Journal Articles:

Concepts and applications of information theory to immuno-oncology Trends in Cancer, Special Issue: Quantitative Cancer Biology 7(4) (2021)

A.Karolak, S.Poonja, DA.Markov, LJ.McCawley, KA.Rejniak Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential Plos.Comp.Biol. 15(7): e1007214 (2019)

A.Khabibullin, A.Karolak, M.Budzevich, M.Mclaughlin, D.Morse, L.Woods Structure and properties of DOTA-chelated radiopharmaceuticals within the 225Ac decay pathway, Med.Chem.Comm.,6;9(7), p155 (2018)

A.Karolak, DA.Markov, LJ.McCawley, KA.Rejniak, Toward personalized computational oncology: from spatial models of tumor spheroids to organoids to tissues, J.R.Soc Interface, 15:20170703 (2018)

A.Karolak, KA.Rejniak Micropharmacology: an in silico approach for assessing drug efficacy within a tumor tissue, Bull. Math. Biol. p1 (2018)

A.Karolak, V.Estrella, T.Chen, AS.Huynh, DL.Morse, KA.Rejniak Targeting imaging agents efficacy linked to tumor tissue topological heterogeneity via single-cell micro-pharmacological modelling, Scientific Reports, 8 (1), p3638 (2018)

S.Mukherjee, A.Karolak, Y.Renaudineau, M.Debant, P.Buscaglia, O.Mignen, WC.Guida, WH.Brooks Molecular dynamics simulations of membrane bound STIM1 to investigate conformational changes during STIM1 activation upon calcium release, J. Chem. Inf. Model. 57 (2), p335 (2017)

TA.Word, A.Karolak, C.Cioce, A.van der Vaart, RW.Larsen, Using photoacoustic calorimetry to study the cis to trans photo isomerization of the [Ru(II)(2,2’-bipyridine)2(H2O)2]2+ complex in aqueous solution, Comment. Inorg. Chem. 36, p343 (2016)

A.Karolak, A.van der Vaart Molecular dynamics simulations of 5-hydroxycytosine damaged DNA J. Phys. Chem. B, 120, p42 (2016)

A.Karolak, A.van der Vaart BII stability and base step flexibility of N6-adenine methylated GATC motifs Biophys. Chem. 203, p22 (2015)

TA.Word, CL.Whittington, A.Karolak, MT.Kemp, HL.Woodcock, A.van der Vaart, RW. Larsen Photoacoustic calorimetry study of ligand photorelease from the Ru(II)bis(2,2'-bipyridine)(6,6'-dimethyl-2,2'-bipyridine) complex in aqueous solution Chem. Phys. Lett. 619, p214 (2015)

A.Karolak, A.van der Vaart Enhanced sampling simulations of DNA step parameters J. Comp. Chem. 35, 2297-2304 (2014)

A.Karolak, A.van der Vaart Importance of local interactions for the ETS1 stability of inhibitory helix 1 Biophys. Chem. 165, p74 (2012)

H.Maciejewski, B.Marciniec, J.Gulinski, A.Karolak, NK.Skvortsov From isothiocyanato- to silyl-nickel complexes Inorg. Chem. Comm. 5, p464 (2002)

Preprints:

A.Karolak, J. Levatic, F. Supek A framework for mutational signature analysis based on DNA shape parameters, BioRXiv doi: https://doi.org/10.1101/2020.09.28.316794 (2020)

M.Damaghi, S.Byrne, L.Xu, N.Tafreshi, B.Fang, JM. Koomen, A.Karolak, T.Chen, J.Johnson, ND. Gallant, A.Marusyk, RJ.Gillies Collagen production and niche engineering: a novel strategy for cancer cells to survive acidosis and evolve. BioRXiv 711978; doi: https://doi.org/10.1101/711978 (2019)

S.Nizzero, JC. Alfonso, A.Alvarez-Arenas, I.Mirzaev, I. Zervantonakis, T.Lewin, A.Rishi, E.Piretto, T. Joshi, DN. Santiago, A.Karolak, R.Howard, H.Enderling, FA.Karreth, J.Torres-Roca Overcoming non-small cell lung cancer radiation resistance by modulating the tumor-immune ecosystem BioRXiv https://doi.org/10.1101/458372 (2018)

A.Karolak, B.Huffstutler, Z.Khan, KA.Rejniak Assessment of patient-specific efficacy of chemo- and targeted-therapies: a micro pharmacology approach NIH/NCI Handbook of Mathematical Methods in Cancer Biology, BioRxiv, doi.org/10.1101/236653 (2017)

R.Walker, PE.Navas, SH.Friedman, S.Galliani, A.Karolak, F.Macfarlane, R.Noble, J.Poleszczuk, S.Russell,  KA.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 doi: 10.1101/055988 (2016)

Research monographs, chapters in collective volumes:

A.Karolak, S.Agrawal, S.Lee, KA.Rejniak Dissecting tumor heterogeneity with single-cell-based in silico models, Chapter in “Encyclopedia of Biomedical Engineering: Single Cell Mathematical Models”, Wiley (2019)

A.Karolak, KA.Rejniak Mathematical modeling of tumor organoids: toward personalized medicine, Chapter in “Tumor Organoids: Cancer Drug Delivery and Development”, Springer (2017)

J.Pérez-Velázquez, JL.Gevertz, A.Karolak, KA.Rejniak Microenvironmental niches and sanctuaries: A route to acquired resistance, Chapter in “Advances in Experimental Medicine and Biology”, Springer (2016)