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Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study.

Sudderuddin H, Kinloch NN, Jin SW, Miller RL, Jones BR, Brumme CJ, Joy JB, Brockman MA, Brumme ZL.

Retrovirology. 2020 Jan 9;17(1):3. doi: 10.1186/s12977-019-0510-1.


Genetic diversity, compartmentalization and age of HIV proviruses persisting in CD4+ T cell subsets during long-term combination antiretroviral therapy.

Jones BR, Miller RL, Kinloch NN, Tsai O, Rigsby H, Sudderuddin H, Shahid A, Ganase B, Brumme CJ, Harris M, Poon AFY, Brockman MA, Fromentin R, Chomont N, Joy JB, Brumme ZL.

J Virol. 2019 Nov 27. pii: JVI.01786-19. doi: 10.1128/JVI.01786-19. [Epub ahead of print]


Comparative Study on the Effects of Picoloyl Groups in Sialylations Based on Their Substitution Pattern.

Jones B, Behm A, Shadrick M, Geringer SA, Escopy S, Lohman M, De Meo C.

J Org Chem. 2019 Dec 6;84(23):15052-15062. doi: 10.1021/acs.joc.9b01492. Epub 2019 Nov 25.


treeio: an R package for phylogenetic tree input and output with richly annotated and associated data.

Wang LG, Lam TT, Xu S, Dai Z, Zhou L, Feng T, Guo P, Dunn CW, Jones BR, Bradley T, Zhu H, Guan Y, Jiang Y, Yu G.

Mol Biol Evol. 2019 Oct 21. pii: msz240. doi: 10.1093/molbev/msz240. [Epub ahead of print]


Automated matrix-matching calibration using standard dilution analysis with two internal standards and a simple three-port mixing chamber.

Sloop JT, Bonilla HJB, Harville T, Jones BT, Donati GL.

Talanta. 2019 Dec 1;205:120160. doi: 10.1016/j.talanta.2019.120160. Epub 2019 Jul 17.


Tree shape-based approaches for the comparative study of cophylogeny.

Avino M, Ng GT, He Y, Renaud MS, Jones BR, Poon AFY.

Ecol Evol. 2019 May 29;9(12):6756-6771. doi: 10.1002/ece3.5185. eCollection 2019 Jun.


HIV Diversity and Genetic Compartmentalization in Blood and Testes during Suppressive Antiretroviral Therapy.

Miller RL, Ponte R, Jones BR, Kinloch NN, Omondi FH, Jenabian MA, Dupuy FP, Fromentin R, Brassard P, Mehraj V, Chomont N, Poon AFY, Joy JB, Brumme ZL, Routy JP; ORCHID Study Group.

J Virol. 2019 Aug 13;93(17). pii: e00755-19. doi: 10.1128/JVI.00755-19. Print 2019 Sep 1.


Optogenetic control of alcohol-seeking behavior via the dorsomedial striatal circuit.

Roltsch Hellard E, Binette A, Zhuang X, Lu J, Ma T, Jones B, Williams E, Jayavelu S, Wang J.

Neuropharmacology. 2019 Sep 1;155:89-97. doi: 10.1016/j.neuropharm.2019.05.022. Epub 2019 May 20.


Effects of platinum-based anticancer drugs on the trace element profile of liver and kidney tissue from mice.

Sloop JT, Carter JA, Bierbach U, Jones BT, Donati GL.

J Trace Elem Med Biol. 2019 Jul;54:62-68. doi: 10.1016/j.jtemb.2019.04.005. Epub 2019 Apr 12.


Identifying and assessing matrix effect severity in inductively coupled plasma optical emission spectrometry using non-analyte signals and unsupervised learning.

Carter JA, Sloop JT, McSweeney T, Jones BT, Donati GL.

Anal Chim Acta. 2019 Jul 25;1062:37-46. doi: 10.1016/j.aca.2019.03.002. Epub 2019 Mar 7.


Chemical Synthesis of Glycosides of N-Acetylneuraminic Acid.

De Meo C, Jones BT.

Adv Carbohydr Chem Biochem. 2018;75:215-316. doi: 10.1016/bs.accb.2018.09.005. Epub 2018 Nov 23. Review.


Genetic complexity in the replication-competent latent HIV reservoir increases with untreated infection duration in infected youth.

Brumme ZL, Sudderuddin H, Ziemniak C, Luzuriaga K, Jones BR, Joy JB, Cunningham CK, Greenough T, Persaud D.

