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Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor.

Qian Y, Cabeza de Vaca I, Vilseck JZ, Cole DJ, Tirado-Rives J, Jorgensen WL.

J Phys Chem B. 2019 Oct 7. doi: 10.1021/acs.jpcb.9b07588. [Epub ahead of print]


The future of force fields in computer-aided drug design.

Cole DJ, Horton JT, Nelson L, Kurdekar V.

Future Med Chem. 2019 Sep;11(18):2359-2363. doi: 10.4155/fmc-2019-0196. Epub 2019 Sep 23. No abstract available.


Development and Validation of the Quantum Mechanical Bespoke Protein Force Field.

Allen AEA, Robertson MJ, Payne MC, Cole DJ.

ACS Omega. 2019 Aug 27;4(11):14537-14550. doi: 10.1021/acsomega.9b01769. eCollection 2019 Sep 10.


Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields.

Cole DJ, Cabeza de Vaca I, Jorgensen WL.

Medchemcomm. 2019 Feb 27;10(7):1116-1120. doi: 10.1039/c9md00017h. eCollection 2019 Jul 1.


Maintenance of Certification: Comment.

Cole DJ, Culley DJ, Fahy BG, Warner DO.

Anesthesiology. 2019 Jun;130(6):1091-1092. doi: 10.1097/ALN.0000000000002723. No abstract available.


Defective Fibrillar Collagen Organization by Fibroblasts Contributes to Airway Remodeling in Asthma.

Mostaço-Guidolin LB, Osei ET, Ullah J, Hajimohammadi S, Fouadi M, Li X, Li V, Shaheen F, Yang CX, Chu F, Cole DJ, Brandsma CA, Heijink IH, Maksym GN, Walker D, Hackett TL.

Am J Respir Crit Care Med. 2019 Aug 15;200(4):431-443. doi: 10.1164/rccm.201810-1855OC.


Estimating age-dependent survival from age-aggregated ringing data-extending the use of historical records.

Jiménez-Muñoz M, Cole DJ, Freeman SN, Robinson RA, Baillie SR, Matechou E.

Ecol Evol. 2019 Feb 5;9(2):769-779. doi: 10.1002/ece3.4820. eCollection 2019 Jan. Review.


QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics.

Horton JT, Allen AEA, Dodda LS, Cole DJ.

J Chem Inf Model. 2019 Apr 22;59(4):1366-1381. doi: 10.1021/acs.jcim.8b00767. Epub 2019 Feb 22.


Postoperative Brain Function: Toward a Better Understanding and the American Society of Anesthesiologists Perioperative Brain Health Initiative.

Cole DJ, Kharasch ED.

Anesthesiology. 2018 Nov;129(5):861-863. doi: 10.1097/ALN.0000000000002085. No abstract available.


The "two-tone" testis.

Cole DJ, Wolfman N, Dyer RB.

Abdom Radiol (NY). 2019 Feb;44(2):798-799. doi: 10.1007/s00261-018-1756-0. Review. No abstract available.


Removal models accounting for temporary emigration.

Zhou M, McCrea RS, Matechou E, Cole DJ, Griffiths RA.

Biometrics. 2019 Mar;75(1):24-35. doi: 10.1111/biom.12961. Epub 2018 Sep 19.


Enhanced Lymphodepletion Is Insufficient to Replace Exogenous IL2 or IL15 Therapy in Augmenting the Efficacy of Adoptively Transferred Effector CD8+ T Cells.

Johnson CB, May BR, Riesenberg BP, Suriano S, Mehrotra S, Garrett-Mayer E, Salem ML, Jeng EK, Wong HC, Paulos CM, Wrangle JM, Cole DJ, Rubinstein MP.

Cancer Res. 2018 Jun 1;78(11):3067-3074. doi: 10.1158/0008-5472.CAN-17-2153. Epub 2018 Apr 10.


IL-2 and Beyond in Cancer Immunotherapy.

Wrangle JM, Patterson A, Johnson CB, Neitzke DJ, Mehrotra S, Denlinger CE, Paulos CM, Li Z, Cole DJ, Rubinstein MP.

J Interferon Cytokine Res. 2018 Feb;38(2):45-68. doi: 10.1089/jir.2017.0101. Review.


Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection.

Allen AEA, Payne MC, Cole DJ.

