{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:22:33Z","timestamp":1792783353341,"version":"4.5.0"},"reference-count":159,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support","award":["# MCB140228"],"award-info":[{"award-number":["# MCB140228"]}],"id":[{"id":"https:\/\/ror.org\/01v6d0b34","id-type":"ROR","asserted-by":"crossref"}]},{"name":"University of Michigan - Department of Microbiology & Immunology","id":[{"id":"https:\/\/ror.org\/00jmfr291","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Center for Data-Driven Drug Development and Treatment Assessment"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Bull Math Biol"],"published-print":{"date-parts":[[2026,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Small cell lung cancer (SCLC) and tuberculosis (TB) are both deadly diseases that present with spatially complex lung lesions. These lesions share similarities, including spatial interactions between T cells and macrophages. Both SCLC and TB exhibit heterogeneous disease progression and responses to treatment; current experimental methods have few tools to investigate the spatiotemporal evolution of these lesions within human lungs. We have applied our computational agent-based model (ABM),\n                    <jats:italic>GranSim<\/jats:italic>\n                    , to extensively study heterogeneity of TB granuloma formation and treatment efficacy. We introduce\n                    <jats:italic>TumorSim<\/jats:italic>\n                    , an analogous ABM designed to understand heterogeneity of SCLC lung tumors.\n                    <jats:italic>TumorSim<\/jats:italic>\n                    mechanistically captures immune-tumor interactions, many of which are well-studied in isolation, including cytokine-based recruitment of immune cells and PD-1\/PD-L1-based inhibition of cytotoxic T cells. Drawing from lung immunology literature, we define and explore wide parameter ranges to characterize\n                    <jats:italic>TumorSim<\/jats:italic>\n                    behavior using global sensitivity analysis. We compare factors that drive both tumor and granuloma outcomes. As model validation, sensitivity analysis captures several well-known correlates of improved SCLC outcomes including macrophage-mediated cytotoxic T-cell recruitment. Surprisingly, both models predict a two-phase formation process occurring with an abrupt change in tumor\/granuloma dynamics upon arrival of adaptive immune cells into the lung. Simulations suggest that while C\u2013C motif chemokine ligand 5 (CCL5) is associated with improved tumor control later during tumor growth, CCL5 plays a pro-tumor role early during tumor growth by recruiting regulatory T cells. We find that, like virtual granulomas,\n                    <jats:italic>TumorSim<\/jats:italic>\n                    tumors become enlarged when immunosuppressive mechanisms outweigh pro-inflammatory responses. This novel tumor model enables future studies of both immunotherapeutics and anti-cancer drugs.\n                  <\/jats:p>","DOI":"10.1007\/s11538-026-01763-8","type":"journal-article","created":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T17:30:12Z","timestamp":1791307812000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Comparison of Mechanisms Driving Lesion Outcomes During Lung Tumor and Tuberculosis Granuloma Formation"],"prefix":"10.1007","volume":"88","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3583-6097","authenticated-orcid":false,"given":"Christian T.","family":"Michael","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7934-4230","authenticated-orcid":false,"given":"Maral","family":"Budak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1053-2591","authenticated-orcid":false,"given":"Denise","family":"Kirschner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,6]]},"reference":[{"key":"1763_CR1","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1038\/ni794","volume":"3","author":"M Afkarian","year":"2002","unstructured":"Afkarian M, Sedy JR, Yang J, Jacobson NG, Cereb N, Yang SY, Murphy TL, Murphy KM (2002) T-bet is a STAT1-induced regulator of IL-12R expression in naive CD4+ T cells. Nat Immunol 3:549\u2013557. https:\/\/doi.org\/10.1038\/ni794","journal-title":"Nat Immunol"},{"key":"1763_CR2","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1177\/10812865241230269","volume":"30","author":"MM Almudarra","year":"2024","unstructured":"Almudarra MM, Ram\u00edrez-Torres A (2024) Examining avascular tumour growth dynamics: a variable-order non-local modelling perspective. Math Mech Solids 30:501\u2013526. https:\/\/doi.org\/10.1177\/10812865241230269","journal-title":"Math Mech Solids"},{"key":"1763_CR3","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/s40425-019-0717-7","volume":"7","author":"A Anastasopoulou","year":"2019","unstructured":"Anastasopoulou A, Ziogas DC, Samarkos M, Kirkwood JM, Gogas H (2019) Reactivation of tuberculosis in cancer patients following administration of immune checkpoint inhibitors: current evidence and clinical practice recommendations. J Immunother Cancer 7:239. https:\/\/doi.org\/10.1186\/s40425-019-0717-7","journal-title":"J Immunother Cancer"},{"key":"1763_CR4","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.1059725","volume":"13","author":"S Ashenafi","year":"2022","unstructured":"Ashenafi S, Brighenti S (2022) Reinventing the human tuberculosis (TB) granuloma: learning from the cancer field. Front Immunol 13:1059725. https:\/\/doi.org\/10.3389\/fimmu.2022.1059725","journal-title":"Front Immunol"},{"key":"1763_CR5","doi-asserted-by":"publisher","first-page":"38022","DOI":"10.18632\/oncotarget.16723","volume":"8","author":"R Bayat Mokhtari","year":"2017","unstructured":"Bayat Mokhtari R, Homayouni TS, Baluch N, Morgatskaya E, Kumar S, Das B, Yeger H (2017) Combination therapy in combating cancer. Oncotarget 8:38022\u201338043. https:\/\/doi.org\/10.18632\/oncotarget.16723","journal-title":"Oncotarget"},{"key":"1763_CR6","doi-asserted-by":"publisher","first-page":"231","DOI":"10.2174\/138920111794295783","volume":"12","author":"PM Biava","year":"2011","unstructured":"Biava PM, Basevi M, Biggiero L, Borgonovo A, Borgonovo E, Burigana F (2011) Cancer cell reprogramming: stem cell differentiation stage factors and an agent based model to optimize cancer treatment. Curr Pharm Biotechnol 12:231\u2013242. https:\/\/doi.org\/10.2174\/138920111794295783","journal-title":"Curr Pharm Biotechnol"},{"key":"1763_CR7","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21176136","author":"TE Bickett","year":"2020","unstructured":"Bickett TE, Karam SD (2020) Tuberculosis-cancer parallels in immune response regulation. Int J Mol Sci. https:\/\/doi.org\/10.3390\/ijms21176136","journal-title":"Int J Mol Sci"},{"key":"1763_CR8","doi-asserted-by":"publisher","first-page":"2011","DOI":"10.4049\/jimmunol.180.4.2011","volume":"180","author":"SK Biswas","year":"2008","unstructured":"Biswas SK, Sica A, Lewis CE (2008) Plasticity of macrophage function during tumor progression: regulation by distinct molecular mechanisms. J Immunol 180:2011\u20132017. https:\/\/doi.org\/10.4049\/jimmunol.180.4.2011","journal-title":"J Immunol"},{"key":"1763_CR9","doi-asserted-by":"publisher","first-page":"14590","DOI":"10.18632\/aging.203113","volume":"13","author":"NC Blessin","year":"2021","unstructured":"Blessin NC, Abu-Hashem R, Mandelkow T, Li W, Simon R, Hube-Magg C, Moller-Koop C, Witt M, Schmidt A, Buscheck F, Fraune C, Luebke AM, Moller K, Jacobsen F, Lutz F, Lennartz M, Steurer S, Sauter G, Hoflmayer D, Tsourlakis MC, Hinsch A, Burandt E, Wilczak W, Minner S, Clauditz TS (2021) Prevalence of proliferating CD8(+) cells in normal lymphatic tissues, inflammation and cancer. Aging (Albany NY) 13:14590\u201314603. https:\/\/doi.org\/10.18632\/aging.203113","journal-title":"Aging (Albany NY)"},{"key":"1763_CR10","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1093\/cid\/cix247","volume":"65","author":"LJ Bonnett","year":"2017","unstructured":"Bonnett LJ, Ken-Dror G, Koh GCKW, Davies GR (2017) Comparing the efficacy of drug regimens for pulmonary tuberculosis: meta-analysis of endpoints in early-phase clinical trials. Clin Infect Dis 65:46\u201354. https:\/\/doi.org\/10.1093\/cid\/cix247","journal-title":"Clin Infect Dis"},{"key":"1763_CR11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007635","volume":"16","author":"RR Bravo","year":"2020","unstructured":"Bravo RR, Baratchart E, West J, Schenck RO, Miller AK, Gallaher J, Gatenbee CD, Basanta D, Robertson-Tessi M, Anderson ARA (2020) Hybrid automata library: a flexible platform for hybrid modeling with real-time visualization. PLoS Comput Biol 16:e1007635. https:\/\/doi.org\/10.1371\/journal.pcbi.1007635","journal-title":"PLoS Comput Biol"},{"key":"1763_CR12","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1010823","volume":"19","author":"M Budak","year":"2023","unstructured":"Budak M, Cicchese JM, Maiello P, Borish HJ, White AG, Chishti HB, Tomko J, Frye LJ, Fillmore D, Kracinovsky K, Sakal J, Scanga CA, Lin PL, Dartois V, Linderman JJ, Flynn JL, Kirschner DE (2023) Optimizing tuberculosis treatment efficacy: comparing the standard regimen with Moxifloxacin-containing regimens. PLoS Comput Biol 19:e1010823. https:\/\/doi.org\/10.1371\/journal.pcbi.1010823","journal-title":"PLoS Comput Biol"},{"key":"1763_CR13","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1002\/psp4.13117","volume":"13","author":"M