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, Chapter of "Encyclopedia of Biomedical Engineering", Narayan S. (Ed), Elsevier ISBN 978-0-128-04829-0 (June 2018); link do the book

A. Karolak, K.A. Rejniak, Mathematical modeling of tumor organoids: toward personalized medicine, Chapter X of “Tumor Organoids”, Soker S., Skardal A. (Eds), Springer 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;

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

Five papers from this special topic issue made to the top 10 most viewed Frontiers Oncology research articles in 2013!

"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. 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;
  2. 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 the publication
  3. 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 the publication

 

Journal articles:

  1. J. Pérez-Velázquez, J.L. Gevertz, A. Karolak, K.A. Rejniak, “Microenvironmental niches and sanctuaries: a route to acquired resistance”, Advances in Experimental Medicine and Biology, 936:149-164, 2016, Pubmed #27739047; PMCID:PMC5113820; link to the article
  2. K.A. Rejniak, “Circulating Tumor Cells: When solid tumor meets fluid microenvironment”, Advances in Experimental Medicine and Biology, 936:93-106, 2016, Pubmed #27739044; PMCID:PMC5113997; link to the article
  3. A.B. Shah, K.A. Rejniak, J.L. Gevertz, "Limiting the development of anti-cancer drug resistance in a spatial model of micrometastases", Mathematical Biosciences & Engineering, 13(6):1185-1206, 2016, Pubmed #27775375, PMCID:PMC5113823, link to the article
  4. K.A. Rejniak, M.C. Lloyd, D. Reed, M.M. Bui, "Diagnostic assessment of osteosarcoma chemoresistance based on virtual clinical trials", Medical Hypotheses Elsevier, 85:348-354, 2015, PubMed #26130106, PMCID:PMC4549200, link to the article
  5. M.C. Lloyd, K.A. Rejniak, J.S. Brown, R.A. Gatenby, E. Minor, M.M. Bui, "Pathology to enhance precision medicine in oncology: lessons from landscape ecology", Advances in Anatomical Pathology, 22(4):267-72, 2015, Pubmed #26050264,PMCID:PMC4729443, link to the article
  6. 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, "Pyruvate sensitizes pancreatic tumors to hypoxia-activated prodrug TH-302", Cancer & Metabolism, 3:2, 2015, Pubmed #25635223, PMCID:PMC4310189, open access
  7. M.J. Kim, K.A. Rejniak, "Mechanical aspects of microtubule bundling in taxane-treated circulating tumor cells", Biophyscial Journal, 107(5): 1236-1246, 2014; Pubmed #25185559, PMCID:PMC4156678, and included in the Biophysical Journal Collection on Cancer Biophysics; link to the article ; link to the collection
  8. M.J. Kim, D. Reed, K.A. Rejniak, "The formation of tight tumor clusters affects the efficacy of cell cycle inhibitors: a hybrid model study", Journal of Theoretical Biology, 352:31-50, 2014; Pubmed #24607745, open access
  9. J.E. Macias-Diaz, K.A. Rejniak, "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, 2014, link to article
  10. M.J. Kim, R.J. Gillies, K.A. Rejniak, "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, 2013, Pubmed #24303366, PMCID:PMC3831268, open access
  11. H. Enderling, K.A. Rejniak, "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, 2013, Pubmed #24062986, PMCID:PMC3772565, open access
  12. K.A. Rejniak, V. Estrella., T. Chen., A.S. Cohen., M.C. Lloyd, D.L. Morse,"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, 2013, Pubmed #23717812, PMCID:PMC3650652, open access 
  13. K.A. Rejniak, "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, 2012, Pubmed #23024961, PMCID:PMC3444760, open access
  14. K.A. Rejniak, "Homeostatic imbalance in epithelial ducts and its role in carcinogenesis", Scientifica, ID:132978, 2012, Pubmed #24278670, PMCID:PMC3820568, open access
