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Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.

Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, van Soolingen D, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z.

Wellcome Open Res. 2019 Dec 2;4:191. doi: 10.12688/wellcomeopenres.15603.1. eCollection 2019.


Controversies in the surgical management of sporadic medullary thyroid carcinoma.

Fussey JM, Bradley PJ, Smith JA.

Curr Opin Otolaryngol Head Neck Surg. 2020 Jan 31. doi: 10.1097/MOO.0000000000000612. [Epub ahead of print]


Infratemporal fossa surgical approaches to primary/recurrent malignancies of salivary origin: paradigm surgical shift, patient selection, and oncologic outcomes.

Bradley PJ.

Curr Opin Otolaryngol Head Neck Surg. 2020 Jan 31. doi: 10.1097/MOO.0000000000000613. [Epub ahead of print]


Multi-region assessment of pharmaceutical exposures and predicted effects in USA wadeable urban-gradient streams.

Bradley PM, Journey CA, Button DT, Carlisle DM, Huffman BJ, Qi SL, Romanok KM, Van Metre PC.

PLoS One. 2020 Jan 30;15(1):e0228214. doi: 10.1371/journal.pone.0228214. eCollection 2020.


Exposure and potential effects of pesticides and pharmaceuticals in protected streams of the US National park Service southeast region.

Bradley PM, Romanok KM, Duncan JR, Battaglin WA, Clark JM, Hladik ML, Huffman BJ, Iwanowicz LR, Journey CA, Smalling KL.

Sci Total Environ. 2020 Feb 20;704:135431. doi: 10.1016/j.scitotenv.2019.135431. Epub 2019 Nov 23.


Using BioID for the Identification of Interacting and Proximal Proteins in Subcellular Compartments in Toxoplasma gondii.

Bradley PJ, Rayatpisheh S, Wohlschlegel JA, Nadipuram SM.

Methods Mol Biol. 2020;2071:323-346. doi: 10.1007/978-1-4939-9857-9_18.


Projected urban growth in the southeastern USA puts small streams at risk.

Van Metre PC, Waite IR, Qi S, Mahler B, Terando A, Wieczorek M, Meador M, Bradley P, Journey C, Schmidt T, Carlisle D.

PLoS One. 2019 Oct 16;14(10):e0222714. doi: 10.1371/journal.pone.0222714. eCollection 2019.


Biological Assessment of Coral Reefs in Southern Puerto Rico: A Technical Approach for Coral Reef Protection Under the U.S. Clean Water Act.

Fisher WS, Vivian DN, Campbell J, Lobue C, Hemmer RL, Wilkinson S, Harris P, Santavy DL, Parsons M, Bradley P, Humphrey A, Oliver LM, Harwell L.

Coast Manage. 2019;47(5):429-452. doi: 10.1080/08920753.2019.1641039.


phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.

Bradley PH, Pollard KS.

Bioinformatics. 2020 Feb 15;36(4):1289-1290. doi: 10.1093/bioinformatics/btz722.


A photoactivatable crosslinking system reveals protein interactions in the Toxoplasma gondii inner membrane complex.

Choi CP, Moon AS, Back PS, Jami-Alahmadi Y, Vashisht AA, Wohlschlegel JA, Bradley PJ.

PLoS Biol. 2019 Oct 4;17(10):e3000475. doi: 10.1371/journal.pbio.3000475. eCollection 2019 Oct.


Shifts in temperature influence how Batrachochytrium dendrobatidis infects amphibian larvae.

Bradley PW, Brawner MD, Raffel TR, Rohr JR, Olson DH, Blaustein AR.

PLoS One. 2019 Sep 19;14(9):e0222237. doi: 10.1371/journal.pone.0222237. eCollection 2019.


A lipid-binding protein mediates rhoptry discharge and invasion in Plasmodium falciparum and Toxoplasma gondii parasites.

Suarez C, Lentini G, Ramaswamy R, Maynadier M, Aquilini E, Berry-Sterkers L, Cipriano M, Chen AL, Bradley P, Striepen B, Boulanger MJ, Lebrun M.

Nat Commun. 2019 Sep 6;10(1):4041. doi: 10.1038/s41467-019-11979-z.


