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Center for Research in Scientific Computation

Journal Papers

Noteworthy Journal Papers 2023

  • Identifying multicellular spatiotemporal organization of cells with SpaceFlow
  • Authors: Honglei Ren, Benjamin L. Walker, Zixuan Cang, Qing Nie
  • Publisher: Nature Communications
  • Abstract: One major challenge in analyzing spatial transcriptomic datasets is to simultaneously incorporate the cell transcriptome similarity and their spatial locations. This paper introduces SpaceFlow, which generates spatially consistent low-dimensional embeddings by incorporating both expression similarity and spatial information using spatially regularized deep graph networks.
  • Quantifying rare events in spotting: How far do wildfires spread?
  • Authors: Alexander Mendez, Mohammad Farazmand
  • Publisher: Fire Safety Journal
  • Abstract: Spotting refers to the transport of burning pieces of firebrand by wind which, at the time of landing, may ignite new fires beyond the direct ignition zone of the main fire. Spot fires that occur far from the original burn unit are rare but have consequential ramifications since their prediction and control remains challenging. To facilitate their prediction, the paper examines three methods for quantifying the landing distribution of firebands.
  • Unsupervised learning methods for efficient geographic clustering and identification of disease disparities with applications to county-level colorectal cancer incidence in California
  • Authors: Mallory E McMahon, Lyubov Doroshenko, Javad Roostaei, Hyunsoon Cho, Mansoor A Haider
  • Publisher: Health Care Management Science
  • Abstract: Many public health policymaking questions involve data subsets representing application-specific attributes and geographic location. Techniques presented in this paper are relevant to applications including the delivery of health care resources and identifying disparities among identity groups, and to questions involving coordination between county- and state-level policy makers.

Noteworthy Journal Papers 2024

  • An electro-hydrodynamics modeling of droplet actuation on solid surface by surfactant-mediated electro-dewetting
  • Authors: Weiqi Chu, Hangjie Ji, Qining Wang, Chang-Jin “CJ” Kim, and Andrea L. Bertozzi
  • Publisher: Physical Review Fluids
  • Abstract: This paper proposed an electro-hydrodynamics model to describe the dynamic evolution of a slender drop containing a dilute ionic surfactant on a naturally wettable surface, with a varying external electric field. This unified model reproduces fundamental microfluidic operations controlled by electrical signals, including dewetting, rewetting, and droplet shifting.
  • Bulk and mosaic deletions of Egfr reveal regionally defined gliogenesis in the developing mouse forebrain
  • Authors: Xuying Zhang, Guanxi Xiao, Caroline Johnson, Yuheng Cai, Zachary K Horowitz, Christine Mennicke, Robert Coffey, Mansoor Haider, David Threadgill, Rebecca Eliscu, Michael C Oldham, Alon Greenbaum, H Troy Ghashghaei
  • Publisher: iScience
  • Abstract: The epidermal growth factor receptor (EGFR) plays a role in cell proliferation and differentiation during healthy development and tumor growth; however, its requirement for brain development remains unclear. This work used a conditional mouse allele for Egfr to examine its contributions to perinatal forebrain development at the tissue level.
  • Physical models of notochord cell packing reveal how tension ratios determine morphometry
  • Authors: Evan J. Curcio and Sharon R. Lubkin
  • Publisher: Cells & Development (cover article)
  • Abstract: This paper investigated the physical and geometric aspects of notochords using a model of finite- length notochords, with interior vacuolated cells arranged in two common packing configurations, and sheath modeled as homogeneous and thin. This work provided a framework for further work which may provide insight into the roles of mechanosensing and pressure-volume regulation in the notochord.
  • Stochastic compartmental models of the COVID-19 pandemic must have temporally correlated uncertainties.
  • Authors: Konstantinos Mamis and Mohammad Farazmand
  • Publisher: Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
  • Abstract: This paper showed that the white noise stochastic model systematically underestimates the severity of the Omicron variant of COVID-19, whereas the Ornstein-Uhlenbeck model correctly forecasts the course of this variant. The results strongly support the need for temporal correlations in modelling of uncertainties in compartmental models of infectious disease.
  • Towards an optimal contraception dosing strategy
  • Authors: Brenda Lyn A. Gavina, Aurelio A. de los Reyes V, Mette S. Olufsen, Suzanne Lenhart, Johnny T. Ottesen
  • Publisher: PLOS Computational Biology
  • Abstract: Anovulation refers to a menstrual cycle characterized by the absence of ovulation. This study utilizes optimal control theory on a modified menstrual cycle model to determine the minimum total exogenous estrogen/progesterone dose, and timing of administration to induce anovulation.