John S. Lowengrub

66 papers Journal 66

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	BiLO: Bilevel Local Operator Learning for PDE Inverse Problems. J. Comput. Phys. Ray Zirui Zhang, Christopher E. Miles, Xiaohui Xie, John S. Lowengrub
2025	J	`jnl`	BiLO: Bilevel Local Operator Learning for PDE Inverse Problems. Part II: Efficient Uncertainty Quantification with Low-Rank Adaptation. CoRR Ray Zirui Zhang, Christopher E. Miles, Xiaohui Xie, John S. Lowengrub
2025	J	`jnl`	Personalized predictions of Glioblastoma infiltration: Mathematical models, Physics-Informed Neural Networks and multimodal scans. Medical Image Anal. Ray Zirui Zhang, Ivan Ezhov, Michal Balcerak, Andy Zhu, Benedikt Wiestler, Bjoern H. Menze, John S. Lowengrub
2024	J	`jnl`	BiLO: Bilevel Local Operator Learning for PDE inverse problems. CoRR Ray Zirui Zhang, Xiaohui Xie, John S. Lowengrub
2024	J	`jnl`	PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration. PLoS Comput. Biol. Jinghao Chen, Jesse R. Holt, Elizabeth L. Evans, John S. Lowengrub, Medha M. Pathak
2023	J	`jnl`	Individualizing Glioma Radiotherapy Planning by Optimization of a Data and Physics Informed Discrete Loss. CoRR Michal Balcerak, Ivan Ezhov, Petr Karnakov, Sergey Litvinov, Petros Koumoutsakos, Jonas Weidner, Ray Zirui Zhang, John S. Lowengrub, Benedikt Wiestler, Bjoern H. Menze
2023	J	`jnl`	Personalized Predictions of Glioblastoma Infiltration: Mathematical Models, Physics-Informed Neural Networks and Multimodal Scans. CoRR Ray Zirui Zhang, Ivan Ezhov, Michal Balcerak, Andy Zhu, Benedikt Wiestler, Bjoern H. Menze, John S. Lowengrub
2023	J	`jnl`	Sharp-interface problem of the Ohta-Kawasaki model for symmetric diblock copolymers. J. Comput. Phys. Amlan K. Barua, Ray Chew, Shuwang Li, John S. Lowengrub, Andreas Münch, Barbara Wagner
2023	J	`jnl`	The Liver Tumor Segmentation Benchmark (LiTS). Medical Image Anal. 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, Wieland H. Sommer, Felix Hofmann, Alexandre Hostettler, Naama Lev-Cohain, Michal Drozdzal, Michal Marianne Amitai, Refael Vivanti, Jacob Sosna, Ivan Ezhov, Anjany Sekuboyina, Fernando Navarro, Florian Kofler, Johannes C. Paetzold, Suprosanna Shit, Xiaobin Hu, Jana Lipková, Markus Rempfler, Marie Piraud, Jan Kirschke, Benedikt Wiestler, Zhiheng Zhang, Christian Hülsemeyer, Marcel Beetz, Florian Ettlinger, Michela Antonelli, Woong Bae, Miriam Bellver, Lei Bi, Hao Chen, Grzegorz Chlebus, Erik B. Dam, Qi Dou, Chi-Wing Fu, Bogdan Georgescu, Xavier Giró-i-Nieto, Felix Grün, Xu Han, Pheng-Ann Heng, Jürgen Hesser, Jan Hendrik Moltz, Christian Igel, Fabian Isensee, Paul Jäger, Fucang Jia, Krishna Chaitanya Kaluva, Mahendra Khened, Ildoo Kim, Jae-Hun Kim, Sungwoong Kim, Simon Kohl, Tomasz K. Konopczynski, Avinash Kori, Ganapathy Krishnamurthi, Fan Li, Hongchao Li, Junbo Li, Xiaomeng Li, John S. Lowengrub, Jun Ma, Klaus H. Maier-Hein, Kevis-Kokitsi Maninis, Hans Meine, Dorit Merhof, Akshay Pai, Mathias Perslev, Jens Petersen, Jordi Pont-Tuset, Jin