  15. K.A. Rejniak, A.R.A. Anderson, "State of the art in computational modelling of cancer", editorial, IMA Journal on Mathematical Medicine and Biology, 29(1):1-2, 2012, Pubmed #22200587
  16. K.A. Rejniak, V. Quaranta, A.R.A. Anderson, "Computational investigations of intrinsic and extrinsic mechanisms underlying the formation of carcinoma", IMA Journal on Mathematical Medicine and Biology, 29(1):67-84, 2012, Pubmed #21106672, PMCID:PMC3499074, Free PMC Article
  17. Y. Kam, K.A. Rejniak, A.R.A. Anderson, "Cellular modeling of cancer invasion: integration of in silico and in vitro approaches", Journal of Cellular Physiology, 227(2): 431-438, 2012, (invited review and the highlights section), Pubmed #21465465, PMCID:PMC3687536, Free PMC Article
  18. K.A. Rejniak, A.R.A. Anderson, "Hybrid models of tumor growth", Wiley Interdisciplinary Reviews: System Biology and Medicine, 3(1):115-125, 2011, (invited review), Pubmed #2106403, PMCID:PMC3057876, Free PMC Article
  19. 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, "Linking changes in epithelial morphogenesis to cancer mutations using computational modeling" PLoS Computational Biology, 2010, 6(8):e1000900, Pubmed #20865159, PMCID:PMC2928778, open access
  20. K.A. Rejniak, L.J. McCawley, "Current trends in mathematical modeling of tumor-microenvironment interactions: a survey of tools and applications", Experimental Biology and Medicine, 2010, 235:411-423, Pubmed #20407073; link to article
  21. A.R.A. Anderson, K.A. Rejniak, P. Gerlee, V. Quaranta, "Microenvironment driven invasion: a multiscale multimodel investigation", Journal of Mathematical Biology, 2009, 58:579-624, Pubmed #18839176; link to article
  22. V. Quaranta, K.A. Rejniak, P. Gerlee, A.R.A. Anderson, "Invasion emerges from cancer cell adaptation to competitive microenvironments: quantitative predictions from multiscale mathematical models", Seminars in Cancer Biology, 2008, 18:338-348, Pubmed #18524624, PMCID:PMC3789515, Free PMC Article
  23. K.A. Rejniak, A.R.A. Anderson, "A computational study of the development of epithelial acini: II. Necessary conditions for structure and lumen stability", Bulletin of Mathematical Biology, 2008, 70(5):1450-1479, Pubmed #18401665; link to article
  24. K.A. Rejniak, A.R.A. Anderson, "A computational study of the development of epithelial acini: I. Sufficient conditions for the formation of a hollow structure", Bulletin of Mathematical Biology, 2008, 70(3):677-712, Pubmed #18188652; link to article
  25. A.R.A. Anderson, K.A. Rejniak, P. Gerlee, V. Quaranta, "Modelling of cancer growth, evolution and invasion: bridging scales and models", Mathematical Modelling of Natural Phenomena, 2007, 2(3):1-29, special issue on cancer modelling; link to article
  26. K.A. Rejniak, R.H. Dillon, "A single cell based model of the ductal tumour microarchitecture", Computational and Mathematical Methods in Medicine, 2007 8(1):51-69, open access
  27. K.A. Rejniak, "An immersed boundary framework for modelling the growth of individual cells: an application to the early tumour development", Journal of Theoretical Biology, 2007, 247:186-204, Pubmed #17416390; link to article
  28. K.A. Rejniak, "A single cell approach in modeling the dynamics of tumor microregions", Mathematical Biosciences and Engineering, 2005, 2(3):643-655, Pubmed #20369945; link to article
  29. C. Popesco, A. Frostholm, K.A. Rejniak, A. Rotter, "Digital transcriptome analysis in the aging cerebellum", Annals New York Acad. Sci, 2004, 1019:58-63, Pubmed #15246995; link to article
  30. K.A. Rejniak, H.J. Kliman, L.J. Fauci, "A computational model of the mechanics of growth of the villous trophoblast bilayer", Bulletin of Mathematical Biology, 2004, 66(2):199-232, Pubmed #14871565; link to article