Profile of James Sluka

2024 Davidson-Fritz SE, Ring CL, Evans MV, Schacht CM, Chang X, Breen M, Honda GS, Kenyon E, Linakis MW, Meade A, Pearce RG, PuruckerT, Sfeir MA, Sluka JP, Devito MJ, and Wambaugh JF. Enabling Transparent Toxicokinetic Modeling for Public Health Risk Assessment. PLOS Comp Bio, submitted 8/2024.

2024 Lubin KE, Zu Z, Sluka JP, Knipp G. Development of an in vitro model of the neurovascular unit for BBB permeability-linked neuroactivity screening. Medicinal Chemistry Research. 2024 July. https://doi.org/10.1007/s00044-024-03290-4

2024 Dietrich SW, Ma W, Ding Y, Watanabe KH, Zelinski MB, Sluka JP. MOTHER-DB: A Database for Sharing Nonhuman Ovarian Histology Images. IEEE/ACM Trans Comput Biol Bioinform. 2024 Jul 12;PP. doi: 10.1109/TCBB.2024.3426999. [Epub ahead of print] PubMed PMID: 38995706.

2024 Chandrasegaran S, Sluka JP, Shanley D. Modelling the spatiotemporal dynamics of senescent cells in wound healing, chronic wounds, and fibrosis. bioRxiv. 2024 Jul 8;. doi: 10.1101/2024.07.04.602041. PubMed PMID: 39026713; PubMed Central PMCID: PMC11257496.

2024 Watanabe KH, Dietrich SB, Ding Y, Ma W, Sluka JP, Zelinski MB. Overview of the multispecies ovary tissue histology electronic repository (MOTHER). Biol Reprod. 2024 Jun 20;. doi: 10.1093/biolre/ioae101. [Epub ahead of print] PubMed PMID: 38900906.

2024 Zha L, Matsu-Ura T, Sluka JP, Murakawa T, Tsuta K. Morphological basis of the lung adenocarcinoma subtypes. iScience. 2024 May 17;27(5):109742. doi: 10.1016/j.isci.2024.109742. eCollection 2024 May 17. PubMed PMID: 38706836; PubMed Central PMCID: PMC11066476.

2023 Sego TJ, Sluka JP, Sauro HM, Glazier JA. Tissue Forge: Interactive biological and biophysics simulation environment. PLoS Comput Biol. 2023 Oct;19(10):e1010768. doi: 10.1371/journal.pcbi.1010768. eCollection 2023 Oct. PubMed PMID: 37871133; PubMed Central PMCID: PMC10621971.

2023 Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, Allocca C, Betsou F, Burdett T, Cancio I, Chapman A, Chapman M, Courtot M, Curcin V, Eder J, Elliot M, Exter K, Goble C, Golebiewski M, Kisler B, Kremer A, Leo S, Lin-Gibson S, Marsano A, Mattavelli M, Moore J, Nakae H, Perseil I, Salman A, Sluka J, Soiland-Reyes S, Strambio-De-Castillia C, Sussman M, Swedlow JR, Zatloukal K, Geiger J. Toward a common standard for data and specimen provenance in life sciences. Learn Health Syst. 2023 Apr 18;8(1):e10365. doi: 10.1002/lrh2.10365. PMID: 38249839; PMCID: PMC10797572.

2023 Gianlupi JF, Sego TJ, Sluka JP, Glazier JA. PhenoCellPy: A Python package for biological cell behavior modeling. bioRxiv. 2023 April. doi: 2023.04.12.535625.

2022 Ferrari Gianlupi J, Mapder T, Sego TJ, Sluka JP, Quinney SK, Craig M, Stratford RE Jr, Glazier JA. Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2. Viruses. 2022 Mar 14;14(3). doi: 10.3390/v14030605. PubMed PMID: 35337012; PubMed Central PMCID: PMC8953050.

2022 ct Tikka P, Mercker M, Skovorodkin I, Saarela U, Vainio S, Ronkainen VP, Sluka JP, Glazier JA, Marciniak-Czochra A, Schaefer F. Computational modelling of nephron progenitor cell movement and aggregation during kidney organogenesis. Math Biosci. 2022 Feb;344:108759. doi: 10.1016/j.mbs.2021.108759. Epub 2021 Dec 7. PubMed PMID: 34883105.

