1007/s11103-017-0646-0. Epub 2017 Aug 9. Erratum in: Plant Mol Biol. 2017 Dec;95(6):647.


Public-Private Partnership: Targeting Real-World Data for Hepatitis C Direct-Acting Antivirals.

Mishra P, Florian J, Peter J, Vainorius M, Fried MW, Nelson DR, Birnkrant D.

Gastroenterology. 2017 Sep;153(3):626-631. doi: 10.1053/j.gastro.2017.07.025. Epub 2017 Jul 27. No abstract available.


Spatial gene drives and pushed genetic waves.

Tanaka H, Stone HA, Nelson DR.

Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):8452-8457. doi: 10.1073/pnas.1705868114. Epub 2017 Jul 25.


Characterization of the cytochrome P450 monooxygenase genes (P450ome) from the carotenogenic yeast Xanthophyllomyces dendrorhous.

Córdova P, Gonzalez AM, Nelson DR, Gutiérrez MS, Baeza M, Cifuentes V, Alcaíno J.

BMC Genomics. 2017 Jul 19;18(1):540. doi: 10.1186/s12864-017-3942-9.


Genome-wide identification of 52 cytochrome P450 (CYP) genes in the copepod Tigriopus japonicus and their B[α]P-induced expression patterns.

Han J, Kim DH, Kim HS, Nelson DR, Lee JS.

Comp Biochem Physiol Part D Genomics Proteomics. 2017 Sep;23:49-57. doi: 10.1016/j.cbd.2017.06.002. Epub 2017 Jul 6.


Pulmonary Hemorrhage Treated With Oxidized Regenerated Cellulose.

Sakata KK, Nelson DR, Midthun DE.

J Bronchology Interv Pulmonol. 2017 Jul;24(3):42-44. doi: 10.1097/LBR.0000000000000390. No abstract available.


Safety of the 2D/3D direct-acting antiviral regimen in HCV-induced Child-Pugh A cirrhosis - A pooled analysis.

Poordad F, Nelson DR, Feld JJ, Fried MW, Wedemeyer H, Larsen L, Cohen DE, Cohen E, Mobashery N, Tatsch F, Foster GR.

J Hepatol. 2017 Oct;67(4):700-707. doi: 10.1016/j.jhep.2017.06.011. Epub 2017 Jun 21.


HBV reactivation after HCV eradication: Deja Vu.

Reau N, Nelson DR.

Liver Int. 2017 Jul;37(7):1088. doi: 10.1111/liv.13358. No abstract available.


The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization.

Nelson DR, Khraiwesh B, Fu W, Alseekh S, Jaiswal A, Chaiboonchoe A, Hazzouri KM, O'Connor MJ, Butterfoss GL, Drou N, Rowe JD, Harb J, Fernie AR, Gunsalus KC, Salehi-Ashtiani K.

Elife. 2017 Jun 17;6. pii: e25783. doi: 10.7554/eLife.25783.


A Transcriptome Survey Spanning Life Stages and Sexes of the Harlequin Bug, Murgantia histrionica.

Sparks ME, Rhoades JH, Nelson DR, Kuhar D, Lancaster J, Lehner B, Tholl D, Weber DC, Gundersen-Rindal DE.

Insects. 2017 May 25;8(2). pii: E55. doi: 10.3390/insects8020055.


Elbasvir plus grazoprevir in patients with hepatitis C virus infection and stage 4-5 chronic kidney disease: clinical, virological, and health-related quality-of-life outcomes from a phase 3, multicentre, randomised, double-blind, placebo-controlled trial.

Bruchfeld A, Roth D, Martin P, Nelson DR, Pol S, Londoño MC, Monsour H Jr, Silva M, Hwang P, Arduino JM, Robertson M, Nguyen BY, Wahl J, Barr E, Greaves W.

Lancet Gastroenterol Hepatol. 2017 Aug;2(8):585-594. doi: 10.1016/S2468-1253(17)30116-4. Epub 2017 May 30.


Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants.

