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Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of -1 Frameshifting by tRNASer3.

Caulfield T, Coban M, Tek A, Flores SC.

Biomolecules. 2019 Nov 18;9(11). pii: E745. doi: 10.3390/biom9110745.


Nontuberculous Mycobacteria Show Differential Infectivity and Use Phospholipids to Antagonize LL-37.

Honda JR, Hess T, Carlson R, Kandasamy P, Nieto Ramirez LM, Norton GJ, Virdi R, Islam MN, Mehaffy C, Hasan NA, Epperson LE, Hesser D, Alper S, Strong M, Flores SC, Voelker DR, Dobos KM, Chan ED.

Am J Respir Cell Mol Biol. 2019 Sep 23. doi: 10.1165/rcmb.2018-0278OC. [Epub ahead of print]


Lung Vascular Remodeling, Cardiac Hypertrophy, and Inflammatory Cytokines in SHIVnef-Infected Macaques.

Almodovar S, Swanson J, Giavedoni LD, Kanthaswamy S, Long CS, Voelkel NF, Edwards MG, Folkvord JM, Connick E, Westmoreland SV, Luciw PA, Flores SC.

Viral Immunol. 2018 Apr;31(3):206-222. doi: 10.1089/vim.2017.0051. Epub 2017 Dec 19.


Insights from engineering the Affibody-Fc interaction with a computational-experimental method.

Nosrati M, Solbak S, Nordesjö O, Nissbeck M, Dourado DFAR, Andersson KG, Housaindokht MR, Löfblom J, Virtanen A, Danielson UH, Flores SC.

Protein Eng Des Sel. 2017 Sep 1;30(9):593-601. doi: 10.1093/protein/gzx023.


Mechanisms Underlying HIV-Associated Noninfectious Lung Disease.

Presti RM, Flores SC, Palmer BE, Atkinson JJ, Lesko CR, Lau B, Fontenot AP, Roman J, McDyer JF, Twigg HL 3rd.

Chest. 2017 Nov;152(5):1053-1060. doi: 10.1016/j.chest.2017.04.154. Epub 2017 Apr 17. Review.


Study of the Lung Microbiome. Have We Reached the End of the Beginning?

Morris A, Flores SC.

Am J Respir Crit Care Med. 2017 Jan 1;195(1):15-16. doi: 10.1164/rccm.201608-1635ED. No abstract available.


Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes.

Cheng RR, Nordesjö O, Hayes RL, Levine H, Flores SC, Onuchic JN, Morcos F.

Mol Biol Evol. 2016 Dec;33(12):3054-3064. Epub 2016 Sep 7.


Modeling and fitting protein-protein complexes to predict change of binding energy.

Dourado DF, Flores SC.

Sci Rep. 2016 May 13;6:25406. doi: 10.1038/srep25406.


National Heart, Lung, and Blood Institute Workshop Summary: Enhancing Opportunities for Training and Retention of a Diverse Biomedical Workforce.

Duncan GA, Lockett A, Villegas LR, Almodovar S, Gomez JL, Flores SC, Wilkes DS, Tigno XT.

Ann Am Thorac Soc. 2016 Apr;13(4):562-7. doi: 10.1513/AnnalsATS.201509-624OT.


Risk Factors Associated With Quantitative Evidence of Lung Emphysema and Fibrosis in an HIV-Infected Cohort.

Leader JK, Crothers K, Huang L, King MA, Morris A, Thompson BW, Flores SC, Drummond MB, Rom WN, Diaz PT.

J Acquir Immune Defic Syndr. 2016 Apr 1;71(4):420-7. doi: 10.1097/QAI.0000000000000894.


MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory.

Tek A, Korostelev AA, Flores SC.

Nucleic Acids Res. 2016 Jan 8;44(1):95-105. doi: 10.1093/nar/gkv1457. Epub 2015 Dec 15.


Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

Beck JM, Schloss PD, Venkataraman A, Twigg H 3rd, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2015 Dec 1;192(11):1335-44. doi: 10.1164/rccm.201501-0128OC.