Budak","year":"2024","unstructured":"Budak M, Via LE, Weiner DM, Barry CE 3rd, Nanda P, Michael G, Mdluli K, Kirschner D (2024) A systematic efficacy analysis of tuberculosis treatment with BPaL-containing regimens using a multiscale modeling approach. CPT Pharmacomet Syst Pharmacol 13:673\u2013685. https:\/\/doi.org\/10.1002\/psp4.13117","journal-title":"CPT Pharmacomet Syst Pharmacol"},{"key":"1763_CR14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1010994","volume":"19","author":"JA Bull","year":"2023","unstructured":"Bull JA, Byrne HM (2023) Quantification of spatial and phenotypic heterogeneity in an agent-based model of tumour-macrophage interactions. PLoS Comput Biol 19:e1010994. https:\/\/doi.org\/10.1371\/journal.pcbi.1010994","journal-title":"PLoS Comput Biol"},{"key":"1763_CR15","doi-asserted-by":"publisher","DOI":"10.1016\/j.smim.2019.05.002","volume":"43","author":"JD Burke","year":"2019","unstructured":"Burke JD, Young HA (2019) IFN-gamma: a cytokine at the right time, is in the right place. Semin Immunol 43:101280. https:\/\/doi.org\/10.1016\/j.smim.2019.05.002","journal-title":"Semin Immunol"},{"key":"1763_CR16","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1007\/s11095-024-03715-0","volume":"41","author":"MC Calopiz","year":"2024","unstructured":"Calopiz MC, Linderman JJ, Thurber GM (2024) Optimizing solid tumor treatment with antibody-drug conjugates using agent-based modeling: considering the role of a carrier dose and payload class. Pharm Res 41:1109\u20131120. https:\/\/doi.org\/10.1007\/s11095-024-03715-0","journal-title":"Pharm Res"},{"key":"1763_CR17","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1046\/j.1365-3083.2001.00842.x","volume":"53","author":"PJ Cardona","year":"2001","unstructured":"Cardona PJ, Llatjos R, Gordillo S, Diaz J, Vinado B, Ariza A, Ausina V (2001) Towards a \u2018human-like\u2019 model of tuberculosis: intranasal inoculation of LPS induces intragranulomatous lung necrosis in mice infected aerogenically with Mycobacterium tuberculosis. Scand J Immunol 53:65\u201371. https:\/\/doi.org\/10.1046\/j.1365-3083.2001.00842.x","journal-title":"Scand J Immunol"},{"key":"1763_CR18","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1016\/j.vaccine.2004.09.008","volume":"23","author":"PJ Cardona","year":"2005","unstructured":"Cardona PJ, Amat I, Gordillo S, Arcos V, Guirado E, Diaz J, Vilaplana C, Tapia G, Ausina V (2005) Immunotherapy with fragmented Mycobacterium tuberculosis cells increases the effectiveness of chemotherapy against a chronical infection in a murine model of tuberculosis. Vaccine 23:1393\u20131398. https:\/\/doi.org\/10.1016\/j.vaccine.2004.09.008","journal-title":"Vaccine"},{"key":"1763_CR19","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1016\/j.jtbi.2005.04.024","volume":"237","author":"F Castiglione","year":"2005","unstructured":"Castiglione F, Toschi F, Bernaschi M, Succi S, Benedetti R, Falini B, Liso A (2005) Computational modeling of the immune response to tumor antigens. J Theor Biol 237:390\u2013400. https:\/\/doi.org\/10.1016\/j.jtbi.2005.04.024","journal-title":"J Theor Biol"},{"key":"1763_CR20","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines4030028","author":"B Chaudhary","year":"2016","unstructured":"Chaudhary B, Elkord E (2016) Regulatory T cells in the tumor microenvironment and cancer progression: role and therapeutic targeting. Vaccines (Basel). https:\/\/doi.org\/10.3390\/vaccines4030028","journal-title":"Vaccines (Basel)"},{"key":"1763_CR21","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2021.716042","volume":"11","author":"WW Chen","year":"2021","unstructured":"Chen WW, Liu W, Li Y, Wang J, Ren Y, Wang G, Chen C, Li H (2021) Deciphering the immune-tumor interplay during early-stage lung cancer development via single-cell technology. Front Oncol 11:716042. https:\/\/doi.org\/10.3389\/fonc.2021.716042","journal-title":"Front Oncol"},{"key":"1763_CR22","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1007\/s00432-021-03895-x","volume":"148","author":"Y Chen","year":"2022","unstructured":"Chen Y, Jin Y, Hu X, Chen M (2022) Infiltrating T lymphocytes in the tumor microenvironment of small cell lung cancer: a state of knowledge review. J Cancer Res Clin Oncol 148:881\u2013895. https:\/\/doi.org\/10.1007\/s00432-021-03895-x","journal-title":"J Cancer Res Clin Oncol"},{"key":"1763_CR23","doi-asserted-by":"publisher","unstructured":"Cicchese J, Sambarey A, Kirschner D, Linderman J, Chandrasekaran S (2020a) A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs. https:\/\/doi.org\/10.1101\/2020.09.03.281550","DOI":"10.1101\/2020.09.03.281550"},{"key":"1763_CR24","doi-asserted-by":"publisher","first-page":"333","DOI":"10.3389\/fphar.2020.00333","volume":"11","author":"JM Cicchese","year":"2020","unstructured":"Cicchese JM, Dartois V, Kirschner DE, Linderman JJ (2020b) Both pharmacokinetic variability and granuloma heterogeneity impact the ability of the first-line antibiotics to sterilize tuberculosis granulomas. Front Pharmacol 11:333. https:\/\/doi.org\/10.3389\/fphar.2020.00333","journal-title":"Front Pharmacol"},{"key":"1763_CR25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0068680","volume":"8","author":"NA Cilfone","year":"2013","unstructured":"Cilfone NA, Perry CR, Kirschner DE, Linderman JJ (2013) Multi-scale modeling predicts a balance of tumor necrosis factor-alpha and interleukin-10 controls the granuloma environment during Mycobacterium tuberculosis infection. PLoS ONE 8:e68680. https:\/\/doi.org\/10.1371\/journal.pone.0068680","journal-title":"PLoS ONE"},{"key":"1763_CR26","doi-asserted-by":"publisher","DOI":"10.1007\/s12195-014-0363-6","author":"NA Cilfone","year":"2014","unstructured":"Cilfone NA, Kirschner DE, Linderman JJ (2014) Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems. Cel Mol Bioeng. https:\/\/doi.org\/10.1007\/s12195-014-0363-6","journal-title":"Cel Mol Bioeng"},{"key":"1763_CR27","doi-asserted-by":"publisher","first-page":"664","DOI":"10.4049\/jimmunol.1400734","volume":"194","author":"NA Cilfone","year":"2015","unstructured":"Cilfone NA, Ford CB, Marino S, Mattila JT, Gideon HP, Flynn JL, Kirschner DE, Linderman JJ (2015a) Computational modeling predicts IL-10 control of lesion sterilization by balancing early host immunity-mediated antimicrobial responses with caseation during Mycobacterium tuberculosis infection. J Immunol 194:664\u2013677. https:\/\/doi.org\/10.4049\/jimmunol.1400734","journal-title":"J Immunol"},{"key":"1763_CR28","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1002\/psp4.22","volume":"4","author":"NA Cilfone","year":"2015","unstructured":"Cilfone NA, Pienaar E, Thurber GM, Kirschner DE, Linderman JJ (2015b) Systems pharmacology approach toward the design of inhaled formulations of rifampicin and isoniazid for treatment of tuberculosis. CPT Pharmacometrics Syst Pharmacol 4:193\u2013203. https:\/\/doi.org\/10.1002\/psp4.22","journal-title":"CPT Pharmacometrics Syst Pharmacol"},{"key":"1763_CR29","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1016\/j.jtbi.2017.07.016","volume":"430","author":"C Cockrell","year":"2017","unstructured":"Cockrell C, An G (2017) Sepsis reconsidered: identifying novel metrics for behavioral landscape characterization with a high-performance computing implementation of an agent-based model. J Theor Biol 430:157\u2013168. https:\/\/doi.org\/10.1016\/j.jtbi.2017.07.016","journal-title":"J Theor Biol"},{"key":"1763_CR30","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1038\/nature13490","volume":"513","author":"OR Colegio","year":"2014","unstructured":"Colegio OR, Chu NQ, Szabo AL, Chu T, Rhebergen AM, Jairam V, Cyrus N, Brokowski CE, Eisenbarth SC, Phillips GM, Cline GW, Phillips AJ, Medzhitov R (2014) Functional polarization of tumour-associated macrophages by tumour-derived lactic acid. Nature 513:559\u2013563. https:\/\/doi.org\/10.1038\/nature13490","journal-title":"Nature"},{"key":"1763_CR31","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1016\/j.ccell.2019.05.004","volume":"35","author":"D Dangaj","year":"2019","unstructured":"Dangaj D, Bruand M, Grimm AJ, Ronet C, Barras D, Duttagupta PA, Lanitis E, Duraiswamy J, Tanyi JL, Benencia F, Conejo-Garcia J, Ramay HR, Montone KT, Powell DJ Jr., Gimotty PA, Facciabene A, Jackson DG, Weber JS, Rodig SJ, Hodi SF, Kandalaft LE, Irving M, Zhang L, Foukas P, Rusakiewicz S, Delorenzi M, Coukos G (2019) Cooperation between constitutive and inducible chemokines enables T cell engraftment and immune attack in solid tumors. Cancer Cell 35:885-900 e810. https:\/\/doi.org\/10.1016\/j.ccell.2019.05.004","journal-title":"Cancer Cell"},{"key":"1763_CR32","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1424563112","author":"M Datta","year":"2015","unstructured":"Datta M, Via LE, Kamoun WS, Liu C, Chen W, Seano G, Weiner DM, Schimel D, England K, Martin JD, Gao X, Xu L, Barry CE 3rd, Jain RK (2015) Anti-vascular endothelial growth factor treatment normalizes tuberculosis granuloma vasculature and improves small molecule delivery. Proc Natl Acad Sci U S A. https:\/\/doi.org\/10.1073\/pnas.1424563112","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1763_CR33","doi-asserted-by":"publisher","first-page":"2721","DOI":"10.1021\/acs.molpharmaceut.8b00237","volume":"15","author":"MB Deci","year":"2018","unstructured":"Deci MB, Ferguson