Personalized predictions of Glioblastoma infiltration: Mathematical models, Physics-Informed Neural Networks and multimodal scans - Ray Zirui Zhang; Ivan Ezhov; Michal Balcerak; Andy Zhu; Benedikt Wiestler; Bjoern H. Menze; John S. Lowengrub (Medical Image Anal., 2025)

PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration - Jinghao Chen; Jesse R. Holt; Elizabeth L. Evans; John S. Lowengrub; Medha M. Pathak (PLoS Comput. Biol., 2024)

BiLO: Bilevel Local Operator Learning for PDE inverse problems - Ray Zirui Zhang; Xiaohui Xie; John S. Lowengrub (CoRR, 2024)

Sharp-interface problem of the Ohta-Kawasaki model for symmetric diblock copolymers - Amlan K. Barua; Ray Chew; Shuwang Li; John S. Lowengrub; Andreas Münch; Barbara Wagner (J. Comput. Phys., 2023)

The Liver Tumor Segmentation Benchmark (LiTS) - Patrick Bilic; Patrick Ferdinand Christ; Hongwei Li; Eugene Vorontsov; Avi Ben-Cohen; Georgios Kaissis; Adi Szeskin; Colin Jacobs; Gabriel Efrain Humpire Mamani; Gabriel Chartrand; Fabian Lohöfer; Julian Walter Holch; et al. (Medical Image Anal., 2023)

Personalized Predictions of Glioblastoma Infiltration: Mathematical Models, Physics-Informed Neural Networks and Multimodal Scans - Ray Zirui Zhang; Ivan Ezhov; Michal Balcerak; Andy Zhu; Benedikt Wiestler; Bjoern H. Menze; John S. Lowengrub (CoRR, 2023)

Individualizing Glioma Radiotherapy Planning by Optimization of a Data and Physics Informed Discrete Loss - Michal Balcerak; Ivan Ezhov; Petr Karnakov; Sergey Litvinov; Petros Koumoutsakos; Jonas Weidner; Ray Zirui Zhang; John S. Lowengrub; Benedikt Wiestler; Bjoern H. Menze (CoRR, 2023)

Second order approximation for a quasi-incompressible Navier-Stokes Cahn-Hilliard system of two-phase flows with variable density - Zhenlin Guo; Qing Cheng; Ping Lin; Chun Liu; John S. Lowengrub (J. Comput. Phys., 2022)

Nonlinear simulation of vascular tumor growth with chemotaxis and the control of necrosis - Min-Jhe Lu; Wenrui Hao; Chun Liu; John S. Lowengrub; Shuwang Li (J. Comput. Phys., 2022)

Mathematical modeling of cancer immunotherapy for personalized clinical translation - Joseph D. Butner; Prashant Dogra; Caroline Chung; Renata Pasqualini; Wadih Arap; John S. Lowengrub; Vittorio Cristini; Zhihui Wang (Nat. Comput. Sci., 2022)

Spatial dynamics of feedback and feedforward regulation in cell lineages - Peter Uhl; John S. Lowengrub; Natalia L. Komarova; Dominik Wodarz (PLoS Comput. Biol., 2022)

Correction: Stress generation, relaxation and size control in confined tumor growth - Huaming Yan; Daniel Ramirez-Guerrero; John S. Lowengrub; Min Wu (PLoS Comput. Biol., 2022)

Numerical study on viscous fingering using electric fields in a Hele-Shaw cell - Meng Zhao; Pedro Anjos; John S. Lowengrub; Wenjun Ying; Shuwang Li (CoRR, 2022)

Phase field modeling and computation of vesicle growth or shrinkage - Xiaoxia Tang; Shuwang Li; John S. Lowengrub; Steven M. Wise (CoRR, 2022)

Stress generation, relaxation and size control in confined tumor growth - Huaming Yan; Daniel Ramirez-Guerrero; John S. Lowengrub; Min Wu (PLoS Comput. Biol., 2021)

Corrections to "A multiscale Agent-Based Model of Ductal Carcinoma in Situ" - Joseph D. Butner; David Fuentes; Bulent Ozpolat; George A. Calin; Xiaobo Zhou; John S. Lowengrub; Vittorio Cristini; Zhihui Wang (IEEE Trans. Biomed. Eng., 2021)

Sharp-interface problem of the Ohta-Kawasaki model for symmetric diblock copolymers - Amlan K. Barua; Ray Chew; Shuwang Li; John S. Lowengrub; Andreas Münch; Barbara Wagner (CoRR, 2021)

Nonlinear simulation of vascular tumor growth with chemotaxis and the control of necrosis - Min-Jhe Lu; Wenrui Hao; Chun Liu; John S. Lowengrub; Shuwang Li (CoRR, 2021)

Higher-order accurate diffuse-domain methods for partial differential equations with Dirichlet boundary conditions in complex, evolving geometries - Fei Yu; Zhenlin Guo; John S. Lowengrub (J. Comput. Phys., 2020)

