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Items: 1 to 50 of 454

1.

Genome Sequence of Bacillus subtilis natto VK161, a Novel Strain That Produces Vitamin K2.

Parks D, Chung IH, Lee IK, Kim EJ, Niraula S, Chang WS.

Microbiol Resour Announc. 2019 Aug 29;8(35). pii: e00444-19. doi: 10.1128/MRA.00444-19.

2.

Efficacy and safety of dolutegravir-rilpivirine for maintenance of virological suppression in adults with HIV-1: 100-week data from the randomised, open-label, phase 3 SWORD-1 and SWORD-2 studies.

Aboud M, Orkin C, Podzamczer D, Bogner JR, Baker D, Khuong-Josses MA, Parks D, Angelis K, Kahl LP, Blair EA, Adkison K, Underwood M, Matthews JE, Wynne B, Vandermeulen K, Gartland M, Smith K.

Lancet HIV. 2019 Sep;6(9):e576-e587. doi: 10.1016/S2352-3018(19)30149-3. Epub 2019 Jul 12.

PMID:
31307948
3.

High-fidelity detection and sorting of nanoscale vesicles in viral disease and cancer.

Morales-Kastresana A, Musich TA, Welsh JA, Telford W, Demberg T, Wood JCS, Bigos M, Ross CD, Kachynski A, Dean A, Felton EJ, Van Dyke J, Tigges J, Toxavidis V, Parks DR, Overton WR, Kesarwala AH, Freeman GJ, Rosner A, Perfetto SP, Pasquet L, Terabe M, McKinnon K, Kapoor V, Trepel JB, Puri A, Kobayashi H, Yung B, Chen X, Guion P, Choyke P, Knox SJ, Ghiran I, Robert-Guroff M, Berzofsky JA, Jones JC.

J Extracell Vesicles. 2019 Jun 19;8(1):1597603. doi: 10.1080/20013078.2019.1597603. eCollection 2019.

4.

Biodistribution and Systemic Effects in Mice Following Intravenous Administration of Cadmium Telluride Quantum Dot Nanoparticles.

Nguyen KC, Zhang Y, Todd J, Kittle K, Patry D, Caldwell D, Lalande M, Smith S, Parks D, Navarro M, Massarsky A, Moon TW, Willmore WG, Tayabali AF.

Chem Res Toxicol. 2019 Aug 19;32(8):1491-1503. doi: 10.1021/acs.chemrestox.8b00397. Epub 2019 Jul 11.

PMID:
31251591
5.

Automated subset identification and characterization pipeline for multidimensional flow and mass cytometry data clustering and visualization.

Meehan S, Kolyagin GA, Parks D, Youngyunpipatkul J, Herzenberg LA, Walther G, Ghosn EEB, Orlova DY.

Commun Biol. 2019 Jun 20;2:229. doi: 10.1038/s42003-019-0467-6. eCollection 2019.

6.

Comparative efficacy and safety and dolutegravir and lamivudine in treatment naive HIV patients.

Radford M, Parks DC, Ferrante S, Punekar Y.

AIDS. 2019 Sep 1;33(11):1739-1749. doi: 10.1097/QAD.0000000000002285.

7.

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales.

Low SJ, Džunková M, Chaumeil PA, Parks DH, Hugenholtz P.

Nat Microbiol. 2019 Aug;4(8):1306-1315. doi: 10.1038/s41564-019-0448-z. Epub 2019 May 20.

PMID:
31110365
8.

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.

Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC.

Nucleic Acids Res. 2019 May 21;47(9):4442-4448. doi: 10.1093/nar/gkz246.

9.

Indirect Comparison of Ropinirole and Pramipexole as Levodopa Adjunctive Therapy in Advanced Parkinson's Disease: A Systematic Review and Network Meta-Analysis.

Zhao H, Ning Y, Cooper J, Refoios Camejo R, Ni X, Yi B, Parks D.

Adv Ther. 2019 Jun;36(6):1252-1265. doi: 10.1007/s12325-019-00938-1. Epub 2019 Apr 8. Review.

PMID:
30963514
10.

An evolving view of methane metabolism in the Archaea.

Evans PN, Boyd JA, Leu AO, Woodcroft BJ, Parks DH, Hugenholtz P, Tyson GW.