SW, Scatigno SL, Nguyen J (2018) Modulating macrophage polarization through CCR2 inhibition and multivalent engagement. Mol Pharm 15:2721\u20132731. https:\/\/doi.org\/10.1021\/acs.molpharmaceut.8b00237","journal-title":"Mol Pharm"},{"key":"1763_CR34","doi-asserted-by":"publisher","first-page":"2789","DOI":"10.1172\/JCI136288","volume":"130","author":"A Dorhoi","year":"2020","unstructured":"Dorhoi A, Kotze LA, Berzofsky JA, Sui Y, Gabrilovich DI, Garg A, Hafner R, Khader SA, Schaible UE, Kaufmann SH, Walzl G, Lutz MB, Mahon RN, Ostrand-Rosenberg S, Bishai W, Du Plessis N (2020) Therapies for tuberculosis and AIDS: myeloid-derived suppressor cells in focus. J Clin Invest 130:2789\u20132799. https:\/\/doi.org\/10.1172\/JCI136288","journal-title":"J Clin Invest"},{"key":"1763_CR35","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1038\/nm.1947","volume":"15","author":"M Economopoulou","year":"2009","unstructured":"Economopoulou M, Langer HF, Celeste A, Orlova VV, Choi EY, Ma M, Vassilopoulos A, Callen E, Deng C, Bassing CH, Boehm M, Nussenzweig A, Chavakis T (2009) Histone H2AX is integral to hypoxia-driven neovascularization. Nat Med 15:553\u2013558. https:\/\/doi.org\/10.1038\/nm.1947","journal-title":"Nat Med"},{"key":"1763_CR36","doi-asserted-by":"publisher","first-page":"8814","DOI":"10.1158\/0008-5472.CAN-09-2115","volume":"69","author":"H Enderling","year":"2009","unstructured":"Enderling H, Anderson AR, Chaplain MA, Beheshti A, Hlatky L, Hahnfeldt P (2009a) Paradoxical dependencies of tumor dormancy and progression on basic cell kinetics. Cancer Res 69:8814\u20138821. https:\/\/doi.org\/10.1158\/0008-5472.CAN-09-2115","journal-title":"Cancer Res"},{"key":"1763_CR37","doi-asserted-by":"publisher","first-page":"1917","DOI":"10.1038\/sj.bjc.6605071","volume":"100","author":"H Enderling","year":"2009","unstructured":"Enderling H, Hlatky L, Hahnfeldt P (2009b) Migration rules: tumours are conglomerates of self-metastases. Br J Cancer 100:1917\u20131925. https:\/\/doi.org\/10.1038\/sj.bjc.6605071","journal-title":"Br J Cancer"},{"key":"1763_CR38","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1093\/imammb\/dqq015","volume":"29","author":"H Enderling","year":"2012","unstructured":"Enderling H, Hlatky L, Hahnfeldt P (2012) The promoting role of a tumour-secreted chemorepellent in self-metastatic tumour progression. Math Med Biol 29:21\u201329. https:\/\/doi.org\/10.1093\/imammb\/dqq015","journal-title":"Math Med Biol"},{"key":"1763_CR39","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1111\/j.1749-6632.1964.tb40991.x","volume":"114","author":"TC Everson","year":"1964","unstructured":"Everson TC (1964) Spontaneous regression of cancer. Ann N Y Acad Sci 114:721\u2013735. https:\/\/doi.org\/10.1111\/j.1749-6632.1964.tb40991.x","journal-title":"Ann N Y Acad Sci"},{"key":"1763_CR40","doi-asserted-by":"publisher","DOI":"10.3390\/ijms262210997","author":"FP Fabrizio","year":"2025","unstructured":"Fabrizio FP (2025) Unlocking lung cancer cell dormancy: an epigenetic perspective. Int J Mol Sci. https:\/\/doi.org\/10.3390\/ijms262210997","journal-title":"Int J Mol Sci"},{"key":"1763_CR41","doi-asserted-by":"publisher","first-page":"3472","DOI":"10.4049\/jimmunol.1003299","volume":"186","author":"M Fallahi-Sichani","year":"2011","unstructured":"Fallahi-Sichani M, El-Kebir M, Marino S, Kirschner DE, Linderman JJ (2011) Multiscale computational modeling reveals a critical role for TNF-alpha receptor 1 dynamics in tuberculosis granuloma formation. J Immunol 186:3472\u20133483. https:\/\/doi.org\/10.4049\/jimmunol.1003299","journal-title":"J Immunol"},{"key":"1763_CR42","doi-asserted-by":"publisher","first-page":"3169","DOI":"10.4049\/jimmunol.1103298","volume":"188","author":"M Fallahi-Sichani","year":"2012","unstructured":"Fallahi-Sichani M, Flynn JL, Linderman JJ, Kirschner DE (2012) Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability. J Immunol 188:3169\u20133178. https:\/\/doi.org\/10.4049\/jimmunol.1103298","journal-title":"J Immunol"},{"key":"1763_CR43","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2025.1561719","volume":"16","author":"C Fang","year":"2025","unstructured":"Fang C, He X, Tang F, Wang Z, Pan C, Zhang Q, Wu J, Wang Q, Liu D, Zhang Y (2025) Where lung cancer and tuberculosis intersect: recent advances. Front Immunol 16:1561719. https:\/\/doi.org\/10.3389\/fimmu.2025.1561719","journal-title":"Front Immunol"},{"key":"1763_CR44","doi-asserted-by":"publisher","first-page":"5829","DOI":"10.1038\/onc.2017.188","volume":"36","author":"J Feng","year":"2017","unstructured":"Feng J, Yang H, Zhang Y, Wei H, Zhu Z, Zhu B, Yang M, Cao W, Wang L, Wu Z (2017) Tumor cell-derived lactate induces TAZ-dependent upregulation of PD-L1 through GPR81 in human lung cancer cells. Oncogene 36:5829\u20135839. https:\/\/doi.org\/10.1038\/onc.2017.188","journal-title":"Oncogene"},{"key":"1763_CR45","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines10112709","author":"S Filiberti","year":"2022","unstructured":"Filiberti S, Russo M, Lonardi S, Bugatti M, Vermi W, Tournier C, Giurisato E (2022) Self-renewal of macrophages: tumor-released factors and signaling pathways. Biomedicines. https:\/\/doi.org\/10.3390\/biomedicines10112709","journal-title":"Biomedicines"},{"key":"1763_CR46","doi-asserted-by":"publisher","first-page":"3812","DOI":"10.1182\/blood-2006-07-035972","volume":"109","author":"K Fischer","year":"2007","unstructured":"Fischer K, Hoffmann P, Voelkl S, Meidenbauer N, Ammer J, Edinger M, Gottfried E, Schwarz S, Rothe G, Hoves S, Renner K, Timischl B, Mackensen A, Kunz-Schughart L, Andreesen R, Krause SW, Kreutz M (2007) Inhibitory effect of tumor cell-derived lactic acid on human T cells. Blood 109:3812\u20133819. https:\/\/doi.org\/10.1182\/blood-2006-07-035972","journal-title":"Blood"},{"key":"1763_CR47","doi-asserted-by":"publisher","first-page":"4682","DOI":"10.1016\/j.cell.2022.10.025","volume":"185","author":"JL Flynn","year":"2022","unstructured":"Flynn JL, Chan J (2022) Immune cell interactions in tuberculosis. Cell 185:4682\u20134702. https:\/\/doi.org\/10.1016\/j.cell.2022.10.025","journal-title":"Cell"},{"key":"1763_CR48","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/s41573-018-0007-y","volume":"18","author":"J Galon","year":"2019","unstructured":"Galon J, Bruni D (2019) Approaches to treat immune hot, altered and cold tumours with combination immunotherapies. Nat Rev Drug Discov 18:197\u2013218. https:\/\/doi.org\/10.1038\/s41573-018-0007-y","journal-title":"Nat Rev Drug Discov"},{"key":"1763_CR49","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1137\/040603127","volume":"3","author":"D Gammack","year":"2005","unstructured":"Gammack D, Ganguli S, Marino S, Segovia-Juarez J, Kirschner DE (2005) Understanding the immune response in tuberculosis using different mathematical models and biological scales. Multiscale Model Simul 3:312\u2013345","journal-title":"Multiscale Model Simul"},{"key":"1763_CR50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005991","volume":"14","author":"A Ghaffarizadeh","year":"2018","unstructured":"Ghaffarizadeh A, Heiland R, Friedman SH, Mumenthaler SM, Macklin P (2018) PhysiCell: an open source physics-based cell simulator for 3-D multicellular systems. PLoS Comput Biol 14:e1005991. https:\/\/doi.org\/10.1371\/journal.pcbi.1005991","journal-title":"PLoS Comput Biol"},{"key":"1763_CR51","unstructured":"Global Tuberculosis Report 2025. 1st edn, (World Health Organization, 2025)"},{"key":"1763_CR52","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.01089-2018","author":"D Goletti","year":"2018","unstructured":"Goletti D, Arlehamn CSL, Scriba TJ, Anthony R, Cirillo DM, Alonzi T, Denkinger CM, Cobelens F (2018) Can we predict tuberculosis cure? What tools are available? Eur Respir J. https:\/\/doi.org\/10.1183\/13993003.01089-2018","journal-title":"Eur Respir J"},{"key":"1763_CR53","doi-asserted-by":"publisher","DOI":"10.1098\/rsif.2017.0320","author":"C Gong","year":"2017","unstructured":"Gong C, Milberg O, Wang B, Vicini P, Narwal R, Roskos L, Popel AS (2017) A computational multiscale agent-based model for simulating spatio-temporal tumour immune response to PD1 and PDL1 inhibition. J R Soc Interface. https:\/\/doi.org\/10.1098\/rsif.2017.0320","journal-title":"J R Soc Interface"},{"key":"1763_CR54","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1080\/10543406.2022.2162066","volume":"33","author":"J Gou","year":"2023","unstructured":"Gou J (2023) On dependence assumption in p-value based multiple test procedures. J Biopharm Stat 33:596\u2013610. https:\/\/doi.org\/10.1080\/10543406.2022.2162066","journal-title":"J Biopharm Stat"},{"key":"1763_CR55","doi-asserted-by":"publisher","DOI":"10.18564\/jasss.4259","author":"V Grimm","year":"2020","unstructured":"Grimm V, Railsback SF, Vincenot CE, Berger U, Gallagher C, Deangelis DL, Edmonds B, Ge J, Giske J, Groeneveld J, Johnston ASA, Milles A, Nabe-Nielsen J, Polhill JG, Radchuk V, Rohw\u00e4der M-S, Stillman RA, Thiele JC, Ayll\u00f3n D (2020) The ODD protocol for describing agent-based and other simulation models: a second update to improve clarity, replication, and structural realism. J Artif Soc Soc Simul. https:\/\/doi.org\/10.18564\/jasss.4259","journal-title":"J Artif Soc Soc Simul"},{"key":"1763_CR56","doi-asserted-by":"publisher","DOI":"10.15761\/icst.1000204","author":"O Guttman","year":"2016","unstructured":"Guttman