Recent Publications


  • 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.


  • 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.
  • 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:
  • Skaf Y, Laubenbacher R. Toward Student-Centric Graduate Training. [Students and Education] SIAM News. 2021 Oct 01;54(08). url:
  • 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:
  • 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:
  • 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.
  • 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.