Host age alters amphibian susceptibility to Batrachochytrium dendrobatidis, an emerging infectious fungal pathogen.

Bradley PW, Snyder PW, Blaustein AR.

PLoS One. 2019 Sep 6;14(9):e0222181. doi: 10.1371/journal.pone.0222181. eCollection 2019.


Deep generative models for T cell receptor protein sequences.

Davidsen K, Olson BJ, DeWitt WS 3rd, Feng J, Harkins E, Bradley P, Matsen FA 4th.

Elife. 2019 Sep 5;8. pii: e46935. doi: 10.7554/eLife.46935.


Refined carbohydrates, phenotypic plasticity and the obesity epidemic.

Bradley P.

Med Hypotheses. 2019 Oct;131:109317. doi: 10.1016/j.mehy.2019.109317. Epub 2019 Jul 20.


Urban Stormwater: An Overlooked Pathway of Extensive Mixed Contaminants to Surface and Groundwaters in the United States.

Masoner JR, Kolpin DW, Cozzarelli IM, Barber LB, Burden DS, Foreman WT, Forshay KJ, Furlong ET, Groves JF, Hladik ML, Hopton ME, Jaeschke JB, Keefe SH, Krabbenhoft DP, Lowrance R, Romanok KM, Rus DL, Selbig WR, Williams BH, Bradley PM.

Environ Sci Technol. 2019 Sep 3;53(17):10070-10081. doi: 10.1021/acs.est.9b02867. Epub 2019 Aug 21.


Advances in protein structure prediction and design.

Kuhlman B, Bradley P.

Nat Rev Mol Cell Biol. 2019 Nov;20(11):681-697. doi: 10.1038/s41580-019-0163-x. Epub 2019 Aug 15. Review.


Corticospinal circuit remodeling after central nervous system injury is dependent on neuronal activity.

Bradley PM, Denecke CK, Aljovic A, Schmalz A, Kerschensteiner M, Bareyre FM.

J Exp Med. 2019 Nov 4;216(11):2503-2514. doi: 10.1084/jem.20181406. Epub 2019 Aug 7.


Predictive Analysis Using Chemical-Gene Interaction Networks Consistent with Observed Endocrine Activity and Mutagenicity of U.S. Streams.

Berninger JP, DeMarini DM, Warren SH, Simmons JE, Wilson VS, Conley JM, Armstrong MD, Iwanowicz LR, Kolpin DW, Kuivila KM, Reilly TJ, Romanok KM, Villeneuve DL, Bradley PM.

Environ Sci Technol. 2019 Aug 6;53(15):8611-8620. doi: 10.1021/acs.est.9b02990. Epub 2019 Jul 22.


Cell-Based Metabolomics for Untargeted Screening and Prioritization of Vertebrate-Active Stressors in Streams Across the United States.

Collette TW, Ekman DR, Zhen H, Nguyen H, Bradley PM, Teng Q.

Environ Sci Technol. 2019 Aug 6;53(15):9232-9240. doi: 10.1021/acs.est.9b02736. Epub 2019 Jul 18.


Corrigendum: Neospora Caninum Activates p38 MAPK as an Evasion Mechanism against Innate Immunity.

Mota CM, Oliveira ACM, Davoli-Ferreira M, Silva MV, Santiago FM, Nadipuram SM, Vashisht AA, Wohlschlegel JA, Bradley PJ, Silva JS, Mineo JR, Mineo TWP.

Front Microbiol. 2019 Mar 26;10:548. doi: 10.3389/fmicb.2019.00548. eCollection 2019.


Treatment Options for Hypopharyngeal Cancer.

Eckel HE, Bradley PJ.

Adv Otorhinolaryngol. 2019;83:47-53. doi: 10.1159/000492308. Epub 2019 Feb 12. Review.


Symptoms and Signs, Staging and Co-Morbidity of Hypopharyngeal Cancer.

Bradley PJ.

Adv Otorhinolaryngol. 2019;83:15-26. doi: 10.1159/000492304. Epub 2019 Feb 12. Review.


Epidemiology of Hypopharyngeal Cancer.

Bradley PJ.

Adv Otorhinolaryngol. 2019;83:1-14. doi: 10.1159/000492299. Epub 2019 Feb 5.