J Chem Theory Comput. 2018 Jan 9;14(1):274-281. doi: 10.1021/acs.jctc.7b00785. Epub 2017 Dec 6.


Distance dependent photoacoustics revealed through DNA nanostructures.

Joseph J, Baumann KN, Koehler P, Zuehlsdorff TJ, Cole DJ, Weber J, Bohndiek SE, Hernández-Ainsa S.

Nanoscale. 2017 Nov 2;9(42):16193-16199. doi: 10.1039/c7nr05353c.


Association between wetland presence and incidence of Salmonella enterica serotype Javiana infections in selected US sites, 2005-2011.

Huang JY, Patrick ME, Manners J, Sapkota AR, Scherzinger KJ, Tobin-D'Angelo M, Henao OL, Cole DJ, Vieira AR.

Epidemiol Infect. 2017 Oct;145(14):2991-2997. doi: 10.1017/S0950268817001790. Epub 2017 Aug 14.


Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.

Cole DJ, Janecek M, Stokes JE, Rossmann M, Faver JC, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR, Huggins DJ, Jorgensen WL.

Chem Commun (Camb). 2017 Aug 17;53(67):9372-9375. doi: 10.1039/c7cc05379g.


Evaluation of the Use of Zero-Augmented Regression Techniques to Model Incidence of Campylobacter Infections in FoodNet.

Tremblay M, Crim SM, Cole DJ, Hoekstra RM, Henao OL, Döpfer D.

Foodborne Pathog Dis. 2017 Oct;14(10):587-592. doi: 10.1089/fpd.2017.2308. Epub 2017 Jul 18.


Evidence of Correlated Static Disorder in the Fenna-Matthews-Olson Complex.

Fokas AS, Cole DJ, Hine NDM, Wells SA, Payne MC, Chin AW.

J Phys Chem Lett. 2017 May 18;8(10):2350-2356. doi: 10.1021/acs.jpclett.7b00669. Epub 2017 May 11.


Vaccination with poly(IC:LC) and peptide-pulsed autologous dendritic cells in patients with pancreatic cancer.

Mehrotra S, Britten CD, Chin S, Garrett-Mayer E, Cloud CA, Li M, Scurti G, Salem ML, Nelson MH, Thomas MB, Paulos CM, Salazar AM, Nishimura MI, Rubinstein MP, Li Z, Cole DJ.

J Hematol Oncol. 2017 Apr 7;10(1):82. doi: 10.1186/s13045-017-0459-2.


Murine Th17 cells utilize IL-2 receptor gamma chain cytokines but are resistant to cytokine withdrawal-induced apoptosis.

Neitzke DJ, Bowers JS, Andrijauskaite K, O'Connell NS, Garrett-Mayer E, Wrangle J, Li Z, Paulos CM, Cole DJ, Rubinstein MP.

Cancer Immunol Immunother. 2017 Jun;66(6):737-751. doi: 10.1007/s00262-017-1965-3. Epub 2017 Mar 9.


Corrigendum: Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis.

Fokas AS, Cole DJ, Ahnert SE, Chin AW.

Sci Rep. 2017 Feb 27;7:42654. doi: 10.1038/srep42654. No abstract available.


Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis.

Fokas AS, Cole DJ, Ahnert SE, Chin AW.

Sci Rep. 2016 Sep 14;6:33213. doi: 10.1038/srep33213. Erratum in: Sci Rep. 2017 Feb 27;7:42654.


Successful chemoimmunotherapy against hepatocellular cancer in a novel murine model.

Li G, Liu D, Cooper TK, Kimchi ET, Qi X, Avella DM, Li N, Yang QX, Kester M, Rountree CB, Kaifi JT, Cole DJ, Rockey DC, Schell TD, Staveley-O'Carroll KF.

J Hepatol. 2017 Jan;66(1):75-85. doi: 10.1016/j.jhep.2016.07.044. Epub 2016 Aug 9.


Applications of large-scale density functional theory in biology.

Cole DJ, Hine ND.

J Phys Condens Matter. 2016 Oct 5;28(39):393001. doi: 10.1088/0953-8984/28/39/393001. Epub 2016 Aug 5. Review.


Molecular Programming of Tumor-Infiltrating CD8+ T Cells and IL15 Resistance.

