Rejniak Lab Publications

 

Books written/edited:

"Systems Biology of Tumor Microenvironment",edited by K.A. Rejniak (2016), Springer, Advances in Experimental Medicine and Biology series, ISBN 978-3-319-42023-3, link to the book
"Computational Models in Oncology: from Tumor Initiation to Progression to Treatment", edited by K.A. Rejniak and H. Enderling (2013), Frontiers in Oncology link to the eBook
"Single-Cell-Based Models in Biology and Medicine" edited by A. Anderson, M. Chaplain, K.A. Rejniak (2007) Birkhauser-Verlag, Mathematics and Biosciences in Interaction (MBI) series, ISBN 978-3-7643-8101-1; link to the book
J. Jedrzejowicz, K. Rejniak, "Introduction to the Theory of Databases with Practical Examples for Btrieve" (in Polish), ISBN 83-7017-745-X, Gdansk University Press, 1997 and 1999 (2nd edition).
J. Jedrzejowicz, K. Rejniak, "Languages, Automata and Computational Complexity--exercise book" (in Polish), ISBN 83-7017-551-1, Gdansk University Press, 1994.

 

Contributed book chapters :

A. Karolak, S. Agrawal, S. Lee, K.A. Rejniak, Single-Cell-Based In Silico Models: A Tool for Dissecting Tumor Heterogeneity, "Encyclopedia of Biomedical Engineering", vol.3 pp. 130-143, Narayan S. (Ed), Elsevier (2019) ISBN 978-0-128-04829-0; link to the publication

A. Karolak, K.A. Rejniak, Mathematical modeling of tumor organoids: toward personalized medicine, in “Tumor Organoids”, Soker S., Skardal A. (Eds), Cancer Drug Discovery and Development, Springer (2018) ISBN 978-3-319-60509-8 (printed), ISBN 978-3-319-60511-1(ebook); link to the book

CSBC/PS-ON Handbook of Mathematical Oncology; a collection of mathematical methods from Cancer Systems Biology Constortium (CSBC) and Physical Sciences-Oncology Network (PS-ON); link to the collection

our contributions: (1) 10.1101/031294; (2) 10.1101/235653; (3) 10.1101/629907;

J.L. Gevertz, Z. Aminzare, K.A. Norton, J. Pérez-Velázquez, A. Volkening, K.A. Rejniak, "Emergence of Anti-Cancer Drug Resistance: Exploring the Importance of the Microenvironmental Niche via a Spatial Model", Chapter I of the book "Applications of Dynamical Systems in Biology and Medicine", edited by A. Radunskaya and T. Jackson, IMA Volumes in Mathematics and Its Applications, Springer-Verlag, (2015), ISBN 978-1-4939-2781-4; link to the book

K.A. Rejniak, "IBCell Morphocharts: a computational model for linking cell molecular activity with emerging tissue morphology", Chapter XXIII, of the book "Discrete and Toplogical Models in Molecular Biology", edited by N. Jonoska and M. Saito, Springer, Natural Computing Series (2014), ISBN 978-3-642-40192-3; link to the book
A. Anderson, D. Basanta, P. Gerlee, K.A. Rejniak, "Evolution, regulation and disruption of homeostasis and its role in carcinogenesis", in T.S. Deisboeck, G. Stamatakos (Eds.), "Multiscale Cancer Modeling", Chapman & Hall-CRC, Mathematical and Computational Biology Series (2010), ISBN 978-1-4398-1440-6; link to the book
K.A. Rejniak, "Modelling the development of complex tissues using individual viscoelastic cells", Chapter IV.3 of the book "Single-Cell-Based Models in Biology and Medicine" edited by A. Anderson, M. Chaplain, K.A. Rejniak, Birkhauser-Verlag, Mathematics and Biosciences in Interaction (MBI) series (2007), ISBN 978-3-7643-8101-1; link to the book

 

Special journal issues edited:

"Computational Models in Oncology: from Tumor Initiation to Progression to Treatment", a special topic of the Frontiers in Oncology Journal, speciality: Frontiers in Molecular and Cellular Oncology, (2013), edited by K.A. Rejniak and H. Enderling, open access & ebook
"Computational Modeling of Cancer", a special issue of the IMA Journal on Mathematical Medicine and Biology 29(1), (2012), edited by A. Anderson and K.A. Rejniak

 

 

Special collection papers:

  1. C. Berrouet, N. Dorilas, K.A.Rejniak, N. Tuncer, "Comparison of drug inhibitory effects in monolayer and spheroid cultures", BioRxiv 2020, https://doi.org/10.1101/2020.05.05.079285; link to publication
  2. J. Perez-Velazquez, K.A.Rejniak, "Drug-induced resistance in micrometastases: analysis of spatio-temporal cell lineages", BioRxiv 2020, https://doi.org/10.1101/2020.03.01.972406; link to publication
  3. H. Enderling, P.M. Altrock, N. Andor, D. Basanta, J. S. Brown, R. A. Gatenby, A. Marusyk, K.A. Rejniak, A. Silva, A.R.A. Anderson, "High school Intership Program in Integrated Mathematical Oncology (HIP-IMO) - five-year experience at Moffitt Cancer Center", BioRxiv, 2020, https://doi.org/10.1101/2020.02.27/967950; link to publication
  4. P. Bhatt, M. Kambara, S. Pilon-Thomas, K.A. Rejniak, I. Chamseddine, "Modeling vaccine-induced immunotherapy: treatment scheduling and robustness with virtual nice cohorts", BioRxiv 2019, https://doi.org/10.1101/740878; link to publication
  5. N. Vitos, S. Chen, S. Mathur, I. Chamseddine, K.A. Rejniak, “Hypoxia in cancer chemo- and immunotherapy: foe or friend?”, BioRxiv 2019, https://doi.org/10.1101/629907; link to publication
  6. P.M. Altrock,N. Yoon.,J.A. Bull,H. Wu, J. Ruiz-Ramírez, D. Miroshnychenko, G.J. Kimmel, E. Kim, R.J. Vander Velde, K. Rejniak, B.J. Manley, F. Spill, A. Marusyk, "The impact of tumor stromal architecture on therapy response and clinical progression", BioRxiv 2018, doi: https://doi.org/10.1101/451047; link to publication
  7. A. Karolak, B. Huffstutler, Z. Khan, K.A. Rejniak,"Assessment of patient-specific efficacy of chemo- and targeted- therapies: a micropharmacology approach", NIH/NCI Handbook of Mathematical Methods in Cancer Biology, BioRxiv 2017; doi: http://dx.doi.org/10.1101/236653; link to publication
  8. R. Walker, P.E. Navas, S.H. Friedman, S. Galliani, A. Karola., F. MacFarlan, R. Noble, J. Poleszczuk, S. Russell, K.A. Rejniak, A. Shahmoradi, F. Ziebell, J. Brayer, D. Abate-Daga, H. Enderling, "Enhancing synergy of CAR T cell therapy and oncolytic virus therapy for pancreatic cancer". Biorxiv, 2016, doi: http://dx.doi.org/10.1101/055988; link to publication
  9. K.A. Rejniak, "Micro-Pharmacodynamics: bridging in vitro and in vivo experimental scales in testing drug efficacy and resistance", NIH/NCI Handbook of Mathematical Methods in Cancer Biology, Biorxiv, 2016, doi: http://dx.doi.org/10.1101/031294; link to publication

Journal articles:

