Interdisciplinary Center for Quantitative Modeling in Biology

Mark Alber

• Ali Nematbakhsh, Megan Levis, Nilay Kumar, Weitao Chen, Jeremiah Zartman andMark Albre [2020], Epithelial organ shape is generated by patterned actomyosincontractility and maintained by the extracellular matrix, PLoS Computational Biology,16(8): e1008105. https://doi.org/10.1371/journal.pcbi.1008105
• Samuel Britton, Mark Alber and William R. Cannon [2020], Enzyme ActivitiesPredicted by Metabolite Concentrations and Solvent Capacity in the Cell, Journal of theRoyal Society Interface 17(171), 20200656.
• Oleg V. Kim, Rustem I. Litvinov, Mark S. Alber and John W. Weisel [2017],Quantitative Structural Mechanobiology of Platelet-Driven Blood Clot Contraction,Nature Communications 8: 1274. https://www.nature.com/articles/s41467-017-00885-x.pdf (authors for correspondence: J.W. Weisel and M. Alber).
• Special Issue on "Multi-scale Modeling of Tissue Growth and Shape", Bulletin of Mathematical Biology, Mark Alber, Christophe Godin, Philip Maini, Roeland Merks,Eric Mjolsness, Editors, Volume 81, Issue 8 (2019).

William Cannon

• Cannon, W. R., Zucker, J. D., Baxter, D. J., Kumar, N., Baker, S. E., Hurley, J. M. and Dunlap, J. C., Prediction of Metabolite Concentrations, Rate Constants and Post-translational Regulation using Maximum Entropy-based Simulations with Application to Central Metabolism of Neurospora crassa," Processes (2018) 6, 63, doi:10.3390/pr6060063.
• Alber, M., Buganza Tepole, A., Cannon, W.R. et al. Integrating Machine Learning and Multiscale Modeling—Perspectives, Challenges, and Opportunities in the Biological, Biomedical, and Behavioral Sciences. npj Digit. Med. 2, 115 (2019) doi:10.1038/s41746-019-0193-y
• Britton, S., Alber, M, and Cannon, W. R., Enzyme Activities Predicted by Metabolite Concentrations and Solvent Capacity in the Cell, Journal of The Royal Society Interface (2020), 17(171): 20200656, doi:10.1098/rsif.2020.0656

Weitao Chen

• Kevin Tsai, Samuel Britton, Ali Nematbakhsh, Roya Zandi, Weitao Chen*, Mark Alber* (2020). Role of combined cell membrane and wall mechanical properties regulated by polarity signals in cell budding. (* co-corresponding author) Physical Biology 17 065011.
• Xue Pan, Linjing Fang, Jianfeng Liu, Betul Senay-Aras, Wenwei Lin, Shuan Zheng, Tong Zhang, Jingzhe Guo, Uri Manor, Jaimie Van Norman, Weitao Chen*, Zhenbiao Yang* (2020). Auxin-induced signaling protein nanoclustering contributes to cell polarity formation. (* co-corresponding author) Nature Communications, 11(1), pp.1-14.
• Yilun Zhu, Yuchi Qiu, Weitao Chen, Qing Nie, Arthur Lander. Scaling a Dpp morphogen gradient through feedback control of receptors and co-receptors. Developmental Cell, 53, no.6 (2020), pp.724-739.

Heyrim Cho

• H. Cho, A. Lewis, K. Storey, 'Bayesian Information-Theoretic Calibration of Radiotherapy Sensitivity Parameters for Informing Effective Scanning Protocols in Cancer', J Clin Med. 9, 2020
• H. Cho, K. Ayers, L. DePillis, Y-H. Kuo, J. Park, A. Radunskaya, R. Rockne, ‘Modeling acute myeloid leukemia in a continuum of differentiation states’, Lett. Biomath., 5, 2018
• H. Cho, D. Venturi, G. E. Karniadakis, ‘Numerical methods for high-dimensional probability density function equations', J. Comput. Phys. 305, 2016

Yat Tin Chow

• Y.T. Chow, J. Darbon, S. Osher, W. Yin, Algorithm for Overcoming the Curse of Dimensionality for State-dependent Hamilton-Jacobi equations, Journal of Computational Physics 387, pp. 376-409, 2019.
• H. Ammari, Y.T. Chow, J. Zou, Super-resolution in imaging high contrast targets from the perspective of scattering coefficients, Journal de Mathematiques Pures et Appliquees 111, pp. 192-226, 2018.
• Y.T. Chow, K. Ito, K. Liu, J. Zou, Direct sampling method for diffusive optical tomography, SIAM Journal of Scientific Computing 37(4), A1658–A1684, 2015.

