Mark S. Alber

42 papers B 4Misc 2Journal 26Unranked 9
YearRankTypeTitle / Venue / Authors
2025 J jnl
DEGAST3D: Learning Deformable 3D Graph Similarity to Track Plant Cells in Unregistered Time Lapse Images.
IEEE Trans. Comput. Biol. Bioinform.
Md Shazid Islam, Arindam Dutta, Calvin-Khang Ta, Kevin Rodriguez, Christian Michael, Mark S. Alber, G. Venugopala Reddy, Amit K. Roy-Chowdhury
2024 J jnl
Study of impacts of two types of cellular aging on the yeast bud morphogenesis.
PLoS Comput. Biol.
Kevin Tsai, Zhen Zhou, Jiadong Yang, Zhiliang Xu, Shixin Xu, Roya Zandi, Nan Hao, Weitao Chen, Mark S. Alber
2023 J jnl
Learning Deformable 3D Graph Similarity to Track Plant Cells in Unregistered Time Lapse Images.
CoRR
Md Shazid Islam, Arindam Dutta, Calvin-Khang Ta, Kevin Rodriguez, Christian Michael, Mark S. Alber, G. Venugopala Reddy, Amit K. Roy-Chowdhury
2022 J jnl
Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance.
PLoS Comput. Biol.
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
2021 J jnl
Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease.
PLoS Comput. Biol.
Noelia Grande Gutiérrez, Mark S. Alber, Andrew M. Kahn, Jane C. Burns, Mathew Mathew, Brian W. McCrindle, Alison L. Marsden
2020 J jnl
Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix.
PLoS Comput. Biol.
Ali Nematbakhsh, Megan Levis, Nilay Kumar, Weitao Chen, Jeremiah J. Zartman, Mark S. Alber
2019 J jnl
Integrating machine learning and multiscale modeling - perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences.
npj Digit. Medicine
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
2017 J jnl
Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia.
PLoS Comput. Biol.
Ali Nematbakhsh, Wenzhao Sun, Pavel A. Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J. Zartman, Mark S. Alber
2016 J jnl
A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms.
IEEE Trans. Medical Imaging
Jianxu Chen, Mark S. Alber, Danny Ziyi Chen
2016 — conf
Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation.
NIPS
Jianxu Chen, Lin Yang, Yizhe Zhang, Mark S. Alber, Danny Ziyi Chen
2016 J jnl
Combining Fully Convolutional and Recurrent Neural Networks for 3D Biomedical Image Segmentation.
CoRR
Jianxu Chen, Lin Yang, Yizhe Zhang, Mark S. Alber, Danny Z. Chen
2016 — conf
Segmentation and tracking of Pseudomonas aeruginosa for cell dynamics analysis in time-lapse images.
ISBI
Jianxu Chen, Yiqing Cai, Chen Wei, Lin Yang, Mark S. Alber, Danny Ziyi Chen
2015 — conf
A Hybrid Approach for Segmentation and Tracking of Myxococcus Xanthus Swarms.
MICCAI (3)
Jianxu Chen, Shant Mahserejian, Mark S. Alber, Danny Z. Chen
2014 — conf
A Matching Model Based on Earth Mover's Distance for Tracking Myxococcus Xanthus.
MICCAI (2)
Jianxu Chen, Cameron W. Harvey, Mark S. Alber, Danny Ziyi Chen
2014 B conf
An Automated Approach for Fibrin Network Segmentation and Structure Identification in 3D Confocal Microscopy Images.
CBMS
Jianxu Chen, Oleg V. Kim, Rustem I. Litvinov, John W. Weisel, Mark S. Alber, Danny Ziyi Chen
2013 J jnl
Fibrin Networks Regulate Protein Transport during Thrombus Development.
PLoS Comput. Biol.
Oleg V. Kim, Zhiliang Xu, Elliot D. Rosen, Mark S. Alber
2012 B conf
Automatic segmentation and analysis of fibrin networks in 3D confocal microscopy images.
Image Processing
Xiaomin Liu, Jian Mu, Kellie R. Machlus, Alisa S. Wolberg, Elliot D. Rosen, Zhiliang Xu, Mark S. Alber, Danny Z. Chen
2012 — conf
Detecting and Tracking Motion of Myxococcus xanthus Bacteria in Swarms.
MICCAI (1)
Xiaomin Liu, Cameron W. Harvey, Haitao Wang, Mark S. Alber, Danny Z. Chen
2012 J jnl
Interconnected Cavernous Structure of Bacterial Fruiting Bodies.