Systemic Therapy, Palliation and Supportive Care of Patients with Hypopharyngeal Cancer.

Bradley PJ, Füreder T, Eckel HE.

Adv Otorhinolaryngol. 2019;83:148-158. doi: 10.1159/000492359. Epub 2019 Feb 12. Review.


Natural History of Treated and Untreated Hypopharyngeal Cancer.

Eckel HE, Bradley PJ.

Adv Otorhinolaryngol. 2019;83:27-34. doi: 10.1159/000492305. Epub 2019 Feb 12. Review.


Future Perspectives in Hypopharyngeal Cancer Care.

Eckel HE, Bradley PJ.

Adv Otorhinolaryngol. 2019;83:167-175. doi: 10.1159/000492361. Epub 2019 Feb 12. Review.


Behavior of major and trace elements in a transient surface water/groundwater system following removal of a long-term wastewater treatment facility source.

Keefe SH, Barber LB, Hubbard LE, Bradley PM, Roth DA, Kolpin DW.

Sci Total Environ. 2019 Jun 10;668:867-880. doi: 10.1016/j.scitotenv.2019.02.358. Epub 2019 Feb 25.


Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.

Bradley PH, Gibney PA, Botstein D, Troyanskaya OG, Rabinowitz JD.

mSystems. 2019 Feb 26;4(1). pii: e00170-18. doi: 10.1128/mSystems.00170-18. eCollection 2019 Jan-Feb.


SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex.

Lipworth S, Jajou R, de Neeling A, Bradley P, van der Hoek W, Maphalala G, Bonnet M, Sanchez-Padilla E, Diel R, Niemann S, Iqbal Z, Smith G, Peto T, Crook D, Walker T, van Soolingen D.

Emerg Infect Dis. 2019 Mar;25(3):482-488. doi: 10.3201/eid2503.180894.


Ultrafast search of all deposited bacterial and viral genomic data.

Bradley P, den Bakker HC, Rocha EPC, McVean G, Iqbal Z.

Nat Biotechnol. 2019 Feb;37(2):152-159. doi: 10.1038/s41587-018-0010-1. Epub 2019 Feb 4.


Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition.

Bradley P, Thomas PG.

Annu Rev Immunol. 2019 Apr 26;37:547-570. doi: 10.1146/annurev-immunol-042718-041757. Epub 2019 Jan 30.


Potential Toxicity of Complex Mixtures in Surface Waters from a Nationwide Survey of United States Streams: Identifying in Vitro Bioactivities and Causative Chemicals.

Blackwell BR, Ankley GT, Bradley PM, Houck KA, Makarov SS, Medvedev AV, Swintek J, Villeneuve DL.

Environ Sci Technol. 2019 Jan 15;53(2):973-983. doi: 10.1021/acs.est.8b05304. Epub 2018 Dec 21.


Wound Exudate.

Bradley P.

Br J Community Nurs. 2018 Dec 1;23(Sup12):S28-S32. doi: 10.12968/bjcn.2018.23.Sup12.S28.


Open-neck organ preservation surgery for hypopharyngeal cancer: indications, techniques, limits, and outcomes.

Bradley PJ, Liu L.

Curr Opin Otolaryngol Head Neck Surg. 2019 Apr;27(2):123-129. doi: 10.1097/MOO.0000000000000501. Review.


Comment on: "The Use of Microtechnology to Quantify the Peak Match Demands of the Football Codes: A Systematic Review".

Carling C, McCall A, Harper D, Bradley PS.

Sports Med. 2019 Feb;49(2):343-345. doi: 10.1007/s40279-018-1032-z. No abstract available.


Mixed-chemical exposure and predicted effects potential in wadeable southeastern USA streams.

Bradley PM, Journey CA, Berninger JP, Button DT, Clark JM, Corsi SR, DeCicco LA, Hopkins KG, Huffman BJ, Nakagaki N, Norman JE, Nowell LH, Qi SL, VanMetre PC, Waite IR.

Sci Total Environ. 2019 Mar 10;655:70-83. doi: 10.1016/j.scitotenv.2018.11.186. Epub 2018 Nov 13.


