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ORCIDMark S. Alber
Person information
- affiliation: University of California Riverside, CA, USA
- affiliation (former): University of Notre Dame, IN, USA
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Journal Articles
- 2024
[j23]Kevin Tsai, Zhen Zhou, Jiadong Yang, Zhiliang Xu, Shixin Xu, Roya Zandi, Nan Hao, Weitao Chen, Mark S. Alber
:
Study of impacts of two types of cellular aging on the yeast bud morphogenesis. PLoS Comput. Biol. 20(9): 1012491 (2024)- 2022
- [j22]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:
Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance. PLoS Comput. Biol. 18(6) (2022) - 2021
- [j21]Noelia Grande Gutiérrez, Mark S. Alber, Andrew M. Kahn, Jane C. Burns, Mathew Mathew, Brian W. McCrindle, Alison L. Marsden:
Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease. PLoS Comput. Biol. 17(9) (2021) - 2020
- [j20]Ali Nematbakhsh, Megan Levis, Nilay Kumar, Weitao Chen, Jeremiah J. Zartman, Mark S. Alber:
Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix. PLoS Comput. Biol. 16(8) (2020) - 2019
- [j19]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:
Integrating machine learning and multiscale modeling - perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences. npj Digit. Medicine 2 (2019) - 2017
- [j18]Ali Nematbakhsh, Wenzhao Sun, Pavel A. Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J. Zartman, Mark S. Alber:
Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia. PLoS Comput. Biol. 13(5) (2017) - 2016
- [j17]Jianxu Chen, Mark S. Alber, Danny Ziyi Chen:
A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms. IEEE Trans. Medical Imaging 35(9): 2074-2084 (2016) - 2013
- [j16]Oleg V. Kim, Zhiliang Xu, Elliot D. Rosen, Mark S. Alber:
Fibrin Networks Regulate Protein Transport during Thrombus Development. PLoS Comput. Biol. 9(6) (2013) - 2012
- [j15]Cameron W. Harvey, Huijing Du, Zhiliang Xu, Dale Kaiser, Igor S. Aranson, Mark S. Alber:
Interconnected Cavernous Structure of Bacterial Fruiting Bodies. PLoS Comput. Biol. 8(12) (2012) - 2010
- [j14]Jian Mu, Xiaomin Liu, Malgorzata M. Kamocka, Zhiliang Xu, Mark S. Alber, Elliot D. Rosen, Danny Z. Chen:
Segmentation, Reconstruction, and Analysis of Blood Thrombus Formation in 3D 2-Photon Microscopy Images. EURASIP J. Adv. Signal Process. 2010 (2010) - [j13]Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre:
Belief propagation estimation of protein and domain interactions using the sum-product algorithm. IEEE Trans. Inf. Theory 56(2): 742-755 (2010) - 2009
- [j12]Mark S. Alber, Richard Gejji, Bogdan Kazmierczak:
Existence of global solutions of a macroscopic model of cellular motion in a chemotactic field. Appl. Math. Lett. 22(11): 1645-1648 (2009) - [j11]Jianfeng Zhu, Yong-Tao Zhang, Stuart A. Newman, Mark S. Alber:
Application of Discontinuous Galerkin Methods for Reaction-Diffusion Systems in Developmental Biology. J. Sci. Comput. 40(1-3): 391-418 (2009) - 2007
- [j10]Scott Christley, Xuelian Zhu, Stuart A. Newman, Mark S. Alber:
Multiscale Agent-based Simulation for Chondrogenic Pattern Formation in Vitro. Cybern. Syst. 38(7): 707-727 (2007) - [j9]Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber:
A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis. Comput. Phys. Commun. 176(11-12): 670-681 (2007) - [j8]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:
From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development. Comput. Sci. Eng. 9(4): 50-60 (2007) - [j7]Scott Christley, Mark S. Alber, Stuart A. Newman:
Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model. PLoS Comput. Biol. 3(4) (2007) - [j6]Yilin Wu, Yi Jiang, Dale Kaiser, Mark S. Alber:
Social Interactions in Myxobacterial Swarming. PLoS Comput. Biol. 3(12) (2007) - 2006
- [j5]Yi Jiang, Olga Sozinova, Mark S. Alber:
On Modeling Complex Collective Behavior in Myxobacteria. Adv. Complex Syst. 9(4): 353-367 (2006) - 2005
- [j4]Mark S. Alber, Thomas Yizhao Hou, James A. Glazier, Yi Jiang:
Special Issue on Multiscale Modeling in Biology. Multiscale Model. Simul. 3(2) (2005) - [j3]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:
A Framework for Three-Dimensional Simulation of Morphogenesis. IEEE ACM Trans. Comput. Biol. Bioinform. 2(4): 273-288 (2005) - 2004
- [j2]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:
COMPUCELL, a multi-model framework for simulation of morphogenesis. Bioinform. 20(7): 1129-1137 (2004) - 2001
- [j1]Mark S. Alber, Charles Miller:
Peakon solutions of the shallow water equation. Appl. Math. Lett. 14(1): 93-98 (2001)
Conference and Workshop Papers
- 2016
- [c15]Jianxu Chen, Yiqing Cai, Chen Wei, Lin Yang, Mark S. Alber, Danny Ziyi Chen:
Segmentation and tracking of Pseudomonas aeruginosa for cell dynamics analysis in time-lapse images. ISBI 2016: 968-971 - [c14]Jianxu Chen, Lin Yang, Yizhe Zhang, Mark S. Alber, Danny Ziyi Chen:
Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation. NIPS 2016: 3036-3044 - 2015
- [c13]Jianxu Chen, Shant Mahserejian, Mark S. Alber, Danny Z. Chen:
A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms. MICCAI (3) 2015: 284-291 - 2014
- [c12]Jianxu Chen, Oleg V. Kim, Rustem I. Litvinov, John W. Weisel, Mark S. Alber, Danny Ziyi Chen:
An Automated Approach for Fibrin Network Segmentation and Structure Identification in 3D Confocal Microscopy Images. CBMS 2014: 173-178 - [c11]Jianxu Chen, Cameron W. Harvey, Mark S. Alber, Danny Ziyi Chen:
A Matching Model Based on Earth Mover's Distance for Tracking Myxococcus Xanthus. MICCAI (2) 2014: 113-120 - 2012
- [c10]Xiaomin Liu, Cameron W. Harvey, Haitao Wang, Mark S. Alber, Danny Z. Chen:
Detecting and Tracking Motion of Myxococcus xanthus Bacteria in Swarms. MICCAI (1) 2012: 373-380 - [c9]Xiaomin Liu, Jian Mu, Kellie R. Machlus, Alisa S. Wolberg, Elliot D. Rosen, Zhiliang Xu, Mark S. Alber, Danny Z. Chen:
Automatic segmentation and analysis of fibrin networks in 3D confocal microscopy images. Image Processing 2012: 831439 - 2011
- [c8]Xiaomin Liu, Alvernia F. Setiadi, Mark S. Alber, Peter P. Lee, Danny Z. Chen:
Identification and classification of cells in multispectral microscopy images of lymph nodes. Image Processing 2011: 79620J - 2010
- [c7]Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre:
Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus Xanthus. Pacific Symposium on Biocomputing 2010: 157-165 - 2009
- [c6]Jian Mu, Xiaomin Liu, Malgorzata M. Kamocka, Zhiliang Xu, Mark S. Alber, Elliot D. Rosen, Danny Z. Chen:
Segmentation, reconstruction, and analysis of blood thrombi in 2-photon microscopy images. CBMS 2009: 1-8 - 2006
- [c5]Nan Chen, James A. Glazier, Mark S. Alber:
A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis. ACRI 2006: 58-67 - [c4]Yilin Wu, Nan Chen, Matthew Rissler, Yi Jiang, Dale Kaiser, Mark S. Alber:
CA Models of Myxobacteria Swarming. ACRI 2006: 192-203 - 2004
- [c3]Rajiv Chaturvedi, Chengbang Huang, Jesús A. Izaguirre, Stuart A. Newman, James A. Glazier, Mark S. Alber:
A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb. ACRI 2004: 543-552 - [c2]Arancha Casal, Cenk Sumen, Tim Reddy, Mark S. Alber, Peter P. Lee:
A Cellular Automata Model of Early T Cell Recognition. ACRI 2004: 553-560 - 2003
- [c1]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:
Multi-model Simulations of Chicken Limb Morphogenesis. International Conference on Computational Science 2003: 39-49
Parts in Books or Collections
- 2003
- [p1]Mark S. Alber, Maria A. Kiskowski, James A. Glazier, Yi Jiang:
On Cellular Automaton Approaches to Modeling Biological Cells. Mathematical Systems Theory in Biology, Communications, Computation, and Finance 2003: 1-39
Informal and Other Publications
- 2023
- [i2]Md Shazid Islam, Arindam Dutta, Calvin-Khang Ta, Kevin Rodriguez, Christian Michael, Mark S. Alber, G. Venugopala Reddy, Amit K. Roy-Chowdhury:
Learning Deformable 3D Graph Similarity to Track Plant Cells in Unregistered Time Lapse Images. CoRR abs/2309.11157 (2023) - 2016
- [i1]Jianxu Chen, Lin Yang, Yizhe Zhang, Mark S. Alber, Danny Z. Chen:
Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation. CoRR abs/1609.01006 (2016)
Coauthor Index
aka: Danny Z. Chen
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