O, Lewis EC (2016) M2-like macrophages and tumor-associated macrophages: overlapping and distinguishing properties en route to a safe therapeutic potential. Integr Cancer Sci Ther. https:\/\/doi.org\/10.15761\/icst.1000204","journal-title":"Integr Cancer Sci Ther"},{"key":"1763_CR57","doi-asserted-by":"publisher","first-page":"1190333","DOI":"10.3389\/fimmu.2023.1190333","volume":"14","author":"J Han","year":"2023","unstructured":"Han J, Wu M, Liu Z (2023) Dysregulation in IFN-gamma signaling and response: the barricade to tumor immunotherapy. Front Immunol 14:1190333. https:\/\/doi.org\/10.3389\/fimmu.2023.1190333","journal-title":"Front Immunol"},{"key":"1763_CR58","doi-asserted-by":"publisher","DOI":"10.4137\/CMO.S9633","author":"K Harris","year":"2012","unstructured":"Harris K, Khachaturova I, Azab B, Maniatis T, Murukutla S, Chalhoub M, Hatoum H, Kilkenny T, Elsayegh D, Maroun R, Alkaied H (2012) Small cell lung cancer doubling time and its effect on clinical presentation: a concise review. Clin Med Insights Oncol. https:\/\/doi.org\/10.4137\/CMO.S9633","journal-title":"Clin Med Insights Oncol"},{"key":"1763_CR59","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0250531","volume":"16","author":"LJ Ho","year":"2021","unstructured":"Ho LJ, Yang HY, Chung CH, Chang WC, Yang SS, Sun CA, Chien WC, Su RY (2021) Increased risk of secondary lung cancer in patients with tuberculosis: a nationwide, population-based cohort study. PLoS ONE 16:e0250531. https:\/\/doi.org\/10.1371\/journal.pone.0250531","journal-title":"PLoS ONE"},{"key":"1763_CR60","doi-asserted-by":"publisher","first-page":"13806","DOI":"10.1073\/pnas.95.23.13806","volume":"95","author":"J Hodge-Dufour","year":"1998","unstructured":"Hodge-Dufour J, Marino MW, Horton MR, Jungbluth A, Burdick MD, Strieter RM, Noble PW, Hunter CA, Pure E (1998) Inhibition of interferon gamma induced interleukin 12 production: a potential mechanism for the anti-inflammatory activities of tumor necrosis factor. Proc Natl Acad Sci U S A 95:13806\u201313811. https:\/\/doi.org\/10.1073\/pnas.95.23.13806","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1763_CR61","doi-asserted-by":"publisher","first-page":"7924","DOI":"10.4049\/jimmunol.179.11.7924","volume":"179","author":"AA Hombach","year":"2007","unstructured":"Hombach AA, Kofler D, Hombach A, Rappl G, Abken H (2007) Effective proliferation of human regulatory T cells requires a strong costimulatory CD28 signal that cannot be substituted by IL-2. J Immunol 179:7924\u20137931. https:\/\/doi.org\/10.4049\/jimmunol.179.11.7924","journal-title":"J Immunol"},{"key":"1763_CR62","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1016\/j.lungcan.2006.05.011","volume":"53","author":"T Horino","year":"2006","unstructured":"Horino T, Takao T, Yamamoto M, Geshi T, Hashimoto K (2006) Spontaneous remission of small cell lung cancer: a case report and review in the literature. Lung Cancer 53:249\u2013252. https:\/\/doi.org\/10.1016\/j.lungcan.2006.05.011","journal-title":"Lung Cancer"},{"key":"1763_CR63","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s13014-016-0744-1","volume":"12","author":"N Ishibashi","year":"2017","unstructured":"Ishibashi N, Maebayashi T, Aizawa T, Sakaguchi M, Nishimaki H, Masuda S (2017) Correlation between the Ki-67 proliferation index and response to radiation therapy in small cell lung cancer. Radiat Oncol 12:16. https:\/\/doi.org\/10.1186\/s13014-016-0744-1","journal-title":"Radiat Oncol"},{"key":"1763_CR64","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-93113-y","volume":"11","author":"T Iwai","year":"2021","unstructured":"Iwai T, Sugimoto M, Patil NS, Bower D, Suzuki M, Kato C, Yorozu K, Kurasawa M, Shames DS, Kondoh O (2021) Both T cell priming in lymph node and CXCR3-dependent migration are the key events for predicting the response of atezolizumab. Sci Rep 11:13912. https:\/\/doi.org\/10.1038\/s41598-021-93113-y","journal-title":"Sci Rep"},{"key":"1763_CR65","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1038\/s41421-024-00755-z","volume":"10","author":"Y Jin","year":"2024","unstructured":"Jin Y, Wu Y, Reuben A, Zhu L, Gay CM, Wu Q, Zhou X, Mo H, Zheng Q, Ren J, Fang Z, Peng T, Wang N, Ma L, Lungevity PIC, Fan Y, Song H, Zhang J, Chen M (2024) Author correction: single-cell and spatial proteo-transcriptomic profiling reveals immune infiltration heterogeneity associated with neuroendocrine features in small cell lung cancer. Cell Discov 10:126. https:\/\/doi.org\/10.1038\/s41421-024-00755-z","journal-title":"Cell Discov"},{"key":"1763_CR66","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1111\/imr.12671","volume":"285","author":"C Jm","year":"2018","unstructured":"Jm C, Evans S, Hult C, Lr J, Wessler T, Ja M, Marino S, Na C, Jt M, Jj L, De K (2018) Dynamic balance of pro- and anti-inflammatory signals controls disease and limits pathology. Immunol Rev 285:147\u2013167","journal-title":"Immunol Rev"},{"key":"1763_CR67","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1007\/s12195-020-00650-z","volume":"14","author":"LR Joslyn","year":"2021","unstructured":"Joslyn LR, Kirschner DE, Linderman JJ (2021) CaliPro: a calibration protocol that utilizes parameter density estimation to explore parameter space and calibrate complex biological models. Cell Mol Bioeng 14:31\u201347. https:\/\/doi.org\/10.1007\/s12195-020-00650-z","journal-title":"Cell Mol Bioeng"},{"key":"1763_CR68","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1038\/ni.2046","volume":"12","author":"C Kao","year":"2011","unstructured":"Kao C, Oestreich KJ, Paley MA, Crawford A, Angelosanto JM, Ali MA, Intlekofer AM, Boss JM, Reiner SL, Weinmann AS, Wherry EJ (2011) Transcription factor T-bet represses expression of the inhibitory receptor PD-1 and sustains virus-specific CD8+ T cell responses during chronic infection. Nat Immunol 12:663\u2013671. https:\/\/doi.org\/10.1038\/ni.2046","journal-title":"Nat Immunol"},{"key":"1763_CR69","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01586-16","author":"CA Kerantzas","year":"2017","unstructured":"Kerantzas CA, Jacobs WR Jr. (2017) Origins of combination therapy for tuberculosis: lessons for future antimicrobial development and application. Mbio. https:\/\/doi.org\/10.1128\/mBio.01586-16","journal-title":"Mbio"},{"key":"1763_CR70","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002742","volume":"8","author":"PS Kim","year":"2012","unstructured":"Kim PS, Lee PP (2012) Modeling protective anti-tumor immunity via preventative cancer vaccines using a hybrid agent-based and delay differential equation approach. PLoS Comput Biol 8:e1002742. https:\/\/doi.org\/10.1371\/journal.pcbi.1002742","journal-title":"PLoS Comput Biol"},{"key":"1763_CR71","doi-asserted-by":"publisher","first-page":"1906","DOI":"10.1001\/jama.2025.0560","volume":"333","author":"SY Kim","year":"2025","unstructured":"Kim SY, Park HS, Chiang AC (2025) Small cell lung cancer: a review. JAMA 333:1906\u20131917. https:\/\/doi.org\/10.1001\/jama.2025.0560","journal-title":"JAMA"},{"key":"1763_CR72","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/s41417-021-00303-x","volume":"29","author":"K Kohli","year":"2022","unstructured":"Kohli K, Pillarisetty VG, Kim TS (2022) Key chemokines direct migration of immune cells in solid tumors. Cancer Gene Ther 29:10\u201321. https:\/\/doi.org\/10.1038\/s41417-021-00303-x","journal-title":"Cancer Gene Ther"},{"key":"1763_CR73","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1007\/s00430-023-00768-7","volume":"212","author":"L Kretschmer","year":"2023","unstructured":"Kretschmer L, Fuchs N, Busch DH, Buchholz VR (2023) Picking up speed: cell cycle regulation during effector CD8(+) T cell differentiation. Med Microbiol Immunol 212:253\u2013260. https:\/\/doi.org\/10.1007\/s00430-023-00768-7","journal-title":"Med Microbiol Immunol"},{"key":"1763_CR74","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1013033","volume":"21","author":"KC Krupinsky","year":"2025","unstructured":"Krupinsky KC, Michael CT, Nanda P, Mattila JT, Kirschner D (2025) Distinguishing multiple roles of T cell and macrophage involvement in determining lymph node fates during Mycobacterium tuberculosis infection. PLoS Comput Biol 21:e1013033. https:\/\/doi.org\/10.1371\/journal.pcbi.1013033","journal-title":"PLoS Comput Biol"},{"key":"1763_CR75","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/s41571-023-00846-y","volume":"21","author":"SA Lasser","year":"2024","unstructured":"Lasser SA, Ozbay Kurt FG, Arkhypov I, Utikal J, Umansky V (2024) Myeloid-derived suppressor cells in cancer and cancer therapy. Nat Rev Clin Oncol 21:147\u2013164. https:\/\/doi.org\/10.1038\/s41571-023-00846-y","journal-title":"Nat Rev Clin Oncol"},{"key":"1763_CR76","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1007\/s12013-014-0477-4","volume":"72","author":"J Li","year":"2015","unstructured":"Li J, Jiang E, Wang X, Shangguan AJ, Zhang L, Yu Z (2015) Dormant cells: the original cause of tumor recurrence and metastasis. Cell Biochem Biophys 72:317\u2013320. https:\/\/doi.org\/10.1007\/s12013-014-0477-4","journal-title":"Cell Biochem Biophys"},{"key":"1763_CR77","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1016\/j.semcancer.2022.09.005","volume":"86","author":"T Li","year":"2022","unstructured":"Li T, Qiao T (2022) Unraveling tumor microenvironment of small-cell lung cancer: implications for immunotherapy. Semin Cancer Biol 