Doedens AL, Rubinstein MP, Gross ET, Best JA, Craig DH, Baker MK, Cole DJ, Bui JD, Goldrath AW.

Cancer Immunol Res. 2016 Sep 2;4(9):799-811. doi: 10.1158/2326-6066.CIR-15-0178. Epub 2016 Aug 2.


Harnessing the IL-7/IL-7Rα axis to improve tumor immunotherapy.

Johnson CB, Wrangle J, Mehrotra S, Li Z, Paulos CM, Cole DJ, Surh CD, Rubinstein MP.

Oncoimmunology. 2016 Jan 19;5(5):e1122865. doi: 10.1080/2162402X.2015.1122865. eCollection 2016 May.


Lack of p53 Augments Antitumor Functions in Cytolytic T Cells.

Banerjee A, Thyagarajan K, Chatterjee S, Chakraborty P, Kesarwani P, Soloshchenko M, Al-Hommrani M, Andrijauskaite K, Moxley K, Janakiraman H, Scheffel MJ, Helke K, Armenson K, Palanisamy V, Rubinstein MP, Mayer EG, Cole DJ, Paulos CM, Christina-Voelkel-Johnson, Nishimura MI, Mehrotra S.

Cancer Res. 2016 Sep 15;76(18):5229-5240. doi: 10.1158/0008-5472.CAN-15-1798. Epub 2016 Jul 27.


Crossroads-2016 Southeastern Surgical Congress Presidential Address.

Cole DJ.

Am Surg. 2016 Jul;82(7):571-4. No abstract available.


Parameter redundancy in discrete state-space and integrated models.

Cole DJ, McCrea RS.

Biom J. 2016 Sep;58(5):1071-90. doi: 10.1002/bimj.201400239. Epub 2016 Jun 30.


A review of human sensory dynamics for application to models of driver steering and speed control.

Nash CJ, Cole DJ, Bigler RS.

Biol Cybern. 2016 Jun;110(2-3):91-116. doi: 10.1007/s00422-016-0682-x. Epub 2016 Apr 16. Review.


Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL.

J Chem Theory Comput. 2016 May 10;12(5):2312-23. doi: 10.1021/acs.jctc.6b00027. Epub 2016 Apr 21.


The Mandate to Measure Patient Experience: How Can Patients "Value" Anesthesia Care?

Meyer MJ, Hyder JA, Cole DJ, Kamdar NV.

Anesth Analg. 2016 Apr;122(4):1211-5. doi: 10.1213/ANE.0000000000001198. Review. No abstract available.


Attribution of Salmonella enterica serotype Hadar infections using antimicrobial resistance data from two points in the food supply system.

Vieira AR, Grass J, Fedorka-Cray PJ, Plumblee JR, Tate H, Cole DJ.

Epidemiol Infect. 2016 Jul;144(9):1983-90. doi: 10.1017/S0950268816000066. Epub 2016 Feb 3.


The CaSm (LSm1) oncogene promotes transformation, chemoresistance and metastasis of pancreatic cancer cells.

Little EC, Camp ER, Wang C, Watson PM, Watson DK, Cole DJ.

Oncogenesis. 2016 Jan 11;5:e182. doi: 10.1038/oncsis.2015.45.


Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms.

Lee LP, Limas NG, Cole DJ, Payne MC, Skylaris CK, Manz TA.

J Chem Theory Comput. 2014 Dec 9;10(12):5377-90. doi: 10.1021/ct500766v.


IL-2Rα mediates temporal regulation of IL-2 signaling and enhances immunotherapy.

Su EW, Moore CJ, Suriano S, Johnson CB, Songalia N, Patterson A, Neitzke DJ, Andrijauskaite K, Garrett-Mayer E, Mehrotra S, Paulos CM, Doedens AL, Goldrath AW, Li Z, Cole DJ, Rubinstein MP.

Sci Transl Med. 2015 Oct 28;7(311):311ra170. doi: 10.1126/scitranslmed.aac8155.


Effector CD8+ T-cell Engraftment and Antitumor Immunity in Lymphodepleted Hosts Is IL7Rα Dependent.

Johnson CB, Riesenberg BP, May BR, Gilreath SC, Li G, Staveley-O'Carroll KF, Garrett-Mayer E, Mehrotra S, Cole DJ, Rubinstein MP.