Qi, Xiaojuan Qi, Oliver Rippel, Karsten Roth, Ignacio Sarasua, Andrea Schenk, Zengming Shen, Jordi Torres, Christian Wachinger, Chunliang Wang, Leon Weninger, Jianrong Wu, Daguang Xu, Xiaoping Yang, Simon Chun-Ho Yu, Yading Yuan, Miao Yue, Liping Zhang, Manuel Jorge Cardoso, Spyridon Bakas, Rickmer Braren, Volker Heinemann, Christopher Pal, An Tang, Samuel Kadoury, Luc Soler, Bram van Ginneken, Hayit Greenspan, Leo Joskowicz, Bjoern H. Menze
2022	J	`jnl`	Correction: Stress generation, relaxation and size control in confined tumor growth. PLoS Comput. Biol. Huaming Yan, Daniel Ramirez-Guerrero, John S. Lowengrub, Min Wu
2022	J	`jnl`	Mathematical modeling of cancer immunotherapy for personalized clinical translation. Nat. Comput. Sci. Joseph D. Butner, Prashant Dogra, Caroline Chung, Renata Pasqualini, Wadih Arap, John S. Lowengrub, Vittorio Cristini, Zhihui Wang
2022	J	`jnl`	Nonlinear simulation of vascular tumor growth with chemotaxis and the control of necrosis. J. Comput. Phys. Min-Jhe Lu, Wenrui Hao, Chun Liu, John S. Lowengrub, Shuwang Li
2022	J	`jnl`	Numerical study on viscous fingering using electric fields in a Hele-Shaw cell. CoRR Meng Zhao, Pedro Anjos, John S. Lowengrub, Wenjun Ying, Shuwang Li
2022	J	`jnl`	Phase field modeling and computation of vesicle growth or shrinkage. CoRR Xiaoxia Tang, Shuwang Li, John S. Lowengrub, Steven M. Wise
2022	J	`jnl`	Second order approximation for a quasi-incompressible Navier-Stokes Cahn-Hilliard system of two-phase flows with variable density. J. Comput. Phys. Zhenlin Guo, Qing Cheng, Ping Lin, Chun Liu, John S. Lowengrub
2022	J	`jnl`	Spatial dynamics of feedback and feedforward regulation in cell lineages. PLoS Comput. Biol. Peter Uhl, John S. Lowengrub, Natalia L. Komarova, Dominik Wodarz
2021	J	`jnl`	Corrections to "A multiscale Agent-Based Model of Ductal Carcinoma in Situ". IEEE Trans. Biomed. Eng. Joseph D. Butner, David Fuentes, Bulent Ozpolat, George A. Calin, Xiaobo Zhou, John S. Lowengrub, Vittorio Cristini, Zhihui Wang
2021	J	`jnl`	Nonlinear simulation of vascular tumor growth with chemotaxis and the control of necrosis. CoRR Min-Jhe Lu, Wenrui Hao, Chun Liu, John S. Lowengrub, Shuwang Li
2021	J	`jnl`	Sharp-interface problem of the Ohta-Kawasaki model for symmetric diblock copolymers. CoRR Amlan K. Barua, Ray Chew, Shuwang Li, John S. Lowengrub, Andreas Münch, Barbara Wagner
2021	J	`jnl`	Stress generation, relaxation and size control in confined tumor growth. PLoS Comput. Biol. Huaming Yan, Daniel Ramirez-Guerrero, John S. Lowengrub, Min Wu
2020	J	`jnl`	A Multiscale Agent-Based Model of Ductal Carcinoma In Situ. IEEE Trans. Biomed. Eng. Joseph D. Butner, David Fuentes, Bulent Ozpolat, George A. Calin, Xiaobo Zhou, John S. Lowengrub, Vittorio Cristini, Zhihui Wang
2020	J	`jnl`	Higher-order accurate diffuse-domain methods for partial differential equations with Dirichlet boundary conditions in complex, evolving geometries. J. Comput. Phys. Fei Yu, Zhenlin Guo, John S. Lowengrub
