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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]


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]


Evolution of aerial spider webs coincided with repeated structural optimization of silk anchorages.

Wolff JO, Paterno GB, Liprandi D, Ramírez MJ, Bosia F, van der Meijden A, Michalik P, Smith HM, Jones BR, Ravelo AM, Pugno N, Herberstein ME.

Evolution. 2019 Oct;73(10):2122-2134. doi: 10.1111/evo.13834. Epub 2019 Sep 10.


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.


Parasitic Nematode and Protozoa Status of Working Sheepdogs on the North Island of New Zealand.

O'Connell A, Scott I, Cogger N, Jones BR, Hill KE.

Animals (Basel). 2019 Mar 18;9(3). pii: E94. doi: 10.3390/ani9030094.


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.


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.


Medium-Term Outcome and CT Assessment of Lateral Foraminotomy at the Lumbosacral Junction in Dogs with Degenerative Lumbosacral Stenosis.

Worth AJ, Hartman A, Bridges JP, Jones BR, Mayhew JIG.

Vet Comp Orthop Traumatol. 2018 Jan;31(1):37-43. doi: 10.3415/vcot-17-05-0061. Epub 2018 Jan 11.


Highly selective and sensitive measurement of active forms of FGF21 using novel immunocapture enrichment with LC-MS/MS.

Zhao Y, Liu G, Kwok S, Jones BR, Liu J, Marchisin D, Joyce PE, Peterson J, Shen JX.

Bioanalysis. 2018 Jan;10(1):23-33. doi: 10.4155/bio-2017-0208. Epub 2017 Dec 14.


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.

13. dating ancestors in phylogenetic trees in R.

Jones BR, Poon AFY.

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


Pre-control relationship of onchocercal skin disease with onchocercal infection in Guinea Savanna, Northern Nigeria.

Murdoch ME, Murdoch IE, Evans J, Yahaya H, Njepuome N, Cousens S, Jones BR, Abiose A.

PLoS Negl Trop Dis. 2017 Mar 29;11(3):e0005489. doi: 10.1371/journal.pntd.0005489. eCollection 2017 Mar.


Divergent Soybean Calmodulins Respond Similarly to Calcium Transients: Insight into Differential Target Regulation.

Walton SD, Chakravarthy H, Shettigar V, O'Neil AJ, Siddiqui JK, Jones BR, Tikunova SB, Davis JP.

Front Plant Sci. 2017 Feb 15;8:208. doi: 10.3389/fpls.2017.00208. eCollection 2017.


Computed tomographic evaluation of dynamic alteration of the canine lumbosacral intervertebral neurovascular foramina.

Worth AJ, Hartman A, Bridges JP, Jones BR, Mayhew JI.

Vet Surg. 2017 Feb;46(2):255-264. doi: 10.1111/vsu.12599. Epub 2017 Jan 11.


Effect of dorsal laminectomy and dorsal annulectomy with partial lumbosacral discectomy on the volume of the lateral intervertebral neuroforamina in dogs when the lumbosacral junction is extended.

Worth AJ, Hartman A, Bridges JP, Jones BR, Mayhew JI.

Vet Surg. 2017 Feb;46(2):265-270. doi: 10.1111/vsu.12606. Epub 2017 Jan 11.


Assessing geotechnical centrifuge modelling in addressing variably saturated flow in soil and fractured rock.

Jones BR, Brouwers LB, Van Tonder WD, Dippenaar MA.

Environ Sci Pollut Res Int. 2017 May;24(15):13203-13223. doi: 10.1007/s11356-016-8333-2. Epub 2017 Jan 5.


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.


HRMS using a Q-Exactive series mass spectrometer for regulated quantitative bioanalysis: how, when, and why to implement.

Sturm RM, Jones BR, Mulvana DE, Lowes S.

Bioanalysis. 2016 Aug;8(16):1709-21. doi: 10.4155/bio-2016-0079. Epub 2016 Jul 27.


Adaptation of hybrid immunoaffinity LC-MS methods for protein bioanalysis in a Contract Research Organization.

Jones BR, Schultz GA.

Bioanalysis. 2016 Aug;8(15):1545-1549. Epub 2016 Jun 9. No abstract available.


Nitric oxide treatments as adjuncts to reperfusion in acute myocardial infarction: a systematic review of experimental and clinical studies.

Bice JS, Jones BR, Chamberlain GR, Baxter GF.

Basic Res Cardiol. 2016 Mar;111(2):23. doi: 10.1007/s00395-016-0540-y. Epub 2016 Feb 24. Review.


Endothelial HIF signaling regulates pulmonary fibrosis-associated pulmonary hypertension.

Bryant AJ, Carrick RP, McConaha ME, Jones BR, Shay SD, Moore CS, Blackwell TR, Gladson S, Penner NL, Burman A, Tanjore H, Hemnes AR, Karwandyar AK, Polosukhin VV, Talati MA, Dong HJ, Gleaves LA, Carrier EJ, Gaskill C, Scott EW, Majka SM, Fessel JP, Haase VH, West JD, Blackwell TS, Lawson WE.

