An improved geometry-aware curvature discretization for level set methods: Application to tumor growth. - Paul Macklin; John S. Lowengrub (J. Comput. Phys., 2006)

A New Ghost Cell/Level Set Method for Moving Boundary Problems: Application to Tumor Growth. - Paul Macklin; John S. Lowengrub (J. Sci. Comput., 2008)

BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. - Ahmadreza Ghaffarizadeh; Samuel H. Friedman; Paul Macklin (Bioinform., 2016)

Quantifying differences in cell line population dynamics using CellPD. - Edwin F. Juarez; Roy Lau; Samuel H. Friedman; Ahmadreza Ghaffarizadeh; Edmond A. Jonckheere; David B. Agus; Shannon M. Mumenthaler; Paul Macklin (BMC Syst. Biol., 2016)

An Evolutionary Model of Tumor Cell Kinetics and the Emergence of Molecular Heterogeneity Driving Gompertzian Growth. - Jeffrey West; Zaki Hasnain; Paul Macklin; Paul K. Newton (SIAM Rev., 2016)

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow. - Jonathan Ozik; Nicholson T. Collier; Justin M. Wozniak; Charles M. Macal; Chase Cockrell; Samuel H. Friedman; Ahmadreza Ghaffarizadeh; Randy W. Heiland; Gary An; Paul Macklin (BMC Bioinform., 2018)

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems. - Ahmadreza Ghaffarizadeh; Randy W. Heiland; Samuel H. Friedman; Shannon M. Mumenthaler; Paul Macklin (PLoS Comput. Biol., 2018)

Students' Use of Metacognitive Skills in Undergraduate Research Experiences in Computational Modeling. - Aasakiran Madamanchi; Randy W. Heiland; Paul Macklin; Alejandra J. Magana (FIE, 2019)

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. - Gaëlle Letort; Arnau Montagud; Gautier Stoll; Randy W. Heiland; Emmanuel Barillot; Paul Macklin; Andrei Yu. Zinovyev; Laurence Calzone (Bioinform., 2019)

xml2jupyter: Mapping parameters between XML and Jupyter widgets. - Randy W. Heiland; Daniel Mishler; Tyler Zhang; Eric Bower; Paul Macklin (J. Open Source Softw., 2019)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics. - Zaki Hasnain; Andrew K. Fraser; Dan Georgess; Alex Choi; Paul Macklin; Joel S. Bader; Shelly R. Peyton; Andrew J. Ewald; Paul K. Newton (Bioinform., 2020)

OpenACC Acceleration of an Agent-Based Biological Simulation Framework. - Matt Stack; Paul Macklin; Robert Searles; Sunita Chandrasekaran (Comput. Sci. Eng., 2022)

Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. - Eric A. Stahlberg; Mohamed Abdel-Rahman; Boris Aguilar; Alireza Asadpoure; Robert A. Beckman; Lynn L. Borkon; Jeffrey N. Bryan; Colleen M. Cebulla; Young Hwan Chang; Ansu Chatterjee; Jun Deng; Sepideh Dolatshahi; et al. (Frontiers Digit. Health, 2022)

Building digital twins of the human immune system: toward a roadmap. - Reinhard C. Laubenbacher; Anna Niarakis; Tomás Helikar; Gary An; B. Shapiro; Rahuman S. Malik-Sheriff; T. J. Sego; Adam C. Knapp; Paul Macklin; James A. Glazier (npj Digit. Medicine, 2022)

Aboveground biomass and carbon stock estimation using UAV photogrammetry in Indonesian mangroves and other competing land uses. - Mohammad Basyuni; Anindya Wirasatriya; Sigit Bayhu Iryanthony; Rizka Amelia; Bejo Slamet; Nurdin Sulistiyono; Rudhi Pribadi; Elham Sumarga; Syaiful Eddy; Shofiyah S. Al Mustaniroh; Sigit D. Sasmito; Frida Sidik; et al. (Ecol. Informatics, 2023)

An agent-based modeling approach for lung fibrosis in response to COVID-19. - Mohammad Aminul Islam; Michael Getz; Paul Macklin; Ashlee N. Ford Versypt (PLoS Comput. Biol., 2023)

Building multiscale models with PhysiBoSS, an agent-based modeling tool. - Marco Ruscone; Andrea Checcoli; Randy W. Heiland; Emmanuel Barillot; Paul Macklin; Laurence Calzone; Vincent Noël (Briefings Bioinform., 2024)

Toward mechanistic medical digital twins: some use cases in immunology. - Reinhard C. Laubenbacher; Fred Adler; Gary An; Filippo Castiglione; Stephen Eubank 002; Luis L. Fonseca; James A. Glazier; Tomás Helikar; Marti Jett-Tilton; Denise Kirschner; Paul Macklin; Borna Mehrad; et al. (Frontiers Digit. Health, 2024)