AIDS. 2019 Feb 1;33(2):211-218. doi: 10.1097/QAD.0000000000002045.


Phylogenetic approach to recover integration dates of latent HIV sequences within-host.

Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Harrigan PR, Jones RB, Brockman MA, Joy JB, Poon AFY, Brumme ZL.

Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):E8958-E8967. doi: 10.1073/pnas.1802028115. Epub 2018 Sep 5.


Analysis of single, cisplatin-induced DNA bends by atomic force microscopy and simulations.

Dutta S, Rivetti C, Gassman NR, Young CG, Jones BT, Scarpinato K, Guthold M.

J Mol Recognit. 2018 Oct;31(10):e2731. doi: 10.1002/jmr.2731. Epub 2018 Jun 3.


The Ability to Acquire Iron Is Inversely Related to Virulence and the Protective Efficacy of Francisella tularensis Live Vaccine Strain.

Fletcher JR, Crane DD, Wehrly TD, Martens CA, Bosio CM, Jones BD.

Front Microbiol. 2018 Apr 4;9:607. doi: 10.3389/fmicb.2018.00607. eCollection 2018.


Immunization with outer membrane vesicles displaying conserved surface polysaccharide antigen elicits broadly antimicrobial antibodies.

Stevenson TC, Cywes-Bentley C, Moeller TD, Weyant KB, Putnam D, Chang YF, Jones BD, Pier GB, DeLisa MP.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):E3106-E3115. doi: 10.1073/pnas.1718341115. Epub 2018 Mar 19.


The global origins of resistance-associated variants in the non-structural proteins 5A and 5B of the hepatitis C virus.

Jones BR, Howe AYM, Harrigan PR, Joy JB.

Virus Evol. 2018 Jan 16;4(1):vex041. doi: 10.1093/ve/vex041. eCollection 2018 Jan.


Bacterial lipoproteins and other factors released by Francisella tularensis modulate human neutrophil lifespan: Effects of a TLR1 SNP on apoptosis inhibition.

Kinkead LC, Whitmore LC, McCracken JM, Fletcher JR, Ketelsen BB, Kaufman JW, Jones BD, Weiss DS, Barker JH, Allen LH.

Cell Microbiol. 2018 Feb;20(2). doi: 10.1111/cmi.12795. Epub 2017 Nov 21.


Characterization of Inner and Outer Membrane Proteins from Francisella tularensis Strains LVS and Schu S4 and Identification of Potential Subunit Vaccine Candidates.

Post DMB, Slütter B, Schilling B, Chande AT, Rasmussen JA, Jones BD, D'Souza AK, Reinders LM, Harty JT, Gibson BW, Apicella MA.

mBio. 2017 Oct 10;8(5). pii: e01592-17. doi: 10.1128/mBio.01592-17.


Iatrogenic type A aortic dissection during idiopathic ventricular tachycardia ablation.

Yeshwant SC, Tsai MH, Jones BR, Hamlin MP, Bensimhon AD, Lustgarten DL.

HeartRhythm Case Rep. 2017 Jun 10;3(8):396-399. doi: 10.1016/j.hrcr.2017.05.008. eCollection 2017 Aug. No abstract available.


Melanoma Metastasis to the Mandible-Case Report and Comprehensive Literature Review.

Cervenka PD, Perez L Jr, Perez DE, Jones B.

J Oral Maxillofac Surg. 2017 Sep;75(9):2025.e1-2025.e12. doi: 10.1016/j.joms.2017.05.029. Epub 2017 Jun 1. Review.

22. dating ancestors in phylogenetic trees in R.

Jones BR, Poon AFY.

Bioinformatics. 2017 Mar 15;33(6):932-934. doi: 10.1093/bioinformatics/btw744.


How Different Forms of Health Matter to Political Participation.

Burden BC, Fletcher JM, Herd P, Jones BM, Moynihan DP.

J Polit. 2017;79(1):166-178. doi: 10.1086/687536. Epub 2016 Nov 2.


Scalable Synthesis of Enantiopure Bis-3,4-diazaphospholane Ligands for Asymmetric Catalysis.

Jones BR, Abrams ML, Landis CR, May SA, Campbell AN, Martinelli JR, Calvin JR.

J Org Chem. 2016 Dec 2;81(23):11965-11970. Epub 2016 Nov 9.


Inductively coupled plasma mass spectrometry and standard dilution analysis applied to concentrated acids.