Am J Physiol Lung Cell Mol Physiol. 2016 Feb 1;310(3):L249-62. doi: 10.1152/ajplung.00258.2015. Epub 2015 Dec 4.


Genetic Consequences of Pleistocene Sea-Level Change on Hawaiian Megalagrion Damselflies.

Jones BR, Jordan S.

J Hered. 2015 Sep-Oct;106(5):618-27. doi: 10.1093/jhered/esv036. Epub 2015 Jun 19.


Regional variations in percutaneous absorption of methimazole: an in vitro study on cat skin.

Hill KE, Chambers JP, Jones BR, Bolwell CF, Aberdein D, Mills PC.

J Vet Pharmacol Ther. 2015 Dec;38(6):616-8. doi: 10.1111/jvp.12220. Epub 2015 Feb 26.


Understanding genetics: why should vets care?

Jones BR, Little S, Lyons LA, Malik R, Nicholas F, O'Brien DP, Pedersen NC.

J Feline Med Surg. 2015 Mar;17(3):201-2. doi: 10.1177/1098612X15571877. No abstract available.


Percutaneous absorption of methimazole: an in vitro study of the absorption pharmacokinetics for two different vehicles.

Hill KE, Mills PC, Jones BR, Bolwell CF, Aberdein D, Chambers JP.

J Vet Pharmacol Ther. 2015 Dec;38(6):581-9. doi: 10.1111/jvp.12213. Epub 2015 Feb 16.


Trans-pinnal movement of methimazole: an in vitro study showing that methimazole can cross from the inner to outer pinna of cats.

Hill KE, Chambers JP, Jones BR, Bolwell CF, Aberdein D, Mills PC.

J Feline Med Surg. 2015 Dec;17(12):1005-11. doi: 10.1177/1098612X14567548. Epub 2015 Jan 19.


Extensive phenotyping of individuals at risk for familial interstitial pneumonia reveals clues to the pathogenesis of interstitial lung disease.

Kropski JA, Pritchett JM, Zoz DF, Crossno PF, Markin C, Garnett ET, Degryse AL, Mitchell DB, Polosukhin VV, Rickman OB, Choi L, Cheng DS, McConaha ME, Jones BR, Gleaves LA, McMahon FB, Worrell JA, Solus JF, Ware LB, Lee JW, Massion PP, Zaynagetdinov R, White ES, Kurtis JD, Johnson JE, Groshong SD, Lancaster LH, Young LR, Steele MP, Phillips Iii JA, Cogan JD, Loyd JE, Lawson WE, Blackwell TS.

Am J Respir Crit Care Med. 2015 Feb 15;191(4):417-26. doi: 10.1164/rccm.201406-1162OC.


A novel mutation in CLCN1 associated with feline myotonia congenita.

Gandolfi B, Daniel RJ, O'Brien DP, Guo LT, Youngs MD, Leach SB, Jones BR, Shelton GD, Lyons LA.

PLoS One. 2014 Oct 30;9(10):e109926. doi: 10.1371/journal.pone.0109926. eCollection 2014.


Pediatric medulloblastoma - update on molecular classification driving targeted therapies.

DeSouza RM, Jones BR, Lowis SP, Kurian KM.

Front Oncol. 2014 Jul 22;4:176. doi: 10.3389/fonc.2014.00176. eCollection 2014. Review.


The prevalence of ocular lesions associated with hypertension in a population of geriatric cats in Auckland, New Zealand.

Carter JM, Irving AC, Bridges JP, Jones BR.

N Z Vet J. 2014 Jan;62(1):21-9. doi: 10.1080/00480169.2013.823827. Epub 2013 Oct 18.


Lessons learned, challenges, and opportunities: the U.S. Endocrine Disruptor Screening Program.

Juberg DR, Borghoff SJ, Becker RA, Casey W, Hartung T, Holsapple MP, Marty MS, Mihaich EM, Van Der Kraak G, Wade MG, Willett CE, Andersen ME, Borgert CJ, Coady KK, Dourson ML, Fowle JR 3rd, Gray LE, Lamb JC, Ortego LS, Schug TT, Toole CM, Zorrilla LM, Kroner OL, Patterson J, Rinckel LA, Jones BR.

ALTEX. 2014;31(1):63-78. doi: 10.14573/altex.1309171. Epub 2013 Oct 10.


Early morning headache with vomiting in a 5 year old boy.

Jones BR, Renowden SA, Lowis SP, Kurian KM.

BMJ. 2013 May 29;346:f3315. doi: 10.1136/bmj.f3315. No abstract available.


β-catenin in the alveolar epithelium protects from lung fibrosis after intratracheal bleomycin.

Tanjore H, Degryse AL, Crossno PF, Xu XC, McConaha ME, Jones BR, Polosukhin VV, Bryant AJ, Cheng DS, Newcomb DC, McMahon FB, Gleaves LA, Blackwell TS, Lawson WE.