2019	J	`jnl`	Boundary integral methods for dispersive equations, Airy flow and the modified Korteweg de Vries equation. Adv. Comput. Math. Mariano Franco-de-Leon, John S. Lowengrub
2019	J	`jnl`	Complex far-field geometries determine the stability of solid tumor growth with chemotaxis. CoRR Min-Jhe Lu, Chun Liu, John S. Lowengrub, Shuwang Li
2019	J	`jnl`	Efficient simulation of thermally fluctuating biopolymers immersed in fluids on 1-micron, 1-second scales. J. Comput. Phys. Kai Liu, John S. Lowengrub, Jun Allard
2019	J	`jnl`	Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length. PLoS Comput. Biol. Kai Liu, Brian Chu, Jay M. Newby, Elizabeth L. Read, John S. Lowengrub, Jun Allard
2019	J	`jnl`	Morphological stability of an elastic tumor-host interface. J. Comput. Appl. Math. Emma Turian, Kai Liu, John S. Lowengrub, Shuwang Li
2019	J	`jnl`	Personalized Radiotherapy Design for Glioblastoma: Integrating Mathematical Tumor Models, Multimodal Scans, and Bayesian Inference. IEEE Trans. Medical Imaging 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, John S. Lowengrub, Bjoern H. Menze
2019	J	`jnl`	The Liver Tumor Segmentation Benchmark (LiTS). CoRR 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, Miao Le, Chunming Li, Xiaomeng Li, Jana Lipková, John S. Lowengrub, Hans Meine, Jan Hendrik Moltz, Chris Pal, Marie Piraud, Xiaojuan Qi, Jin Qi, Markus Rempfler, Karsten Roth, Andrea Schenk, Anjany Sekuboyina, Ping Zhou, Christian Hülsemeyer, Marcel Beetz, Florian Ettlinger, Felix Grün, Georgios Kaissis, Fabian Lohöfer, Rickmer Braren, Julian Holch, Felix Hofmann, Wieland H. Sommer, Volker Heinemann, Colin Jacobs, Gabriel Efrain Humpire Mamani, Bram van Ginneken, Gabriel Chartrand, An Tang, Michal Drozdzal, Avi Ben-Cohen, Eyal Klang, Michal Marianne Amitai, Eli Konen, Hayit Greenspan, Johan Moreau, Alexandre Hostettler, Luc Soler, Refael Vivanti, Adi Szeskin, Naama Lev-Cohain, Jacob Sosna, Leo Joskowicz, Bjoern H. Menze
2018	J	`jnl`	A Uniquely Solvable, Energy Stable Numerical Scheme for the Functionalized Cahn-Hilliard Equation and Its Convergence Analysis. J. Sci. Comput. Wenqiang Feng, Zhen Guan, John S. Lowengrub, Cheng Wang, Steven M. Wise, Ying Chen
2018	J	`jnl`	A mass-conservative adaptive FAS multigrid solver for cell-centered finite difference methods on block-structured, locally-cartesian grids. J. Comput. Phys. Wenqiang Feng, Zhenlin Guo, John S. Lowengrub, Steven M. Wise
2018	J	`jnl`	Computation of a Shrinking Interface in a Hele-Shaw Cell. SIAM J. Sci. Comput. Meng Zhao, Xiaofan Li, Wenjun Ying, Andrew Belmonte, John S. Lowengrub, Shuwang Li
2018	J	`jnl`	Efficient energy stable schemes for isotropic and strongly anisotropic Cahn-Hilliard systems with the Willmore regularization. J. Comput. Phys. Ying Chen, John S. Lowengrub, Jie Shen, Cheng Wang, Steven M. Wise
2018	J	`jnl`	Personalized Radiotherapy Planning for Glioma Using Multimodal Bayesian Model Calibration. CoRR 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, John S. Lowengrub, Bjoern H. Menze