86:117\u2013125. https:\/\/doi.org\/10.1016\/j.semcancer.2022.09.005","journal-title":"Semin Cancer Biol"},{"key":"1763_CR78","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/nm.3412","volume":"20","author":"PL Lin","year":"2014","unstructured":"Lin PL, Ford CB, Coleman MT, Myers AJ, Gawande R, Ioerger T, Sacchettini J, Fortune SM, Flynn JL (2014) Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing. Nat Med 20:75\u201379. https:\/\/doi.org\/10.1038\/nm.3412","journal-title":"Nat Med"},{"key":"1763_CR79","doi-asserted-by":"publisher","first-page":"e1005739","DOI":"10.1371\/journal.ppat.1005739","volume":"12","author":"PL Lin","year":"2016","unstructured":"Lin PL, Maiello P, Gideon HP, Coleman MT, Cadena AM, Rodgers MA, Gregg R, O\u2019malley M, Tomko J, Fillmore D, Frye LJ, Rutledge T, Difazio RM, Janssen C, Klein E, Andersen PL, Fortune SM, Flynn JL (2016) PET CT identifies reactivation risk in cynomolgus macaques with latent M. Tuberculosis. PLoS Pathog 12:e1005739. https:\/\/doi.org\/10.1371\/journal.ppat.1005739","journal-title":"PLoS Pathog"},{"key":"1763_CR80","doi-asserted-by":"publisher","first-page":"2541","DOI":"10.4049\/jimmunol.1800993","volume":"201","author":"PL Lin","year":"2018","unstructured":"Lin PL, Flynn JL (2018) The end of the binary era: revisiting the spectrum of tuberculosis. J Immunol 201:2541\u20132548. https:\/\/doi.org\/10.4049\/jimmunol.1800993","journal-title":"J Immunol"},{"key":"1763_CR81","doi-asserted-by":"publisher","first-page":"2873","DOI":"10.4049\/jimmunol.0903117","volume":"184","author":"JJ Linderman","year":"2010","unstructured":"Linderman JJ, Riggs T, Pande M, Miller M, Marino S, Kirschner DE (2010) Characterizing the dynamics of CD4+ T cell priming within a lymph node. J Immunol 184:2873\u20132885. https:\/\/doi.org\/10.4049\/jimmunol.0903117","journal-title":"J Immunol"},{"key":"1763_CR82","doi-asserted-by":"publisher","first-page":"045026","DOI":"10.1088\/1361-6560\/abd4f9","volume":"66","author":"R Liu","year":"2021","unstructured":"Liu R, Higley KA, Swat MH, Chaplain MJ, Powathil GG, Glazier JA (2021) Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D. Phys Med Biol 66:045026. https:\/\/doi.org\/10.1088\/1361-6560\/abd4f9","journal-title":"Phys Med Biol"},{"key":"1763_CR83","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1186\/1471-2105-7-352","volume":"7","author":"PL Lollini","year":"2006","unstructured":"Lollini PL, Motta S, Pappalardo F (2006) Discovery of cancer vaccination protocols with a genetic algorithm driving an agent based simulator. BMC Bioinformatics 7:352. https:\/\/doi.org\/10.1186\/1471-2105-7-352","journal-title":"BMC Bioinformatics"},{"key":"1763_CR84","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1111\/j.1440-1843.2006.00789.x","volume":"11","author":"SY Low","year":"2006","unstructured":"Low SY, Eng P, Keng GH, Ng DC (2006) Positron emission tomography with CT in the evaluation of non-small cell lung cancer in populations with a high prevalence of tuberculosis. Respirology 11:84\u201389. https:\/\/doi.org\/10.1111\/j.1440-1843.2006.00789.x","journal-title":"Respirology"},{"key":"1763_CR85","doi-asserted-by":"publisher","first-page":"1994","DOI":"10.1038\/s41591-025-03627-5","volume":"31","author":"FJ Lowery","year":"2025","unstructured":"Lowery FJ, Goff SL, Gasmi B, Parkhurst MR, Ratnam NM, Halas HK, Shelton TE, Langhan MM, Bhasin A, Dinerman AJ, Dulemba V, Goldlust IS, Gustafson AM, Hakim AA, Hitscherich KJ, Kenney LM, Levy L, Rault-Wang JG, Bera A, Ray S, Seavey CD, Hoang CD, Hernandez JM, Gartner JJ, Sindiri S, Prickett TD, Mcintyre LS, Krishna S, Robbins PF, Klemen ND, Kwong MLM, Yang JC, Rosenberg SA (2025) Neoantigen-specific tumor-infiltrating lymphocytes in gastrointestinal cancers: a phase 2 trial. Nat Med 31:1994\u20132003. https:\/\/doi.org\/10.1038\/s41591-025-03627-5","journal-title":"Nat Med"},{"key":"1763_CR86","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1016\/j.jtbi.2003.11.023","volume":"227","author":"S Marino","year":"2004","unstructured":"Marino S, Kirschner DE (2004) The human immune response to Mycobacterium tuberculosis in lung and lymph node. J Theor Biol 227:463\u2013486","journal-title":"J Theor Biol"},{"key":"1763_CR87","doi-asserted-by":"publisher","first-page":"1909","DOI":"10.1371\/journal.pcbi.0030194","volume":"3","author":"S Marino","year":"2007","unstructured":"Marino S, Sud D, Plessner H, Lin PL, Chan J, Flynn JL, Kirschner DE (2007) Differences in reactivation of tuberculosis induced from anti-TNF treatments are based on bioavailability in granulomatous tissue. PLoS Comput Biol 3:1909\u20131924. https:\/\/doi.org\/10.1371\/journal.pcbi.0030194","journal-title":"PLoS Comput Biol"},{"key":"1763_CR88","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.jtbi.2008.04.011","volume":"254","author":"S Marino","year":"2008","unstructured":"Marino S, Hogue IB, Ray CJ, Kirschner DE (2008) A methodology for performing global uncertainty and sensitivity analysis in systems biology. J Theor Biol 254:178\u2013196. https:\/\/doi.org\/10.1016\/j.jtbi.2008.04.011","journal-title":"J Theor Biol"},{"key":"1763_CR89","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1073\/pnas.1311322111","volume":"111","author":"S Marino","year":"2014","unstructured":"Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD (2014) Mathematical modeling of primary succession of murine intestinal microbiota. Proc Natl Acad Sci U S A 111:439\u2013444. https:\/\/doi.org\/10.1073\/pnas.1311322111","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1763_CR90","doi-asserted-by":"publisher","DOI":"10.3390\/computation6040058","author":"S Marino","year":"2018","unstructured":"Marino S, Hult C, Wolberg P, Linderman JJ, Kirschner DE (2018) The role of dimensionality in understanding granuloma formation. Computation. https:\/\/doi.org\/10.3390\/computation6040058","journal-title":"Computation"},{"key":"1763_CR91","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00312-17","author":"CJ Martin","year":"2017","unstructured":"Martin CJ, Cadena AM, Leung VW, Lin PL, Maiello P, Hicks N, Chase MR, Flynn JL, Fortune SM (2017) Digitally barcoding mycobacterium tuberculosis reveals in vivo infection dynamics in the macaque model of tuberculosis. Mbio. https:\/\/doi.org\/10.1128\/mBio.00312-17","journal-title":"Mbio"},{"key":"1763_CR92","doi-asserted-by":"publisher","first-page":"1078","DOI":"10.1128\/jb.184.4.1078-1088.2002","volume":"184","author":"MC Menendez","year":"2002","unstructured":"Menendez MC, Garcia MJ, Navarro MC, Gonzalez-Y-Merchand JA, Rivera-Gutierrez S, Garcia-Sanchez L, Cox RA (2002) Characterization of an rRNA operon (rrnB) of Mycobacterium fortuitum and other mycobacterial species: implications for the classification of mycobacteria. J Bacteriol 184:1078\u20131088. https:\/\/doi.org\/10.1128\/jb.184.4.1078-1088.2002","journal-title":"J Bacteriol"},{"key":"1763_CR93","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1208\/s12248-022-00756-4","volume":"24","author":"B Menezes","year":"2022","unstructured":"Menezes B, Khera E, Calopiz M, Smith MD, Ganno ML, Cilliers C, Abu-Yousif AO, Linderman JJ, Thurber GM (2022) Pharmacokinetics and pharmacodynamics of TAK-164 antibody drug conjugate coadministered with unconjugated antibody. AAPS J 24:107. https:\/\/doi.org\/10.1208\/s12248-022-00756-4","journal-title":"AAPS J"},{"key":"1763_CR94","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1200\/CCI.18.00069","volume":"3","author":"J Metzcar","year":"2019","unstructured":"Metzcar J, Wang Y, Heiland R, Macklin P (2019) A review of cell-based computational modeling in cancer biology. JCO Clin Cancer Inform 3:1\u201313. https:\/\/doi.org\/10.1200\/CCI.18.00069","journal-title":"JCO Clin Cancer Inform"},{"key":"1763_CR95","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.613638","volume":"11","author":"JA Millar","year":"2020","unstructured":"Millar JA, Butler JR, Evans S, Mattila JT, Linderman JJ, Flynn JL, Kirschner DE (2020) Spatial organization and recruitment of non-specific T cells may limit T cell-macrophage interactions within Mycobacterium tuberculosis granulomas. Front Immunol 11:613638. https:\/\/doi.org\/10.3389\/fimmu.2020.613638","journal-title":"Front Immunol"},{"key":"1763_CR96","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002970","volume":"9","author":"GR Mirams","year":"2013","unstructured":"Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, Corrias A, Davit Y, Dunn SJ, Fletcher AG, Harvey DG, Marsh ME, Osborne JM, Pathmanathan P, Pitt-Francis J, Southern J, Zemzemi N, Gavaghan DJ (2013) Chaste: an open source C++ library for computational physiology and biology. PLoS Comput Biol 9:e1002970. https:\/\/doi.org\/10.1371\/journal.pcbi.1002970","journal-title":"PLoS Comput Biol"},{"key":"1763_CR97","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2023.111656","volume":"576","author":"N Mohsin","year":"2024","unstructured":"Mohsin N, Enderling H, Brady-Nicholls R, Zahid MU (2024) Simulating tumor volume dynamics in response to radiotherapy: implications of model selection. J Theor Biol 576:111656. https:\/\/doi.org\/10.1016\/j.jtbi.2023.111656","journal-title":"J Theor Biol"},{"key":"1763_CR98","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1016\/j.immuni.2023.06.003","volume":"56","author":"MA Moreno Ayala","year":"2023","unstructured":"Moreno Ayala MA, Campbell TF, Zhang C, Dahan N, Bockman A, Prakash V, Feng