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A benchmark study of loop modeling methods applied to G protein-coupled receptors.

Wink LH, Baker DL, Cole JA, Parrill AL.

J Comput Aided Mol Des. 2019 Jun;33(6):573-595. doi: 10.1007/s10822-019-00196-x. Epub 2019 May 23.


Impact of public-private partnership on a regional colonoscopy service.

Sakowska MM, Cole JAM, Watters DA, Guest GD.

ANZ J Surg. 2019 May;89(5):552-556. doi: 10.1111/ans.15066. Epub 2019 Mar 19.


Singultus (Hiccups).

Cole JA, Plewa MC.

StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2019 Jan-.
2019 Jun 4.


Soil HONO emissions at high moisture content are driven by microbial nitrate reduction to nitrite: tackling the HONO puzzle.

Wu D, Horn MA, Behrendt T, Müller S, Li J, Cole JA, Xie B, Ju X, Li G, Ermel M, Oswald R, Fröhlich-Nowoisky J, Hoor P, Hu C, Liu M, Andreae MO, Pöschl U, Cheng Y, Su H, Trebs I, Weber B, Sörgel M.

ISME J. 2019 Jul;13(7):1688-1699. doi: 10.1038/s41396-019-0379-y. Epub 2019 Mar 4.


Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges.

Carroll LM, Wiedmann M, Mukherjee M, Nicholas DC, Mingle LA, Dumas NB, Cole JA, Kovac J.

Front Microbiol. 2019 Feb 12;10:144. doi: 10.3389/fmicb.2019.00144. eCollection 2019.


Shared decision-making (SHARE-D) for healthy behaviour change: a feasibility study in general practice.

Cupples ME, Cole JA, Hart ND, Heron N, McKinley MC, Tully MA.

BJGP Open. 2018 Apr 18;2(2):bjgpopen18X101517. doi: 10.3399/bjgpopen18X101517. eCollection 2018 Jul.


GPCR homology model template selection benchmarking: Global versus local similarity measures.

Castleman PN, Sears CK, Cole JA, Baker DL, Parrill AL.

J Mol Graph Model. 2019 Jan;86:235-246. doi: 10.1016/j.jmgm.2018.10.016. Epub 2018 Oct 21.


How Bioinformatic Tools Guide Experiments To Resolve the Chaos of Apparently Unlimited Metabolic Variation.

Cole JA.

J Bacteriol. 2018 Dec 20;201(2). pii: e00628-18. doi: 10.1128/JB.00628-18. Print 2019 Jan 15.


Anaerobic Bacterial Response to Nitrosative Stress.

Cole JA.

Adv Microb Physiol. 2018;72:193-237. doi: 10.1016/bs.ampbs.2018.01.001. Epub 2018 Mar 15.


Development of a generic β-lactamase screening system for improved signal peptides for periplasmic targeting of recombinant proteins in Escherichia coli.

Selas Castiñeiras T, Williams SG, Hitchcock A, Cole JA, Smith DC, Overton TW.

Sci Rep. 2018 May 3;8(1):6986. doi: 10.1038/s41598-018-25192-3.


The Essential Genome of Escherichia coli K-12.

Goodall ECA, Robinson A, Johnston IG, Jabbari S, Turner KA, Cunningham AF, Lund PA, Cole JA, Henderson IR.

MBio. 2018 Feb 20;9(1). pii: e02096-17. doi: 10.1128/mBio.02096-17.


Optimizing host cell physiology and stress avoidance for the production of recombinant human tumour necrosis factor α in Escherichia coli.

Selas Castiñeiras T, Williams SG, Hitchcock A, Cole JA, Smith DC, Overton TW.

Microbiology. 2018 Apr;164(4):440-452. doi: 10.1099/mic.0.000622. Epub 2018 Feb 14.


Simulating biological processes: stochastic physics from whole cells to colonies.

Earnest TM, Cole JA, Luthey-Schulten Z.

Rep Prog Phys. 2018 May;81(5):052601. doi: 10.1088/1361-6633/aaae2c. Epub 2018 Feb 9.


Correction: Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects.

Peterson JR, Cole JA, Luthey-Schulten Z.

PLoS One. 2017 Dec 19;12(12):e0190193. doi: 10.1371/journal.pone.0190193. eCollection 2017.


Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide.

Cadby IT, Faulkner M, Cheneby J, Long J, van Helden J, Dolla A, Cole JA.

Sci Rep. 2017 Nov 24;7(1):16228. doi: 10.1038/s41598-017-16403-4.


Multimodal Assessment of Mesenchymal Stem Cell Therapy for Diabetic Vascular Complications.

Hedhli J, Konopka CJ, Schuh S, Bouvin H, Cole JA, Huntsman HD, Kilian KA, Dobrucki IT, Boppart MD, Dobrucki LW.

Theranostics. 2017 Sep 5;7(16):3876-3888. doi: 10.7150/thno.19547. eCollection 2017.


Population FBA predicts metabolic phenotypes in yeast.

Labhsetwar P, Melo MCR, Cole JA, Luthey-Schulten Z.