Nat Rev Microbiol. 2019 Apr;17(4):219-232. doi: 10.1038/s41579-018-0136-7. Epub 2019 Jan 21. Review.

PMID:
30664670
11.

A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.).

Rinke C, Rubino F, Messer LF, Youssef N, Parks DH, Chuvochina M, Brown M, Jeffries T, Tyson GW, Seymour JR, Hugenholtz P.

ISME J. 2019 Mar;13(3):663-675. doi: 10.1038/s41396-018-0282-y. Epub 2018 Oct 15.

12.

A combination of TLR-4 agonist and saponin adjuvants increases antibody diversity and protective efficacy of a recombinant West Nile Virus antigen.

Van Hoeven N, Wiley S, Gage E, Fiore-Gartland A, Granger B, Gray S, Fox C, Clements DE, Parks DE, Winram S, Stinchcomb DT, Reed SG, Coler RN.

NPJ Vaccines. 2018 Sep 26;3:39. doi: 10.1038/s41541-018-0077-1. eCollection 2018.

13.

Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments.

Parks DR, Moore WA, Brinkman RR, Chen Y, Condello D, El Khettabi F, Nolan JP, Perfetto SP, Redelman D, Spidlen J, Van Dyke J, Wang L, Wood JCS.

Cytometry A. 2018 Nov;93(11):1087-1091. doi: 10.1002/cyto.a.23605. Epub 2018 Sep 23.

PMID:
30244531
14.

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.

Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P.

Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27.

PMID:
30148503
15.

The importance of designating type material for uncultured taxa.

Chuvochina M, Rinke C, Parks DH, Rappé MS, Tyson GW, Yilmaz P, Whitman WB, Hugenholtz P.

Syst Appl Microbiol. 2019 Jan;42(1):15-21. doi: 10.1016/j.syapm.2018.07.003. Epub 2018 Jul 18.

16.

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.

Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE, McSweeney CS, Muir JG, Gibson PR, Cuív PÓ, Hugenholtz P, Tyson GW, Morrison M.

ISME J. 2018 Dec;12(12):2942-2953. doi: 10.1038/s41396-018-0225-7. Epub 2018 Aug 1.

PMID:
30068938
17.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
18.

High prevalence of systemic rheumatic diseases in women with type 1 diabetes.

Bao YK, Salam M, Parks D, McGill JB, Hughes J.

J Diabetes Complications. 2018 Aug;32(8):737-739. doi: 10.1016/j.jdiacomp.2018.06.001. Epub 2018 Jun 7.

19.

Erratum: Addendum: Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).

Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P.

Front Microbiol. 2018 Apr 18;9:772. doi: 10.3389/fmicb.2018.00772. eCollection 2018.

20.

An indirect comparison of intravenous and subcutaneous belimumab efficacy in patients with SLE and high disease activity.

Ramachandran S, Parks D, Kurtinecz M, Roth DA, Alfonso-Cristancho R.

J Comp Eff Res. 2018 Jun;7(6):581-593. doi: 10.2217/cer-2017-0085. Epub 2018 Apr 25.

21.

QFMatch: multidimensional flow and mass cytometry samples alignment.

Orlova DY, Meehan S, Parks D, Moore WA, Meehan C, Zhao Q, Ghosn EEB, Herzenberg LA, Walther G.

Sci Rep. 2018 Feb 19;8(1):3291. doi: 10.1038/s41598-018-21444-4.

22.

Patterns of Carbon Nanotubes by Flow-Directed Deposition on Substrates with Architectured Topographies.

K Jawed M, Hadjiconstantinou NG, Parks DM, Reis PM.

Nano Lett. 2018 Mar 14;18(3):1660-1667. doi: 10.1021/acs.nanolett.7b04676. Epub 2018 Feb 23.

PMID:
29451801
23.

Transcriptional Profiling of Synovial Macrophages Using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid Arthritis.

Mandelin AM 2nd, Homan PJ, Shaffer AM, Cuda CM, Dominguez ST, Bacalao E, Carns M, Hinchcliff M, Lee J, Aren K, Thakrar A, Montgomery AB, Bridges SL Jr, Bathon JM, Atkinson JP, Fox DA, Matteson EL, Buckley CD, Pitzalis C, Parks D, Hughes LB, Geraldino-Pardilla L, Ike R, Phillips K, Wright K, Filer A, Kelly S, Ruderman EM, Morgan V, Abdala-Valencia H, Misharin AV, Budinger GS, Bartom ET, Pope RM, Perlman H, Winter DR.