Jia Gou

• Jia Gou, Lin Lin, Hans G. Othmer, A Model for the Hippo Pathway in the Drosophila Wing Disc, Biophys. J., 115(4), (2018), https://www.sciencedirect.com/science/article/pii/S0006349518307641 .
• Jia Gou, Michael J. Ward, An Asymptotic Analysis of a 2-D Model of Dynamically Active Compartments Coupled by Bulk Diffusion, J. Nonl. Sci., 26(4), (2016), https://link.springer.com/article/10.1007/s00332-016-9296-7 .
• Jia Gou, Yue Xian Li, Wayne Nagata, Michael J. Ward, Synchronized Oscillatory Dynamics for a 1-D Model of Membrane Kinetics Coupled by Linear Bulk Diffusion, SIAM J. Appl. Dyn. Sys., 14(4), (2015), https://epubs.siam.org/doi/abs/10.1137/15M1039122?af=R .

Jim Kelliher

• A characterization at infinity of bounded vorticity, bounded velocity solutions to the 2D Euler equations, Indiana University Mathematics Journal, 64(6), 1643-1666, 2015.
• Observations on the vanishing viscosity limit, Transactions of the American Mathematical Society, 369, 2003-2027, 2017. Published electronically 2 June 2016. Comment.
• With Elaine Cozzi, Well-posedness of the 2D Euler equations when velocity grows at infinity, Discrete & Continuous Dynamical Systems, 39(5), 2361-2392, 2018.

Amir Moradifam

• Publications Listing

Misha Potomkin

• Chi, H., Potomkin, M., Zhang, L., Berlyand, L. and Aranson, I.S., 2020. Surface anchoring controls orientation of a microswimmer in nematic liquid crystal. Communications Physics, 3(1), pp.1-9.
• Berlyand, L., Jabin, P.E., Potomkin, M. and Ratajczyk, E., 2020. A kinetic approach to active rods dynamics in confined domains. Multiscale Modeling & Simulation, 18(1), pp.1-20.
• Potomkin, M., Kaiser, A., Berlyand, L. and Aranson, I.S., 2017. Focusing of active particles in a converging flow. New Journal of Physics, 19(11), p.115005.

Russell Rockne

• Rockne RC, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, Macklin P, Hormuth D, Jarrett AM, Lima EABDF, Oden J, Biros G, Yankeelov TE, Curtius K, Bakir IA, Wodarz D, Komarova N, Aparicio L, Bordyuh M, Rabadan R, Finley S, Enderling H, Caudell JJ, Moros EG, Anderson ARA, Gatenby R, Kaznatcheev A, Jeavons P, Krishnan N, Pelesko J, Wadhwa RR, Yoon N, Nichol D, Marusyk A, Hinczewski M, Scott JG. The 2019 Mathematical Oncology Roadmap. Physical Biology, vol. 16, no. 4, 2019 Apr 16. PMID: 30991381 PMCID: PMC6655440 DOI: 10.1088/1478-3975/ab1a09
• Rockne RC, Branciamore S, Qi J, Frankhouser DE, O’Meally D, Hua W-K, Cook G, Carnahan E, Zhang L, Marmom A, Wu H, Maestrini D, Wu X, Yuan Y-C, Liu Zheng, Wang LD, Forman S, Carlesso N, Kuo Y-H, Marcucci G. State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia. Cancer Research 2020 Aug 1;80(15):3157-3169 PMID: 32414754 PMCID: PMC7416495 DOI: 10.1158/0008-5472.CAN-20-0354
• Abler D., Büchler P., Rockne R.C. (2019) Towards Model-Based Characterization of Biomechanical Tumor Growth Phenotypes. In: Bebis G., Benos T., Chen K., Jahn K., Lima E. (eds) Mathematical and Computational Oncology. ISMCO 2019. Lecture Notes in Computer Science, vol 11826. Springer, Cham. DOI: 10.1007/978-3-030-35210-3_6, ISBN 978-3-030-35209-7

Qixuan Wang

• Qixuan Wang*, Ji Won Oh*, Hye-Lim Lee, Anukriti Dhar, Tao Peng, Raul Ramos, Christian Fernando Guerrero-Juarez, Xiaojie Wang, Ran Zhao, Xiaoling Cao, Jonathan Le, Melisa A Fuentes, Shelby C Jocoy, Antoni R Rossi, Brian Vu, Kim Pham, Xiaoyang Wang, Nanda Maya Mali, Jung Min Park, June- Hyug Choi, Hyunsu Lee, Julien Legrand, Eve Kandyba, Jung Chul Kim, Moonkyu Kim, John Foley, Zhengquan Yu, Krzysztof Kobielak, Bogi Andersen, Kiarash Khosrotehrani, Qing Nie#, Maksim V Plikus#. "A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning." eLife, 6 (2017): e22772. [Link].
• Qixuan Wang*, William R. Holmes*, Julian Sosnik, Thomas Schilling, Qing Nie#. "Cell sorting and noise-induced cell plasticity coordinate to sharpen boundaries between gene expression domains." PLoS Computational Biology, 13.1 (2017): e1005307. [Link]
• Qixuan Wang# and Hans G. Othmer. "Computational analysis of amoeboid swimming at low Reynolds number." Journal of Mathematical Biology, 72.7 (2016): 1893-1926. [Link] [ArXiv]

Special Issue of the Bulletin of Mathematical Biology, Multi-scale Modeling of Tissue Growth and Shape, Mark Alber, Christophe Godin, Philip Maini, Roeland Merks, Eric Mjolsness, Editors (to appear).

