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The Role of Dimensionality in Understanding Granuloma Formation.

Marino S, Hult C, Wolberg P, Linderman JJ, Kirschner DE.

Computation (Basel). 2018 Dec;6(4). pii: 58. doi: 10.3390/computation6040058. Epub 2018 Nov 14.


Evaluating vaccination strategies for tuberculosis in endemic and non-endemic settings.

Renardy M, Kirschner DE.

J Theor Biol. 2019 May 21;469:1-11. doi: 10.1016/j.jtbi.2019.02.020. Epub 2019 Mar 6.


Data-Driven Model Validation Across Dimensions.

Renardy M, Wessler T, Blemker S, Linderman J, Peirce S, Kirschner D.

Bull Math Biol. 2019 Jun;81(6):1853-1866. doi: 10.1007/s11538-019-00590-4. Epub 2019 Mar 4.


Fluoroquinolone Efficacy against Tuberculosis Is Driven by Penetration into Lesions and Activity against Resident Bacterial Populations.

Sarathy J, Blanc L, Alvarez-Cabrera N, O'Brien P, Dias-Freedman I, Mina M, Zimmerman M, Kaya F, Ho Liang HP, Prideaux B, Dietzold J, Salgame P, Savic RM, Linderman J, Kirschner D, Pienaar E, Dartois V.

Antimicrob Agents Chemother. 2019 Apr 25;63(5). pii: e02516-18. doi: 10.1128/AAC.02516-18. Print 2019 May.


The Amazon rain forest plant Uncaria tomentosa (cat's claw) and its specific proanthocyanidin constituents are potent inhibitors and reducers of both brain plaques and tangles.

Snow AD, Castillo GM, Nguyen BP, Choi PY, Cummings JA, Cam J, Hu Q, Lake T, Pan W, Kastin AJ, Kirschner DA, Wood SG, Rockenstein E, Masliah E, Lorimer S, Tanzi RE, Larsen L.

Sci Rep. 2019 Feb 6;9(1):561. doi: 10.1038/s41598-019-38645-0.


Dose finding for new vaccines: The role for immunostimulation/immunodynamic modelling.

Rhodes SJ, Knight GM, Kirschner DE, White RG, Evans TG.

J Theor Biol. 2019 Mar 21;465:51-55. doi: 10.1016/j.jtbi.2019.01.017. Epub 2019 Jan 10.


Integrating Non-human Primate, Human, and Mathematical Studies to Determine the Influence of BCG Timing on H56 Vaccine Outcomes.

Joslyn LR, Pienaar E, DiFazio RM, Suliman S, Kagina BM, Flynn JL, Scriba TJ, Linderman JJ, Kirschner DE.

Front Microbiol. 2018 Aug 17;9:1734. doi: 10.3389/fmicb.2018.01734. eCollection 2018.


Dynamic balance of pro- and anti-inflammatory signals controls disease and limits pathology.

Cicchese JM, Evans S, Hult C, Joslyn LR, Wessler T, Millar JA, Marino S, Cilfone NA, Mattila JT, Linderman JJ, Kirschner DE.

Immunol Rev. 2018 Sep;285(1):147-167. doi: 10.1111/imr.12671. Review.


Low Levels of T Cell Exhaustion in Tuberculous Lung Granulomas.

Wong EA, Joslyn L, Grant NL, Klein E, Lin PL, Kirschner DE, Flynn JL.

Infect Immun. 2018 Aug 22;86(9). pii: e00426-18. doi: 10.1128/IAI.00426-18. Print 2018 Sep.


Emergence and selection of isoniazid and rifampin resistance in tuberculosis granulomas.

Pienaar E, Linderman JJ, Kirschner DE.

PLoS One. 2018 May 10;13(5):e0196322. doi: 10.1371/journal.pone.0196322. eCollection 2018.


Deletion of TGF-β1 Increases Bacterial Clearance by Cytotoxic T Cells in a Tuberculosis Granuloma Model.

Warsinske HC, Pienaar E, Linderman JJ, Mattila JT, Kirschner DE.

Front Immunol. 2017 Dec 20;8:1843. doi: 10.3389/fimmu.2017.01843. eCollection 2017.


Applying optimization algorithms to tuberculosis antibiotic treatment regimens.

Cicchese JM, Pienaar E, Kirschner DE, Linderman JJ.

