Reinhard Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, Tomas Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen. Forum on immune digital twins: a meeting report. 2023, October 26. https://arxiv.org/abs/2310.18374, https://doi.org/10.48550/arXiv.2310.18374
Tien Comlekoglu, Bette J. Dzamba, Gustavo G. Pacheco, David R. Shook, T.J. Sego, James A. Glazier, Shayn M. Peirce, Douglas W. DeSimone. Modeling the roles of cohesotaxis, cell-intercalation, and tissue geometry in collective cell migration of Xenopus mesendoderm. 2023 Oct 16.bioRxiv 2023.10.16.562601; doi: https://doi.org/10.1101/2023.10.16.562601
Chesnais F, Sego TJ, Engstler E, Battilocchi M, Danovi D, Glazier JA, Veschini L. A spatialised agent-based model of NOTCH signalling pathway in Endothelial Cells predicts emergent heterogeneity due to continual dynamic phenotypic adjustments. bioRxiv. 2022 Aug 6. doi: 10.1101/2022.08.06.503043.
Brunson JC, Skaf Y. Fixed and adaptive landmark sets for finite pseudometric spaces. 2022 Dec 21. arXiv: 2212.09826
Kadelka C, Keilty B, Laubenbacher R. Collectively canalizing Boolean functions. 2020 Oct 5. arXiv: 2008.13741
Articles
2024
Laubenbacher R, Adler F, An G, Castiglione F, Eubank S, Fonseca LL, Glazier J, Helikar T, Jett-Tilton M, Kirschner D, Macklin P, Mehrad B, Moore B, Pasour V, Shmulevich I, Smith A, Voigt I, Yankeelov TE and Ziemssen T (2024) Toward mechanistic medical digital twins: some use cases in immunology. Front. Digit. Health 6:1349595. doi: 10.3389/fdgth.2024.1349595
Reinhard Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, Tomas Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen. Forum on immune digital twins: a meeting report. npj Systems Biology and Applications. 2024/02/16. 2056-7189. https://doi.org/10.1038/s41540-024-00345-5
T J Sego, SimService: a lightweight library for building simulation services in Python, Bioinformatics, Volume 40, Issue 1, January 2024, btae009, https://doi.org/10.1093/bioinformatics/btae009
2023
Mochan, E.; Sego, T.J. Mathematical Modeling of the Lethal Synergism of Coinfecting Pathogens in Respiratory Viral Infections: A Review. Microorganisms2023, 11, 2974. https://doi.org/10.3390/microorganisms11122974
Ribeiro HAL, Scindia Y, Mehrad B, Laubenbacher R. COVID-19-associated pulmonary aspergillosis in immunocompetent patients: a virtual patient cohort study. J Math Biol. 2023 Jun 12;87(1):6. doi: 10.1007/s00285-023-01940-6 . PMID: 37306747; PMCID: PMC10258510.
Kadelka C, Wheeler M, Veliz-Cuba A, Murrugarra D, Laubenbacher R. Modularity of biological systems: a link between structure and function. J R Soc Interface. 2023 Oct;20(207):20230505. DOI: 10.1098/rsif.2023.0505 . Epub 2023 Oct 25. PMID: 37876275.
Elena S Dimitrova, Adam C Knapp, Brandilyn Stigler, Michael E Stillman, Cyclone: Open-source package for simulation and analysis of finite dynamical systems, Bioinformatics, 2023;, btad634, https://doi.org/10.1093/bioinformatics/btad634
Sego, T.J., Comlekoglu, T., Peirce, S.M. et al. General, open-source vertex modeling in biological applications using Tissue Forge. Sci Rep13, 17886 (2023). https://doi.org/10.1038/s41598-023-45127-x
Riley EL, Brunson JC, Eydgahi S, Brantly ML, Lascano JE. Development of a risk score to increase detection of severe alpha-1 antitrypsin deficiency. ERJ Open Res. 2023 Sep 18;9(5):00302-2023. PMID: 37727673
Riley L, Brunson JC, Eydgahi S, Brantly M, Lascano J. Development of a Risk Score to Increase Detection of Severe Alpha-1 Antitrypsin Deficiency. ERJ Open Res. Epub ahead of print.
Aghaee M, Ledzewicz U, Robbins M, Bezman N, Jay Cho H, Moore H. Determining Optimal Combination Regimens for Patients with Multiple Myeloma. Eur J Pharm Sci. 2023 Jun 9:106492. doi: 10.1016/j.ejps.2023.106492. Epub ahead of print. PMID: 37302768.