L, Sher T, Dupage M (2023) CXCR3 expression in regulatory T cells drives interactions with type I dendritic cells in tumors to restrict CD8(+) T cell antitumor immunity. Immunity 56:1613\u20131630. https:\/\/doi.org\/10.1016\/j.immuni.2023.06.003","journal-title":"Immunity"},{"key":"1763_CR99","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1016\/j.ccell.2024.01.010","volume":"42","author":"BY Nabet","year":"2024","unstructured":"Nabet BY, Hamidi H, Lee MC, Banchereau R, Morris S, Adler L, Gayevskiy V, Elhossiny AM, Srivastava MK, Patil NS, Smith KA, Jesudason R, Chan C, Chang PS, Fernandez M, Rost S, Mcginnis LM, Koeppen H, Gay CM, Minna JD, Heymach JV, Chan JM, Rudin CM, Byers LA, Liu SV, Reck M, Shames DS (2024) Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade. Cancer Cell 42:429\u2013443. https:\/\/doi.org\/10.1016\/j.ccell.2024.01.010","journal-title":"Cancer Cell"},{"key":"1763_CR100","doi-asserted-by":"publisher","DOI":"10.3389\/fams.2023.1256443","author":"P Nanda","year":"2023","unstructured":"Nanda P, Kirschner DE (2023) Calibration methods to fit parameters within complex biological models. Front Appl Math Stat. https:\/\/doi.org\/10.3389\/fams.2023.1256443","journal-title":"Front Appl Math Stat"},{"key":"1763_CR101","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1084\/jem.158.3.670","volume":"158","author":"CF Nathan","year":"1983","unstructured":"Nathan CF, Murray HW, Wiebe ME, Rubin BY (1983) Identification of interferon-gamma as the lymphokine that activates human macrophage oxidative metabolism and antimicrobial activity. J Exp Med 158:670\u2013689. https:\/\/doi.org\/10.1084\/jem.158.3.670","journal-title":"J Exp Med"},{"key":"1763_CR102","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1016\/0014-4827(59)90130-2","volume":"16","author":"AA Newton","year":"1959","unstructured":"Newton AA, Wildy P (1959) Parasynchronous division of HeLa cells. Exp Cell Res 16:624\u2013635. https:\/\/doi.org\/10.1016\/0014-4827(59)90130-2","journal-title":"Exp Cell Res"},{"key":"1763_CR103","doi-asserted-by":"publisher","first-page":"20140640","DOI":"10.1098\/rsif.2014.0640","volume":"11","author":"KA Norton","year":"2014","unstructured":"Norton KA, Popel AS (2014) An agent-based model of cancer stem cell initiated avascular tumour growth and metastasis: the effect of seeding frequency and location. J R Soc Interface 11:20140640. https:\/\/doi.org\/10.1098\/rsif.2014.0640","journal-title":"J R Soc Interface"},{"key":"1763_CR104","doi-asserted-by":"publisher","DOI":"10.3390\/pr7010037","author":"KA Norton","year":"2019","unstructured":"Norton KA, Gong C, Jamalian S, Popel AS (2019) Multiscale agent-based and hybrid modeling of the tumor immune microenvironment. Processes (Basel). https:\/\/doi.org\/10.3390\/pr7010037","journal-title":"Processes (Basel)"},{"key":"1763_CR105","doi-asserted-by":"publisher","first-page":"8569328","DOI":"10.1155\/2017\/8569328","volume":"2017","author":"ME Oraiopoulou","year":"2017","unstructured":"Oraiopoulou ME, Tzamali E, Tzedakis G, Vakis A, Papamatheakis J, Sakkalis V (2017) In vitro\/in silico study on the role of doubling time heterogeneity among primary glioblastoma cell lines. Biomed Res Int 2017:8569328. https:\/\/doi.org\/10.1155\/2017\/8569328","journal-title":"Biomed Res Int"},{"key":"1763_CR106","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1093\/bmb\/ldh047","volume":"73\u201374","author":"LP Ormerod","year":"2005","unstructured":"Ormerod LP (2005) Multidrug-resistant tuberculosis (MDR-TB): epidemiology, prevention and treatment. Br Med Bull 73\u201374:17\u201324. https:\/\/doi.org\/10.1093\/bmb\/ldh047","journal-title":"Br Med Bull"},{"key":"1763_CR107","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1186\/s12859-018-2510-x","volume":"19","author":"J Ozik","year":"2018","unstructured":"Ozik J, Collier N, Wozniak JM, Macal C, Cockrell C, Friedman SH, Ghaffarizadeh A, Heiland R, An G, Macklin P (2018) High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. BMC Bioinformatics 19:483. https:\/\/doi.org\/10.1186\/s12859-018-2510-x","journal-title":"BMC Bioinformatics"},{"key":"1763_CR108","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1158\/0008-5472.CAN-10-1733","volume":"71","author":"A Palazon","year":"2011","unstructured":"Palazon A, Teijeira A, Martinez-Forero I, Hervas-Stubbs S, Roncal C, Penuelas I, Dubrot J, Morales-Kastresana A, Perez-Gracia JL, Ochoa MC, Ochoa-Callejero L, Martinez A, Luque A, Dinchuk J, Rouzaut A, Jure-Kunkel M, Melero I (2011) Agonist anti-CD137 mAb act on tumor endothelial cells to enhance recruitment of activated T lymphocytes. Cancer Res 71:801\u2013811. https:\/\/doi.org\/10.1158\/0008-5472.CAN-10-1733","journal-title":"Cancer Res"},{"issue":"669\u2013683","key":"1763_CR109","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2017.10.003","volume":"32","author":"A Palazon","year":"2017","unstructured":"Palazon A, Tyrakis PA, Macias D, Velica P, Rundqvist H, Fitzpatrick S, Vojnovic N, Phan AT, Loman N, Hedenfalk I, Hatschek T, Lovrot J, Foukakis T, Goldrath AW, Bergh J, Johnson RS (2017) An HIF-1alpha\/VEGF-A axis in cytotoxic T cells regulates tumor progression. Cancer Cell 32(669\u2013683):e665. https:\/\/doi.org\/10.1016\/j.ccell.2017.10.003","journal-title":"Cancer Cell"},{"key":"1763_CR110","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0026523","volume":"6","author":"F Pappalardo","year":"2011","unstructured":"Pappalardo F, Martinez Forero I, Pennisi M, Palazon A, Melero I, Motta S (2011) SimB16: modeling induced immune system response against B16-melanoma. PLoS ONE 6:e26523. https:\/\/doi.org\/10.1371\/journal.pone.0026523","journal-title":"PLoS ONE"},{"issue":"Suppl 7","key":"1763_CR111","doi-asserted-by":"publisher","first-page":"S13","DOI":"10.1186\/1471-2105-11-S7-S13","volume":"11","author":"M Pennisi","year":"2010","unstructured":"Pennisi M, Pappalardo F, Palladini A, Nicoletti G, Nanni P, Lollini PL, Motta S (2010) Modeling the competition between lung metastases and the immune system using agents. BMC Bioinformatics 11(Suppl 7):S13. https:\/\/doi.org\/10.1186\/1471-2105-11-S7-S13","journal-title":"BMC Bioinformatics"},{"key":"1763_CR112","doi-asserted-by":"publisher","first-page":"E4041","DOI":"10.1073\/pnas.1720948115","volume":"115","author":"E Peranzoni","year":"2018","unstructured":"Peranzoni E, Lemoine J, Vimeux L, Feuillet V, Barrin S, Kantari-Mimoun C, Bercovici N, Guerin M, Biton J, Ouakrim H, Regnier F, Lupo A, Alifano M, Damotte D, Donnadieu E (2018) Macrophages impede CD8 T cells from reaching tumor cells and limit the efficacy of anti-PD-1 treatment. Proc Natl Acad Sci U S A 115:E4041\u2013E4050. https:\/\/doi.org\/10.1073\/pnas.1720948115","journal-title":"Proc Natl Acad Sci U S A"},{"key":"1763_CR113","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1012266","volume":"20","author":"A Petrucciani","year":"2024","unstructured":"Petrucciani A, Hoerter A, Kotze L, Du Plessis N, Pienaar E (2024) Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma. PLoS Comput Biol 20:e1012266. https:\/\/doi.org\/10.1371\/journal.pcbi.1012266","journal-title":"PLoS Comput Biol"},{"key":"1763_CR114","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.jtbi.2014.11.021","volume":"367","author":"E Pienaar","year":"2015","unstructured":"Pienaar E, Cilfone NA, Lin PL, Dartois V, Mattila JT, Butler JR, Flynn JL, Kirschner DE, Linderman JJ (2015a) A computational tool integrating host immunity with antibiotic dynamics to study tuberculosis treatment. J Theor Biol 367:166\u2013179. https:\/\/doi.org\/10.1016\/j.jtbi.2014.11.021","journal-title":"J Theor Biol"},{"key":"1763_CR115","doi-asserted-by":"publisher","DOI":"10.1186\/s12918-015-0221-8","volume":"9","author":"E Pienaar","year":"2015","unstructured":"Pienaar E, Dartois V, Linderman JJ, Kirschner DE (2015b) In silico evaluation and exploration of antibiotic tuberculosis treatment regimens. BMC Syst Biol 9:79. https:\/\/doi.org\/10.1186\/s12918-015-0221-8","journal-title":"BMC Syst Biol"},{"key":"1763_CR116","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0196322","author":"E Pienaar","year":"2018","unstructured":"Pienaar E, Linderman J (2018) Emergence and selection of isoniazid and rifampin resistance in tuberculosis granulomas. PLoS ONE. https:\/\/doi.org\/10.1371\/journal.pone.0196322","journal-title":"PLoS ONE"},{"key":"1763_CR117","doi-asserted-by":"publisher","first-page":"2244","DOI":"10.1158\/1078-0432.CCR-14-2958","volume":"21","author":"MC Pietanza","year":"2015","unstructured":"Pietanza MC, Byers LA, Minna JD, Rudin CM (2015) Small cell lung cancer: will recent progress lead to improved outcomes? Clin Cancer Res 21:2244\u20132255. https:\/\/doi.org\/10.1158\/1078-0432.CCR-14-2958","journal-title":"Clin Cancer Res"},{"key":"1763_CR118","doi-asserted-by":"publisher","first-page":"4079","DOI":"10.4049\/jimmunol.1201061","volume":"189","author":"JM Pitt","year":"2012","unstructured":"Pitt JM, Stavropoulos E, Redford PS, Beebe AM, Bancroft GJ, Young DB, O\u2019garra A (2012) Blockade of IL-10 signaling during bacillus Calmette-Guerin vaccination enhances and sustains Th1, Th17, and innate lymphoid IFN-gamma and IL-17 responses and increases protection to Mycobacterium tuberculosis infection. J Immunol 189:4079\u20134087. https:\/\/doi.org\/10.4049\/jimmunol.1201061","journal-title":"J Immunol"},{"key":"1763_CR119","doi-asserted-by":"publisher","unstructured":"Poleszczuk