Pathogenic nontuberculous mycobacteria resist and inactivate cathelicidin: implication of a novel role for polar mycobacterial lipids.

Honda JR, Hess T, Malcolm KC, Ovrutsky AR, Bai X, Irani VR, Dobos KM, Chan ED, Flores SC.

PLoS One. 2015 May 18;10(5):e0126994. doi: 10.1371/journal.pone.0126994. eCollection 2015.


Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin.

Fiesel FC, Caulfield TR, Moussaud-Lamodière EL, Ogaki K, Dourado DF, Flores SC, Ross OA, Springer W.

Hum Mutat. 2015 Aug;36(8):774-86. doi: 10.1002/humu.22808. Epub 2015 Jun 3.


Lymphocytic alveolitis is associated with the accumulation of functionally impaired HIV-specific T cells in the lung of antiretroviral therapy-naive subjects.

Neff CP, Chain JL, MaWhinney S, Martin AK, Linderman DJ, Flores SC, Campbell TB, Palmer BE, Fontenot AP.

Am J Respir Crit Care Med. 2015 Feb 15;191(4):464-73. doi: 10.1164/rccm.201408-1521OC.


Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin.

Caulfield TR, Fiesel FC, Moussaud-Lamodière EL, Dourado DF, Flores SC, Springer W.

PLoS Comput Biol. 2014 Nov 6;10(11):e1003935. doi: 10.1371/journal.pcbi.1003935. eCollection 2014 Nov.


A multiscale approach to predicting affinity changes in protein-protein interfaces.

Dourado DF, Flores SC.

Proteins. 2014 Oct;82(10):2681-90. doi: 10.1002/prot.24634. Epub 2014 Jul 5.


Plasma LL-37 correlates with vitamin D and is reduced in human immunodeficiency virus-1 infected individuals not receiving antiretroviral therapy.

Honda JR, Connick E, MaWhinney S, Chan ED, Flores SC.

J Med Microbiol. 2014 Jul;63(Pt 7):997-1003. doi: 10.1099/jmm.0.070888-0. Epub 2014 May 12.


Transfer of intracellular HIV Nef to endothelium causes endothelial dysfunction.

Wang T, Green LA, Gupta SK, Kim C, Wang L, Almodovar S, Flores SC, Prudovsky IA, Jolicoeur P, Liu Z, Clauss M.

PLoS One. 2014 Mar 7;9(3):e91063. doi: 10.1371/journal.pone.0091063. eCollection 2014.


Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise.

Twigg HL 3rd, Morris A, Ghedin E, Curtis JL, Huffnagle GB, Crothers K, Campbell TB, Flores SC, Fontenot AP, Beck JM, Huang L, Lynch S, Knox KS, Weinstock G; Lung HIV Microbiome Project.

Lancet Respir Med. 2013 Jul;1(5):354-6. doi: 10.1016/S2213-2600(13)70117-6. Epub 2013 Jul 8. No abstract available.


Muc5b is required for airway defence.

Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O'Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM.

Nature. 2014 Jan 16;505(7483):412-6. doi: 10.1038/nature12807. Epub 2013 Dec 8.


Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome.

Flores SC.

Nucleic Acids Res. 2014 Jan;42(2):e9. doi: 10.1093/nar/gkt906. Epub 2013 Sep 29.


Alterations in the gut microbiota associated with HIV-1 infection.

Lozupone CA, Li M, Campbell TB, Flores SC, Linderman D, Gebert MJ, Knight R, Fontenot AP, Palmer BE.

Cell Host Microbe. 2013 Sep 11;14(3):329-39. doi: 10.1016/j.chom.2013.08.006.


Human immunodeficiency virus, herpes virus infections, and pulmonary vascular disease.

Flores SC, Almodovar S.

Pulm Circ. 2013 Jan;3(1):165-70. doi: 10.4103/2045-8932.109955.