Ribeiro HAL, Scindia Y, Mehrad B, Laubenbacher R. COVID-19-associated pulmonary aspergillosis in immunocompetent patients: a virtual patient cohort study. Journal of Mathematical Biology. 2023 Jun;87:6. doi: 10.1007/s00285-023-01940-6
Chandrasekhar K, Kadelka C, Laubenbacher R, Murrugarra D. Stability of linear Boolean networks. Physica D: Nonlinear Phenomena. 2023 Sep;451:133775. doi: 10.1016/j.physd.2023.133775.
Chung T, Sego TJ, Glazier JA. Cell Modeling in Jupyter Notebook using CompuCell3D. J ATE. 2023 Jan 30;2(1). doi: 10.5281/zenodo.7600786
Kadelka C, Keilty B, Laubenbacher R. Collectively canalizing Boolean functions. Advances in Applied Mathematics 2023 Apr;145:102475. doi: 10.1016/j.aam.2022.102475
2022
Harshman N, Knapp A. Topological Exchange Statistics in One Dimension. 2021 Aug 25. arXiv: 2108.05653
Sordo Vieira L, Guastello A, Nguyen B, Nutley SK, Ordway A, Simpson H, Zakrzewski J, Archer C, Liu N, Jean Gilles ME, Nosheny R, Weiner M, Mackin RS, Mathews CA. Identifying psychiatric and neurological comorbidities associated with hoarding disorder through network analysis. J Psychiatr Res. 2022 Dec;156:16-24. doi: 10.1016/j.jpsychires.2022.09.037. Epub 2022 Sep 27. PMID: 36219904.
Miñoza JMA, Rico JA, Zamora PRF, Bacolod M, Laubenbacher R, Dumancas GG, de Castro R. Biomarker Discovery for Meta-Classification of Melanoma Metastatic Progression Using Transfer Learning. Genes 2022 Dec 7;13(12):2303. doi: 10.3390/genes13122303.
DeBarry JD, Nural MV, Pakala SB, Nayak V, Warrenfeltz S, Humphrey J, Lapp SA, Cabrera-Mora M, Brito CFA, Jiang J, Saney CL, Hankus A, Stealey HM, DeBarry MB, Lackman N, Legall N, Lee K, Tang Y, Gupta A, Trippe ED, Bridger RR, Weatherly DB, Peterson MS, Jiang X, Tran V, Uppal K, Fonseca LL, Joyner CJ, Karpuzoglu E, Cordy RJ, Meyer EVS, Wells LL, Ory DS, Lee FE, Tirouvanziam R, Gutiérrez JB, Ibegbu C, Lamb TJ, Pohl J, Pruett ST, Jones DP, Styczynski MP, Voit EO, Moreno A, Galinski MR, Kissinger JC. MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques. Sci Data. 2022 Nov 24;9(1):722. doi: 10.1038/s41597-022-01755-y. PMID: 36433985.
Nguyen BK, Zakrzewski JJ, Sordo Vieira L, Mathews CA. Impact of Hoarding and Obsessive-Compulsive Disorder Symptomatology on Quality of Life and Their Interaction With Depression Symptomatology. Front Psychol. 2022 Aug 1;13:926048. doi: 10.3389/fpsyg.2022.926048. PMID: 35978775; PMCID: PMC9376220.
Guastello AD, Brunson JC, Sambuco N, Dale LP, Tracy NA, Allen BR, Mathews CA. Predictors of professional burnout and fulfilment in a longitudinal analysis on nurses and healthcare workers in the COVID-19 pandemic. J Clin Nurs. 2022 Aug 10. doi: 10.1111/jocn.16463. Epub ahead of print. PMID: 35949164.
Peterson MS, Joyner CJ, Lapp SA, Brady JA, Wood JS, Cabrera-Mora M, Saney CL, Fonseca LL, Cheng WT, Jiang J, Soderberg SR, Nural MV, Hankus A, Machiah D, Karpuzoglu E, DeBarry JD, Tirouvanziam R, Kissinger JC, Moreno A, Gumber S, Voit EO, Gutierrez JB, Cordy RJ, Galinski MR. Plasmodium knowlesi Cytoadhesion Involves SICA Variant Proteins. Front Cell Infect Microbiol. 2022 Jun 23;12:888496. doi: 10.3389/fcimb.2022.888496. PMID: 35811680; PMCID: PMC9260704.