Arthritis Rheumatol. 2018 Jun;70(6):841-854. doi: 10.1002/art.40453. Epub 2018 May 3.

24.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

25.

Switch from tenofovir disoproxil fumarate combination to dolutegravir with rilpivirine improves parameters of bone health.

McComsey GA, Lupo S, Parks D, Poggio MC, De Wet J, Kahl LP, Angelis K, Wynne B, Vandermeulen K, Gartland M, Cupo M, Aboud M; 202094 Sub-Study Investigators.

AIDS. 2018 Feb 20;32(4):477-485. doi: 10.1097/QAD.0000000000001725.

26.

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2018 Feb;3(2):253. doi: 10.1038/s41564-017-0083-5.

PMID:
29234139
27.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Parks DH, Rinke C, Chuvochina M, Chaumeil PA, Woodcroft BJ, Evans PN, Hugenholtz P, Tyson GW.

Nat Microbiol. 2017 Nov;2(11):1533-1542. doi: 10.1038/s41564-017-0012-7. Epub 2017 Sep 11. Erratum in: Nat Microbiol. 2017 Dec 12;:.

PMID:
28894102
28.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Erratum in: Nat Biotechnol. 2018 Feb 6;36(2):196. Nat Biotechnol. 2018 Jul 6;36(7):660.

29.
30.

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.).

Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P.

Front Microbiol. 2017 Apr 24;8:682. doi: 10.3389/fmicb.2017.00682. eCollection 2017. Erratum in: Front Microbiol. 2018 Apr 18;9:772.

31.

A New Phenomenon: Sub-Tg, Solid-State, Plasticity-Induced Bonding in Polymers.

Padhye N, Parks DM, Trout BL, Slocum AH.

Sci Rep. 2017 Apr 20;7:46405. doi: 10.1038/srep46405.

32.

On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria.

Soo RM, Hemp J, Parks DH, Fischer WW, Hugenholtz P.

Science. 2017 Mar 31;355(6332):1436-1440. doi: 10.1126/science.aal3794.

PMID:
28360330
33.

Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi-level bead data.

Parks DR, El Khettabi F, Chase E, Hoffman RA, Perfetto SP, Spidlen J, Wood JC, Moore WA, Brinkman RR.

Cytometry A. 2017 Mar;91(3):232-249. doi: 10.1002/cyto.a.23052. Epub 2017 Feb 3.

34.

Comparative effectiveness of mepolizumab and omalizumab in severe asthma: An indirect treatment comparison.

Cockle SM, Stynes G, Gunsoy NB, Parks D, Alfonso-Cristancho R, Wex J, Bradford ES, Albers FC, Willson J.

Respir Med. 2017 Feb;123:140-148. doi: 10.1016/j.rmed.2016.12.009. Epub 2016 Dec 21. Review.

35.

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota.

Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, Tyson GW.

Nat Microbiol. 2016 Oct 3;1:16170. doi: 10.1038/nmicrobiol.2016.170.

PMID:
27694807
36.

Enhancing the performance of the T-peel test for thin and flexible adhered laminates.

Padhye N, Parks DM, Slocum AH, Trout BL.

Rev Sci Instrum. 2016 Aug;87(8):085111. doi: 10.1063/1.4960172.

PMID:
27587164
37.

Discovery of novel potent imidazo[1,2-b]pyridazine PDE10a inhibitors.

Meegalla SK, Huang H, Illig CR, Parks DJ, Chen J, Lee YK, Wilson KJ, Patel SK, Cheung WS, Lu T, Kirchner T, Askari HB, Geisler J, Patch RJ, Gibbs AC, Rady B, Connelly M, Player MR.

Bioorg Med Chem Lett. 2016 Sep 1;26(17):4216-22. doi: 10.1016/j.bmcl.2016.07.054. Epub 2016 Jul 25.

PMID:
27491708
38.

A catalogue of 136 microbial draft genomes from Red Sea metagenomes.

Haroon MF, Thompson LR, Parks DH, Hugenholtz P, Stingl U.