Comparison of the respiratory microbiome in healthy nonsmokers and smokers.

Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2013 May 15;187(10):1067-75. doi: 10.1164/rccm.201210-1913OC.


Insights into diseases of human telomerase from dynamical modeling.

Flores SC, Zemora G, Waldsich C.

Pac Symp Biocomput. 2013:200-11.


Widespread colonization of the lung by Tropheryma whipplei in HIV infection.

Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP; Lung HIV Microbiome Project.

Am J Respir Crit Care Med. 2013 May 15;187(10):1110-7. doi: 10.1164/rccm.201211-2145OC.


Role of carboxylate side chains in the cation Hofmeister series.

Kherb J, Flores SC, Cremer PS.

J Phys Chem B. 2012 Jun 28;116(25):7389-97. doi: 10.1021/jp212243c. Epub 2012 Jun 14.


RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction.

Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E.

RNA. 2012 Apr;18(4):610-25. doi: 10.1261/rna.031054.111. Epub 2012 Feb 23.


Multiscale modeling of macromolecular biosystems.

Flores SC, Bernauer J, Shin S, Zhou R, Huang X.

Brief Bioinform. 2012 Jul;13(4):395-405. doi: 10.1093/bib/bbr077. Epub 2012 Jan 6.


Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension.

Almodovar S, Knight R, Allshouse AA, Roemer S, Lozupone C, McDonald D, Widmann J, Voelkel NF, Shelton RJ, Suarez EB, Hammer KW, Goujard C, Petrosillo N, Simonneau G, Hsue PY, Humbert M, Flores SC.

AIDS Res Hum Retroviruses. 2012 Jun;28(6):607-18. doi: 10.1089/AID.2011.0021. Epub 2012 Jan 17.


Immune Responses of HIV-1 Tat Transgenic Mice to Mycobacterium Tuberculosis W-Beijing SA161.

Honda JR, Shang S, Shanley CA, Caraway ML, Henao-Tamayo M, Chan ED, Basaraba RJ, Orme IM, Ordway DJ, Flores SC.

Open AIDS J. 2011;5:86-95. doi: 10.2174/1874613601105010086. Epub 2011 Oct 19.


Predicting protein ligand binding motions with the conformation explorer.

Flores SC, Gerstein MB.

BMC Bioinformatics. 2011 Oct 27;12:417. doi: 10.1186/1471-2105-12-417.


Methyl groups of trimethylamine N-oxide orient away from hydrophobic interfaces.

Sagle LB, Cimatu K, Litosh VA, Liu Y, Flores SC, Chen X, Yu B, Cremer PS.

J Am Chem Soc. 2011 Nov 23;133(46):18707-12. doi: 10.1021/ja205106e. Epub 2011 Oct 27.


HIV-1 Tat increases oxidant burden in the lungs of transgenic mice.

Cota-Gomez A, Flores AC, Ling XF, Varella-Garcia M, Flores SC.

Free Radic Biol Med. 2011 Nov 1;51(9):1697-707. doi: 10.1016/j.freeradbiomed.2011.07.023. Epub 2011 Aug 5.


Fast flexible modeling of RNA structure using internal coordinates.

Flores SC, Sherman MA, Bruns CM, Eastman P, Altman RB.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1247-57. doi: 10.1109/TCBB.2010.104.


Pathogenesis of HIV-associated pulmonary hypertension: potential role of HIV-1 Nef.

Almodovar S, Hsue PY, Morelli J, Huang L, Flores SC; Lung HIV Study.

Proc Am Thorac Soc. 2011 Jun;8(3):308-12. doi: 10.1513/pats.201006-046WR.


HIV-associated lung infections and complications in the era of combination antiretroviral therapy.

Crothers K, Thompson BW, Burkhardt K, Morris A, Flores SC, Diaz PT, Chaisson RE, Kirk GD, Rom WN, Huang L; Lung HIV Study.

Proc Am Thorac Soc. 2011 Jun;8(3):275-81. doi: 10.1513/pats.201009-059WR. Review.


