Aleksandra Karolak, PhD

Dr. Karolak’s background includes application and development of tools from the fields of computational and biophysical chemistry, structural biology, mathematical oncology, machine learning, and information theory. Her interests focus on understanding cancer development, progression, and variability in the response to treatment using models that can be translated into the clinic. She will be leading the application of machine learning in computational biology and drug discovery as part of the Molecular Medicine Program.

Associations

• Machine Learning
• Gastrointestinal Oncology
• Molecular Medicine Program

Education & Training

Graduate:

• University of South Florida, PhD - Biophysical and Computational Chemistry
• Adam Mickiewicz University, MSc - Metal-Organic Chemistry, Maxima Cum Laude, Individual Curriculum

Dr. Karolak’s background includes application and development of tools from the fields of computational and biophysical chemistry, structural biology, mathematical oncology, machine learning, and information theory. Her interests focus on understanding cancer development, progression, and variability in the response to treatment using models that can be translated into the clinic. She will be leading the application of machine learning in computational biology and drug discovery as part of the Molecular Medicine Program.

• Davis EW, Park MA, Basinski TL, Arnoletti JP, Bloomston M, Carson TL, Biachi De Castria T, Chen DT, Cortizas EM, Crowder SL, Genilo-Delgado M, Douglas WG, Huguet KL, Jiang K, Hodul PJ, Karolak A, Kim DW, Koomen JM, Menon AA, Mo Q, Mok SR, Molina-Vega MA, Moreno-Urazan L, Ahmed S, Parker NH, Pimiento JM, Rasool G, Sparks LM, Stewart PA, Tassielli AF, Teer JK, Trevino JG, Velanovich V, Wang X, Whelan CJ, Judge SM, Judge AR, Fleming JB, Malafa MP, Jeong D, Permuth JB. The Impact of Edema on Skeletal Muscle Changes among Patients with Pancreatic Ductal Adenocarcinoma. Cancer Epidemiol Biomarkers Prev. 2025 Sep.34(9):1609-1617. Pubmedid: 40553455.
• Nguyen T, Karolak A. Transformer graph variational autoencoder for generative molecular design. Biophys J. 2025 Jan. Pubmedid: 39885689.
• Wojtulewski A, Sikora A, Dineen S, Raoof M, Karolak A. Using artificial intelligence and statistics for managing peritoneal metastases from gastrointestinal cancers. Brief Funct Genomics. 2025 Jan.24. Pubmedid: 39736152. Pmcid: PMC11735730.
• Karolak A, Urbaniak K, Monastyrskyi A, Duckett DR, Branciamore S, Stewart PA. Structure-independent machine-learning predictions of the CDK12 interactome. Biophys J. 2024 Sep.123(17):2910-2920. Pubmedid: 38762754. Pmcid: PMC11393676.
• Sikora A, Sullivan KM, Dineen S, Raoof M, Karolak A. Emerging therapeutic approaches for peritoneal metastases from gastrointestinal cancers. Mol Ther Oncol. 2024 Mar.32(1):200767. Pubmedid: 38596287. Pmcid: PMC10873742.
• Mukund A, Afridi MA, Karolak A, Park MA, Permuth JB, Rasool G. Pancreatic Ductal Adenocarcinoma (PDAC): A Review of Recent Advancements Enabled by Artificial Intelligence. Cancers (Basel). 2024 Jun.16(12). Pubmedid: 38927945. Pmcid: PMC11201559.
• Park MA, Gumpper-Fedus K, Krishna SG, Genilo-Delgado MC, Brantley S, Hart PA, Dillhoff ME, Gomez MF, Basinski TL, Mok SR, Luthra AK, Fleming JB, Mohammadi A, Centeno BA, Jiang K, Karolak A, Jeong D, Chen DT, Stewart PA, Teer JK, Cruz-Monserrate Z, Permuth JB. Molecular Pathway and Immune Profile Analysis of IPMN-Derived Versus PanIN-Derived Pancreatic Ductal Adenocarcinomas. Int J Mol Sci. 2024 Dec.25(23). Pubmedid: 39684873. Pmcid: PMC11642437.
• El Naqa I, Karolak A, Luo Y, Folio L, Tarhini AA, Rollison D, Parodi K. Translation of AI into oncology clinical practice. Oncogene. 2023 Oct.42(42):3089-3097. Pubmedid: 37684407.
• Schöning V, Khurana A, Karolak A. Editorial: Spotlight on artificial intelligence in experimental pharmacology and drug discovery. Front Pharmacol. 2023 Aug.14:1261141. Pubmedid: 37711179. Pmcid: PMC10498275.
• Shaw TI, Zhao B, Li Y, Wang H, Wang L, Manley B, Stewart PA, Karolak A. Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients. Front Oncol. 2022 Nov.12:1051487. Pubmedid: 36505834. Pmcid: PMC9730332.
• McCune JS, Nakamura R, O'Meally D, Randolph TW, Sandmaier BM, Karolak A, Hockenbery D, Navarro SL. Pharmacometabonomic association of cyclophosphamide 4-hydroxylation in hematopoietic cell transplant recipients. Clin Transl Sci. 2022 May.15(5):1215-1224. Pubmedid: 35106927. Pmcid: PMC9099130.