J, Macklin P, Enderling H (2016) Agent-Based Modeling of Cancer Stem Cell Driven Solid Tumor Growth. Methods in molecular biology (Clifton, N.J 1516:335\u2013346. https:\/\/doi.org\/10.1007\/7651_2016_346","DOI":"10.1007\/7651_2016_346"},{"key":"1763_CR120","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1177\/0037549717699072","volume":"93","author":"F Pourhasanzade","year":"2017","unstructured":"Pourhasanzade F, Sabzpoushan SH, Alizadeh AM, Esmati E (2017) An agent-based model of avascular tumor growth: immune response tendency to prevent cancer development. SIMULATION 93:641\u2013657. https:\/\/doi.org\/10.1177\/0037549717699072","journal-title":"SIMULATION"},{"key":"1763_CR121","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jtbi.2012.05.015","volume":"308","author":"GG Powathil","year":"2012","unstructured":"Powathil GG, Gordon KE, Hill LA, Chaplain MA (2012) Modelling the effects of cell-cycle heterogeneity on the response of a solid tumour to chemotherapy: biological insights from a hybrid multiscale cellular automaton model. J Theor Biol 308:1\u201319. https:\/\/doi.org\/10.1016\/j.jtbi.2012.05.015","journal-title":"J Theor Biol"},{"key":"1763_CR122","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00033","volume":"7","author":"C Prats","year":"2016","unstructured":"Prats C, Vilaplana C, Valls J, Marzo E, Cardona PJ, Lopez D (2016) Local inflammation, dissemination and coalescence of lesions are key for the progression toward active tuberculosis: the bubble model. Front Microbiol 7:33. https:\/\/doi.org\/10.3389\/fmicb.2016.00033","journal-title":"Front Microbiol"},{"key":"1763_CR123","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.1038\/s41591-024-03037-z","volume":"30","author":"C Qi","year":"2024","unstructured":"Qi C, Liu C, Gong J, Liu D, Wang X, Zhang P, Qin Y, Ge S, Zhang M, Peng Z, Zhou J, Lu Z, Lu M, Cao Y, Yuan J, Wang Y, Wang Z, Xue R, Peng X, Wang Y, Yuan D, Li J, Zhang X, Shen L (2024) Claudin18.2-specific CAR T cells in gastrointestinal cancers: phase 1 trial final results. Nat Med 30:2224\u20132234. https:\/\/doi.org\/10.1038\/s41591-024-03037-z","journal-title":"Nat Med"},{"key":"1763_CR124","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1038\/nri3211","volume":"12","author":"L Ramakrishnan","year":"2012","unstructured":"Ramakrishnan L (2012) Revisiting the role of the granuloma in tuberculosis. Nat Rev Immunol 12:352\u2013366. https:\/\/doi.org\/10.1038\/nri3211","journal-title":"Nat Rev Immunol"},{"key":"1763_CR125","doi-asserted-by":"publisher","first-page":"3706","DOI":"10.4049\/jimmunol.0802297","volume":"182","author":"JC Ray","year":"2009","unstructured":"Ray JC, Flynn JL, Kirschner DE (2009) Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection. J Immunol 182:3706\u20133717. https:\/\/doi.org\/10.4049\/jimmunol.0802297","journal-title":"J Immunol"},{"key":"1763_CR126","doi-asserted-by":"publisher","first-page":"1853","DOI":"10.1007\/s11538-019-00590-4","volume":"81","author":"M Renardy","year":"2019","unstructured":"Renardy M, Wessler T, Blemker S, Linderman J, Peirce S, Kirschner D (2019) Data-driven model validation across dimensions. Bull Math Biol 81:1853\u20131866. https:\/\/doi.org\/10.1007\/s11538-019-00590-4","journal-title":"Bull Math Biol"},{"key":"1763_CR127","doi-asserted-by":"publisher","DOI":"10.1016\/j.mbs.2021.108593","volume":"337","author":"M Renardy","year":"2021","unstructured":"Renardy M, Joslyn LR, Millar JA, Kirschner DE (2021) To Sobol or not to Sobol? The effects of sampling schemes in systems biology applications. Math Biosci 337:108593. https:\/\/doi.org\/10.1016\/j.mbs.2021.108593","journal-title":"Math Biosci"},{"key":"1763_CR128","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1010254","volume":"18","author":"A Ruiz-Martinez","year":"2022","unstructured":"Ruiz-Martinez A, Gong C, Wang H, Sove RJ, Mi H, Kimko H, Popel AS (2022) Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model. PLoS Comput Biol 18:e1010254. https:\/\/doi.org\/10.1371\/journal.pcbi.1010254","journal-title":"PLoS Comput Biol"},{"key":"1763_CR129","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1021\/acsinfecdis.6b00051","volume":"2","author":"JP Sarathy","year":"2016","unstructured":"Sarathy JP, Zuccotto F, Hsinpin H, Sandberg L, Via LE, Marriner GA, Masquelin T, Wyatt P, Ray P, Dartois V (2016) Prediction of drug penetration in tuberculosis lesions. ACS Infect Dis 2:552\u2013563. https:\/\/doi.org\/10.1021\/acsinfecdis.6b00051","journal-title":"ACS Infect Dis"},{"key":"1763_CR130","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1164\/rccm.202410-2096ST","volume":"211","author":"JJ Saukkonen","year":"2025","unstructured":"Saukkonen JJ, Duarte R, Munsiff SS, Winston CA, Mammen MJ, Abubakar I, Acuna-Villaorduna C, Barry PM, Bastos ML, Carr W, Chami H, Chen LL, Chorba T, Daley CL, Garcia-Prats AJ, Holland K, Konstantinidis I, Lipman M, Battista Migliori G, Parvez FM, Shapiro AE, Sotgiu G, Starke JR, Starks AM, Thakore S, Wang SH, Wortham JM, Nahid P (2025) Updates on the treatment of drug-susceptible and drug-resistant tuberculosis: an official ATS\/CDC\/ERS\/IDSA clinical practice guideline. Am J Respir Crit Care Med 211:15\u201333. https:\/\/doi.org\/10.1164\/rccm.202410-2096ST","journal-title":"Am J Respir Crit Care Med"},{"key":"1763_CR131","doi-asserted-by":"publisher","first-page":"1565","DOI":"10.1126\/science.1203486","volume":"331","author":"RD Schreiber","year":"2011","unstructured":"Schreiber RD, Old LJ, Smyth MJ (2011) Cancer immunoediting: integrating immunity\u2019s roles in cancer suppression and promotion. Science 331:1565\u20131570. https:\/\/doi.org\/10.1126\/science.1203486","journal-title":"Science"},{"key":"1763_CR132","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/j.jtbi.2004.06.031","volume":"231","author":"JL Segovia-Juarez","year":"2004","unstructured":"Segovia-Juarez JL, Ganguli S, Kirschner D (2004) Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model. J Theor Biol 231:357\u2013376. https:\/\/doi.org\/10.1016\/j.jtbi.2004.06.031","journal-title":"J Theor Biol"},{"key":"1763_CR133","doi-asserted-by":"publisher","first-page":"e13","DOI":"10.1016\/S1470-2045(24)00374-7","volume":"26","author":"T Sen","year":"2025","unstructured":"Sen T, Dotsu Y, Corbett V, Puri S, Sen U, Boyle TA, Mack P, Hirsch F, Aljumaily R, Naqash AR, Sukrithan V, Karim NA (2025) Pulmonary neuroendocrine neoplasms: the molecular landscape, therapeutic challenges, and diagnosis and management strategies. Lancet Oncol 26:e13\u2013e33. https:\/\/doi.org\/10.1016\/S1470-2045(24)00374-7","journal-title":"Lancet Oncol"},{"key":"1763_CR134","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/1745-6150-5-25","volume":"5","author":"AS Silva","year":"2010","unstructured":"Silva AS, Gatenby RA (2010) A theoretical quantitative model for evolution of cancer chemotherapy resistance. Biol Direct 5:25. https:\/\/doi.org\/10.1186\/1745-6150-5-25","journal-title":"Biol Direct"},{"key":"1763_CR135","doi-asserted-by":"publisher","first-page":"1331","DOI":"10.1093\/bioinformatics\/btt772","volume":"30","author":"J Starruss","year":"2014","unstructured":"Starruss J, De Back W, Brusch L, Deutsch A (2014) Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology. Bioinformatics 30:1331\u20131332. https:\/\/doi.org\/10.1093\/bioinformatics\/btt772","journal-title":"Bioinformatics"},{"key":"1763_CR136","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1016\/B978-0-12-388403-9.00013-8","volume":"110","author":"MH Swat","year":"2012","unstructured":"Swat MH, Thomas GL, Belmonte JM, Shirinifard A, Hmeljak D, Glazier JA (2012) Multi-scale modeling of tissues using CompuCell 3D. Methods Cell Biol 110:325\u2013366. https:\/\/doi.org\/10.1016\/B978-0-12-388403-9.00013-8","journal-title":"Methods Cell Biol"},{"issue":"Suppl 1","key":"1763_CR137","doi-asserted-by":"publisher","first-page":"S18","DOI":"10.1038\/modpathol.2011.150","volume":"25","author":"WD Travis","year":"2012","unstructured":"Travis WD (2012) Update on small cell carcinoma and its differentiation from squamous cell carcinoma and other non-small cell carcinomas. Mod Pathol 25(Suppl 1):S18-30. https:\/\/doi.org\/10.1038\/modpathol.2011.150","journal-title":"Mod Pathol"},{"key":"1763_CR138","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1146\/annurev-immunol-031210-101324","volume":"29","author":"MD Vesely","year":"2011","unstructured":"Vesely MD, Kershaw MH, Schreiber RD, Smyth MJ (2011) Natural innate and adaptive immunity to cancer. Annu Rev Immunol 29:235\u2013271. https:\/\/doi.org\/10.1146\/annurev-immunol-031210-101324","journal-title":"Annu Rev Immunol"},{"key":"1763_CR139","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-127","volume":"14","author":"J Von Eichborn","year":"2013","unstructured":"Von Eichborn J, Woelke AL, Castiglione F, Preissner R (2013) VaccImm: simulating peptide vaccination in cancer therapy. BMC Bioinformatics 14:127. https:\/\/doi.org\/10.1186\/1471-2105-14-127","journal-title":"BMC Bioinformatics"},{"key":"1763_CR140","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.semcancer.2014.04.001","volume":"30","author":"Z Wang","year":"2015","unstructured":"Wang Z, Butner JD, Kerketta R, Cristini V, Deisboeck TS (2015) Simulating cancer growth with multiscale agent-based modeling. Semin Cancer Biol 30:70\u201378. https:\/\/doi.org\/10.1016\/j.semcancer.2014.04.001","journal-title":"Semin