Mark S. Alber

Publication Activity (10 Years)

Years Active: 2001-2023
Publications (10 Years): 8

Top Topics

Phase Contrast Microscopy

Computational Model

Image Segmentation

Confocal Microscopy Images

Top Venues

PLoS Comput. Biol.

Publications

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 (2023)
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)
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)
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)
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)
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 (2016)
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) (2016)
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)
Jianxu Chen, Shant Mahserejian, Mark S. Alber, Danny Z. Chen
A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms. MICCAI (3) (2015)
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)
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)
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)
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)
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)
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. Medical Imaging: Image Processing (2012)
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. Medical Imaging: Image Processing (2011)
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)
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)
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) (2010)
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)
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) (2009)
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) (2009)
Scott Christley, Mark S. Alber, Stuart A. Newman
Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model. PLoS Comput. Biol. 3 (4) (2007)
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) (2007)
Scott Christley, Xuelian Zhu, Stuart A. Newman, Mark S. Alber
. Cybern. Syst. 38 (7) (2007)
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) (2007)
Yilin Wu, Yi Jiang, Dale Kaiser, Mark S. Alber
Social Interactions in Myxobacterial Swarming. PLoS Comput. Biol. 3 (12) (2007)
Yilin Wu, Nan Chen, Matthew Rissler, Yi Jiang, Dale Kaiser, Mark S. Alber
CA Models of Myxobacteria Swarming. ACRI (2006)
Yi Jiang, Olga Sozinova, Mark S. Alber
On Modeling Complex Collective Behavior in Myxobacteria. Adv. Complex Syst. 9 (4) (2006)
Nan Chen, James A. Glazier, Mark S. Alber
A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis. ACRI (2006)
Mark S. Alber, Thomas Hou, James A. Glazier, Yi Jiang
Special Issue on Multiscale Modeling in Biology. Multiscale Model. Simul. 3 (2) (2005)
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) (2005)
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)
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) (2004)
Arancha Casal, Cenk Sumen, Tim Reddy, Mark S. Alber, Peter P. Lee
A Cellular Automata Model of Early T Cell Recognition. ACRI (2004)
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)
Mark S. Alber, Charles Miller
Peakon solutions of the shallow water equation. Appl. Math. Lett. 14 (1) (2001)