Publications

Butner JD, Dogra P, Chung C, Koay EJ, Welsh J, Hong DS, Cristini V, Wang Z. Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy. NPJ Syst Biol Appl. 2024 Dec 01; 10(1). PMID: 39143136. doi: 10.1038/s41540-024-00415-8.

Dogra P, Shinglot V, Ruiz Ramírez J, Cave J, Butner JD, Schiavone C, Duda DG, Kaseb A, Chung C, Koay EJ, Cristini V, Ozpolat B, Calin GA, Wang Z. Translational modeling-based evidence for enhanced efficacy of standard-of-care drugs in combination with anti-microRNA-155 in non-small-cell lung cancer. Mol Cancer. 2024 Dec 01; 23(1). PMID: 39095771. PMCID: PMC11295620.

Dogra P, Butner JD, Cristini V, Wang Z. Development of a Multiscale Mechanistic Model for Predicting Tumor Response to Anti-miR-155. Annu Int Conf IEEE Eng Med Biol Soc. 2024 Jul 15. doi: 10.1109/EMBC53108.2024.10782406.

Cave J, Shinglot V, Butner JD, Cristini V, Ozpolat B, Calin GA, Dogra P, Wang Z. Mechanistic modeling of anti-microRNA-155 therapy combinations in lung cancer. Annu Int Conf IEEE Eng Med Biol Soc. 2023 Jul; 2023:1-4. PMID: 38083518. doi: 10.1109/EMBC40787.2023.10341114.

Syed M, Cagely M, Dogra P, Hollmer L, Butner JD, Cristini V, Koay EJ. Immune-checkpoint inhibitor therapy response evaluation using oncophysics-based mathematical models. Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2023 Mar; 15(2):e1855. PMID: 36148978. doi: 10.1002/wnan.1855.

Butner JD, Dogra P, Cristini V, Deisboeck TS, Wang Z. Computational Approaches for Multiscale Modeling. In: Encyclopedia of Cell Biology (Second Edition). United States of America: Elsevier; 2023; pages 251-260.

Butner JD, Farhat M, Cristini V, Chung C, Wang Z. Protocol for mathematical prediction of patient response and survival to immune checkpoint inhibitor immunotherapy. STAR Protoc. 2022 Dec; 3(4):101886. PMID: 36595890. PMCID: PMC9719106.

Butner JD, Dogra P, Chung C, Pasqualini R, Arap W, Lowengrub J, Cristini V, Wang Z. Mathematical modeling of cancer immunotherapy for personalized clinical translation. Nat Comput Sci. 2022 Dec; 2(12):785-796. PMID: 38126024. PMCID: PMC10732566.

Sun K, Xu Y, Zhang L, Niravath P, Darcourt J, Patel T, Teh BS, Farach AM, Guerrero C, Mathur S, Sultenfuss MA, Gupta N, Schwartz MR, Haley SL, Nair S, Li X, Nguyen TTA, Butner JD, Ensor J, Mejia JA, Mei Z, Butler EB, Chen SH, Bernicker EH, Chang JC. A Phase 2 Trial of Enhancing Immune Checkpoint Blockade by Stereotactic Radiation and In Situ Virus Gene Therapy in Metastatic Triple-Negative Breast Cancer. Clin Cancer Res. 2022 Oct; 28(20):4392-4401. PMID: 35877117. PMCID: PMC9561553.

Wang CX, Elganainy D, Zaid MM, Butner JD, Agrawal A, Nizzero S, Minsky BD, Holliday EB, Taniguchi CM, Smith GL, Koong AC, Herman JM, Das P, Maitra A, Wang H, Wolff RA, Katz MHG, Crane CH, Cristini V, Koay EJ. Mass Transport Model of Radiation Response: Calibration and Application to Chemoradiation for Pancreatic Cancer. Int J Radiat Oncol Biol Phys. 2022 Sep; 114(1):163-172. PMID: 35643254. PMCID: PMC10042520.

Butner JD, Dogra P, Chung C, Ruiz-Ramírez J, Nizzero S, Plodinec M, Li X, Pan PY, Chen SH, Cristini V, Ozpolat B, Calin GA, Wang Z. Dedifferentiation-mediated stem cell niche maintenance in early-stage ductal carcinoma in situ progression: insights from a multiscale modeling study. Cell Death Dis. 2022 May; 13(5):485. PMID: 35597788. PMCID: PMC9124196.

