Mark S. Alber

According to our database, Mark S. Alber authored at least 40 papers between 2001 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Study of impacts of two types of cellular aging on the yeast bud morphogenesis.

Kevin Tsai, Zhen Zhou, Jiadong Yang, Zhiliang Xu, Shixin Xu, Roya Zandi, Nan Hao, Weitao Chen, Mark S. Alber

PLoS Comput. Biol., 2024

2023

Learning Deformable 3D Graph Similarity to Track Plant Cells in Unregistered Time Lapse Images.

Md Shazid Islam, Arindam Dutta, Calvin-Khang Ta, Kevin Rodriguez, Christian Michael, Mark S. Alber, G. Venugopala Reddy, Amit K. Roy-Chowdhury

CoRR, 2023

2022

Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance.

Mikahl Banwarth-Kuhn, Kevin Rodriguez, Christian Michael, Calvin-Khang Ta, Alexander Plong, Eric Bourgain-Chang, Ali Nematbakhsh, Weitao Chen, Amit K. Roy-Chowdhury, G. Venugopala Reddy, Mark S. Alber

PLoS Comput. Biol., 2022

2021

Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease.

Noelia Grande Gutiérrez, Mark S. Alber, Andrew M. Kahn, Jane C. Burns, Mathew Mathew, Brian W. McCrindle, Alison L. Marsden

PLoS Comput. Biol., 2021

2020

Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix.

Ali Nematbakhsh, Megan Levis, Nilay Kumar, Weitao Chen, Jeremiah J. Zartman, Mark S. Alber

PLoS Comput. Biol., 2020

2019

Integrating machine learning and multiscale modeling - perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences.

Mark S. Alber, Adrian Buganza Tepole, William R. Cannon, Suvranu De, Salvador Dura-Bernal, Krishna C. Garikipati, George E. Karniadakis, William W. Lytton, Paris Perdikaris, Linda R. Petzold, Ellen Kuhl

npj Digit. Medicine, 2019

2017

Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia.

Ali Nematbakhsh, Wenzhao Sun, Pavel A. Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J. Zartman, Mark S. Alber

PLoS Comput. Biol., 2017

2016

A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms.

Jianxu Chen, Mark S. Alber, Danny Ziyi Chen

IEEE Trans. Medical Imaging, 2016

Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation.

Jianxu Chen, Lin Yang, Yizhe Zhang, Mark S. Alber, Danny Ziyi Chen

Proceedings of the Advances in Neural Information Processing Systems 29: Annual Conference on Neural Information Processing Systems 2016, 2016

Segmentation and tracking of Pseudomonas aeruginosa for cell dynamics analysis in time-lapse images.

Jianxu Chen, Yiqing Cai, Chen Wei, Lin Yang, Mark S. Alber, Danny Ziyi Chen

Proceedings of the 13th IEEE International Symposium on Biomedical Imaging, 2016

2015

A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms.

Jianxu Chen, Shant Mahserejian, Mark S. Alber, Danny Z. Chen

Proceedings of the Medical Image Computing and Computer-Assisted Intervention - MICCAI 2015 - 18th International Conference Munich, Germany, October 5, 2015

2014

A Matching Model Based on Earth Mover's Distance for Tracking Myxococcus Xanthus.

Jianxu Chen, Cameron W. Harvey, Mark S. Alber, Danny Ziyi Chen

Proceedings of the Medical Image Computing and Computer-Assisted Intervention - MICCAI 2014, 2014

An Automated Approach for Fibrin Network Segmentation and Structure Identification in 3D Confocal Microscopy Images.

Jianxu Chen, Oleg V. Kim, Rustem I. Litvinov, John W. Weisel, Mark S. Alber, Danny Ziyi Chen

Proceedings of the 2014 IEEE 27th International Symposium on Computer-Based Medical Systems, 2014

2013

Fibrin Networks Regulate Protein Transport during Thrombus Development.

Oleg V. Kim, Zhiliang Xu, Elliot D. Rosen, Mark S. Alber

PLoS Comput. Biol., 2013

2012

Interconnected Cavernous Structure of Bacterial Fruiting Bodies.

Cameron W. Harvey, Huijing Du, Zhiliang Xu, Dale Kaiser, Igor S. Aranson, Mark S. Alber

PLoS Comput. Biol., 2012

Automatic segmentation and analysis of fibrin networks in 3D confocal microscopy images.

Xiaomin Liu, Jian Mu, Kellie R. Machlus, Alisa S. Wolberg, Elliot D. Rosen, Zhiliang Xu, Mark S. Alber, Danny Z. Chen

Proceedings of the Medical Imaging 2012: Image Processing, 2012

Detecting and Tracking Motion of Myxococcus xanthus Bacteria in Swarms.