Adhikari B, Starkweather A, Xu W, Acabchuk RL, Ramesh D, Eze B, Yang Y, Yang GS, Walker J, Laubenbacher R, Park CL. A feasibility study on yoga’s mechanism of action for chronic low back pain: psychological and neurophysiological changes, including global gene expression and DNA methylation, following a yoga intervention for chronic low back pain. Pilot Feasibility Stud. 2022 Jul 7;8(1):142. doi: 10.1186/s40814-022-01103-2. PMID: 35794661; PMCID: PMC9260994.
Laubenbacher R, Niarakis A, Helikar T, An G, Shapiro B, Malik-Sheriff RS, Sego TJ, Knapp A, Macklin P, Glazier JA. Building digital twins of the human immune system: toward a roadmap. npj Digit. Med. 2022 May 20;5,64. doi: 10.1038/s41746-022-00610-z.
Skaf Y, Laubenbacher R. Topological Data Analysis in Biomedicine: A Review. J Biomed Inform. 2022 May 1:104082. doi: 10.1016/j.jbi.2022.104082. Epub ahead of print. PMID: 35508272.
Sordo Vieira L, Nguyen B, Nutley SK, Bertolace L, Ordway A, Simpson H, Zakrzewski J, Gilles MEJ, Nosheny R, Weiner M, Mackin RS, Mathews CA. Self-reporting of psychiatric illness in an online patient registry is a good indicator of the existence of psychiatric illness. J Psychiatr Res. 2022 Jul;151:34-41. doi: 10.1016/j.jpsychires.2022.03.022. Epub 2022 Apr 15.
Ribeiro HAL, Sordo Vieira L, Scindia Y, Adhikari B, Wheeler M, Knapp A, Schroeder W, Mehrad B, Laubenbacher R. Multi-scale mechanistic modelling of the host defence in invasive aspergillosis reveals leucocyte activation and iron acquisition as drivers of infection outcome. J R Soc Interface. 2022 Apr;19(189):20210806. doi: 10.1098/rsif.2021.0806. Epub 2022 Apr 13. PMID: 35414216.
Schlauch KA, Read RW, Neveux I, Lipp B, Slonim A, Grzymski JJ. The Impact of ACEs on BMI: An Investigation of the Genotype–Environment Effects of BMI. Front. Genet. 2022 Mar;13:816660. doi: 10.3389/fgene.2022.816660.
Michels K, Solomon AL, Scindia Y, Sordo Vieira L, Yana G, Whitten S, Vaulont S, Burdick MD, Atkinson C, Laubenbacher R, Mehrad B. Aspergillus utilizes extracellular heme as an iron source during invasive pneumonia, driving infection severity. J Infect Dis. 2022 Mar 10:jiac079. doi: 10.1093/infdis/jiac079. Epub ahead of print. PMID: 35267014.
Sordo Vieira L, Laubenbacher R. Computational models in systems biology: standards, dissemination, and best practices. Curr Opin Biotechnol. 2022 Jun;75:102702. doi: 10.1016/j.copbio.2022.102702. Epub ahead of print.
Knapp AC, Sordo Vieira L, Laubenbacher R, Chifman J. SteadyCellPhenotype: A web-based tool for the modeling of biological networks with ternary logic. Bioinformatics. 2022 Feb 18. doi: 10.1093/bioinformatics/btac097. Epub ahead of print.
2021
Braakman S, Pathmanathan P, Moore H. Evaluation framework for systems models. CPT Pharmacometrics Syst Pharmacol. 2021 Dec 18. doi: 10.1002/psp4.12755. Epub ahead of print. PMID: 34921743.
Peterson MS, Joyner CJ, Brady JA, Wood JS, Cabrera-Mora M, Saney CL, Fonseca LL, Cheng WT, Jiang J, Lapp SA, Soderberg SR, Nural MV, Humphrey JC, Hankus A, Machiah D, Karpuzoglu E, DeBarry JD; MaHPIC-Consortium, Tirouvanziam R, Kissinger JC, Moreno A, Gumber S, Voit EO, Gutiérrez JB, Cordy RJ, Galinski MR. Clinical recovery of Macaca fascicularis infected with Plasmodium knowlesi. Malar J. 2021 Dec 30;20(1):486. doi: 10.1186/s12936-021-03925-6. PMID: 34969401; PMCID: PMC8719393.