Dogra P, Ramírez JR, Butner JD, Peláez MJ, Chung C, Hooda-Nehra A, Pasqualini R, Arap W, Cristini V, Calin GA, Ozpolat B, Wang Z. Translational Modeling Identifies Synergy between Nanoparticle-Delivered miRNA-22 and Standard-of-Care Drugs in Triple-Negative Breast Cancer. Pharm Res. 2022 Mar; 39(3):511-528. PMID: 35294699. PMCID: PMC8986735.

Dogra P, Ramirez JR, Butner JD, Pelaez MJ, Cristini V, Wang Z. A Multiscale Model to Identify Limiting Factors in Nanoparticle-Based miRNA Delivery for Tumor Inhibition. Annu Int Conf IEEE Eng Med Biol Soc. 2021 Nov; 2021:4230-4233. PMID: 34892157. PMCID: PMC8712117.

Butner JD, Martin GV, Wang Z, Corradetti B, Ferrari M, Esnaola N, Chung C, Hong DS, Welsh JW, Hasegawa N, Mittendorf EA, Curley SA, Chen SH, Pan PY, Libutti SK, Ganesan S, Sidman RL, Pasqualini R, Arap W, Koay EJ, Cristini V. Early prediction of clinical response to checkpoint inhibitor therapy in human solid tumors through mathematical modeling. Elife. 2021 Nov; 10. PMID: 34749885. PMCID: PMC8629426.

Butner JD, Wang Z, Elganainy D, Al Feghali KA, Plodinec M, Calin GA, Dogra P, Nizzero S, Ruiz-Ramírez J, Martin GV, Tawbi HA, Chung C, Koay EJ, Welsh JW, Hong DS, Cristini V. A mathematical model for the quantification of a patient's sensitivity to checkpoint inhibitors and long-term tumour burden. Nat Biomed Eng. 2021 Apr; 5(4):297-308. PMID: 33398132. PMCID: PMC8669771.

Dogra P, Ruiz-Ramírez J, Sinha K, Butner JD, Peláez MJ, Rawat M, Yellepeddi VK, Pasqualini R, Arap W, Sostman HD, Cristini V, Wang Z. Innate Immunity Plays a Key Role in Controlling Viral Load in COVID-19: Mechanistic Insights from a Whole-Body Infection Dynamics Model. ACS Pharmacol Transl Sci. 2021 Feb; 4(1):248-265. PMID: 33615177. PMCID: PMC7805603.

Anaya DA, Dogra P, Wang Z, Haider M, Ehab J, Jeong DK, Ghayouri M, Lauwers GY, Thomas K, Kim R, Butner JD, Nizzero S, Ramírez JR, Plodinec M, Sidman RL, Cavenee WK, Pasqualini R, Arap W, Fleming JB, Cristini V. A Mathematical Model to Estimate Chemotherapy Concentration at the Tumor-Site and Predict Therapy Response in Colorectal Cancer Patients with Liver Metastases. Cancers (Basel). 2021 Jan; 13(3):1-18. PMID: 33503971. PMCID: PMC7866038.

Noureddine A, Butner JD, Zhu W, Naydenkov P, Pelaez MJ, Goel S, Wang Z, Brinker CJ, Cristini V, Dogra P. Emerging Lipid-Coated Silica Nanoparticles for Cancer Therapy. In: Cancer Nanotheranostics. United States of America: Springer, Cham; 2021; pages 335-361.

Dogra P, Butner JD, Nizzero S, Ruiz Ramírez J, Noureddine A, Peláez MJ, Elganainy D, Yang Z, Le AD, Goel S, Leong HS, Koay EJ, Brinker CJ, Cristini V, Wang Z. Image-guided mathematical modeling for pharmacological evaluation of nanomaterials and monoclonal antibodies. Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2020 Sep; 12(5):e1628. PMID: 32314552. PMCID: PMC7507140.

Dogra P, Butner JD, Ramirez JR, Cristini V, Wang Z. Investigating the Effect of Aging on the Pharmacokinetics and Tumor Delivery of Nanomaterials using Mathematical Modeling. Annu Int Conf IEEE Eng Med Biol Soc. 2020 Jul; 2020:2447-2450. PMID: 33018501.