PLoS Comput Biol. 2017 Sep 8;13(9):e1005728. doi: 10.1371/journal.pcbi.1005728. eCollection 2017 Sep.


Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects.

Peterson JR, Cole JA, Luthey-Schulten Z.

PLoS One. 2017 Aug 18;12(8):e0182570. doi: 10.1371/journal.pone.0182570. eCollection 2017. Erratum in: PLoS One. 2017 Dec 19;12 (12 ):e0190193.


MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis.

Isom GL, Davies NJ, Chong ZS, Bryant JA, Jamshad M, Sharif M, Cunningham AF, Knowles TJ, Chng SS, Cole JA, Henderson IR.

Sci Rep. 2017 Aug 17;7(1):8608. doi: 10.1038/s41598-017-09111-6.


Living rain gauges: cumulative precipitation explains the emergence schedules of California protoperiodical cicadas.

Chatfield-Taylor W, Cole JA.

Ecology. 2017 Oct;98(10):2521-2527. doi: 10.1002/ecy.1980.


Careful accounting of extrinsic noise in protein expression reveals correlations among its sources.

Cole JA, Luthey-Schulten Z.

Phys Rev E. 2017 Jun;95(6-1):062418. doi: 10.1103/PhysRevE.95.062418. Epub 2017 Jun 27.


Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain.

Dunne KA, Chaudhuri RR, Rossiter AE, Beriotto I, Browning DF, Squire D, Cunningham AF, Cole JA, Loman N, Henderson IR.

Microb Genom. 2017 Mar 23;3(3):mgen000106. doi: 10.1099/mgen.0.000106. eCollection 2017 Mar.


Synthesis, Chemical Characterization and Multiscale Biological Evaluation of a Dimeric-cRGD Peptide for Targeted Imaging of α V β 3 Integrin Activity.

Hedhli J, Czerwinski A, Schuelke M, Płoska A, Sowinski P, Hood L, Mamer SB, Cole JA, Czaplewska P, Banach M, Dobrucki IT, Kalinowski L, Imoukhuede P, Dobrucki LW.

Sci Rep. 2017 Jun 9;7(1):3185. doi: 10.1038/s41598-017-03224-8.


A new species of Megatibicen endemic to Mescalero-Monahans shinnery sands (Hemiptera: <i>Auchenorrhyncha</i>: Cicadidae).

Cole JA.

Zootaxa. 2017 Feb 23;4236(3):zootaxa.4236.3.9. doi: 10.11646/zootaxa.4236.3.9.


Steatorrhea and Hyperoxaluria in Severely Obese Patients Before and After Roux-en-Y Gastric Bypass.

Moreland AM, Santa Ana CA, Asplin JR, Kuhn JA, Holmes RP, Cole JA, Odstrcil EA, Van Dinter TG Jr, Martinez JG, Fordtran JS.

Gastroenterology. 2017 Apr;152(5):1055-1067.e3. doi: 10.1053/j.gastro.2017.01.004. Epub 2017 Jan 12.


Regulation, sensory domains and roles of two Desulfovibrio desulfuricans ATCC27774 Crp family transcription factors, HcpR1 and HcpR2, in response to nitrosative stress.

Cadby IT, Ibrahim SA, Faulkner M, Lee DJ, Browning D, Busby SJ, Lovering AL, Stapleton MR, Green J, Cole JA.

Mol Microbiol. 2016 Dec;102(6):1120-1137. doi: 10.1111/mmi.13540. Epub 2016 Oct 20.


Ribosome biogenesis in replicating cells: Integration of experiment and theory.

Earnest TM, Cole JA, Peterson JR, Hallock MJ, Kuhlman TE, Luthey-Schulten Z.

Biopolymers. 2016 Oct;105(10):735-751. doi: 10.1002/bip.22892.


Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn's disease: an observational study.

Walton C, Montoya MP, Fowler DP, Turner C, Jia W, Whitehead RN, Griffiths L, Waring RH, Ramsden DB, Cole JA, Cauchi M, Bessant C, Naylor SJ, Hunter JO.

Eur J Clin Nutr. 2016 Sep;70(9):1052-6. doi: 10.1038/ejcn.2016.74. Epub 2016 May 11.


Control of hexuronate metabolism in Escherichia coli by the two interdependent regulators, ExuR and UxuR: derepression by heterodimer formation.

Tutukina MN, Potapova AV, Cole JA, Ozoline ON.

Microbiology. 2016 Jul;162(7):1220-1231. doi: 10.1099/mic.0.000297. Epub 2016 Apr 29.


Role of EGF receptor ligands in TCDD-induced EGFR down-regulation and cellular proliferation.

Campion CM, Leon Carrion S, Mamidanna G, Sutter CH, Sutter TR, Cole JA.

Chem Biol Interact. 2016 Jun 25;253:38-47. doi: 10.1016/j.cbi.2016.04.031. Epub 2016 Apr 23.


Implications of aligning full registration of doctors with medical school graduation: a qualitative study of stakeholder perspectives.

Mattick KL, Kaufhold K, Kelly N, Cole JA, Scheffler G, Rees CE, Bullock A, Gormley GJ, Monrouxe LV.