Atuegwu NC, Litt MD, Krishnan-Sarin S, Laubenbacher RC, Perez MF, Mortensen EM. E-Cigarette Use in Young Adult Never Cigarette Smokers with Disabilities: Results from the Behavioral Risk Factor Surveillance System Survey. Int J Environ Res Public Health. 2021 May 20;18(10):5476. doi: 10.3390/ijerph18105476. PMID: 34065407; PMCID: PMC8160823.
Masison J, Beezley J, Mei Y, Ribeiro HAL, Knapp AC, Sordo Vieira L, Adhikari B, Scindia Y, Grauer M, Helba B, Schroeder W, Mehrad B, Laubenbacher R. A modular computational framework for medical digital twins. Proc Natl Acad Sci U S A. 2021 May 18;118(20):e2024287118. doi: 10.1073/pnas.2024287118. PMID: 33972437; PMCID: PMC8157963.
Dalvi-Garcia F, Fonseca LL, Vasconcelos ATR, Hedin-Pereira C, Voit EO. A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression. PLoS Comput Biol. 2021 May 10;17(5):e1008956. doi: 10.1371/journal.pcbi.1008956. PMID: 33970902; PMCID: PMC8136856.
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.
Koshy-Chenthittayil S, Archambault L, Senthilkumar D, Laubenbacher R, Mendes P, Dongari-Bagtzoglou A. Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review. Microorganisms. 2021 Feb 17;9(2):417. doi: 10.3390/microorganisms9020417. PMID: 33671308; PMCID: PMC7922883.
Wooten DJ, Zañudo JGT, Murrugarra D, Perry AM, Dongari-Bagtzoglou A, Laubenbacher R, Nobile CJ, Albert R. Mathematical modeling of the Candida albicans yeast to hyphal transition reveals novel control strategies. PLoS Comput Biol. 2021 Mar 29;17(3):e1008690. doi: 10.1371/journal.pcbi.1008690. PMID: 33780439; PMCID: PMC8031856.
2020
Terasaki M, Brunson JC, Sardi J. Analysis of the three dimensional structure of the kidney glomerulus capillary network. Sci Rep. 2020 Nov 23;10(1):20334. doi: 10.1038/s41598-020-77211-x. PMID: 33230129; PMCID: PMC7683536.
Nutley SK, Bertolace L, Sordo Vieira L, Nguyen B, Ordway A, Simpson H, Zakrzewski J, Camacho MR, Eichenbaum J, Nosheny R, Weiner M, Mackin RS, Mathews CA. Internet-based hoarding assessment: The reliability and predictive validity of the internet-based Hoarding Rating Scale, Self-Report. Psychiatry Res. 2020 Dec;294:113505. doi: 10.1016/j.psychres.2020.113505. Epub 2020 Oct 11. PMID: 33070108; PMCID: PMC8080473.
Atuegwu NC, Oncken C, Laubenbacher RC, Perez MF, Mortensen EM. Factors Associated with E-Cigarette Use in U.S. Young Adult Never Smokers of Conventional Cigarettes: A Machine Learning Approach. Int J Environ Res Public Health. 2020 Oct 5;17(19):7271. doi: 10.3390/ijerph17197271. PMID: 33027932; PMCID: PMC7579019.
Software
Brunson JC, Paul E. R Package ordr: A ‘tidyverse’ Extension for Ordinations and Biplots (version 0.1.0). CRAN 2022 Aug 18. url: https://cran.r-project.org/package=ordr
Brunson JC, Skaf Y. R Package interplex: Coercion Methods for Simplicial Complex Data Structures (version 0.1.0). CRAN 2022 Jun 21. url: https://cran.r-project.org/package=interplex
Brunson JC, Demkowicz B, Choudhary S. R Package tdaunif: Uniform Manifold Samplers for Topological Data Analysis (version 0.1.0). CRAN 2020 Oct 26. url: https://cran.r-project.org/package=tdaunif
Piekenbrock M, Brunson JC, Hinnant H. R Package simplextree: Provides Tools for Working with General Simplicial Complexes (version 1.0.1). CRAN 2020 Sep 12. url: https://cran.r-project.org/package=simplextree.
Presentations
2023
Fonseca, Luis L. Treatment Optimization in Medical Digital Twins, UF Pulmonary Research Conference Seminar Series, Gainesville, FL, 2023 Oct 25
Moore, H. How to Calculate an Optimal Drug Regimen, UF Pulmonary Research Conference Seminar Series, Gainesville, FL, 2023 Oct 18
Laubenbacher RC. Alliance Discussion, Research!America, 2023 June 15.