Butner JD, Fuentes D, Ozpolat B, Calin GA, Zhou X, Lowengrub J, Cristini V, Wang Z. A Multiscale Agent-Based Model of Ductal Carcinoma In Situ. IEEE Trans Biomed Eng. 2020 May; 67(5):1450-1461. PMID: 31603768. PMCID: PMC8445608.

Butner JD, Elganainy D, Wang CX, Wang Z, Chen SH, Esnaola NF, Pasqualini R, Arap W, Hong DS, Welsh J, Koay EJ, Cristini V. Mathematical prediction of clinical outcomes in advanced cancer patients treated with checkpoint inhibitor immunotherapy. Sci Adv. 2020 May; 6(18):eaay6298. PMID: 32426472. PMCID: PMC7190324.

Dogra P, Butner JD, Ruiz Ramírez J, Chuang YL, Noureddine A, Jeffrey Brinker C, Cristini V, Wang Z. A mathematical model to predict nanomedicine pharmacokinetics and tumor delivery. Comput Struct Biotechnol J. 2020; 18:518-531. PMID: 32206211. PMCID: PMC7078505.

Dogra P, Chuang YL, Butner JD, Cristini V, Wang Z. Development of a Physiologically-Based Mathematical Model for Quantifying Nanoparticle Distribution in Tumors. Annu Int Conf IEEE Eng Med Biol Soc. 2019 Jul; 2019:2852-2855. PMID: 31946487. PMCID: PMC7234807.

Dogra P, Butner JD, Chuang YL, Caserta S, Goel S, Brinker CJ, Cristini V, Wang Z. Mathematical modeling in cancer nanomedicine: a review. Biomed Microdevices. 2019 Apr; 21(2):40. PMID: 30949850. PMCID: PMC6449316.

Butner JD, Cristini V, Wang Z. Understanding Ductal Carcinoma in Situ Invasion using a Multiscale Agent-Based Model. Annu Int Conf IEEE Eng Med Biol Soc. 2018 Oct; 2018-July:5846-5849.

Butner JD, Cristini V, Wang Z. Development of a three dimensional, multiscale agent-based model of ductal carcinoma in situ. Annu Int Conf IEEE Eng Med Biol Soc. 2017 Sep; :86-89.

Cristini V, Koay EJ, Wang Z, Butner JD. Developing More Successful Cancer Treatments with Physical Oncology. In: An Introduction to Physical Oncology. United States of America: CRC Press; 2017; pages 13-30.

Cristini V, Koay EJ, Wang Z, Butner JD. Mathematical Modeling of Drug Response. In: An Introduction to Physical Oncology. 1st Edition ed. United States of America: CRC Press; 2017; pages 53-74.

Butner JD, Cristini V, Wang Z. Development of a three dimensional, lattice-free multiscale model of the mammary terminal end bud. Annu Int Conf IEEE Eng Med Biol Soc. 2016 Oct; 2016-October:6134-6137.

Butner JD, Chuang Y, Simbawa E, Al-Fhaid AS, Mahmoud SR, Cristini V, Wang Z. A hybrid agent-based model of the developing mammary terminal end bud. Journal Theor Biol. 2016 Oct; 407:259-270.

Wang Z, Kerketta R, Chuang Y, Dogra P, Butner JD, Brocato TA, Day A, Xu R, Shen H, Simbawa E, Al-Fhaid AS, Mahmoud SR. Theory and Experimental Validation of a Spatio-temporal Model of Chemotherapy Transport to Enhance Tumor Cell Kill. PLoS Comput Biol. 2016 Jun; 12(6).

Butner JD, Cristini V, Wang Z. A modeling approach to study the normal mammary gland growth process. Annu Int Conf IEEE Eng Med Biol Soc. 2015 Nov; 2015-November:1444-1447.

Wang Z, Butner JD, Cristini V, Deisboeck TS. Integrated PK-PD and agent-based modeling in oncology. J Pharmacokinet Pharmacodyn. 2015 Mar; 42(2):179-189.

Wang Z, Butner JD, Kerketta R, Cristini V, Deisboeck TS. Simulating cancer growth with multiscale agent-based modeling. Semin Cancer Biol. 2015 Feb; 30:70-78.

Pascal J, Ashley CE, Wang Z, Brocato TA, Butner JD, Carnes EC, Koay EJ, Brinker CJ, Cristini V. Mechanistic modeling identifies drug-uptake history as predictor of tumor drug resistance and nano-carrier-mediated response. ACS Nano. 2013 Dec; 7(12):11174-11182.