Cancer Biol"},{"key":"1763_CR141","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.canlet.2019.03.015","volume":"452","author":"S Wang","year":"2019","unstructured":"Wang S, Liu R, Yu Q, Dong L, Bi Y, Liu G (2019) Metabolic reprogramming of macrophages during infections and cancer. Cancer Lett 452:14\u201322. https:\/\/doi.org\/10.1016\/j.canlet.2019.03.015","journal-title":"Cancer Lett"},{"key":"1763_CR142","doi-asserted-by":"publisher","first-page":"399","DOI":"10.4103\/jcrt.jcrt_1965_21","volume":"18","author":"J Wang","year":"2022","unstructured":"Wang J, Hu L, Yang X, Ye X, Ni Y, Meng M, Huang G, Zhang T, Li W, Han X, Wei Z, Dai J, Zou Z (2022) A study of microwave ablation for small cell lung cancer. J Cancer Res Ther 18:399\u2013404. https:\/\/doi.org\/10.4103\/jcrt.jcrt_1965_21","journal-title":"J Cancer Res Ther"},{"key":"1763_CR143","doi-asserted-by":"publisher","first-page":"2233","DOI":"10.1007\/s11538-006-9103-y","volume":"68","author":"C Warrender","year":"2006","unstructured":"Warrender C, Forrest S, Koster F (2006) Modeling intercellular interactions in early Mycobacterium infection. Bull Math Biol 68:2233\u20132261. https:\/\/doi.org\/10.1007\/s11538-006-9103-y","journal-title":"Bull Math Biol"},{"key":"1763_CR144","doi-asserted-by":"publisher","DOI":"10.1186\/s12885-018-5233-5","volume":"19","author":"G Werutsky","year":"2019","unstructured":"Werutsky G, Hochhegger B, Lopes De Figueiredo Pinto JA, Martinez-Mesa J, Zanini ML, Berdichevski EH, Vilas E, Da Silva VD, Tsukazan MTR, Vieira A, Fritscher LG, Hartmann L, Alba M, Sartori G, Matushita C, Bortolotto V, Do Amaral RR, Junior LCA, Zaffaroni F, Barrios CH, Debiasi M, Frietscher CC (2019) PET-CT has low specificity for mediastinal staging of non-small-cell lung cancer in an endemic area for tuberculosis: a diagnostic test study (LACOG 0114). BMC Cancer 19:5. https:\/\/doi.org\/10.1186\/s12885-018-5233-5","journal-title":"BMC Cancer"},{"key":"1763_CR145","doi-asserted-by":"publisher","first-page":"5904","DOI":"10.1038\/onc.2008.271","volume":"27","author":"TL Whiteside","year":"2008","unstructured":"Whiteside TL (2008) The tumor microenvironment and its role in promoting tumor growth. Oncogene 27:5904\u20135912. https:\/\/doi.org\/10.1038\/onc.2008.271","journal-title":"Oncogene"},{"key":"1763_CR146","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20230707","author":"CG Winchell","year":"2023","unstructured":"Winchell CG, Nyquist SK, Chao MC, Maiello P, Myers AJ, Hopkins F, Chase M, Gideon HP, Patel KV, Bromley JD, Simonson AW, Floyd-O\u2019sullivan R, Wadsworth M, Rosenberg JM, Uddin R, Hughes T, Kelly RJ, Griffo J, Tomko J, Klein E, Berger B, Scanga CA, Mattila J, Fortune SM, Shalek AK, Lin PL, Flynn JL (2023) CD8+ lymphocytes are critical for early control of tuberculosis in macaques. J Exp Med. https:\/\/doi.org\/10.1084\/jem.20230707","journal-title":"J Exp Med"},{"key":"1763_CR147","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0023257","volume":"6","author":"AL Woelke","year":"2011","unstructured":"Woelke AL, Von Eichborn J, Murgueitio MS, Worth CL, Castiglione F, Preissner R (2011) Development of immune-specific interaction potentials and their application in the multi-agent-system VaccImm. PLoS ONE 6:e23257. https:\/\/doi.org\/10.1371\/journal.pone.0023257","journal-title":"PLoS ONE"},{"key":"1763_CR148","doi-asserted-by":"publisher","first-page":"644","DOI":"10.4049\/jimmunol.1901211","volume":"204","author":"EA Wong","year":"2020","unstructured":"Wong EA, Evans S, Kraus CR, Engelman KD, Maiello P, Flores WJ, Cadena AM, Klein E, Thomas K, White AG, Causgrove C, Stein B, Tomko J, Mattila JT, Gideon H, Lin PL, Reimann KA, Kirschner DE, Flynn JL (2020) IL-10 impairs local immune response in lung granulomas and lymph nodes during early Mycobacterium tuberculosis infection. J Immunol 204:644\u2013659. https:\/\/doi.org\/10.4049\/jimmunol.1901211","journal-title":"J Immunol"},{"key":"1763_CR149","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1002\/cncr.25616","volume":"117","author":"CY Wu","year":"2011","unstructured":"Wu CY, Hu HY, Pu CY, Huang N, Shen HC, Li CP, Chou YJ (2011) Pulmonary tuberculosis increases the risk of lung cancer: a population-based cohort study. Cancer 117:618\u2013624. https:\/\/doi.org\/10.1002\/cncr.25616","journal-title":"Cancer"},{"key":"1763_CR150","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1016\/j.canlet.2014.03.013","volume":"347","author":"Q Wu","year":"2014","unstructured":"Wu Q, Yang Z, Nie Y, Shi Y, Fan D (2014) Multi-drug resistance in cancer chemotherapeutics: mechanisms and lab approaches. Cancer Lett 347:159\u2013166. https:\/\/doi.org\/10.1016\/j.canlet.2014.03.013","journal-title":"Cancer Lett"},{"key":"1763_CR151","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1016\/j.csbj.2019.03.006","volume":"17","author":"X Wu","year":"2019","unstructured":"Wu X, Gu Z, Chen Y, Chen B, Chen W, Weng L, Liu X (2019) Application of PD-1 blockade in cancer immunotherapy. Comput Struct Biotechnol J 17:661\u2013674. https:\/\/doi.org\/10.1016\/j.csbj.2019.03.006","journal-title":"Comput Struct Biotechnol J"},{"key":"1763_CR152","doi-asserted-by":"publisher","first-page":"1576","DOI":"10.1098\/rsif.2011.0726","volume":"9","author":"ML Wynn","year":"2012","unstructured":"Wynn ML, Kulesa PM, Schnell S (2012) Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour. J R Soc Interface 9:1576\u20131588. https:\/\/doi.org\/10.1098\/rsif.2011.0726","journal-title":"J R Soc Interface"},{"key":"1763_CR153","doi-asserted-by":"publisher","first-page":"2494","DOI":"10.1182\/blood-2006-11-058271","volume":"110","author":"Y Yang","year":"2007","unstructured":"Yang Y, Ochando JC, Bromberg JS, Ding Y (2007) Identification of a distant T-bet enhancer responsive to IL-12\/Stat4 and IFNgamma\/Stat1 signals. Blood 110:2494\u20132500. https:\/\/doi.org\/10.1182\/blood-2006-11-058271","journal-title":"Blood"},{"key":"1763_CR154","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2025.1657441","volume":"15","author":"Y Yang","year":"2025","unstructured":"Yang Y, Liu N, Wu J, Wu Q, Zhao J, Shi Y, Shen M, Xu Z, Shi Y, Yu J, Yi P, Cheng J, Sun J, Xu Y, Wang K (2025) Intratumoral heterogeneity and potential treatment strategies in small cell lung cancer. Front Oncol 15:1657441. https:\/\/doi.org\/10.3389\/fonc.2025.1657441","journal-title":"Front Oncol"},{"key":"1763_CR155","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0015423","volume":"5","author":"H Yoon","year":"2010","unstructured":"Yoon H, Kim TS, Braciale TJ (2010) The cell cycle time of CD8+ T cells responding in vivo is controlled by the type of antigenic stimulus. PLoS ONE 5:e15423. https:\/\/doi.org\/10.1371\/journal.pone.0015423","journal-title":"PLoS ONE"},{"key":"1763_CR156","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1097\/JTO.0b013e3181fb4fcc","volume":"6","author":"YH Yu","year":"2011","unstructured":"Yu YH, Liao CC, Hsu WH, Chen HJ, Liao WC, Muo CH, Sung FC, Chen CY (2011) Increased lung cancer risk among patients with pulmonary tuberculosis: a population cohort study. J Thorac Oncol 6:32\u201337. https:\/\/doi.org\/10.1097\/JTO.0b013e3181fb4fcc","journal-title":"J Thorac Oncol"},{"key":"1763_CR157","doi-asserted-by":"publisher","first-page":"1094","DOI":"10.1097\/JTO.0b013e3181a97e31","volume":"4","author":"P Zhan","year":"2009","unstructured":"Zhan P, Wang J, Lv XJ, Wang Q, Qiu LX, Lin XQ, Yu LK, Song Y (2009) Prognostic value of vascular endothelial growth factor expression in patients with lung cancer: a systematic review with meta-analysis. J Thorac Oncol 4:1094\u20131103. https:\/\/doi.org\/10.1097\/JTO.0b013e3181a97e31","journal-title":"J Thorac Oncol"},{"key":"1763_CR158","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.canlet.2020.11.034","volume":"499","author":"Y Zheng","year":"2021","unstructured":"Zheng Y, Wang Z, Wei S, Liu Z, Chen G (2021) Epigenetic silencing of chemokine CCL2 represses macrophage infiltration to potentiate tumor development in small cell lung cancer. Cancer Lett 499:148\u2013163. https:\/\/doi.org\/10.1016\/j.canlet.2020.11.034","journal-title":"Cancer Lett"},{"key":"1763_CR159","doi-asserted-by":"publisher","unstructured":"Zhong X, Ji P & Yang L (2026) Small cell lung cancer: from immunobiological mechanisms to clinical advances. Front Immunol 17:1765497. https:\/\/doi.org\/10.3389\/fimmu.2026.1765497","DOI":"10.3389\/fimmu.2026.1765497"}],"container-title":["Bulletin of Mathematical Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11538-026-01763-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11538-026-01763-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11538-026-01763-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T17:30:15Z","timestamp":1791307815000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11538-026-01763-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,6]]},"references-count":159,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["1763"],"URL":"https:\/\/doi.org\/10.1007\/s11538-026-01763-8","relation":{},"ISSN":["0092-8240","1522-9602"],"issn-type":[{"value":"0092-8240","type":"print"},{"value":"1522-9602","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,6]]},"assertion":[{"value":"26 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 September 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 October 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"197"}}