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UF Health University of Florida
Laboratory for Systems Medicine Division of Pulmonary, Critical Care & Sleep Medicine

Publications

Preprints

  • Brunson JC, Skaf Y. Fixed and adaptive landmark sets for finite pseudometric spaces. 2022 Dec 21. arXiv: 2212.09826
  • Aghaee M, Ledzewicz U, Robbins M, Bezman N, Cho HJ, Moore H. Determining Optimal Combination Regimens for Patients with Multiple Myeloma. 2022 Nov 17. arXiv: 2211.09280
  • Kadelka C, Laubenbacher R, Murrugarra D, Veliz-Cuba A, Wheeler M. Decomposition of Boolean networks: An approach to modularity of biological systems. 2022 Jun 9. arXiv: 2206.04217
  • Harshman N, Knapp A. Topological Exchange Statistics in One Dimension. 2021 Aug 25. arXiv: 2108.05653
  • Kadelka C, Keilty B, Laubenbacher R. Collectively canalizing Boolean functions. 2020 Oct 5. arXiv: 2008.13741
  • Ribeiro HAL, Scindia Y, Mehrad B, Laubenbacher R. COVID-associated pulmonary aspergillosis in immunocompetent patients. 2022 Jul 19. bioRxiv, doi: 10.1101/2022.07.18.500514v1

Articles

2023

  • Skaf Y, Laubenbacher R. Topological data analysis in biomedicine: A review. J Biomed Inform. 2022 Jun;130:104082. doi: 10.1016/j.jbi.2022.104082. Epub 2022 May 1. PMID: 35508272
  • 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

  • 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.
  • Skaf Y, Laubenbacher R. Student-Centric Graduate Training: Challenges and Opportunities. [Students and Education] SIAM News. 2021 Nov 01;54(08). url: https://sinews.siam.org/Details-Page/student-centric-graduate-training-challenges-and-opportunities.
  • Skaf Y, Laubenbacher R. Toward Student-Centric Graduate Training. [Students and Education] SIAM News. 2021 Oct 01;54(08). url: https://sinews.siam.org/Details-Page/toward-student-centric-graduate-training.
  • Koshy-Chenthittayil S, Mendes P, Laubenbacher R. Optimization of agent-based models through coarse-graining: A case study in microbial ecology. Lett. Biomath. 2021 Sep 24;8(1):167–178. url: https://lettersinbiomath.journals.publicknowledgeproject.org/index.php/lib/article/view/431.
  • Gupta A, Styczynski MP, Galinski MR, Voit EO, Fonseca LL. Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections. Sci Rep. 2021 Sep 30;11(1):19519. doi: 10.1038/s41598-021-98024-6. PMID: 34593836; PMCID: PMC8484567.
  • Laubenbacher R. The Why and How of Manuscript Review: What Goes Around Comes Around. [Programs and Publications] SIAM News. 2021 Sep 01;54(07). url: https://sinews.siam.org/Details-Page/the-why-and-how-of-manuscript-review-what-goes-around-comes-around.
  • 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

Presentations

2022

  • Fonseca LL. “Generating ODE Approximations of Agent Based Models for Control Purposes”. Minisymposium on Boolean networks and related modeling frameworks at the 12th European Conference on Mathematical and Theoretical Biology (ECMTB 2022). Heidelberg, Germany, 2022 Sep 19.
  • 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.
  • Laubenbacher RC. “Multiscale Computational Models for Lung Immunity”. Keynote Presentation at the 30th Conference on Intelligent Systems for Molecular Biology of the International Society for Computational Biology. 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.