Sci Data. 2016 Jul 5;3:160050. doi: 10.1038/sdata.2016.50.

39.

Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

Robbins SJ, Evans PN, Parks DH, Golding SD, Tyson GW.

Front Microbiol. 2016 Jun 8;7:731. doi: 10.3389/fmicb.2016.00731. eCollection 2016.

40.

A Quantitative Method for Comparing the Brightness of Antibody-dye Reagents and Estimating Antibodies Bound per Cell.

Kantor AB, Moore WA, Meehan S, Parks DR.

Curr Protoc Cytom. 2016 Jul 1;77:1.30.1-1.30.23. doi: 10.1002/cpcy.6.

PMID:
27367287
41.

Mechanistic Origin of the Ultrastrong Adhesion between Graphene and a-SiO2: Beyond van der Waals.

Kumar S, Parks D, Kamrin K.

ACS Nano. 2016 Jul 26;10(7):6552-62. doi: 10.1021/acsnano.6b00382. Epub 2016 Jul 5.

PMID:
27347793
42.

An indirect comparison of HbA1c treatment effect with albiglutide and exenatide 2.0 mg QW using the Bucher method.

Martin AA, Parks D.

Diabetes Metab Syndr Obes. 2016 May 19;9:163-8. doi: 10.2147/DMSO.S100775. eCollection 2016.

43.

Dynamic quantification of antigen molecules with flow cytometry.

Moskalensky AE, Chernyshev AV, Yurkin MA, Nekrasov VM, Polshchitsin AA, Parks DR, Moore WA, Filatenkov A, Maltsev VP, Orlova DY.

J Immunol Methods. 2015 Dec;427:139-47.

PMID:
27030828
44.

Genome-Based Microbial Taxonomy Coming of Age.

Hugenholtz P, Skarshewski A, Parks DH.

Cold Spring Harb Perspect Biol. 2016 Jun 1;8(6). pii: a018085. doi: 10.1101/cshperspect.a018085. Review.

45.

A Novel Synthetic TLR-4 Agonist Adjuvant Increases the Protective Response to a Clinical-Stage West Nile Virus Vaccine Antigen in Multiple Formulations.

Van Hoeven N, Joshi SW, Nana GI, Bosco-Lauth A, Fox C, Bowen RA, Clements DE, Martyak T, Parks DE, Baldwin S, Reed SG, Coler RN.

PLoS One. 2016 Feb 22;11(2):e0149610. doi: 10.1371/journal.pone.0149610. eCollection 2016.

46.

Radiographic evaluation of short-stem press-fit total shoulder arthroplasty: short-term follow-up.

Casagrande DJ, Parks DL, Torngren T, Schrumpf MA, Harmsen SM, Norris TR, Kelly JD 2nd.

J Shoulder Elbow Surg. 2016 Jul;25(7):1163-9. doi: 10.1016/j.jse.2015.11.067. Epub 2016 Feb 17.

PMID:
26897311
47.

Incremental Hospital Costs Associated With Comorbidities of Prematurity.

Black L, Hulsey T, Lee K, Parks DC, Ebeling MD.

Manag Care. 2015 Dec;24(12):54-60.

48.

A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres.

Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P.

Front Microbiol. 2016 Jan 7;6:1469. doi: 10.3389/fmicb.2015.01469. eCollection 2015.

49.

Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

Yeoh YK, Sekiguchi Y, Parks DH, Hugenholtz P.

Mol Biol Evol. 2016 Apr;33(4):915-27. doi: 10.1093/molbev/msv281. Epub 2015 Nov 28.

50.

2015 American College of Rheumatology Guideline for the Treatment of Rheumatoid Arthritis.

Singh JA, Saag KG, Bridges SL Jr, Akl EA, Bannuru RR, Sullivan MC, Vaysbrot E, McNaughton C, Osani M, Shmerling RH, Curtis JR, Furst DE, Parks D, Kavanaugh A, O'Dell J, King C, Leong A, Matteson EL, Schousboe JT, Drevlow B, Ginsberg S, Grober J, St Clair EW, Tindall E, Miller AS, McAlindon T.

Arthritis Rheumatol. 2016 Jan;68(1):1-26. doi: 10.1002/art.39480. Epub 2015 Nov 6. Review.

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