Renault H, De Marothy M, Jonasson G, Lara P, Nelson DR, Nilsson I, André F, von Heijne G, Werck-Reichhart D.

Mol Biol Evol. 2017 Aug 1;34(8):2041-2056. doi: 10.1093/molbev/msx160.


Safety and efficacy of current direct-acting antiviral regimens in kidney and liver transplant recipients with hepatitis C: Results from the HCV-TARGET study.

Saxena V, Khungar V, Verna EC, Levitsky J, Brown RS Jr, Hassan MA, Sulkowski MS, O'Leary JG, Koraishy F, Galati JS, Kuo AA, Vainorius M, Akushevich L, Nelson DR, Fried MW, Terrault N, Reddy KR.

Hepatology. 2017 Oct;66(4):1090-1101. doi: 10.1002/hep.29258. Epub 2017 Sep 4.


Cytochrome P450 diversity in the tree of life.

Nelson DR.

Biochim Biophys Acta. 2018 Jan;1866(1):141-154. doi: 10.1016/j.bbapap.2017.05.003. Epub 2017 May 11.


Pragmatic trial of a Study Navigator Model (NAU) vs. Ambassador Model (N+) to increase enrollment to health research among community members who use illicit drugs.

Cottler LB, Striley CW, Elliott AL, Zulich AE, Kwiatkowski E, Nelson DR.

Drug Alcohol Depend. 2017 Jun 1;175:146-150. doi: 10.1016/j.drugalcdep.2016.12.031. Epub 2017 Apr 4.


Institutional profile: University of Florida Health Personalized Medicine Program.

Cavallari LH, Weitzel KW, Elsey AR, Liu X, Mosley SA, Smith DM, Staley BJ, Winterstein AG, Mathews CA, Franchi F, Rollini F, Angiolillo DJ, Starostik P, Clare-Salzler MJ, Nelson DR, Johnson JA.

Pharmacogenomics. 2017 Apr;18(5):421-426. doi: 10.2217/pgs-2017-0028. Epub 2017 Mar 27. Review.


Patient engagement and study design of PROP UP: A multi-site patient-centered prospective observational study of patients undergoing hepatitis C treatment.

Evon DM, Golin CE, Stewart P, Fried MW, Alston S, Reeve B, Lok AS, Sterling RK, Lim JK, Reau N, Sarkar S, Nelson DR, Reddy KR, Di Bisceglie AM.

Contemp Clin Trials. 2017 Jun;57:58-68. doi: 10.1016/j.cct.2017.03.013. Epub 2017 Mar 22.


Oral Direct-Acting Agent Therapy for Hepatitis C Virus Infection: A Systematic Review.

Falade-Nwulia O, Suarez-Cuervo C, Nelson DR, Fried MW, Segal JB, Sulkowski MS.

Ann Intern Med. 2017 May 2;166(9):637-648. doi: 10.7326/M16-2575. Epub 2017 Mar 21. Review.


The ancient CYP716 family is a major contributor to the diversification of eudicot triterpenoid biosynthesis.

Miettinen K, Pollier J, Buyst D, Arendt P, Csuk R, Sommerwerk S, Moses T, Mertens J, Sonawane PD, Pauwels L, Aharoni A, Martins J, Nelson DR, Goossens A.

Nat Commun. 2017 Feb 6;8:14153. doi: 10.1038/ncomms14153.


CYPome of the conifer pathogen Heterobasidion irregulare: Inventory, phylogeny, and transcriptional analysis of the response to biocontrol.

Mgbeahuruike AC, Kovalchuk A, Ubhayasekera W, Nelson DR, Yadav JS.

Fungal Biol. 2017 Feb;121(2):158-171. doi: 10.1016/j.funbio.2016.11.006. Epub 2016 Dec 8.


Assessing the identity and expression level of the cytochrome P450 20A1 (CYP20A1) gene in the BPA-, BDE-47, and WAF-exposed copepods Tigriopus japonicus and Paracyclopina nana.