Cell Mol Bioeng. 2017 Dec;10(6):523-535. doi: 10.1007/s12195-017-0507-6. Epub 2017 Aug 30.


Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach.

Pienaar E, Sarathy J, Prideaux B, Dietzold J, Dartois V, Kirschner DE, Linderman JJ.

PLoS Comput Biol. 2017 Aug 17;13(8):e1005650. doi: 10.1371/journal.pcbi.1005650. eCollection 2017 Aug.


The A2V mutation as a new tool for hindering Aβ aggregation: A neutron and x-ray diffraction study.

Cantu' L, Colombo L, Stoilova T, Demé B, Inouye H, Booth R, Rondelli V, Di Fede G, Tagliavini F, Del Favero E, Kirschner DA, Salmona M.

Sci Rep. 2017 Jul 14;7(1):5510. doi: 10.1038/s41598-017-05582-9.


Myelin structure in unfixed, single nerve fibers: Scanning X-ray microdiffraction with a beam size of 200nm.

Inouye H, Kuo FH, Denninger AR, Weinhausen B, Burghammer M, Kirschner DA.

J Struct Biol. 2017 Dec;200(3):229-243. doi: 10.1016/j.jsb.2017.07.001. Epub 2017 Jul 8.


Identifying mechanisms driving formation of granuloma-associated fibrosis during Mycobacterium tuberculosis infection.

Warsinske HC, DiFazio RM, Linderman JJ, Flynn JL, Kirschner DE.

J Theor Biol. 2017 Sep 21;429:1-17. doi: 10.1016/j.jtbi.2017.06.017. Epub 2017 Jun 20.


A review of computational and mathematical modeling contributions to our understanding of Mycobacterium tuberculosis within-host infection and treatment.

Kirschner D, Pienaar E, Marino S, Linderman JJ.

Curr Opin Syst Biol. 2017 Jun;3:170-185. doi: 10.1016/j.coisb.2017.05.014. Epub 2017 May 22.


Acidotoxicity via ASIC1a Mediates Cell Death during Oxygen Glucose Deprivation and Abolishes Excitotoxicity.

Bhowmick S, Moore JT, Kirschner DL, Curry MC, Westbrook EG, Rasley BT, Drew KL.

ACS Chem Neurosci. 2017 Jun 21;8(6):1204-1212. doi: 10.1021/acschemneuro.6b00355. Epub 2017 Mar 1.


Computational Modeling Predicts Simultaneous Targeting of Fibroblasts and Epithelial Cells Is Necessary for Treatment of Pulmonary Fibrosis.

Warsinske HC, Wheaton AK, Kim KK, Linderman JJ, Moore BB, Kirschner DE.

Front Pharmacol. 2016 Jun 23;7:183. doi: 10.3389/fphar.2016.00183. eCollection 2016.


Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome.

Marino S, Gideon HP, Gong C, Mankad S, McCrone JT, Lin PL, Linderman JJ, Flynn JL, Kirschner DE.

PLoS Comput Biol. 2016 Apr 11;12(4):e1004804. doi: 10.1371/journal.pcbi.1004804. eCollection 2016 Apr.


rAAV Gene Therapy in a Canavan's Disease Mouse Model Reveals Immune Impairments and an Extended Pathology Beyond the Central Nervous System.

Ahmed SS, Schattgen SA, Frakes AE, Sikoglu EM, Su Q, Li J, Hampton TG, Denninger AR, Kirschner DA, Kaspar B, Matalon R, Gao G.

Mol Ther. 2016 Jun;24(6):1030-1041. doi: 10.1038/mt.2016.68. Epub 2016 Apr 4.


Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions.

Pienaar E, Matern WM, Linderman JJ, Bader JS, Kirschner DE.

Infect Immun. 2016 Apr 22;84(5):1650-1669. doi: 10.1128/IAI.01438-15. Print 2016 May.


In silico models of M. tuberculosis infection provide a route to new therapies.

Linderman JJ, Kirschner DE.

Drug Discov Today Dis Models. 2015 Spring;15:37-41. Epub 2014 May 9.


Strategic Priming with Multiple Antigens can Yield Memory Cell Phenotypes Optimized for Infection with Mycobacterium tuberculosis: A Computational Study.

Ziraldo C, Gong C, Kirschner DE, Linderman JJ.

Front Microbiol. 2016 Jan 6;6:1477. doi: 10.3389/fmicb.2015.01477. eCollection 2015.