Autoimmune-mediated vascular injury occurs prior to sustained hyperglycemia in a murine model of type I diabetes mellitus.

Zimmerman MA, Haskins K, Bradley B, Gilman J, Gamboni-Robertson F, Flores SC.

J Surg Res. 2011 Jun 15;168(2):e195-202. doi: 10.1016/j.jss.2011.01.021. Epub 2011 Feb 26.


Dependence of Golgi apparatus integrity on nitric oxide in vascular cells: implications in pulmonary arterial hypertension.

Lee JE, Patel K, Almodóvar S, Tuder RM, Flores SC, Sehgal PB.

Am J Physiol Heart Circ Physiol. 2011 Apr;300(4):H1141-58. doi: 10.1152/ajpheart.00767.2010. Epub 2011 Jan 7.


Strategies for articulated multibody-based adaptive coarse grain simulation of RNA.

Poursina M, Bhalerao KD, Flores SC, Anderson KS, Laederach A.

Methods Enzymol. 2011;487:73-98. doi: 10.1016/B978-0-12-381270-4.00003-2.


Structural insights into pre-translocation ribosome motions.

Flores SC, Altman R.

Pac Symp Biocomput. 2011:205-11.


Efficacy of transcranial magnetic stimulation (TMS) in depression: naturalistic study.

Aliño JJ, Jiménez JL, Flores SC, Alcocer MI.

Actas Esp Psiquiatr. 2010 Mar-Apr;38(2):87-93. Epub 2010 Mar 1.


Turning limited experimental information into 3D models of RNA.

Flores SC, Altman RB.

RNA. 2010 Sep;16(9):1769-78. doi: 10.1261/rna.2112110. Epub 2010 Jul 22.


Specific anion effects on water structure adjacent to protein monolayers.

Chen X, Flores SC, Lim SM, Zhang Y, Yang T, Kherb J, Cremer PS.

Langmuir. 2010 Nov 2;26(21):16447-54. doi: 10.1021/la1015862.


Pulmonary hypertension associated with HIV infection: pulmonary vascular disease: the global perspective.

Almodovar S, Cicalini S, Petrosillo N, Flores SC.

Chest. 2010 Jun;137(6 Suppl):6S-12S. doi: 10.1378/chest.09-3065.


Predicting RNA structure by multiple template homology modeling.

Flores SC, Wan Y, Russell R, Altman RB.

Pac Symp Biocomput. 2010:216-27.


Golgi dysfunction is a common feature in idiopathic human pulmonary hypertension and vascular lesions in SHIV-nef-infected macaques.

Sehgal PB, Mukhopadhyay S, Patel K, Xu F, Almodóvar S, Tuder RM, Flores SC.

Am J Physiol Lung Cell Mol Physiol. 2009 Oct;297(4):L729-37. doi: 10.1152/ajplung.00087.2009. Epub 2009 Jul 31.


Inflammation, growth factors, and pulmonary vascular remodeling.

Hassoun PM, Mouthon L, Barberà JA, Eddahibi S, Flores SC, Grimminger F, Jones PL, Maitland ML, Michelakis ED, Morrell NW, Newman JH, Rabinovitch M, Schermuly R, Stenmark KR, Voelkel NF, Yuan JX, Humbert M.

J Am Coll Cardiol. 2009 Jun 30;54(1 Suppl):S10-9. doi: 10.1016/j.jacc.2009.04.006. Review.


A potential role for reactive oxygen species and the HIF-1alpha-VEGF pathway in hypoxia-induced pulmonary vascular leak.

Irwin DC, McCord JM, Nozik-Grayck E, Beckly G, Foreman B, Sullivan T, White M, T Crossno J Jr, Bailey D, Flores SC, Majka S, Klemm D, van Patot MC.

Free Radic Biol Med. 2009 Jul 1;47(1):55-61. doi: 10.1016/j.freeradbiomed.2009.03.027. Epub 2009 Apr 7.

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