Am J Respir Crit Care Med. 2013 Mar 15;187(6):630-9. doi: 10.1164/rccm.201205-0972OC. Epub 2013 Jan 10.


Choanal atresia in a cat.

Azarpeykan S, Stickney A, Hill KE, Hartman AC, Jones BR, Acke E.

N Z Vet J. 2013 Jul;61(4):237-41. doi: 10.1080/00480169.2012.745208. Epub 2013 Jan 7.


First WNK4-hypokalemia animal model identified by genome-wide association in Burmese cats.

Gandolfi B, Gruffydd-Jones TJ, Malik R, Cortes A, Jones BR, Helps CR, Prinzenberg EM, Erhardt G, Lyons LA.

PLoS One. 2012;7(12):e53173. doi: 10.1371/journal.pone.0053173. Epub 2012 Dec 28.


Surrogate matrix and surrogate analyte approaches for definitive quantitation of endogenous biomolecules.

Jones BR, Schultz GA, Eckstein JA, Ackermann BL.

Bioanalysis. 2012 Oct;4(19):2343-56. doi: 10.4155/bio.12.200.


A serological survey of leptospiral antibodies in dogs in New Zealand.

Harland AL, Cave NJ, Jones BR, Benschop J, Donald JJ, Midwinter AC, Squires RA, Collins-Emerson JM.

N Z Vet J. 2013 Mar;61(2):98-106. doi: 10.1080/00480169.2012.719212. Epub 2012 Sep 27.


Permanent monoparesis in a dog after intramedullary injection of iohexol into the lumbar spinal cord.

Leitch BJ, Hartman AC, Mayhew IG, Jones BR, Worth AJ.

N Z Vet J. 2013 Jan;61(1):53-9. doi: 10.1080/00480169.2012.704846. Epub 2012 Sep 18.


Twitch or no twitch? The cutaneous trunci reflex.

Jones BR.

J Small Anim Pract. 2012 Aug;53(8):431. doi: 10.1111/j.1748-5827.2012.01267.x. No abstract available.


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.


A retrospective study of gastric dilatation and gastric dilatation and volvulus in working farm dogs in New Zealand.

Hendriks MM, Hill KE, Cogger N, Jones BR, Cave NJ.

N Z Vet J. 2012 May;60(3):165-70. doi: 10.1080/00480169.2011.644758.


Intratracheal bleomycin causes airway remodeling and airflow obstruction in mice.

Polosukhin VV, Degryse AL, Newcomb DC, Jones BR, Ware LB, Lee JW, Loyd JE, Blackwell TS, Lawson WE.

Exp Lung Res. 2012 Apr;38(3):135-46. doi: 10.3109/01902148.2012.658595.


Telomerase deficiency does not alter bleomycin-induced fibrosis in mice.

Degryse AL, Xu XC, Newman JL, Mitchell DB, Tanjore H, Polosukhin VV, Jones BR, McMahon FB, Gleaves LA, Phillips JA 3rd, Cogan JD, Blackwell TS, Lawson WE.

Exp Lung Res. 2012 Apr;38(3):124-34. doi: 10.3109/01902148.2012.658148.


Specificity and sensitivity of serum canine pancreatic elastase-1 concentration in the diagnosis of pancreatitis.

Mansfield CS, Watson PD, Jones BR.

J Vet Diagn Invest. 2011 Jul;23(4):691-7. doi: 10.1177/1040638711407875.


Genotypic characterisation and cluster analysis of Campylobacter jejuni isolates from domestic pets, human clinical cases and retail food.

Acke E, Carroll C, O'Leary A, McGill K, Kelly L, Lawlor A, Madden RH, Moran L, Scates P, McNamara E, Moore JE, Jones BR, Fanning S, Whyte P.

Ir Vet J. 2011 Mar 31;64(1):6. doi: 10.1186/2046-0481-64-6.


Endoplasmic reticulum stress enhances fibrotic remodeling in the lungs.

Lawson WE, Cheng DS, Degryse AL, Tanjore H, Polosukhin VV, Xu XC, Newcomb DC, Jones BR, Roldan J, Lane KB, Morrisey EE, Beers MF, Yull FE, Blackwell TS.

Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10562-7. doi: 10.1073/pnas.1107559108. Epub 2011 Jun 13.


Congenital hypothyroidism of dogs and cats: a review.

Bojanic K, Acke E, Jones BR.

N Z Vet J. 2011 May;59(3):115-22. doi: 10.1080/00480169.2011.567964. Review.


TGFβ signaling in lung epithelium regulates bleomycin-induced alveolar injury and fibroblast recruitment.

Degryse AL, Tanjore H, Xu XC, Polosukhin VV, Jones BR, Boomershine CS, Ortiz C, Sherrill TP, McMahon FB, Gleaves LA, Blackwell TS, Lawson WE.

Am J Physiol Lung Cell Mol Physiol. 2011 Jun;300(6):L887-97. doi: 10.1152/ajplung.00397.2010. Epub 2011 Mar 25.

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