2021 Toledo-Marín JQ, Fox G, Sluka JP, Glazier JA. Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations. Front Physiol. 2021 Jun 24;12:667828. doi: 10.3389/fphys.2021.667828. PMID: 34248661; PMCID: PMC8264663.

2021 Laubenbacher R, Sluka JP, Glazier JA. Using digital twins in viral infection. Science. 2021 Mar 12;371(6534):1105-1106. doi: 10.1126/science.abf3370. PMID: 33707255; PMCID: PMC8170388.

2020 Adhyapok P, Fu X, Sluka JP, Clendenon SG, Sluka VD, Wang Z, Dunn K, Klaunig JE, Glazier JA. A computational model of liver tissue damage and repair. PLoS One. 2020 Dec 21;15(12):e0243451. doi: 10.1371/journal.pone.0243451. PMID: 33347443; PMCID: PMC7752149.

2020 Dunn KW, Martinez MM, Wang Z, Mang HE, Clendenon SG, Sluka JP, Glazier JA, Klaunig JE. Mitochondrial depolarization and repolarization in the early stages of acetaminophen hepatotoxicity in mice. Toxicology. 2020 Jun;439:152464. doi: 10.1016/j.tox.2020.152464. Epub 2020 Apr 19. PMID: 32315716; PMCID: PMC7270714.

2019 Clendenon SG, Fu X, Von Hoene RA, Clendenon JL, Sluka JP, Winfree S, Mang H, Martinez M, Filson A, Klaunig JE, Glazier JA, Dunn KW. Spatial Temporal Analysis of Fieldwise Flow in Microvasculature. J Vis Exp. 2019 Nov 18;(153). doi: 10.3791/60493. PMID: 31789313.

2019 Rockne RC, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, Macklin P, Hormuth DA, Jarrett AM, Lima EABF, Tinsley Oden J, Biros G, Yankeelov TE, Curtius K, Al Bakir I, Wodarz D, Komarova N, Aparicio L, Bordyuh M, Rabadan R, Finley SD, Enderling H, Caudell J, Moros EG, Anderson ARA, Gatenby RA, Kaznatcheev A, Jeavons P, Krishnan N, Pelesko J, Wadhwa RR, Yoon N, Nichol D, Marusyk A, Hinczewski M, Scott JG. The 2019 mathematical oncology roadmap. Phys Biol. 2019 Jun 19;16(4):041005. doi: 10.1088/1478-3975/ab1a09. PMID: 30991381; PMCID: PMC6655440.

2018 Fu X, Sluka JP, Clendenon SG, Dunn KW, Wang Z, Klaunig JE, Glazier JA. Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models. PLoS One. 2018 Sep 13;13(9):e0198060. doi: 10.1371/journal.pone.0198060. PMID: 30212461; PMCID: PMC6136710.

2018 Clendenon SG, Fu X, Von Hoene RA, Clendenon JL, Sluka JP, Winfree S, Mang H, Martinez M, Filson AJ, Klaunig JE, Glazier JA, Dunn KW. A simple automated method for continuous fieldwise measurement of microvascular hemodynamics. Microvasc Res. 2019 May;123:7-13. doi: 10.1016/j.mvr.2018.11.010. Epub 2018 Nov 28. PubMed PMID: 30502365; PubMed Central PMCID: PMC6379124.

2016 JP Sluka, X Fu, M Swat, JM Belmonte, A Cosmanescu, SG Clendenon, JF Wambaugh and JA Glazier “A Liver-centric Multiscale Modeling Framework for Xenobiotics”, PLoS One. 2016 Sep 16;11(9):e0162428. doi: 10.1371/journal.pone.0162428. “2016 Best Biological Modeling Paper Award” from the Biological Modeling Specialty Section of the Society of Toxicology.

2016 CE Clancy, G An, WR Cannon, Y Liu, EE May, P Ortoleva, AS Popel, JP Sluka, J Su, P Vicini, X Zhou and DM Eckmann “Multiscale Modeling in the Clinic: Drug Design and Development”, Annals of Biomedical Engineering, 2016 Feb 17; PMID: 26885640.

