Mark Alber
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Integrating machine learning and multiscale modeling—perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences
M Alber, A Buganza Tepole, WR Cannon, S De, S Dura-Bernal, ...
NPJ digital medicine 2 (1), 115, 2019
Combining fully convolutional and recurrent neural networks for 3d biomedical image segmentation
J Chen, L Yang, Y Zhang, M Alber, DZ Chen
Advances in neural information processing systems 29, 2016
CompuCell, a multi-model framework for simulation of morphogenesis
JA Izaguirre, R Chaturvedi, C Huang, T Cickovski, J Coffland, G Thomas, ...
Bioinformatics 20 (7), 1129-1137, 2004
A multiscale model of thrombus development
Z Xu, N Chen, MM Kamocka, ED Rosen, M Alber
Journal of the Royal Society Interface 5 (24), 705-722, 2008
Multiscale modeling meets machine learning: What can we learn?
GCY Peng, M Alber, A Buganza Tepole, WR Cannon, S De, ...
Archives of Computational Methods in Engineering 28, 1017-1037, 2021
The geometry of peaked solitons and billiard solutions of a class of integrable PDE's
MS Alber, R Camassa, DD Holm, JE Marsden
Letters in Mathematical Physics 32, 137-151, 1994
Quantitative structural mechanobiology of platelet-driven blood clot contraction
OV Kim, RI Litvinov, MS Alber, JW Weisel
Nature communications 8 (1), 1274, 2017
On cellular automaton approaches to modeling biological cells
MS Alber, MA Kiskowski, JA Glazier, Y Jiang
Mathematical systems theory in biology, communications, computation, andá…, 2003
Periodic reversal of direction allows Myxobacteria to swarm
Y Wu, AD Kaiser, Y Jiang, MS Alber
Proceedings of the National Academy of Sciences 106 (4), 1222-1227, 2009
A framework for three-dimensional simulation of morphogenesis
TM Cickovski, C Huang, R Chaturvedi, T Glimm, HGE Hentschel, ...
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2 (4), 273-288, 2005
Study of blood flow impact on growth of thrombi using a multiscale model
Z Xu, N Chen, SC Shadden, JE Marsden, MM Kamocka, ED Rosen, ...
Soft Matter 5 (4), 769-779, 2009
On multiscale approaches to three-dimensional modelling of morphogenesis
R Chaturvedi, C Huang, B Kazmierczak, T Schneider, JA Izaguirre, ...
Journal of the Royal Society interface 2 (3), 237-253, 2005
A multiscale model of venous thrombus formation with surface-mediated control of blood coagulation cascade
Z Xu, J Lioi, J Mu, MM Kamocka, X Liu, DZ Chen, ED Rosen, M Alber
Biophysical journal 98 (9), 1723-1732, 2010
Structural basis for the nonlinear mechanics of fibrin networks under compression
OV Kim, RI Litvinov, JW Weisel, MS Alber
Biomaterials 35 (25), 6739-6749, 2014
A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis
N Chen, JA Glazier, JA Izaguirre, MS Alber
Computer physics communications 176 (11-12), 670-681, 2007
The mechanisms of microtubule catastrophe and rescue: implications from analysis of a dimer-scale computational model
G Margolin, IV Gregoretti, TM Cickovski, C Li, W Shi, MS Alber, ...
Molecular biology of the cell 23 (4), 642-656, 2012
Bare bones pattern formation: a core regulatory network in varying geometries reproduces major features of vertebrate limb development and evolution
J Zhu, YT Zhang, MS Alber, SA Newman
PLoS One 5 (5), e10892, 2010
The Complex Geometry of Weak Piecewise Smooth Solutions of Integrable Nonlinear PDE's of Shallow Water and Dym Type
MS Alber, R Camassa, YN Fedorov, DD Holm, JE Marsden
Communications in Mathematical Physics 221, 197-227, 2001
Type IV pili interactions promote intercellular association and moderate swarming of Pseudomonas aeruginosa
ME Anyan, A Amiri, CW Harvey, G Tierra, N Morales-Soto, CM Driscoll, ...
Proceedings of the National Academy of Sciences 111 (50), 18013-18018, 2014
Mechanism for the catastrophe-promoting activity of the microtubule destabilizer Op18/stathmin
KK Gupta, C Li, A Duan, EO Alberico, OV Kim, MS Alber, HV Goodson
Proceedings of the National Academy of Sciences 110 (51), 20449-20454, 2013
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