A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection.

Marino S, Kirschner DE.

Computation (Basel). 2016;4(4). pii: 39. doi: 10.3390/computation4040039. Epub 2016 Oct 21.


In silico evaluation and exploration of antibiotic tuberculosis treatment regimens.

Pienaar E, Dartois V, Linderman JJ, Kirschner DE.

BMC Syst Biol. 2015 Nov 14;9:79. doi: 10.1186/s12918-015-0221-8.


Evolution of myelin ultrastructure and the major structural myelin proteins.

Inouye H, Kirschner DA.

Brain Res. 2016 Jun 15;1641(Pt A):43-63. doi: 10.1016/j.brainres.2015.10.037. Epub 2015 Oct 28. Review.


Claudin-11 Tight Junctions in Myelin Are a Barrier to Diffusion and Lack Strong Adhesive Properties.

Denninger AR, Breglio A, Maheras KJ, LeDuc G, Cristiglio V, Demé B, Gow A, Kirschner DA.

Biophys J. 2015 Oct 6;109(7):1387-97. doi: 10.1016/j.bpj.2015.08.012.


Validation of hand motion analysis as an objective assessment tool for the Focused Assessment with Sonography for Trauma examination.

Ziesmann MT, Park J, Unger B, Kirkpatrick AW, Vergis A, Pham C, Kirschner D, Logestty S, Gillman LM.

J Trauma Acute Care Surg. 2015 Oct;79(4):631-7. doi: 10.1097/TA.0000000000000813.


Identifying Mechanisms of Homeostatic Signaling in Fibroblast Differentiation.

Warsinske HC, Ashley SL, Linderman JJ, Moore BB, Kirschner DE.

Bull Math Biol. 2015 Aug;77(8):1556-82. doi: 10.1007/s11538-015-0096-2. Epub 2015 Sep 18.


Systems Pharmacology Approach Toward the Design of Inhaled Formulations of Rifampicin and Isoniazid for Treatment of Tuberculosis.

Cilfone NA, Pienaar E, Thurber GM, Kirschner DE, Linderman JJ.

CPT Pharmacometrics Syst Pharmacol. 2015 Mar;4(3):e00022. doi: 10.1002/psp4.22. Epub 2015 Mar 11.


Effectiveness of contact investigations for tuberculosis control in Arkansas.

Guzzetta G, Ajelli M, Yang Z, Mukasa LN, Patil N, Bates JH, Kirschner DE, Merler S.

J Theor Biol. 2015 Sep 7;380:238-46. doi: 10.1016/j.jtbi.2015.05.031. Epub 2015 Jun 5.


A multi-scale approach to designing therapeutics for tuberculosis.

Linderman JJ, Cilfone NA, Pienaar E, Gong C, Kirschner DE.

Integr Biol (Camb). 2015 May;7(5):591-609. doi: 10.1039/c4ib00295d. Epub 2015 Apr 30.


Validation of the quality of ultrasound imaging and competence (QUICk) score as an objective assessment tool for the FAST examination.

Ziesmann MT, Park J, Unger BJ, Kirkpatrick AW, Vergis A, Logsetty S, Pham C, Kirschner D, Gillman LM.

J Trauma Acute Care Surg. 2015 May;78(5):1008-13. doi: 10.1097/TA.0000000000000639.


A population model capturing dynamics of tuberculosis granulomas predicts host infection outcomes.

Gong C, Linderman JJ, Kirschner D.

Math Biosci Eng. 2015 Jun;12(3):625-42. doi: 10.3934/mbe.2015.12.625.


Plasmalogen phospholipids protect internodal myelin from oxidative damage.

Luoma AM, Kuo F, Cakici O, Crowther MN, Denninger AR, Avila RL, Brites P, Kirschner DA.

Free Radic Biol Med. 2015 Jul;84:296-310. doi: 10.1016/j.freeradbiomed.2015.03.012. Epub 2015 Mar 21.


Myelin abnormalities in the optic and sciatic nerves in mice with GM1-gangliosidosis.

Heinecke KA, Luoma A, d'Azzo A, Kirschner DA, Seyfried TN.

ASN Neuro. 2015 Feb 18;7(1). pii: 1759091415568913. doi: 10.1177/1759091415568913. Print 2015 Jan-Feb.