Cancer Immunol Res. 2015 Dec;3(12):1364-74. doi: 10.1158/2326-6066.CIR-15-0087-T. Epub 2015 Aug 21.


The rise and decline in Salmonella enterica serovar Enteritidis outbreaks attributed to egg-containing foods in the United States, 1973-2009.

Wright AP, Richardson L, Mahon BE, Rothenberg R, Cole DJ.

Epidemiol Infect. 2016 Mar;144(4):810-9. doi: 10.1017/S0950268815001867. Epub 2015 Aug 20.


Large-Scale Density Functional Theory Transition State Searching in Enzymes.

Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris CK, Payne MC.

J Phys Chem Lett. 2014 Nov 6;5(21):3614-9. doi: 10.1021/jz5018703. Epub 2014 Oct 9.


Paclitaxel tumor priming promotes delivery and transfection of intravenous lipid-siRNA in pancreatic tumors.

Wang J, Lu Z, Wang J, Cui M, Yeung BZ, Cole DJ, Wientjes MG, Au JL.

J Control Release. 2015 Oct 28;216:103-10. doi: 10.1016/j.jconrel.2015.08.012. Epub 2015 Aug 10.


IL-12 conditioning improves retrovirally mediated transduction efficiency of CD8+ T cells.

Andrijauskaite K, Suriano S, Cloud CA, Li M, Kesarwani P, Stefanik LS, Moxley KM, Salem ML, Garrett-Mayer E, Paulos CM, Mehrotra S, Kochenderfer JN, Cole DJ, Rubinstein MP.

Cancer Gene Ther. 2015 Jul;22(7):360-7. doi: 10.1038/cgt.2015.28. Epub 2015 Jul 17.


The impact of surgical diversion before neoadjuvant therapy for rectal cancer.

Anderson BJ, Hill EG, Sweeney RE, Wahlquist AE, Marshall DT, Staveley O'Carroll KF, Cole DJ, Camp ER.

Am Surg. 2015 May;81(5):444-9.


Dendritic Cells in Irradiated Mice Trigger the Functional Plasticity and Antitumor Activity of Adoptively Transferred Tc17 Cells via IL12 Signaling.

Bowers JS, Nelson MH, Kundimi S, Bailey SR, Huff LW, Schwartz KM, Cole DJ, Rubinstein MP, Paulos CM.

Clin Cancer Res. 2015 Jun 1;21(11):2546-57. doi: 10.1158/1078-0432.CCR-14-2294. Epub 2015 Apr 22.


Interleukin-12 enhances the function and anti-tumor activity in murine and human CD8(+) T cells.

Rubinstein MP, Su EW, Suriano S, Cloud CA, Andrijauskaite K, Kesarwani P, Schwartz KM, Williams KM, Johnson CB, Li M, Scurti GM, Salem ML, Paulos CM, Garrett-Mayer E, Mehrotra S, Cole DJ.

Cancer Immunol Immunother. 2015 May;64(5):539-49. doi: 10.1007/s00262-015-1655-y. Epub 2015 Feb 13.


The inducible costimulator augments Tc17 cell responses to self and tumor tissue.

Nelson MH, Kundimi S, Bowers JS, Rogers CE, Huff LW, Schwartz KM, Thyagarajan K, Little EC, Mehrotra S, Cole DJ, Rubinstein MP, Paulos CM.

J Immunol. 2015 Feb 15;194(4):1737-47. doi: 10.4049/jimmunol.1401082. Epub 2015 Jan 9.


Does your species have memory? Analyzing capture-recapture data with memory models.

Cole DJ, Morgan BJ, McCrea RS, Pradel R, Gimenez O, Choquet R.

Ecol Evol. 2014 Jun;4(11):2124-33. doi: 10.1002/ece3.1037. Epub 2014 Apr 30.


Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design.

Cole DJ, Tirado-Rives J, Jorgensen WL.

Biochim Biophys Acta. 2015 May;1850(5):966-971. doi: 10.1016/j.bbagen.2014.08.018. Epub 2014 Sep 6.


Constrained geometric dynamics of the Fenna-Matthews-Olson complex: the role of correlated motion in reducing uncertainty in excitation energy transfer.

Fokas AS, Cole DJ, Chin AW.

Photosynth Res. 2014 Dec;122(3):275-92. doi: 10.1007/s11120-014-0027-3. Epub 2014 Jul 18.


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