Xiaomin Liu, Cameron W. Harvey, Haitao Wang, Mark S. Alber, Danny Z. Chen

Proceedings of the Medical Image Computing and Computer-Assisted Intervention - MICCAI 2012, 2012

2011

Identification and classification of cells in multispectral microscopy images of lymph nodes.

Xiaomin Liu, Alvernia F. Setiadi, Mark S. Alber, Peter P. Lee, Danny Z. Chen

Proceedings of the Medical Imaging 2011: Image Processing, 2011

2010

Belief propagation estimation of protein and domain interactions using the sum-product algorithm.

Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre

IEEE Trans. Inf. Theory, 2010

Segmentation, Reconstruction, and Analysis of Blood Thrombus Formation in 3D 2-Photon Microscopy Images.

Jian Mu, Xiaomin Liu, Malgorzata M. Kamocka, Zhiliang Xu, Mark S. Alber, Elliot D. Rosen, Danny Z. Chen

EURASIP J. Adv. Signal Process., 2010

Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus Xanthus.

Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

Application of Discontinuous Galerkin Methods for Reaction-Diffusion Systems in Developmental Biology.

Jianfeng Zhu, Yong-Tao Zhang, Stuart A. Newman, Mark S. Alber

J. Sci. Comput., 2009

Existence of global solutions of a macroscopic model of cellular motion in a chemotactic field.

Mark S. Alber, Richard Gejji, Bogdan Kazmierczak

Appl. Math. Lett., 2009

Segmentation, reconstruction, and analysis of blood thrombi in 2-photon microscopy images.

Jian Mu, Xiaomin Liu, Malgorzata M. Kamocka, Zhiliang Xu, Mark S. Alber, Elliot D. Rosen, Danny Z. Chen

Proceedings of the Twenty-Second IEEE International Symposium on Computer-Based Medical Systems, 2009

2007

Social Interactions in Myxobacterial Swarming.

Yilin Wu, Yi Jiang, Dale Kaiser, Mark S. Alber

PLoS Comput. Biol., 2007

Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model.

Scott Christley, Mark S. Alber, Stuart A. Newman

PLoS Comput. Biol., 2007

From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development.

Trevor M. Cickovski, Kedar Aras, Maciej Swat, Roeland Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre

Comput. Sci. Eng., 2007

A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis.

Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber

Comput. Phys. Commun., 2007

Multiscale Agent-based Simulation for Chondrogenic Pattern Formation <i>in Vitro</i>.

Scott Christley, Xuelian Zhu, Stuart A. Newman, Mark S. Alber

Cybern. Syst., 2007

2006

On Modeling Complex Collective Behavior in Myxobacteria.

Yi Jiang, Olga Sozinova, Mark S. Alber

Adv. Complex Syst., 2006

CA Models of Myxobacteria Swarming.

Yilin Wu, Nan Chen, Matthew Rissler, Yi Jiang, Dale Kaiser, Mark S. Alber

Proceedings of the Cellular Automata, 2006

A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis.

Nan Chen, James A. Glazier, Mark S. Alber

Proceedings of the Cellular Automata, 2006

2005

A Framework for Three-Dimensional Simulation of Morphogenesis.

Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre

IEEE ACM Trans. Comput. Biol. Bioinform., 2005

Special Issue on Multiscale Modeling in Biology.

Mark S. Alber, Thomas Yizhao Hou, James A. Glazier, Yi Jiang

Multiscale Model. Simul., 2005

2004

COMPUCELL, a multi-model framework for simulation of morphogenesis.

Jesús A. Izaguirre, Rajiv Chaturvedi, Chengbang Huang, Trevor M. Cickovski, J. Coffland, Gilberto L. Thomas, Gabor Forgacs, Mark S. Alber, H. George E. Hentschel, Stuart A. Newman, James A. Glazier

Bioinform., 2004

A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb.

Rajiv Chaturvedi, Chengbang Huang, Jesús A. Izaguirre, Stuart A. Newman, James A. Glazier, Mark S. Alber

Proceedings of the Cellular Automata, 2004

A Cellular Automata Model of Early T Cell Recognition.

Arancha Casal, Cenk Sumen, Tim Reddy, Mark S. Alber, Peter P. Lee

Proceedings of the Cellular Automata, 2004

2003

Multi-model Simulations of Chicken Limb Morphogenesis.

Rajiv Chaturvedi, Jesús A. Izaguirre, Chengbang Huang, Trevor M. Cickovski, P. Virtue, Gilberto L. Thomas, Gabor Forgacs, Mark S. Alber, H. George E. Hentschel, Stuart A. Newman, James A. Glazier

Proceedings of the Computational Science - ICCS 2003, 2003

On Cellular Automaton Approaches to Modeling Biological Cells.

Mark S. Alber, Maria A. Kiskowski, James A. Glazier, Yi Jiang

Proceedings of the Mathematical Systems Theory in Biology, 2003

2001

Peakon solutions of the shallow water equation.

Mark S. Alber, Charles Miller

Appl. Math. Lett., 2001