Virgilio A, Schiavo D, Costa LM, Nóbrega JA, Jones BT, Donati GL.

Talanta. 2016 Dec 1;161:826-829. doi: 10.1016/j.talanta.2016.09.047. Epub 2016 Sep 19.


Inclusion of Epitopes That Expand High-Avidity CD4+ T Cells Transforms Subprotective Vaccines to Efficacious Immunogens against Virulent Francisella tularensis.

Roberts LM, Crane DD, Wehrly TD, Fletcher JR, Jones BD, Bosio CM.

J Immunol. 2016 Oct 1;197(7):2738-47. doi: 10.4049/jimmunol.1600879. Epub 2016 Aug 19.


Outer membrane vesicles displaying engineered glycotopes elicit protective antibodies.

Chen L, Valentine JL, Huang CJ, Endicott CE, Moeller TD, Rasmussen JA, Fletcher JR, Boll JM, Rosenthal JA, Dobruchowska J, Wang Z, Heiss C, Azadi P, Putnam D, Trent MS, Jones BD, DeLisa MP.

Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):E3609-18. doi: 10.1073/pnas.1518311113. Epub 2016 Jun 6.


Metabolic Reprogramming of Host Cells by Virulent Francisella tularensis for Optimal Replication and Modulation of Inflammation.

Wyatt EV, Diaz K, Griffin AJ, Rasmussen JA, Crane DD, Jones BD, Bosio CM.

J Immunol. 2016 May 15;196(10):4227-36. doi: 10.4049/jimmunol.1502456. Epub 2016 Mar 30.


Standard dilution analysis of beverages by microwave-induced plasma optical emission spectrometry.

Goncalves DA, McSweeney T, Santos MC, Jones BT, Donati GL.

Anal Chim Acta. 2016 Feb 25;909:24-9. doi: 10.1016/j.aca.2015.12.046. Epub 2016 Jan 12.


Interactions of Francisella tularensis with Alveolar Type II Epithelial Cells and the Murine Respiratory Epithelium.

Faron M, Fletcher JR, Rasmussen JA, Apicella MA, Jones BD.

PLoS One. 2015 May 26;10(5):e0127458. doi: 10.1371/journal.pone.0127458. eCollection 2015.


Characterization of Francisella tularensis Schu S4 mutants identified from a transposon library screened for O-antigen and capsule deficiencies.

Rasmussen JA, Fletcher JR, Long ME, Allen LA, Jones BD.

Front Microbiol. 2015 May 5;6:338. doi: 10.3389/fmicb.2015.00338. eCollection 2015.


Gill histopathologies following exposure to nanosilver or silver nitrate.

Hawkins AD, Thornton C, Kennedy AJ, Bu K, Cizdziel J, Jones BW, Steevens JA, Willett KL.

J Toxicol Environ Health A. 2015;78(5):301-15. doi: 10.1080/15287394.2014.971386.


Standard dilution analysis.

Jones WB, Donati GL, Calloway CP Jr, Jones BT.

Anal Chem. 2015 Feb 17;87(4):2321-7. doi: 10.1021/ac504152x. Epub 2015 Jan 30.


Two-component regulators control hilA expression by controlling fimZ and hilE expression within Salmonella enterica serovar Typhimurium.

Baxter MA, Jones BD.

Infect Immun. 2015 Mar;83(3):978-85. doi: 10.1128/IAI.02506-14. Epub 2014 Dec 29.


Differential response of MCF7, MDA-MB-231, and MCF 10A cells to hyperthermia, silver nanoparticles and silver nanoparticle-induced photothermal therapy.

Thompson EA, Graham E, MacNeill CM, Young M, Donati G, Wailes EM, Jones BT, Levi-Polyachenko NH.

Int J Hyperthermia. 2014 Aug;30(5):312-23. doi: 10.3109/02656736.2014.936051.


Characterization of missense alleles of the glial cells missing gene of Drosophila.

Jones BW.

Genesis. 2014 Oct;52(10):864-9. doi: 10.1002/dvg.22801. Epub 2014 Jul 21.


Metabolic engineering of Salmonella vaccine bacteria to boost human Vγ2Vδ2 T cell immunity.

Workalemahu G, Wang H, Puan KJ, Nada MH, Kuzuyama T, Jones BD, Jin C, Morita CT.

J Immunol. 2014 Jul 15;193(2):708-21. doi: 10.4049/jimmunol.1302746. Epub 2014 Jun 18.