Han J, Kim DH, Seo JS, Kim IC, Nelson DR, Puthumana J, Lee JS.

Comp Biochem Physiol C Toxicol Pharmacol. 2017 Mar;193:42-49. doi: 10.1016/j.cbpc.2017.01.001. Epub 2017 Jan 11.


Algal Cell Factories: Approaches, Applications, and Potentials.

Fu W, Chaiboonchoe A, Khraiwesh B, Nelson DR, Al-Khairy D, Mystikou A, Alzahmi A, Salehi-Ashtiani K.

Mar Drugs. 2016 Dec 13;14(12). pii: E225. Review.


The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance.

Chen W, Hasegawa DK, Kaur N, Kliot A, Pinheiro PV, Luan J, Stensmyr MC, Zheng Y, Liu W, Sun H, Xu Y, Luo Y, Kruse A, Yang X, Kontsedalov S, Lebedev G, Fisher TW, Nelson DR, Hunter WB, Brown JK, Jander G, Cilia M, Douglas AE, Ghanim M, Simmons AM, Wintermantel WM, Ling KS, Fei Z.

BMC Biol. 2016 Dec 14;14(1):110.


HCVerso1 and 2: faldaprevir with deleobuvir (BI 207127) and ribavirin for treatment-naïve patients with chronic hepatitis C virus genotype-1b infection.

Sarrazin C, Castelli F, Andreone P, Buti M, Colombo M, Pol S, Calinas F, Puoti M, Olveira A, Shiffman M, Stern JO, Kukolj G, Roehrle M, Aslanyan S, Deng Q, Vinisko R, Mensa FJ, Nelson DR.

Clin Exp Gastroenterol. 2016 Nov 24;9:351-363. eCollection 2016.


Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

McKenna DD, Scully ED, Pauchet Y, Hoover K, Kirsch R, Geib SM, Mitchell RF, Waterhouse RM, Ahn SJ, Arsala D, Benoit JB, Blackmon H, Bledsoe T, Bowsher JH, Busch A, Calla B, Chao H, Childers AK, Childers C, Clarke DJ, Cohen L, Demuth JP, Dinh H, Doddapaneni H, Dolan A, Duan JJ, Dugan S, Friedrich M, Glastad KM, Goodisman MA, Haddad S, Han Y, Hughes DS, Ioannidis P, Johnston JS, Jones JW, Kuhn LA, Lance DR, Lee CY, Lee SL, Lin H, Lynch JA, Moczek AP, Murali SC, Muzny DM, Nelson DR, Palli SR, Panfilio KA, Pers D, Poelchau MF, Quan H, Qu J, Ray AM, Rinehart JP, Robertson HM, Roehrdanz R, Rosendale AJ, Shin S, Silva C, Torson AS, Jentzsch IM, Werren JH, Worley KC, Yocum G, Zdobnov EM, Gibbs RA, Richards S.

Genome Biol. 2016 Nov 11;17(1):227.


The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii.

Itkin M, Davidovich-Rikanati R, Cohen S, Portnoy V, Doron-Faigenboim A, Oren E, Freilich S, Tzuri G, Baranes N, Shen S, Petreikov M, Sertchook R, Ben-Dor S, Gottlieb H, Hernandez A, Nelson DR, Paris HS, Tadmor Y, Burger Y, Lewinsohn E, Katzir N, Schaffer A.

Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):E7619-E7628. Epub 2016 Nov 7.


All-oral direct-acting antiviral therapy in HCV-advanced liver disease is effective in real-world practice: observations through HCV-TARGET database.

Reddy KR, Lim JK, Kuo A, Di Bisceglie AM, Galati JS, Morelli G, Everson GT, Kwo PY, Brown RS Jr, Sulkowski MS, Akuschevich L, Lok AS, Pockros PJ, Vainorius M, Terrault NA, Nelson DR, Fried MW, Manns MP; HCV-TARGET Study Group.

Aliment Pharmacol Ther. 2017 Jan;45(1):115-126. doi: 10.1111/apt.13823. Epub 2016 Oct 28.