Sego TJ. CompuCell3D: Overview and Applications in Complex Biological Systems Modeling. Building Immune Digital Twins Workshop, Institut Pascal, Paris, France, 2023 May 15–June 2
Sordo Vieira L. Can Non-Hoarding Specific Markers of Problems in Mental Health Predict Populations at Risk of Compulsive Hoarding? Society of Biological Psychiatry Annual Meeting, San Diego CA, 2023 Apr 27–29.
Sego TJ. Cell State Dynamics in Multicellular Contexts: Current Capabilities and Future Directions. HARMONY 2023, University of Washington, 2023 Apr 24–27.
Sego TJ. Interactive Biological and Biophysics Simulation with Tissue Forge. HARMONY 2023, University of Washington, 2023 Apr 24–27.
Sego TJ. Enabling the Future of Biological and Biomedical Sciences with Advanced Modeling, Software and Computing. Mechanical and Energy Engineering Research Seminar Series, Purdue School of Engineering & Technology, Indiana University–Purdue University Indianapolis, 2023 Mar 2.
Fonseca LL. Modeling Host-Parasite Interactions in Malaria Blood-Stage Infections in Rhesus Macaques. Emerging Pathogens Institute Research Day, University of Florida, Gainesville, FL, 2023 Feb 16.
Cruz DA. Estimating the Long-term Behavior of Biologically Inspired Agent-based Models. Biomathematics Seminar, University of Florida, Gainesville, FL, 2023 Feb 16.
Cruz DA. Topological data analysis of pattern formation in stem cell colonies. Invited by Prof. Vincent Martinez. Mathematics Colloquium, Hunter College, New York, NY, 2023 Feb 16.
Sego TJ. Introduction to Particle-based Modeling in Tissue Forge. Invited by Prof. Herbert Sauro. Center for Reproducible Biomedical Modeling Tutorial Series, Department of Bioengineering, University of Washington, Seattle, WA, 2023 Feb 8.
Cruz DA. Topological data analysis of pattern formation in stem cell colonies. Invited oral presentation, Cal Poly Mathematics Department Colloquium, San Luis Obispo, CA, US, 2023 Feb 3.
Sego, TJ. Developing Software Tools in Computational Biology. Invited by Prof. Jared Ashcroft. Micro Nano Technology Education Center, Pasadena City College, Pasadena, CA. 2023 Jan 27.
Brunson JC. Toward Tidy Principles for Matrix-Decomposed Data. Invited panel on New Developments in Graphing Multivariate Data at the Joint Statistical Meetings. Washington, DC, 2022 Aug 8.
Laubennbacher R. Multiscale computational models of lung immunity. University of Idaho, 2022 Nov 1.
Laubennbacher R. Multiscale computational models of lung immunity. U.S. Food and Drug Administration (virtual), 2022 Oct 26.
Laubennbacher R. Boolean networks in systems biology. Max Planck Institute for Mathematics in the Natural Sciences, Leipzig, Germany, 2022 Sep 23.
Laubennbacher R. Mathematics in 21st century medicine: digital twins. Annual meeting of the Society for Mathematical Biology, Heidelberg, Germany, 2022 Sep 22.
Walker M. Implications of Disease Spread Due to Variability in Body Mass from Larval Stages in Aedes Aegypti. MS35: Advances in Epidemiology, 2022 SIAM Conference on the Life Sciences (hybrid), 2022 Jul 12.
Laubennbacher R. Multiscale computational models for lung immunity. Keynote Lecture, 30th Conference on Intelligent Systems for Molecular Biology, SYSMOD, Madison, WI, 2022 Jul 11.
Brunson JC. Toward a tidy package ecosystem for topological data analysis. Special session on Expanding Tidyverse at useR! 2022. Virtual, 2022 Jun 23.
Brunson JC. Post-Transplant Disparities Amongst Sarcoidosis-Indicated Lung Recipients. Mini-symposium on Advances in Pre- and Post-Lung Transplant Care: From Selection to CLAD at the American Thoracic Society International Conference. San Francisco, CA, 2022 May 18.
Cruz DA. Invited panelist, professional development panel. Undergraduate Mathematics Research Conference, Georgia Tech, Atlanta, GA, 2022 Apr 23.
Laubennbacher R. Medical digital twins: mathematics for 21st century medicine, Geller Lecture, Texas A&M University, College Station, TX, 2022 Apr 12.