  1. J. Perez-Velazquez, K.A.Rejniak, (2020) "Drug-induced resistance in micrometastases: analysis of spatio-temporal cell lineages", special topic on Advances in Mathematical and Computational Oncology, Froniers in Physiology 11:319. Pubmed#:32362836 ; link to the article
  2. I. Chamseddine, K.A. Rejniak, (2020) "Hybrid modeling frameworks of tumor development and treatment", WIREs Systems Biology and Medicine, 12(1):e1461. Pubmed#:31313504; link to the article
  3. A. Karolak, S. Poonja, K.A. Rejniak, (2019) "Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential", PLoS Computational Biology, 15(7):e1007214, Pubmed#31310602; link to the article
  4. A. Karolak, K.A. Rejniak, (2019) "Micropharamacology: An In Silico Approach for Assesing Drug Efficacy Within a Tumor Tissue", Bulletin of Mathematical Biology; 81(9):3623-3641, Pubmed#:29423880; link to the article; link to the article viewer
  5. A. Karolak, V.C. Estrella, A.S. Huynh, T. Chen, J. Vagner, D.L. Morse, K.A. Rejniak, (2018) "Targeting Ligand Specificity Linked to Tumor Tissue Topological Heterogeneity via Single-Cell Micro-Pharmacological Modeling", Scientific Reports, 8:3638, Pubmed#:29483578; link to the article
  6. A. Karolak, D.A. Markov, L.J. McCawley, K.A. Rejniak, (2018) "Toward Personalized Computational Oncology: from Spatial Models of Tumor Spheroids, to Organoids, to Tissues", Journal of Royal Society Interface, 15:20170703, Pubmed #29367239; link to the article
  7. J. Pérez-Velázquez, J.L. Gevertz, A. Karolak, K.A. Rejniak, (2016) “Microenvironmental niches and sanctuaries: a route to acquired resistance”, Advances in Experimental Medicine and Biology, 936:149-164, Pubmed #27739047; PMCID:PMC5113820; link to the article
  8. K.A. Rejniak, (2016) “Circulating Tumor Cells: When solid tumor meets fluid microenvironment”, Advances in Experimental Medicine and Biology, 936:93-106, Pubmed #27739044; PMCID:PMC5113997; link to the article
  9. A.B. Shah, K.A. Rejniak, J.L. Gevertz, (2016) "Limiting the development of anti-cancer drug resistance in a spatial model of micrometastases", Mathematical Biosciences & Engineering, 13(6):1185-1206, Pubmed #27775375, PMCID:PMC5113823, link to the article
  10. K.A. Rejniak, M.C. Lloyd, D. Reed, M.M. Bui, (2015) "Diagnostic assessment of osteosarcoma chemoresistance based on virtual clinical trials", Medical Hypotheses Elsevier, 85:348-354, Pubmed #26130106, PMCID:PMC4549200, link to the article
  11. M.C. Lloyd, K.A. Rejniak, J.S. Brown, R.A. Gatenby, E. Minor, M.M. Bui, (2015) "Pathology to enhance precision medicine in oncology: lessons from landscape ecology", Advances in Anatomical Pathology, 22(4):267-72, Pubmed #26050264,PMCID:PMC4729443, link to the article
  12. J.W. Wojtkowiak, H.C. Cornell, S. Matsumoto, K. Saito,Y. Takakusagi, P. Dutta, M.J. Kim, X. Zhang, R. Leos, K.M. Bailey, G. Martinez, M.C. Lloyd, C. Weber, J.B. Mitchell, R.M. Lynch, A.F. Baker, R.A. Gatenby, K.A. Rejniak, C. Hart, M.C. Krishna, R.J. Gillies, (2015) "Pyruvate sensitizes pancreatic tumors to hypoxia-activated prodrug TH-302", Cancer & Metabolism, 3:2, Pubmed #25635223, PMCID:PMC4310189, open access
  13. M.J. Kim, K.A. Rejniak, (2014) "Mechanical aspects of microtubule bundling in taxane-treated circulating tumor cells", Biophyscial Journal, 107(5): 1236-1246, Pubmed #25185559, PMCID:PMC4156678, and included in the Biophysical Journal Collection on Cancer Biophysics; link to the article ; link to the collection
  14. M.J. Kim, D. Reed, K.A. Rejniak, (2014) "The formation of tight tumor clusters affects the efficacy of cell cycle inhibitors: a hybrid model study", Journal of Theoretical Biology, 352:31-50, Pubmed #24607745, open access
  15. J.E. Macias-Diaz, K.A. Rejniak, (2014) "On a conditionally stable nonlinear method to approximate some monotone and bounded solutions of a generalized population model", Applied Mathematics and Computation, 229(1):273-282, link to article
  16. M.J. Kim, R.J. Gillies, K.A. Rejniak, (2013) "Current advances in mathematical modeling of anti-cancer drug penetration into tumor tissues", Frontiers in Oncology, Special Topic Title: Ways to improve tumor uptake and penetration of drugs into solid tumors, Host Specialty: Frontiers in Pharmacology of Anti-Cancer Drugs, Frontiers in Oncology Journal, 3:278, Pubmed #24303366, PMCID:PMC3831268, open access
  17. H. Enderling, K.A. Rejniak, (2013) "Simulating cancer: computational models in mncology", Editorial, Frontiers in Oncology, Special Topic Title: Computational Models in Oncology: from Tumor Initiation to Progression to Treatment, Host Specialilty: Forntiers in Molecular and Celular Oncology, Frontiers in Oncology Journal, 3:233, Pubmed #24062986, PMCID:PMC3772565, open access