2016 JF Wambaugh, BA Wetmore, R Pearce, C Strope, R Goldsmith, J Sluka, A Sedykh, A Tropsha, S Bosgra, I Shah, R Judson, RS Thomas, and RW Setzer “Toxicokinetic Triage for Environmental Chemicals”, Toxicological Sciences, 147(1):55-67. PMID: 26085347. “Honorable Mention, Society of Toxicology, Toxicological Sciences Paper of the Year Award 2016.”

2016 Somogyi E, Sluka JP, Glazier JA. 2016. Formalizing knowledge in multi-scale agent based simulations. In Proceedings of the ACM/IEEE 19th International Conference on Model Driven Engineering Languages and Systems (MODELS ’16). ACM, New York, NY, USA, 115-122. DOI: https://doi.org/10.1145/2976767.2976790

2014 Sluka, J, Shirinifard A, Swat M, Cosmanescu A, Heiland R, and Glazier JA “The Cell Behavior Ontology: Describing the intrinsic biological behaviors of real and model cells seen as active agents”, Bioinformatics, 30:16, 2367-2374; doi: 10.1093/bioinformatics/ btu210.

2012 Sluka, JP, Glazier, JA, Swat, M “Infrastructure requirements for moving multiscale modeling from research tools to the clinical and regulatory domains”, in VPH NoE Newsletter,7, January 2012.

2012 R Heiland, M Swat, J Sluka, B Zaitlen, A Shirinifard, GL Thomas, A Lumsdaine, and J.A. Glazier. “Visualizing Cells and their Connectivity Graphs for CompuCell3D”. Biological Data Visualization (BioVis), 2012 IEEE Symposium on , pp.85-90, 14-15 Oct. 2012. doi: 10.1109/BioVis. 2012.6378597.

2001-2007 J Sluka, “PDQ_MED A software package for efficient mining of the biomedical literature in conjunction with ’Ohmics experiments”. Commercial software package. Customers included the National Institute of Environmental Health Sciences (NIEHS), MD Anderson Cancer Center, Duke University, Merck, Eli Lily, and Amgen.

2002 Dodge, JA, Jones, CD, Marron, K, Sluka, JP, Stocksdale, MG, “Compounds and compositions with nitrogen-containing non-basic side chains”, US Patent 6,444,688, Issued Sept. 3, 2002.

1999 Schmid, CR, Sluka, JP, Duke, KM, Glasebrook, AW “Novel nonsteroidal selective estrogen receptor modulators. Carbon and heteroatom replacement of oxygen in the ethoxypiperidine region of raloxifene”, Bioorganic and Medicinal Chemistry Letters 9, 523–528. (PMID: 10098655)

1998 Miles, RM, Turner, CH, Santerre, R, Tu, Y, McClelland, ., Argot, J, DeHoff, BS, Mundy, CW, Rosteck, PR Jr., Bidwell, J, Sluka, JP, Hock, J, Onyia, J. “Analysis of differential gene expression in rat tibia after osteogenic stimulus in vivo: mechanical loading regulates Osteopontin and Myeloperoxidase”, Journal of Cellular Biochemistry 68, 355–365.

1997 Grese, TA, Sluka, JP, Bryant, HU, Cullinan, GJ, Glasebrook, AL, Jones, CD, Matsumoto, K, Palkowitz, AD, Termine, JD, Winter, M., Yang, NN, Dodge, JA “Molecular determinants of tissue selectivity in estrogen receptor modulators”, Proceedings of the National Academy of Sciences USA 94, 14105–14110.(PMID: 9391160)

1990 Sluka, JP, Horvath, SJ, Glasglow, AC, Simon, MI, Dervan, PB “The Importance of Minor Groove Contacts in the Recognition of DNA by the DNA Binding Domain 3 of Hin Recombinase”, Biochemistry 29, 6551–6561. (PMID: 2204415)

1990 Sluka, JP, Griffin, JH, Mack, DP, Dervan, PB “Reagents and Methods for the Solid Phase Synthesis of Protein-EDTA for Use in Affinity Cleaving” Journal of the American Chemical Society 112, 6369–6374.

1987 Sluka, JP, Bruist, MF Horvath, SJ, Simon, MI, Dervan, PB “Synthesis of a Sequence Specific DNA Cleaving Peptide”, Science 238, 1129. (PMID: 3120311)