BMJ Open. 2016 Feb 23;6(2):e010246. doi: 10.1136/bmjopen-2015-010246.


The roles of the hybrid cluster protein, Hcp and its reductase, Hcr, in high affinity nitric oxide reduction that protects anaerobic cultures of Escherichia coli against nitrosative stress.

Wang J, Vine CE, Balasiny BK, Rizk J, Bradley CL, Tinajero-Trejo M, Poole RK, Bergaust LL, Bakken LR, Cole JA.

Mol Microbiol. 2016 Jun;100(5):877-92. doi: 10.1111/mmi.13356. Epub 2016 Mar 22.


Effects of DNA replication on mRNA noise.

Peterson JR, Cole JA, Fei J, Ha T, Luthey-Schulten ZA.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15886-91. doi: 10.1073/pnas.1516246112. Epub 2015 Dec 15.


The global aHUS registry: methodology and initial patient characteristics.

Licht C, Ardissino G, Ariceta G, Cohen D, Cole JA, Gasteyger C, Greenbaum LA, Johnson S, Ogawa M, Schaefer F, Vande Walle J, Frémeaux-Bacchi V.

BMC Nephrol. 2015 Dec 10;16:207. doi: 10.1186/s12882-015-0195-1.


Reply to R Schiffmann.

Betesh AL, Santa Ana CA, Cole JA, Fordtran JS.

Am J Clin Nutr. 2015 Dec;102(6):1615-6. doi: 10.3945/ajcn.115.120576. No abstract available.


Is achlorhydria a cause of iron deficiency anemia?

Betesh AL, Santa Ana CA, Cole JA, Fordtran JS.

Am J Clin Nutr. 2015 Jul;102(1):9-19. doi: 10.3945/ajcn.114.097394. Epub 2015 May 20. Review.


Implementing a Community Empowerment Center to Build Capacity for Developing, Implementing, and Sustaining Interventions to Promote Community Health.

Smallwood SW, Freedman DA, Pitner RO, Sharpe PA, Cole JA, Hastie S, Hunter B.

J Community Health. 2015 Dec;40(6):1122-9. doi: 10.1007/s10900-015-0038-9.


Spatially-resolved metabolic cooperativity within dense bacterial colonies.

Cole JA, Kohler L, Hedhli J, Luthey-Schulten Z.

BMC Syst Biol. 2015 Mar 18;9:15. doi: 10.1186/s12918-015-0155-1.


Paracoccus sanguinis sp. nov., isolated from clinical specimens of New York State patients.

McGinnis JM, Cole JA, Dickinson MC, Mingle LA, Lapierre P, Musser KA, Wolfgang WJ.

Int J Syst Evol Microbiol. 2015 Jun;65(Pt 6):1877-82. doi: 10.1099/ijs.0.000193. Epub 2015 Mar 19.


Frequency of exogenous hormone therapy impacts spermiation in male Fowler's toad (Bufo fowleri).

McDonough CE, Martin MW, Vance CK, Cole JA, Kouba AJ.

Reprod Fertil Dev. 2016 Jun;28(7):995-1003. doi: 10.1071/RD14214.


Co-cultured tissue-specific scaffolds for tendon/bone interface engineering.

Cooper JO, Bumgardner JD, Cole JA, Smith RA, Haggard WO.

J Tissue Eng. 2014 Jul 7;5:2041731414542294. doi: 10.1177/2041731414542294. eCollection 2014.


Whole Cell Modeling: From Single Cells to Colonies.

Cole JA, Luthey-Schulten Z.

Isr J Chem. 2014 Aug;54(8-9):1219-1229. Epub 2014 Jul 31.


Most influential FEMS publications.

Prosser JI, Cole JA, Nielsen J, Bavoil PM, Häggblom MM.

FEMS Microbiol Lett. 2014 May;354(2):83-4. doi: 10.1111/1574-6968.12444.


Synthetic biology: old wine in new bottles with an emerging language that ranges from the sublime to the ridiculous?

Cole JA.

FEMS Microbiol Lett. 2014 Feb;351(2):113-5. doi: 10.1111/1574-6968.12388. No abstract available.


Cardiovascular medication use following percutaneous coronary intervention: the Australian experience.

Cole JA, Brennan AL, Ajani AE, Yan BP, Duffy SJ, Loane P, Reid CM, Yudi MB, New G, Black A, Shaw J, Clark DJ, Andrianopoulos N.

Cardiovasc Ther. 2014 Apr;32(2):47-51. doi: 10.1111/1755-5922.12060.


Modeling long-term host cell-Giardia lamblia interactions in an in vitro co-culture system.

Fisher BS, Estraño CE, Cole JA.

PLoS One. 2013 Dec 3;8(12):e81104. doi: 10.1371/journal.pone.0081104. eCollection 2013.


Prostaglandin E(2) in tick saliva regulates macrophage cell migration and cytokine profile.

Poole NM, Mamidanna G, Smith RA, Coons LB, Cole JA.

Parasit Vectors. 2013 Sep 11;6(1):261. doi: 10.1186/1756-3305-6-261.

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