  18. K.A. Rejniak, V. Estrella., T. Chen., A.S. Cohen., M.C. Lloyd, D.L. Morse, (2013) "The role of tumor tissue architecture on treatment penetration and efficacy: an integrative study", Frontiers in Oncology, Special Topic Title: Computational Models in Oncology: from Tumor Initiation to Progression to Treatment, Host Speciality: Frontiers in Molecular and Cellular Oncology, Frontiers in Oncology Journal, 3:111, Pubmed #23717812, PMCID:PMC3650652, open access 
  19. K.A. Rejniak, (2012) "Investigating dynamical deformations of tumor cells in circulation: predictions from a theoretical model", Frontiers in Oncology, Special Topic Title: Therapeutic targeting of circulating tumor cells, Host Specialty: Frontiers in Cancer Molecular Targets and Therapeutics, Frontiers in Oncology Journal, 2:111, Pubmed #23024961, PMCID:PMC3444760, open access
  20. K.A. Rejniak, (2012)"Homeostatic imbalance in epithelial ducts and its role in carcinogenesis", Scientifica, ID:132978, Pubmed #24278670, PMCID:PMC3820568, open access
  21. K.A. Rejniak, A.R.A. Anderson, (2012)"State of the art in computational modelling of cancer", editorial, IMA Journal on Mathematical Medicine and Biology, 29(1):1-2, Pubmed #22200587
  22. K.A. Rejniak, V. Quaranta, A.R.A. Anderson, (2012) "Computational investigations of intrinsic and extrinsic mechanisms underlying the formation of carcinoma", IMA Journal on Mathematical Medicine and Biology, 29(1):67-84, Pubmed #21106672, PMCID:PMC3499074, Free PMC Article
  23. Y. Kam, K.A. Rejniak, A.R.A. Anderson, (2012) "Cellular modeling of cancer invasion: integration of in silico and in vitro approaches", Journal of Cellular Physiology, 227(2): 431-438, (invited review and the highlights section), Pubmed #21465465, PMCID:PMC3687536, Free PMC Article
  24. K.A. Rejniak, A.R.A. Anderson, (2011) "Hybrid models of tumor growth", Wiley Interdisciplinary Reviews: System Biology and Medicine, 3(1):115-125, (invited review), Pubmed #2106403, PMCID:PMC3057876, Free PMC Article
  25. K.A. Rejniak, S.E. Wang, N.S. Bryce, H. Chang, B. Parvin, J. Jourquin, L. Estrada, J.W. Gray, C.L. Arteaga, A.M. Weaver, V. Quaranta, A.R.A. Anderson, (2010) "Linking changes in epithelial morphogenesis to cancer mutations using computational modeling" PLoS Computational Biology, 6(8):e1000900, Pubmed #20865159, PMCID:PMC2928778, open access
  26. K.A. Rejniak, L.J. McCawley, (2010) "Current trends in mathematical modeling of tumor-microenvironment interactions: a survey of tools and applications", Experimental Biology and Medicine, 235:411-423, Pubmed #20407073; link to article
  27. A.R.A. Anderson, K.A. Rejniak, P. Gerlee, V. Quaranta, (2009) "Microenvironment driven invasion: a multiscale multimodel investigation", Journal of Mathematical Biology, 58:579-624, Pubmed #18839176; link to article
  28. V. Quaranta, K.A. Rejniak, P. Gerlee, A.R.A. Anderson, (2008) "Invasion emerges from cancer cell adaptation to competitive microenvironments: quantitative predictions from multiscale mathematical models", Seminars in Cancer Biology, 18:338-348, Pubmed #18524624, PMCID:PMC3789515, Free PMC Article
  29. K.A. Rejniak, A.R.A. Anderson, (2008) "A computational study of the development of epithelial acini: II. Necessary conditions for structure and lumen stability", Bulletin of Mathematical Biology, 70(5):1450-1479, Pubmed #18401665; link to article
  30. K.A. Rejniak, A.R.A. Anderson, (2008) "A computational study of the development of epithelial acini: I. Sufficient conditions for the formation of a hollow structure", Bulletin of Mathematical Biology, 70(3):677-712, Pubmed #18188652; link to article
  31. A.R.A. Anderson, K.A. Rejniak, P. Gerlee, V. Quaranta, (2007) "Modelling of cancer growth, evolution and invasion: bridging scales and models", Mathematical Modelling of Natural Phenomena, 2(3):1-29, special issue on cancer modelling; link to article
  32. K.A. Rejniak, R.H. Dillon, (2007) "A single cell based model of the ductal tumour microarchitecture", Computational and Mathematical Methods in Medicine, 8(1):51-69, open access
  33. K.A. Rejniak, (2007) "An immersed boundary framework for modelling the growth of individual cells: an application to the early tumour development", Journal of Theoretical Biology, 247:186-204, Pubmed #17416390; link to article
  34. K.A. Rejniak, (2005) "A single cell approach in modeling the dynamics of tumor microregions", Mathematical Biosciences and Engineering, 2(3):643-655, Pubmed #20369945; link to article
  35. C. Popesco, A. Frostholm, K.A. Rejniak, A. Rotter ,(2004) "Digital transcriptome analysis in the aging cerebellum", Annals New York Acad. Sci, 1019:58-63, Pubmed #15246995; link to article
  36. K.A. Rejniak, H.J. Kliman, L.J. Fauci, (2004) "A computational model of the mechanics of growth of the villous trophoblast bilayer", Bulletin of Mathematical Biology, 66(2):199-232, Pubmed #14871565; link to article