A Multiscale Agent-Based Model of Ductal Carcinoma In Situ - Joseph D. Butner; David Fuentes; Bulent Ozpolat; George A. Calin; Xiaobo Zhou; John S. Lowengrub; Vittorio Cristini; Zhihui Wang (IEEE Trans. Biomed. Eng., 2020)

Boundary integral methods for dispersive equations, Airy flow and the modified Korteweg de Vries equation - Mariano Franco-de-Leon; John S. Lowengrub (Adv. Comput. Math., 2019)

Morphological stability of an elastic tumor-host interface - Emma Turian; Kai Liu; John S. Lowengrub; Shuwang Li (J. Comput. Appl. Math., 2019)

Efficient simulation of thermally fluctuating biopolymers immersed in fluids on 1-micron, 1-second scales - Kai Liu; John S. Lowengrub; Jun Allard (J. Comput. Phys., 2019)

Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length - Kai Liu; Brian Chu; Jay M. Newby; Elizabeth L. Read; John S. Lowengrub; Jun Allard (PLoS Comput. Biol., 2019)

Personalized Radiotherapy Design for Glioblastoma: Integrating Mathematical Tumor Models, Multimodal Scans, and Bayesian Inference - Jana Lipková; Panagiotis Angelikopoulos; Stephen Wu; Esther Alberts; Benedikt Wiestler; Christian Diehl; Christine Preibisch; Thomas Pyka; Stephanie Combs; Panagiotis E. Hadjidoukas; Koen Van Leemput; Petros Koumoutsakos; et al. (IEEE Trans. Medical Imaging, 2019)

The Liver Tumor Segmentation Benchmark (LiTS) - Patrick Bilic; Patrick Ferdinand Christ; Eugene Vorontsov; Grzegorz Chlebus; Hao Chen; Qi Dou; Chi-Wing Fu; Xiao Han; Pheng-Ann Heng; Jürgen Hesser; Samuel Kadoury; Tomasz K. Konopczynski; et al. (CoRR, 2019)

Complex far-field geometries determine the stability of solid tumor growth with chemotaxis - Min-Jhe Lu; Chun Liu; John S. Lowengrub; Shuwang Li (CoRR, 2019)

A mass-conservative adaptive FAS multigrid solver for cell-centered finite difference methods on block-structured, locally-cartesian grids - Wenqiang Feng; Zhenlin Guo; John S. Lowengrub; Steven M. Wise (J. Comput. Phys., 2018)

Efficient energy stable schemes for isotropic and strongly anisotropic Cahn-Hilliard systems with the Willmore regularization - Ying Chen; John S. Lowengrub; Jie Shen; Cheng Wang; Steven M. Wise (J. Comput. Phys., 2018)

A Uniquely Solvable, Energy Stable Numerical Scheme for the Functionalized Cahn-Hilliard Equation and Its Convergence Analysis - Wenqiang Feng; Zhen Guan; John S. Lowengrub; Cheng Wang; Steven M. Wise; Ying Chen (J. Sci. Comput., 2018)

Computation of a Shrinking Interface in a Hele-Shaw Cell - Meng Zhao; Xiaofan Li; Wenjun Ying; Andrew Belmonte; John S. Lowengrub; Shuwang Li (SIAM J. Sci. Comput., 2018)

Personalized Radiotherapy Planning for Glioma Using Multimodal Bayesian Model Calibration - Jana Lipková; Panagiotis Angelikopoulos; Stephen Wu; Esther Alberts; Benedikt Wiestler; Christian Diehl; Christine Preibisch; Thomas Pyka; Stephanie Combs; Panagiotis E. Hadjidoukas; Koen Van Leemput; Petros Koumoutsakos; et al. (CoRR, 2018)

Multiscale Modeling of Glioblastoma Suggests that the Partial Disruption of Vessel/Cancer Stem Cell Crosstalk Can Promote Tumor Regression Without Increasing Invasiveness - Huaming Yan; Monica Romero-Lopez; Hermann B. Frieboes; Christopher C. W. Hughes; John S. Lowengrub (IEEE Trans. Biomed. Eng., 2017)

Automated Unsupervised Segmentation of Liver Lesions in CT scans via Cahn-Hilliard Phase Separation - Jana Lipková; Markus Rempfler; Patrick Ferdinand Christ; John S. Lowengrub; Bjoern H. Menze (CoRR, 2017)

An interface-fitted adaptive mesh method for elliptic problems and its application in free interface problems with surface tension - Xiaoming Zheng; John S. Lowengrub (Adv. Comput. Math., 2016)

Nonlinear simulations of elastic fingering in a Hele-Shaw cell - Meng Zhao; Andrew Belmonte; Shuwang Li; Xiaofan Li; John S. Lowengrub (J. Comput. Appl. Math., 2016)

Collective Properties of a Transcription Initiation Model Under Varying Environment - Yucheng Hu; John S. Lowengrub (J. Comput. Biol., 2016)

Numerical simulation of endocytosis: Viscous flow driven by membranes with non-uniformly distributed curvature-inducing molecules - John S. Lowengrub; Jun Allard; Sebastian Aland (J. Comput. Phys., 2016)

