Fonseca LL, Böttcher L, Mehrad B, Laubenbacher RC. Optimal control of agent-based models via surrogate modeling. PLoS Comput Biol. 2025 Jan 14;21(1):e1012138. doi: 10.1371/journal.pcbi.1012138. Epub ahead of print. PMID: 39808665.
2024
Niarakis A, Laubenbacher R, An G, Ilan Y, Fisher J, Flobak Å, Reiche K, Rodríguez Martínez M, Geris L, Ladeira L, Veschini L, Blinov ML, Messina F, Fonseca LL, Ferreira S, Montagud A, Noël V, Marku M, Tsirvouli E, Torres MM, Harris LA, Sego TJ, Cockrell C, Shick AE, Balci H, Salazar A, Rian K, Hemedan AA, Esteban-Medina M, Staumont B, Hernandez-Vargas E, Martis B S, Madrid-Valiente A, Karampelesis P, Sordo Vieira L, Harlapur P, Kulesza A, Nikaein N, Garira W, Malik Sheriff RS, Thakar J, Tran VDT, Carbonell-Caballero J, Safaei S, Valencia A, Zinovyev A, Glazier JA. Immune digital twins for complex human pathologies: applications, limitations, and challenges. NPJ Syst Biol Appl. 2024 Nov 30;10(1):141. doi: 10.1038/s41540-024-00450-5. PMID: 39616158; PMCID: PMC11608242.
Matthew Wheeler, Claus Kadelka, Alan Veliz-Cuba, David Murrugarra, Reinhard Laubenbacher. Modular construction of Boolean networks. Physica D: Nonlinear Phenomena, Volume 468, 134278, ISSN 0167-2789. November 2024. doi.org/10.1016/j.physd.2024.134278
Reinhard Laubenbacher, Luis Sordo Vieira. Research in Biomathematics: A guide to Funding from the U.S. Army Research Office. SIAM News, Vol 57, Issue 07. September 2024.
Dasa O, Bai C, Sajdeya R, Kimmel SE, Pepine CJ, Gurka J MJ, Laubenbacher R, Pearson TA, Mardini MT. Identifying Potential Factors Associated With Racial Disparities in COVID-19 Outcomes: Retrospective Cohort Study Using Machine Learning on Real-World Data. JMIR Public Health Surveill. 2024 Sep 26;10:e54421. doi: 10.2196/54421. PMID: 39326040; PMCID: PMC11467607.
Simpson, M.J., Laubenbacher, R.C. & Baker, R.E. Make the Most of Your Society Journal. Bull Math Biol86, 120. 20 August 2024. doi: 10.1007/s11538-024-01349-2
T. Comlekoglu, B. Dzabma, G. Pacheco, D.R. Shook, T.J. Sego, J.A. Glazier, S.M. Peirce, D. DeSimone. Modeling the Roles of Cohesotaxis, Cell-Intercalation, and Tissue Geometry in Collective Cell Migration of Xenopus Mesendoderm. Biology Open, 13(8). 19 August 2024. doi: 10.1242/bio.060615
Sheen, J., Curtin, L., Finley, S. et al. Integrating Diversity, Equity, and Inclusion into Preclinical, Clinical, and Public Health Mathematical Models. Bull Math Biol86, 56. 16 April 2024. doi: 10.1007/s11538-024-01282-4
Walker M, Moore H, Ataya A, Pham A, Corris PA, Laubenbacher R, Bryant AJ. A perfectly imperfect engine: Utilizing the digital twin paradigm in pulmonary hypertension. Pulm Circ. 2024 Jun 25;14(2):e12392. doi: 10.1002/pul2.12392. PMID: 38933181; PMCID: PMC11199193.
Al-Bahou R, Bruner J, Moore H, Zarrinpar A. Quantitative methods for optimizing patient outcomes in liver transplantation. Liver Transpl. 2024 Mar 1;30(3):311-320. doi: 10.1097/LVT.0000000000000325. Epub 2023 Dec 25. PMID: 38153309; PMCID: PMC10932841.
Laubenbacher R, Mehrad B, Shmulevich I, Trayanova N. Digital twins in medicine. Nat Comput Sci. 2024 Mar;4(3):184-191. doi: 10.1038/s43588-024-00607-6. Epub 2024 Mar 26. PMID: 38532133; PMCID: PMC11102043.
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
Shabman RS, Craig M, Laubenbacher R, Reeves D, Brown LL. NIAID/SMB Workshop on Multiscale Modeling of Infectious and Immune-Mediated Diseases. Bull Math Biol. 2024 Mar 21;86(5):44. doi: 10.1007/s11538-024-01276-2. PMID: 38512541; PMCID: PMC10957590.
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.