2017	J	`jnl`	Automated Unsupervised Segmentation of Liver Lesions in CT scans via Cahn-Hilliard Phase Separation. CoRR Jana Lipková, Markus Rempfler, Patrick Ferdinand Christ, John S. Lowengrub, Bjoern H. Menze
2017	J	`jnl`	Multiscale Modeling of Glioblastoma Suggests that the Partial Disruption of Vessel/Cancer Stem Cell Crosstalk Can Promote Tumor Regression Without Increasing Invasiveness. IEEE Trans. Biomed. Eng. Huaming Yan, Monica Romero-Lopez, Hermann B. Frieboes, Christopher C. W. Hughes, John S. Lowengrub
2016	J	`jnl`	An energy stable, hexagonal finite difference scheme for the 2D phase field crystal amplitude equations. J. Comput. Phys. Zhen Guan, Vili Heinonen, John S. Lowengrub, Cheng Wang, Steven M. Wise
2016	J	`jnl`	An interface-fitted adaptive mesh method for elliptic problems and its application in free interface problems with surface tension. Adv. Comput. Math. Xiaoming Zheng, John S. Lowengrub
2016	J	`jnl`	Collective Properties of a Transcription Initiation Model Under Varying Environment. J. Comput. Biol. Yucheng Hu, John S. Lowengrub
2016	J	`jnl`	Feedback, Lineages and Self-Organizing Morphogenesis. PLoS Comput. Biol. Sameeran Kunche, Huaming Yan, Anne L. Calof, John S. Lowengrub, Arthur D. Lander
2016	J	`jnl`	Nonlinear simulations of elastic fingering in a Hele-Shaw cell. J. Comput. Appl. Math. Meng Zhao, Andrew Belmonte, Shuwang Li, Xiaofan Li, John S. Lowengrub
2016	J	`jnl`	Numerical simulation of endocytosis: Viscous flow driven by membranes with non-uniformly distributed curvature-inducing molecules. J. Comput. Phys. John S. Lowengrub, Jun Allard, Sebastian Aland
2015	J	`jnl`	POPE: post optimization posterior evaluation of likelihood free models. BMC Bioinform. Edward Meeds, Michael Chiang, Mary Lee, Olivier Cinquin, John S. Lowengrub, Max Welling
2014	J	`jnl`	A numerical method for the quasi-incompressible Cahn-Hilliard-Navier-Stokes equations for variable density flows with a discrete energy law. J. Comput. Phys. Zhenlin Guo, Ping Lin, John S. Lowengrub
2014	J	`jnl`	Diffuse interface models of locally inextensible vesicles in a viscous fluid. J. Comput. Phys. Sebastian Aland, Sabine Egerer, John S. Lowengrub, Axel Voigt
2014	J	`jnl`	Second order convex splitting schemes for periodic nonlocal Cahn-Hilliard and Allen-Cahn equations. J. Comput. Phys. Zhen Guan, John S. Lowengrub, Cheng Wang, Steven M. Wise
2013	J	`jnl`	Convergence Analysis of a Second Order Convex Splitting Scheme for the Modified Phase Field Crystal Equation. SIAM J. Numer. Anal. Arvind Baskaran, John S. Lowengrub, Cheng Wang, Steven M. Wise
2013	J	`jnl`	Energy stable and efficient finite-difference nonlinear multigrid schemes for the modified phase field crystal equation. J. Comput. Phys. Arvind Baskaran, Zhengzheng Hu, John S. Lowengrub, Cheng Wang, Steven M. Wise, Peng Zhou
2012	J	`jnl`	A level-set continuum method for two-phase flows with insoluble surfactant. J. Comput. Phys. Jian-Jun Xu, Yin Yang, John S. Lowengrub