An energy stable, hexagonal finite difference scheme for the 2D phase field crystal amplitude equations - Zhen Guan; Vili Heinonen; John S. Lowengrub; Cheng Wang; Steven M. Wise (J. Comput. Phys., 2016)

Feedback, Lineages and Self-Organizing Morphogenesis - Sameeran Kunche; Huaming Yan; Anne L. Calof; John S. Lowengrub; Arthur D. Lander (PLoS Comput. Biol., 2016)

POPE: post optimization posterior evaluation of likelihood free models - Edward Meeds; Michael Chiang; Mary Lee; Olivier Cinquin; John S. Lowengrub; Max Welling (BMC Bioinform., 2015)

A numerical method for the quasi-incompressible Cahn-Hilliard-Navier-Stokes equations for variable density flows with a discrete energy law - Zhenlin Guo; Ping Lin; John S. Lowengrub (J. Comput. Phys., 2014)

Diffuse interface models of locally inextensible vesicles in a viscous fluid - Sebastian Aland; Sabine Egerer; John S. Lowengrub; Axel Voigt (J. Comput. Phys., 2014)

Second order convex splitting schemes for periodic nonlocal Cahn-Hilliard and Allen-Cahn equations - Zhen Guan; John S. Lowengrub; Cheng Wang; Steven M. Wise (J. Comput. Phys., 2014)

Energy stable and efficient finite-difference nonlinear multigrid schemes for the modified phase field crystal equation - Arvind Baskaran; Zhengzheng Hu; John S. Lowengrub; Cheng Wang; Steven M. Wise; Peng Zhou (J. Comput. Phys., 2013)

Convergence Analysis of a Second Order Convex Splitting Scheme for the Modified Phase Field Crystal Equation - Arvind Baskaran; John S. Lowengrub; Cheng Wang; Steven M. Wise (SIAM J. Numer. Anal., 2013)

A level-set continuum method for two-phase flows with insoluble surfactant - Jian-Jun Xu; Yin Yang; John S. Lowengrub (J. Comput. Phys., 2012)

Predicting simulation parameters of biological systems using a Gaussian process model - Xiangxin Zhu; Max Welling; Fang Jin; John S. Lowengrub (Stat. Anal. Data Min., 2012)

Modeling an Elastic Fingering Instability in a Reactive Hele-Shaw Flow - Andong He; John S. Lowengrub; Andrew Belmonte (SIAM J. Appl. Math., 2012)

A diffuse-interface method for two-phase flows with soluble surfactants - Knut Erik Teigen; Peng Song; John S. Lowengrub; Axel Voigt (J. Comput. Phys., 2011)

A grid based particle method for solving partial differential equations on evolving surfaces and modeling high order geometrical motion - Shingyu Leung; John S. Lowengrub; Hongkai Zhao (J. Comput. Phys., 2011)

An adaptive multigrid algorithm for simulating solid tumor growth using mixture models - Steven M. Wise; John S. Lowengrub; Vittorio Cristini (Math. Comput. Model., 2011)

Dynamics of multicomponent vesicles in a viscous fluid - Jin Sun Sohn; Yu-Hau Tseng; Shuwang Li; Axel Voigt; John S. Lowengrub (J. Comput. Phys., 2010)

Stable and efficient finite-difference nonlinear-multigrid schemes for the phase field crystal equation - Zhengzheng Hu; Steven M. Wise; Cheng Wang; John S. Lowengrub (J. Comput. Phys., 2009)

An Energy-Stable and Convergent Finite-Difference Scheme for the Phase Field Crystal Equation - Steven M. Wise; Cheng Wang; John S. Lowengrub (SIAM J. Numer. Anal., 2009)

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

A rescaling scheme with application to the long-time simulation of viscous fingering in a Hele-Shaw cell - Shuwang Li; John S. Lowengrub; Perry H. Leo (J. Comput. Phys., 2007)

Solving the regularized, strongly anisotropic Cahn-Hilliard equation by an adaptive nonlinear multigrid method - Steven M. Wise; Junseok Kim; John S. Lowengrub (J. Comput. Phys., 2007)

A level-set method for interfacial flows with surfactant - Jian-Jun Xu; Zhilin Li; John S. Lowengrub; Hongkai Zhao (J. Comput. Phys., 2006)

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

An adaptive coupled level-set/volume-of-fluid interface capturing method for unstructured triangular grids - Xiaofeng Yang; Ashley J. James; John S. Lowengrub; Xiaoming Zheng; Vittorio Cristini (J. Comput. Phys., 2006)

Almost optimal convergence of the point vortex method for vortex sheets using numerical filtering - Russel E. Caflisch; Thomas Y. Hou; John S. Lowengrub (Math. Comput., 1999)

The Convergence of an Exact Desingularization for Vortex Methods - Thomas Y. Hou; John S. Lowengrub; Michael J. Shelley (SIAM J. Sci. Comput., 1993)

High-Order and Efficient Methods for the Vorticity Formulation of the Euler Equations - John S. Lowengrub; Michael J. Shelley; Barry Merriman (SIAM J. Sci. Comput., 1993)