Kim, O.V., Nevzorova, T.A., Mordakhanova, E.R., Ponomareva, A.A., Andrianova, I.A., Le Minh, G., Daminova, A.G., Peshkova, A.D., Alber, M.S., Vagin, O., Litvinov, R.I., Weisel, J.W., Fatal dysfunction and disintegration of thrombin-stimulated platelets. Haematologica. 2019 Feb 21. pii: haematol.2018.202309. doi: 10.3324/haematol.2018.202309. [Epub ahead of print]

Shixin Xu, Mark Alber and Zhiliang Xu [2019], Three-phase Model of Visco-elastic Incompressible Fluid Flow and its Computational Implementation, Communications in Computational Physics 25(2):586-624.

Banwarth-Kuhn, M., Nematbakhsh, A., Rodriguez, K.W., Snipes, S., Rasmussen, C.G., Reddy, G.V., Alber, M. [2018], Cell-Based Model of the Generation and Maintenance of the Shape and Structure of the Multilayered Shoot Apical Meristem of Arabidopsis thaliana. Bull. Math. Biol. 2018 Dec 14. doi: 10.1007/s11538-018-00547-z. [Epub ahead of print]

Shixin Xu, Zhiliang Xu, Oleg Kim, Rustem I. Litvinov, John W. Weisel and Mark Alber [2017], Model Predictions of Deformation, Embolization, and Permeability of Partially Obstructive Blood Clots under Variable Shear Flow, Journal of the Royal Society Interface 14: 20170441. http://dx.doi.org/10.1098/rsif.2017.0441

Oleg, V. Kim, Rustem I. Litvinov, Mark S. Alber and John W. Weisel [2017], Quantitative Structural Mechanobiology of Platelet-Driven Blood Clot Contraction, Nature Communications 8: 1274. https://www.nature.com/articles/s41467-017-00885-x.pdf (authors for correspondence: J.W. Weisel and M. Alber).

Peter Hook, Rustem I. Litvinov, Oleg V. Kim, Shixin Xu, Zhiliang Xu, Joel S. Bennett, Mark S. Alber and John W. Weisel [2017], Strong Binding of Platelet Integrin αIIbβ3 to Fibrin Clots: Potential Target to Destabilize Thrombi, Scientific Reports 7: 13001 (published by Nature) DOI:10.1038/s41598-017-12615-w

Y. Klymenko, O. Kim, E. Loughran, J. Yang, R. Lombard, M. Alber and M.S. Stack [2017], Cadherin composition and multicellular aggregate invasion in organotypic models of epithelial ovarian cancer intraperitoneal metastasis, Oncogene Oct 19;36(42):58405851. doi: 10.1038/onc.2017.171 (published by Springer Nature, authors for correspondence: M.S. Stack and M. Alber).

Peter Hook, Teresa Brito-Robinson, Oleg Kim, Cofy, Narciso, Holly V. Goodson, John W. Weisel, Mark S. Alber and Jeremiah J. Zartman, Whole Blood Clot Optical
Clearing for Nondestructive 3D Imaging and Quantitative Analysis, Biomedical Optics Express, Volume 8, Issue 8, Page 3671. (authors for correspondence: J.Zartman, J.W.Weisel and M. Alber).

Ali Nematbakhsh, Wenzhao Sun, Pavel A. Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J. Zartman, Mark Alber [2017], Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia, PLoS  Computational Biology, 13(5): e1005533. https://doi.org/10.1371/journal.pcbi.1005533

Aranda R. Duan, Erin M. Jonasson, Emily O. Alberico, Chunlei Li, Jared P. Scripture, Rachel A. Miller, Mark S. Alber and Holly V. Goodson [2017], Interactions between Tau and different conformations of tubulin: Implications for Tau function and mechanism, Journal of Molecular Biology 429(9):1424-1438. doi: 10.1016/j.jmb.2017.03.018.

O.V. Kim, R.I. Litvinov, J. Chen, D.Z. Chen, J.W. Weisel and M.S. Alber [2017], Compression-induced structural and mechanical changes of fibrin-collagen composites, Matrix Biol. 2017 Jul;60-61:141-156. doi: 10.1016/j.matbio.2016.10.007. 

Aboutaleb Amiri, Cameron Harvey, Amy Buchmann, Scott Christley, Joshua D. Shrout, Igor S. Aranson, Mark Alber [2017], Reversals and collisions optimize protein exchange in bacterial swarms, Physical Review E 95, 032408.

Martina Bukac and Mark Alber[2017], Multi-component model of intramural hematoma, Journal of Biomechanics 50, 42-49.

Kim O., Liang, X., Litvinov, R.I., Weisel, J.W., Alber, M.S., Purohit, P.K. [2016], Foam-like compression behavior of fibrin networks, Biomech Model Mechanobiol. 15:213-228.

Chen, J., M.S. Alber, and D.Z. Chen, A Hybrid Approach for Segmentation and Tracking of Myxococcus xanthus Swarms [2016], IEEE Transactions on Medical Imaging 35(9):2074-84.