2012	J	`jnl`	Modeling an Elastic Fingering Instability in a Reactive Hele-Shaw Flow. SIAM J. Appl. Math. Andong He, John S. Lowengrub, Andrew Belmonte
2012	J	`jnl`	Predicting simulation parameters of biological systems using a Gaussian process model. Stat. Anal. Data Min. Xiangxin Zhu, Max Welling, Fang Jin, John S. Lowengrub
2011	J	`jnl`	A diffuse-interface method for two-phase flows with soluble surfactants. J. Comput. Phys. Knut Erik Teigen, Peng Song, John S. Lowengrub, Axel Voigt
2011	J	`jnl`	A grid based particle method for solving partial differential equations on evolving surfaces and modeling high order geometrical motion. J. Comput. Phys. Shingyu Leung, John S. Lowengrub, Hongkai Zhao
2011	J	`jnl`	An adaptive multigrid algorithm for simulating solid tumor growth using mixture models. Math. Comput. Model. Steven M. Wise, John S. Lowengrub, Vittorio Cristini
2010	J	`jnl`	Dynamics of multicomponent vesicles in a viscous fluid. J. Comput. Phys. Jin Sun Sohn, Yu-Hau Tseng, Shuwang Li, Axel Voigt, John S. Lowengrub
2009	J	`jnl`	An Energy-Stable and Convergent Finite-Difference Scheme for the Phase Field Crystal Equation. SIAM J. Numer. Anal. Steven M. Wise, Cheng Wang, John S. Lowengrub
2009	J	`jnl`	Stable and efficient finite-difference nonlinear-multigrid schemes for the phase field crystal equation. J. Comput. Phys. Zhengzheng Hu, Steven M. Wise, Cheng Wang, John S. Lowengrub
2008	J	`jnl`	A New Ghost Cell/Level Set Method for Moving Boundary Problems: Application to Tumor Growth. J. Sci. Comput. Paul Macklin, John S. Lowengrub
2007	J	`jnl`	A rescaling scheme with application to the long-time simulation of viscous fingering in a Hele-Shaw cell. J. Comput. Phys. Shuwang Li, John S. Lowengrub, Perry H. Leo
2007	J	`jnl`	Solving the regularized, strongly anisotropic Cahn-Hilliard equation by an adaptive nonlinear multigrid method. J. Comput. Phys. Steven M. Wise, Junseok Kim, John S. Lowengrub
2006	J	`jnl`	A level-set method for interfacial flows with surfactant. J. Comput. Phys. Jian-Jun Xu, Zhilin Li, John S. Lowengrub, Hongkai Zhao
2006	J	`jnl`	An adaptive coupled level-set/volume-of-fluid interface capturing method for unstructured triangular grids. J. Comput. Phys. Xiaofeng Yang, Ashley J. James, John S. Lowengrub, Xiaoming Zheng, Vittorio Cristini
2006	J	`jnl`	An improved geometry-aware curvature discretization for level set methods: Application to tumor growth. J. Comput. Phys. Paul Macklin, John S. Lowengrub
1999	J	`jnl`	Almost optimal convergence of the point vortex method for vortex sheets using numerical filtering. Math. Comput. Russel E. Caflisch, Thomas Y. Hou, John S. Lowengrub
1993	J	`jnl`	High-Order and Efficient Methods for the Vorticity Formulation of the Euler Equations. SIAM J. Sci. Comput. John S. Lowengrub, Michael J. Shelley, Barry Merriman
1993	J	`jnl`	The Convergence of an Exact Desingularization for Vortex Methods. SIAM J. Sci. Comput. Thomas Y. Hou, John S. Lowengrub, Michael J. Shelley