Variability in tuberculosis granuloma T cell responses exists, but a balance of pro- and anti-inflammatory cytokines is associated with sterilization.

Gideon HP, Phuah J, Myers AJ, Bryson BD, Rodgers MA, Coleman MT, Maiello P, Rutledge T, Marino S, Fortune SM, Kirschner DE, Lin PL, Flynn JL.

PLoS Pathog. 2015 Jan 22;11(1):e1004603. doi: 10.1371/journal.ppat.1004603. eCollection 2015 Jan.


Computational modeling predicts IL-10 control of lesion sterilization by balancing early host immunity-mediated antimicrobial responses with caseation during mycobacterium tuberculosis infection.

Cilfone NA, Ford CB, Marino S, Mattila JT, Gideon HP, Flynn JL, Kirschner DE, Linderman JJ.

J Immunol. 2015 Jan 15;194(2):664-77. doi: 10.4049/jimmunol.1400734. Epub 2014 Dec 15.


A computational tool integrating host immunity with antibiotic dynamics to study tuberculosis treatment.

Pienaar E, Cilfone NA, Lin PL, Dartois V, Mattila JT, Butler JR, Flynn JL, Kirschner DE, Linderman JJ.

J Theor Biol. 2015 Feb 21;367:166-179. doi: 10.1016/j.jtbi.2014.11.021. Epub 2014 Dec 9.


Neutron scattering from myelin revisited: bilayer asymmetry and water-exchange kinetics.

Denninger AR, Demé B, Cristiglio V, LeDuc G, Feller WB, Kirschner DA.

Acta Crystallogr D Biol Crystallogr. 2014 Dec 1;70(Pt 12):3198-211. doi: 10.1107/S1399004714023815. Epub 2014 Nov 22.


Macrophage polarization drives granuloma outcome during Mycobacterium tuberculosis infection.

Marino S, Cilfone NA, Mattila JT, Linderman JJ, Flynn JL, Kirschner DE.

Infect Immun. 2015 Jan;83(1):324-38. doi: 10.1128/IAI.02494-14. Epub 2014 Nov 3.


Myelin organization in the nodal, paranodal, and juxtaparanodal regions revealed by scanning x-ray microdiffraction.

Inouye H, Liu J, Makowski L, Palmisano M, Burghammer M, Riekel C, Kirschner DA.

PLoS One. 2014 Jul 1;9(7):e100592. doi: 10.1371/journal.pone.0100592. eCollection 2014.


Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models.

Kirschner DE, Hunt CA, Marino S, Fallahi-Sichani M, Linderman JJ.

Wiley Interdiscip Rev Syst Biol Med. 2014 Jul-Aug;6(4):289-309. doi: 10.1002/wsbm.1270. Epub 2014 May 9. Review.


A bacteriophage capsid protein provides a general amyloid interaction motif (GAIM) that binds and remodels misfolded protein assemblies.

Krishnan R, Tsubery H, Proschitsky MY, Asp E, Lulu M, Gilead S, Gartner M, Waltho JP, Davis PJ, Hounslow AM, Kirschner DA, Inouye H, Myszka DG, Wright J, Solomon B, Fisher RA.

J Mol Biol. 2014 Jun 26;426(13):2500-19. doi: 10.1016/j.jmb.2014.04.015. Epub 2014 Apr 22.


Peripheral nervous system plasmalogens regulate Schwann cell differentiation and myelination.

da Silva TF, Eira J, Lopes AT, Malheiro AR, Sousa V, Luoma A, Avila RL, Wanders RJ, Just WW, Kirschner DA, Sousa MM, Brites P.

J Clin Invest. 2014 Jun;124(6):2560-70. doi: 10.1172/JCI72063. Epub 2014 Apr 24.


Phase variation and host immunity against high molecular weight (HMW) adhesins shape population dynamics of nontypeable Haemophilus influenzae within human hosts.

Davis GS, Marino S, Marrs CF, Gilsdorf JR, Dawid S, Kirschner DE.

J Theor Biol. 2014 Aug 21;355:208-18. doi: 10.1016/j.jtbi.2014.04.010. Epub 2014 Apr 18.


Harnessing the heterogeneity of T cell differentiation fate to fine-tune generation of effector and memory T cells.

Gong C, Linderman JJ, Kirschner D.

Front Immunol. 2014 Feb 19;5:57. doi: 10.3389/fimmu.2014.00057. eCollection 2014.

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