Reconnaissance of Mixed Organic and Inorganic Chemicals in Private and Public Supply Tapwaters at Selected Residential and Workplace Sites in the United States.

Bradley PM, Kolpin DW, Romanok KM, Smalling KL, Focazio MJ, Brown JB, Cardon MC, Carpenter KD, Corsi SR, DeCicco LA, Dietze JE, Evans N, Furlong ET, Givens CE, Gray JL, Griffin DW, Higgins CP, Hladik ML, Iwanowicz LR, Journey CA, Kuivila KM, Masoner JR, McDonough CA, Meyer MT, Orlando JL, Strynar MJ, Weis CP, Wilson VS.

Environ Sci Technol. 2018 Dec 4;52(23):13972-13985. doi: 10.1021/acs.est.8b04622. Epub 2018 Nov 21.


Nutrient enrichment in wadeable urban streams in the Piedmont Ecoregion of the Southeastern United States.

Journey CA, Van Metre PC, Waite IR, Clark JM, Button DT, Nakagaki N, Qi SL, Munn MD, Bradley PM.

Heliyon. 2018 Nov 7;4(11):e00904. doi: 10.1016/j.heliyon.2018.e00904. eCollection 2018 Nov.


Influence of the Varied Pitch Shape on Soccer Players Physiological Responses and Time-Motion Characteristics During Small-Sided Games.

Casamichana D, Bradley PS, Castellano J.

J Hum Kinet. 2018 Oct 15;64:171-180. doi: 10.1515/hukin-2017-0192. eCollection 2018 Sep.


Wound Exudate.

Chambers T, Bradley P.

Br J Nurs. 2018 Nov 8;27(20):S28-S32. doi: 10.12968/bjon.2018.27.Sup20.S28. No abstract available.


Concurrent HPV-related oropharyngeal carcinoma in four couples.

Sathasivam HP, Bhatia R, Bradley P, Robson A, Paleri V, Cocks H, Oozeer N, Milne D, Sloan P, Robinson M.

Oral Oncol. 2018 Nov;86:33-37. doi: 10.1016/j.oraloncology.2018.09.003. Epub 2018 Sep 11.


Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.

Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL.

Nucleic Acids Res. 2019 Jan 10;47(1):450-467. doi: 10.1093/nar/gky1059.


Efferocytosis of apoptotic alveolar epithelial cells is sufficient to initiate lung fibrosis.

Kim KK, Dotson MR, Agarwal M, Yang J, Bradley PB, Subbotina N, Osterholzer JJ, Sisson TH.

Cell Death Dis. 2018 Oct 17;9(11):1056. doi: 10.1038/s41419-018-1074-z.


Prevalence of cystoid macular oedema, epiretinal membrane and cataract in retinitis pigmentosa.

Liew G, Strong S, Bradley P, Severn P, Moore AT, Webster AR, Mitchell P, Kifley A, Michaelides M.

Br J Ophthalmol. 2019 Aug;103(8):1163-1166. doi: 10.1136/bjophthalmol-2018-311964. Epub 2018 Oct 5.


Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B.

N Engl J Med. 2018 Oct 11;379(15):1403-1415. doi: 10.1056/NEJMoa1800474. Epub 2018 Sep 26.


Guidelines to authors publishing a case report: the need for quality improvement.

Bradley PJ.

AME Case Rep. 2018 Apr 10;2:10. doi: 10.21037/acr.2018.04.02. eCollection 2018. No abstract available.


Special section "Case Reports in Otolaryngology".

Bradley PJ, Frcs M.

AME Case Rep. 2018 Jan 22;2:1. doi: 10.21037/acr.2018.01.02. eCollection 2018. No abstract available.


Printable all-dielectric water-based absorber.

Bradley PJ, Torrico MOM, Brennan C, Hao Y.

Sci Rep. 2018 Sep 27;8(1):14490. doi: 10.1038/s41598-018-32395-1.


Quantification of a Professional Football Team's External Load Using a Microcycle Structure.

Martín-García A, Gómez Díaz A, Bradley PS, Morera F, Casamichana D.

J Strength Cond Res. 2018 Dec;32(12):3511-3518. doi: 10.1519/JSC.0000000000002816.


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