Recent Publications

Preprints

  • SteadyCellPhenotype: A web-based tool for the modeling of biological networks with ternary logic. Adam C. Knapp, Luis Sordo Vieira, Reinhard Laubenbacher, Julia Chifman. bioRxiv 2021.08.10.454961; doi: https://doi.org/10.1101/2021.08.10.454961.
  • Harshman, Nathan, Knapp, Adam. (2021). Topological exchange statistics in one dimension. Arxiv. https://arxiv.org/abs/2108.05653.
  • Kadelka, Claus, Benjamin Keilty, and Reinhard Laubenbacher. “Collectively Canalizing Boolean Functions.” ArXiv:2008.13741 [Cs, Math, q-Bio], October 5, 2020. http://arxiv.org/abs/2008.13741.
  • Peterson, Mariko S., et al. “Clinical Recovery of Macaca Fascicularis Infected with Plasmodium Knowlesi.” BioRxiv, Cold Spring Harbor Laboratory, 1 Jan. 2021, www.biorxiv.org/content/10.1101/2021.06.28.448877v1.

Publications

  • Yara Skaf and Reinhard Laubenbacher. 2021. “Toward Student-Centric Graduate Training”. [Students and Education] SIAM News, 54 (08). https://sinews.siam.org/Details-Page/toward-student-centric-graduate-training
  • Koshy-Chenthittayil, Sherli, Pedro Mendes, and Reinhard Laubenbacher. 2021. “Optimization of Agent-Based Models Through Coarse-Graining”. Letters in Biomathematics8 (1), 167–178. https://lettersinbiomath.journals.publicknowledgeproject.org/index.php/lib/article/view/431.
  • Anuj Gupta, Mark P. Styczynski, Mary R. Galinski, Eberhard O. Voit & Luis L. Fonseca. Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections. Sci Rep 11, 19519 (2021). https://doi.org/10.1038/s41598-021-98024-6
  • Laubenbacher, R. (2021, September 1). The Why and How of Manuscript Review: What Goes Around Comes Around. SIAM News. https://sinews.siam.org/Details-Page/the-why-and-how-of-manuscript-review-what-goes-around-comes-around
  • Atuegwu, Nkiruka C.; Litt, Mark D.; Krishnan-Sarin, Suchitra; Laubenbacher, Reinhard C.; Perez, Mario F.; Mortensen, Eric M. 2021. “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 18, no. 10: 5476. https://doi.org/10.3390/ijerph18105476
  • Masison, J., J. Beezley, Y. Mei, H. a. L. Ribeiro, A. C. Knapp, L. Sordo Vieira, B. Adhikari, et al. “A Modular Computational Framework for Medical Digital Twins.” Proceedings of the National Academy of Sciences 118, no. 20 (May 18, 2021). https://doi.org/10.1073/pnas.2024287118.
  • Dalvi-Garcia, Felipe, Luis L. Fonseca, Ana Tereza R. Vasoncelos, Cecilia Hedin-Pereira, and Eberhard O. Voit. “A Model of Dopamine and Serotonin-Kynurenine Metabolism in Cortisolemia: Implications for Depression.” PLOS Computational Biology 17, no. 5 (May 10, 2021): e1008956. https://doi.org/10.1371/journal.pcbi.1008956.
  • Laubenbacher, Reinhard, James P. Sluka, and James A. Glazier. “Using Digital Twins in Viral Infection.” Science 371, no. 6534 (March 12, 2021): 1105. https://doi.org/10.1126/science.abf3370
  • Koshy-Chenthittayil, Sherli; Archambault, Linda; Senthilkumar, Dhananjai; Laubenbacher, Reinhard; Mendes, Pedro; Dongari-Bagtzoglou, Anna. 2021. “Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review” Microorganisms 9, no. 2: 417. https://doi.org/10.3390/microorganisms9020417
  • Wooten, David J., Jorge Gómez Tejeda Zañudo, David Murrugarra, Austin M. Perry, Anna Dongari-Bagtzoglou, Reinhard Laubenbacher, Clarissa J. Nobile, and Réka Albert. “Mathematical Modeling of the Candida Albicans Yeast to Hyphal Transition Reveals Novel Control Strategies.” Preprint. Systems Biology, January 20, 2021. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008690
  • Terasaki, Mark, Jason Cory Brunson, and Justin Sardi. “Analysis of the Three Dimensional Structure of the Kidney Glomerulus Capillary Network.” Scientific Reports 10, no. 1 (December 2020): 20334. nature.com/articles/s41598-020-77211-x.
  • Sara K. Nutley, Lyvia Bertolace, Luis Sordo Vieira, Binh Nguyen, Ashley Ordway, Heather Simpson, Jessica Zakrzewski, Monica R. Camacho, Joseph Eichenbaum, Rachel Nosheny, Michael Weiner, R. Scott Mackin, Carol A. Mathews. Internet-based hoarding assessment: the reliability and predictive validity of the internet-based Hoarding Rating Scale, Self-Report, Psychiatry Research (2020). doi:https://doi.org/10.1016/j.psychres.2020.113505
  • Atuegwu, Nkiruka C., Cheryl Oncken, Reinhard C. Laubenbacher, Mario F. Perez, and Eric M. Mortensen. “Factors Associated with E-Cigarette Use in U.S. Young Adult Never Smokers of Conventional Cigarettes: A Machine Learning Approach.” International Journal of Environmental Research and Public Health 17, no. 19 (January 2020): 7271. https://doi.org/10.3390/ijerph17197271.

Releases

  • Jason Cory Brunson, Brandon Demkowicz, and Sanmati Choudhary, R Package ‘tdaunif’: Uniform Manifold Samplers for Topological Data Analysis (version 0.1.0). https://corybrunson.github.io/tdaunif/, (October 2020). https://cran.r-project.org/package=tdaunif
  • Matt Piekenbrock, Jason Cory Brunson, and Howard Hinnant. R Package ‘simplextree: Provides Tools for Working with General Simplicial Complexes’ (version 1.0.1). https://github.com/peekxc/simplextree, R, (September 2020). https://cran.r-project.org/package=simplextree.