Bismuth as a general internal standard for lead in atomic absorption spectrometry.

Bechlin MA, Fortunato FM, Ferreira EC, Gomes Neto JA, Nóbrega JA, Donati GL, Jones BT.

Anal Chim Acta. 2014 Jun 11;831:24-30. doi: 10.1016/j.aca.2014.05.002. Epub 2014 May 2.


Uncovering the components of the Francisella tularensis virulence stealth strategy.

Jones BD, Faron M, Rasmussen JA, Fletcher JR.

Front Cell Infect Microbiol. 2014 Mar 7;4:32. doi: 10.3389/fcimb.2014.00032. eCollection 2014. Review.


Francisella tularensis Schu S4 lipopolysaccharide core sugar and O-antigen mutants are attenuated in a mouse model of tularemia.

Rasmussen JA, Post DM, Gibson BW, Lindemann SR, Apicella MA, Meyerholz DK, Jones BD.

Infect Immun. 2014 Apr;82(4):1523-39. doi: 10.1128/IAI.01640-13. Epub 2014 Jan 22.


Direct determination of sodium, potassium, chromium and vanadium in biodiesel fuel by tungsten coil atomic emission spectrometry.

Dancsak SE, Silva SG, Nóbrega JA, Jones BT, Donati GL.

Anal Chim Acta. 2014 Jan 2;806:85-90. doi: 10.1016/j.aca.2013.10.055. Epub 2013 Nov 19.


The Francisella tularensis migR, trmE, and cphA genes contribute to F. tularensis pathogenicity island gene regulation and intracellular growth by modulation of the stress alarmone ppGpp.

Faron M, Fletcher JR, Rasmussen JA, Long ME, Allen LA, Jones BD.

Infect Immun. 2013 Aug;81(8):2800-11. doi: 10.1128/IAI.00073-13. Epub 2013 May 28.


Cobalt as chemical modifier to improve chromium sensitivity and minimize matrix effects in tungsten coil atomic emission spectrometry.

Silva SG, Donati GL, Santos LN, Jones BT, Nóbrega JA.

Anal Chim Acta. 2013 May 30;780:7-12. doi: 10.1016/j.aca.2013.04.006. Epub 2013 Apr 15.


Disruption of Francisella tularensis Schu S4 iglI, iglJ, and pdpC genes results in attenuation for growth in human macrophages and in vivo virulence in mice and reveals a unique phenotype for pdpC.

Long ME, Lindemann SR, Rasmussen JA, Jones BD, Allen LA.

Infect Immun. 2013 Mar;81(3):850-61. doi: 10.1128/IAI.00822-12. Epub 2012 Dec 28.


Francisella tularensis live vaccine strain folate metabolism and pseudouridine synthase gene mutants modulate macrophage caspase-1 activation.

Ulland TK, Janowski AM, Buchan BW, Faron M, Cassel SL, Jones BD, Sutterwala FS.

Infect Immun. 2013 Jan;81(1):201-8. doi: 10.1128/IAI.00991-12. Epub 2012 Oct 31.


ANGES: reconstructing ANcestral GEnomeS maps.

Jones BR, Rajaraman A, Tannier E, Chauve C.

Bioinformatics. 2012 Sep 15;28(18):2388-90. doi: 10.1093/bioinformatics/bts457. Epub 2012 Jul 20.


Internal standardization combined with dilute-and-shoot preparation of distilled alcoholic beverages for Cu determination by high-resolution continuum source flame atomic absorption spectrometry.

Raposo JL Jr, de Oliveira AP, Jones BT, Gomes Neto JA.

Talanta. 2012 Apr 15;92:53-7. doi: 10.1016/j.talanta.2012.01.035. Epub 2012 Jan 24.


Characterization of cis-regulatory elements controlling repo transcription in Drosophila melanogaster.

Johnson RW, Wood JL, Jones BW.

Gene. 2012 Jan 15;492(1):167-76. doi: 10.1016/j.gene.2011.10.032. Epub 2011 Oct 25.


Determination of sulfur in biodiesel microemulsions using the summation of the intensities of multiple emission lines.

Young CG, Amais RS, Schiavo D, Garcia EE, Nóbrega JA, Jones BT.

Talanta. 2011 May 15;84(3):995-9. doi: 10.1016/j.talanta.2011.01.008. Epub 2011 Jan 15.


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