PLoS Comput. Biol.
Cameron W. Harvey, Huijing Du, Zhiliang Xu, Dale Kaiser, Igor S. Aranson, Mark S. Alber
2011 B conf
Identification and classification of cells in multispectral microscopy images of lymph nodes.
Image Processing
Xiaomin Liu, Alvernia F. Setiadi, Mark S. Alber, Peter P. Lee, Danny Z. Chen
2010 J jnl
Belief propagation estimation of protein and domain interactions using the sum-product algorithm.
IEEE Trans. Inf. Theory
Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre
2010 Misc conf
Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus Xanthus.
Pacific Symposium on Biocomputing
Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre
2010 J jnl
Segmentation, Reconstruction, and Analysis of Blood Thrombus Formation in 3D 2-Photon Microscopy Images.
EURASIP J. Adv. Signal Process.
Jian Mu, Xiaomin Liu, Malgorzata M. Kamocka, Zhiliang Xu, Mark S. Alber, Elliot D. Rosen, Danny Z. Chen
2009 J jnl
Application of Discontinuous Galerkin Methods for Reaction-Diffusion Systems in Developmental Biology.
J. Sci. Comput.
Jianfeng Zhu, Yong-Tao Zhang, Stuart A. Newman, Mark S. Alber
2009 J jnl
Existence of global solutions of a macroscopic model of cellular motion in a chemotactic field.
Appl. Math. Lett.
Mark S. Alber, Richard Gejji, Bogdan Kazmierczak
2009 B conf
Segmentation, reconstruction, and analysis of blood thrombi in 2-photon microscopy images.
CBMS
Jian Mu, Xiaomin Liu, Malgorzata M. Kamocka, Zhiliang Xu, Mark S. Alber, Elliot D. Rosen, Danny Z. Chen
2007 J jnl
A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis.
Comput. Phys. Commun.
Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber
2007 J jnl
From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development.
Comput. Sci. Eng.
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
2007 J jnl
Multiscale Agent-based Simulation for Chondrogenic Pattern Formation
Cybern. Syst.
Scott Christley, Xuelian Zhu, Stuart A. Newman, Mark S. Alber
2007 J jnl
Patterns of Mesenchymal Condensation in a Multiscale, Discrete Stochastic Model.
PLoS Comput. Biol.
Scott Christley, Mark S. Alber, Stuart A. Newman
2007 J jnl
Social Interactions in Myxobacterial Swarming.
PLoS Comput. Biol.
Yilin Wu, Yi Jiang, Dale Kaiser, Mark S. Alber
2006 — conf
A Parallel Implementation of the Cellular Potts Model for Simulation of Cell-Based Morphogenesis.
ACRI
Nan Chen, James A. Glazier, Mark S. Alber
2006 — conf
CA Models of Myxobacteria Swarming.
ACRI
Yilin Wu, Nan Chen, Matthew Rissler, Yi Jiang, Dale Kaiser, Mark S. Alber
2006 J jnl
On Modeling Complex Collective Behavior in Myxobacteria.
Adv. Complex Syst.
Yi Jiang, Olga Sozinova, Mark S. Alber
2005 J jnl
A Framework for Three-Dimensional Simulation of Morphogenesis.
IEEE ACM Trans. Comput. Biol. Bioinform.
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
2005 J jnl
Special Issue on Multiscale Modeling in Biology.
Multiscale Model. Simul.
Mark S. Alber, Thomas Yizhao Hou, James A. Glazier, Yi Jiang
2004 — conf
A Cellular Automata Model of Early T Cell Recognition.
ACRI
Arancha Casal, Cenk Sumen, Tim Reddy, Mark S. Alber, Peter P. Lee
2004 — conf
A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb.
ACRI
Rajiv Chaturvedi, Chengbang Huang, Jesús A. Izaguirre, Stuart A. Newman, James A. Glazier, Mark S. Alber
2004 J jnl
COMPUCELL, a multi-model framework for simulation of morphogenesis.
Bioinform.
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
2003 Misc conf
Multi-model Simulations of Chicken Limb Morphogenesis.
International Conference on Computational Science
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
2003 — ch.
On Cellular Automaton Approaches to Modeling Biological Cells.
Mathematical Systems Theory in Biology, Communications, Computation, and Finance
Mark S. Alber, Maria A. Kiskowski, James A. Glazier, Yi Jiang
2001 J jnl
Peakon solutions of the shallow water equation.
Appl. Math. Lett.
Mark S. Alber, Charles Miller