Effectiveness of Ledipasvir-Sofosbuvir Combination in Patients With Hepatitis C Virus Infection and Factors Associated With Sustained Virologic Response.

Terrault NA, Zeuzem S, Di Bisceglie AM, Lim JK, Pockros PJ, Frazier LM, Kuo A, Lok AS, Shiffman ML, Ben Ari Z, Akushevich L, Vainorius M, Sulkowski MS, Fried MW, Nelson DR; HCV-TARGET Study Group.

Gastroenterology. 2016 Dec;151(6):1131-1140.e5. doi: 10.1053/j.gastro.2016.08.004. Epub 2016 Aug 24.


Plastic deformation of tubular crystals by dislocation glide.

Beller DA, Nelson DR.

Phys Rev E. 2016 Sep;94(3-1):033004. Epub 2016 Sep 26.


Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s.

Parvez M, Qhanya LB, Mthakathi NT, Kgosiemang IK, Bamal HD, Pagadala NS, Xie T, Yang H, Chen H, Theron CW, Monyaki R, Raselemane SC, Salewe V, Mongale BL, Matowane RG, Abdalla SM, Booi WI, van Wyk M, Olivier D, Boucher CE, Nelson DR, Tuszynski JA, Blackburn JM, Yu JH, Mashele SS, Chen W, Syed K.

Sci Rep. 2016 Sep 12;6:33099. doi: 10.1038/srep33099.


Cytochrome P450 complement (CYPome) of Candida oregonensis, a gut-associated yeast of bark beetle, Dendroctonus rhizophagus.

Hernández-Martínez F, Briones-Roblero CI, Nelson DR, Rivera-Orduña FN, Zúñiga G.

Fungal Biol. 2016 Sep;120(9):1077-89. doi: 10.1016/j.funbio.2016.06.005. Epub 2016 Jun 17.


Reclassification of the larval pathogen for marine bivalves Vibrio tubiashii subsp. europaeus as Vibrio europaeus sp. nov.

Dubert J, Romalde JL, Spinard EJ, Nelson DR, Gomez-Chiarri M, Barja JL.

Int J Syst Evol Microbiol. 2016 Nov;66(11):4791-4796. doi: 10.1099/ijsem.0.001431. Epub 2016 Aug 18.


Cost of Antihyperglycemic Medications in the United States.

Alatorre C, Schultz EH, Nelson DR.

JAMA. 2016 Aug 9;316(6):665. doi: 10.1001/jama.2016.8587. No abstract available.


Resistance Analyses of HCV NS3/4A Protease and NS5B Polymerase from Clinical Studies of Deleobuvir and Faldaprevir.

Berger KL, Sarrazin C, Nelson DR, Scherer J, Sha N, Marquis M, Côté-Martin A, Vinisko R, Stern JO, Mensa FJ, Kukolj G.

PLoS One. 2016 Aug 5;11(8):e0160668. doi: 10.1371/journal.pone.0160668. eCollection 2016.


Draft Genome Sequence of the Emerging Bivalve Pathogen Vibrio tubiashii subsp. europaeus.

Spinard EJ, Dubert J, Nelson DR, Gomez-Chiarri M, Barja JL.

Genome Announc. 2016 Jul 28;4(4). pii: e00625-16. doi: 10.1128/genomeA.00625-16.


Effectiveness and safety of sofosbuvir plus ribavirin for the treatment of HCV genotype 2 infection: results of the real-world, clinical practice HCV-TARGET study.

Welzel TM, Nelson DR, Morelli G, Di Bisceglie A, Reddy RK, Kuo A, Lim JK, Darling J, Pockros P, Galati JS, Frazier LM, Alqahtani S, Sulkowski MS, Vainorius M, Akushevich L, Fried MW, Zeuzem S; HCV-TARGET Study Group.

Gut. 2017 Oct;66(10):1844-1852. doi: 10.1136/gutjnl-2016-311609. Epub 2016 Jul 13.

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