• Karolak A, Levatić J, Supek F. A framework for mutational signature analysis based on DNA shape parameters. PLoS One. 2022 Jan.17(1):e0262495. Pubmedid: 35015788. Pmcid: PMC8752002.
• Karolak A, Levatić J, Supek F. A framework for mutational signature analysis based on DNA shape parameters. bioRxiv. 2021 Sep.
• Karolak A, Branciamore S, McCune JS, Lee PP, Rodin AS, Rockne RC. Concepts and Applications of Information Theory to Immuno-Oncology. Trends Cancer. 2021 Apr.7(4):335-346. Pubmedid: 33618998. Pmcid: PMC8156485.
• Karolak A, Huffstutler B, Khan Z, Rejniak KA. Assessment of patient-specific efficacy of chemo- and targeted-therapies: a micropharmacology approach. bioRxiv. 2019 May.
• Karolak A, Poonja S, Rejniak KA. Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential. PLoS Comput Biol. 2019 Jul.15(7):e1007214. Pubmedid: 31310602. Pmcid: PMC6660094.
• Khabibullin AR, Karolak A, Budzevich MM, McLaughlin ML, Morse DL, Woods LM. Structure and properties of DOTA-chelated radiopharmaceuticals within the 225Ac decay pathway. Medchemcomm. 2018 Jul.9(7):1155-1163. Pubmedid: 30109003. Pmcid: PMC6072494.
• Karolak A, Markov DA, McCawley LJ, Rejniak KA. Towards personalized computational oncology: from spatial models of tumour spheroids, to organoids, to tissues. J R Soc Interface. 2018 Jan.15(138). Pubmedid: 29367239. Pmcid: PMC5805971.
• Karolak A, Estrella VC, Huynh AS, Chen T, Vagner J, Morse DL, Rejniak KA. Targeting Ligand Specificity Linked to Tumor Tissue Topological Heterogeneity via Single-Cell Micro-Pharmacological Modeling. Sci Rep. 2018 Feb.8(1):3638. Pubmedid: 29483578. Pmcid: PMC5827036.
• Mukherjee S, Karolak A, Debant M, Buscaglia P, Renaudineau Y, Mignen O, Guida WC, Brooks WH. Molecular Dynamics Simulations of Membrane-Bound STIM1 to Investigate Conformational Changes during STIM1 Activation upon Calcium Release. J Chem Inf Model. 2017 02.57(2):335-344. Pubmedid: 28151650.
• Karolak A, van der Vaart A. BII stability and base step flexibility of N6-adenine methylated GATC motifs. Biophys Chem. 2016 Mar.203-204:22-27. Pubmedid: 26004863.
• Khabibullin AR, Karolak A, Budzevich MM, Woods LM, Martinez MV, McLaughlin ML, Morse DL. SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals. Med Phys. 2016 Jun.43(6):3314.
• Word TA, Karolak A, Cioce CR, Van Der Vaart A, Larsen RW. Using Photoacoustic Calorimetry to Study the cis- to trans- Photoisomerization of the [Ru(II)(2,2’-bipyridine)2(H2O)2]2+ Complex in Aqueous Solution. Comments Inorg Chem. 2016 Jun.36(6):343-354.
• Karolak A, van der Vaart A. Molecular Dynamics Simulations of 5-Hydroxycytosine Damaged DNA. J Phys Chem B. 2016 Jan.120(1):42-48. Pubmedid: 26654566.
• Pérez-Velázquez J, Gevertz JL, Karolak A, Rejniak KA. Microenvironmental Niches and Sanctuaries: A Route to Acquired Resistance. Adv Exp Med Biol. 2016 Dec.936:149-164. Pubmedid: 27739047. Pmcid: PMC5113820.
• Word TA, Whittington CL, Karolak A, Kemp MT, Woodcock HL, van der Vaart A, Larsen RW. 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. 2015 Jan.619:214-218.
• Karolak A, van der Vaart A. Enhanced sampling simulations of DNA step parameters. J Comput Chem. 2014 Dec.35(32):2297-2304. Pubmedid: 25303338.
• Karolak A, van der Vaart A. Importance of local interactions for the stability of inhibitory helix 1 in apo Ets-1. Biophys Chem. 2012 May.165-166:74-78. Pubmedid: 22494801.
• , Maciejewski H, Marciniec B, Gulinski J, Karolak A, Skvortsov NK. From isothiocyanato– to silyl–nickel complexes. Inorg Chem Commun. 2002 Jul.5(7):464-467.

• Title: Cancer AIKG: a Web-scale Trustworthy AI-Knowledge Graph-LLM hybrid on Cancer, Constructed and Interrogated for Bias using Deep-Learning
  Award Number: 25C06
  Sponsor: Florida State University (FSU)
  Karolak, A. (PD/PI)
• Title: Multi-omic Evaluation of Ovarian Cancer Responses to Heated Intraperitoneal Chemotherapy (HiPEC)
  Award Number: HT9425-21-1-0342
  Sponsor: Department of Defense (DOD)
  Karolak, A. (PD/PI)
• Title: CancerAIKG: A Web-scale Trustworthy AI-Knowledge Graph-LLM hybrid on Cancer, Constructed and Interrogated for Bias Using Deep-Learning
  Award Number: MOABG
  Sponsor: Florida State University (FSU)
  Karolak, A. (PD/PI)