Publications

Mark Alber

Ali Nematbakhsh, Megan Levis, Nilay Kumar, et al. (2020). Epithelial organ shape is generated by patterned actomyosin contractility and maintained by the extracellular matrix. PLoS Computational Biology, 16(8): e1008105. [DOI]
Samuel Britton, Mark Alber, and William R. Cannon (2020). Enzyme Activities Predicted by Metabolite Concentrations and Solvent Capacity in the Cell. Journal of the Royal 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. [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, edited by Mark Alber, Christophe Godin, Philip Maini, Roeland Merks, and Eric Mjolsness, 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. (2018). Prediction of Metabolite Concentrations, Rate Constants and Post-translational Regulation using Maximum Entropy-based Simulations with Application to Central Metabolism of Neurospora crassa. Processes, 6:63. DOI: 10.3390/pr6060063.
Alber, M., Buganza Tepole, A., Cannon, W. R., et al. (2019). Integrating Machine Learning and Multiscale Modeling—Perspectives, Challenges, and Opportunities in the Biological, Biomedical, and Behavioral Sciences. npj Digital Medicine, 2:115. DOI: 10.1038/s41746-019-0193-y.
Britton, S., Alber, M., and Cannon, W. R. (2020). Enzyme Activities Predicted by Metabolite Concentrations and Solvent Capacity in the Cell. Journal of The Royal Society Interface, 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. Physical Biology, 17: 065011. (* co-corresponding author)
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. Nature Communications, 11(1), pp. 1–14. (* co-corresponding author)
Yilun Zhu, Yuchi Qiu, Weitao Chen, Qing Nie, Arthur Lander (2020). Scaling a Dpp morphogen gradient through feedback control of receptors and co-receptors. Developmental Cell, 53(6), pp. 724–739.

Heyrim Cho

H. Cho, A. Lewis, K. Storey (2020). Bayesian Information-Theoretic Calibration of Radiotherapy Sensitivity Parameters for Informing Effective Scanning Protocols in Cancer. Journal of Clinical Medicine, 9.
H. Cho, K. Ayers, L. DePillis, Y-H. Kuo, J. Park, A. Radunskaya, R. Rockne (2018). Modeling acute myeloid leukemia in a continuum of differentiation states. Letters in Biomathematics, 5.
H. Cho, D. Venturi, G. E. Karniadakis (2016). Numerical methods for high-dimensional probability density function equations. Journal of Computational Physics, 305.

Yat Tin Chow

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

Jia Gou

Jia Gou, Lin Lin, Hans G. Othmer (2018). A Model for the Hippo Pathway in the Drosophila Wing Disc. Biophysical Journal, 115(4). [Link]
Jia Gou, Michael J. Ward (2016). An Asymptotic Analysis of a 2-D Model of Dynamically Active Compartments Coupled by Bulk Diffusion. Journal of Nonlinear Science, 26(4). [Link]
Jia Gou, Yue Xian Li, Wayne Nagata, Michael J. Ward (2015). Synchronized Oscillatory Dynamics for a 1-D Model of Membrane Kinetics Coupled by Linear Bulk Diffusion. SIAM Journal on Applied Dynamical Systems, 14(4). [Link]

Jim Kelliher

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

Amir Moradifam

Amir Moradifam. Full list of publications available here .

Mykhailo 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, R.C., Hawkins-Daarud, A., Swanson, K.R., Sluka, J.P., Glazier, J.A., Macklin, P., Hormuth, D., Jarrett, A.M., Lima, E.A.B.D.F., Oden, J., Biros, G., Yankeelov, T.E., Curtius, K., Bakir, I.A., Wodarz, D., Komarova, N., Aparicio, L., Bordyuh, M., Rabadan, R., Finley, S., Enderling, H., Caudell, J.J., Moros, E.G., Anderson, A.R.A., Gatenby, R., Kaznatcheev, A., Jeavons, P., Krishnan, N., Pelesko, J., Wadhwa, R.R., Yoon, N., Nichol, D., Marusyk, A., Hinczewski, M., Scott, J.G. (2019). The 2019 Mathematical Oncology Roadmap. Physical Biology, 16(4). PMID: 30991381 PMCID: PMC6655440 DOI: 10.1088/1478-3975/ab1a09
Rockne, R.C., Branciamore, S., Qi, J., Frankhouser, D.E., O’Meally, D., Hua, W.-K., Cook, G., Carnahan, E., Zhang, L., Marmom, A., Wu, H., Maestrini, D., Wu, X., Yuan, Y.-C., Zheng, L., Wang, L.D., Forman, S., Carlesso, N., Kuo, Y.-H., Marcucci, G. (2020). State-Transition Analysis of Time-Sequential Gene Expression Identifies Critical Points That Predict Development of Acute Myeloid Leukemia. Cancer Research, 80(15), pp. 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. 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 (2017). A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning. eLife, 6: e22772. [Link]
Qixuan Wang*, William R. Holmes*, Julian Sosnik, Thomas Schilling, Qing Nie (2017). Cell sorting and noise-induced cell plasticity coordinate to sharpen boundaries between gene expression domains. PLoS Computational Biology, 13(1): e1005307. [Link]
Qixuan Wang# and Hans G. Othmer (2016). Computational analysis of amoeboid swimming at low Reynolds number. Journal of Mathematical Biology, 72(7): 1893–1926. [Link] [ArXiv]

Other Publications

Mark Alber, Christophe Godin, Philip Maini, Roeland Merks, Eric Mjolsness (Editors). Special Issue of the Bulletin of Mathematical Biology: Multi-scale Modeling of Tissue Growth and Shape. 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. (2019). Fatal dysfunction and disintegration of thrombin-stimulated platelets. Haematologica. doi: 10.3324/haematol.2018.202309. [Epub ahead of print]
Shixin Xu, Mark Alber, 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. Bulletin of Mathematical Biology. doi: 10.1007/s11538-018-00547-z.
Shixin Xu, Zhiliang Xu, Oleg Kim, Rustem I. Litvinov, John W. Weisel, 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. [Link]
Oleg V. Kim, Rustem I. Litvinov, Mark S. Alber, John W. Weisel (2017). Quantitative Structural Mechanobiology of Platelet-Driven Blood Clot Contraction. Nature Communications, 8: 1274. [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, John W. Weisel (2017). Strong Binding of Platelet Integrin αIIbβ3 to Fibrin Clots: Potential Target to Destabilize Thrombi. Scientific Reports, 7: 13001. DOI: 10.1038/s41598-017-12615-w
Y. Klymenko, O. Kim, E. Loughran, J. Yang, R. Lombard, M. Alber, M.S. Stack (2017). Cadherin composition and multicellular aggregate invasion in organotypic models of epithelial ovarian cancer intraperitoneal metastasis. Oncogene, 36(42): 5840–5851. doi: 10.1038/onc.2017.171 (Authors for correspondence: M.S. Stack and M. Alber)
Peter Hook, Teresa Brito-Robinson, Oleg Kim, Cody Narciso, Holly V. Goodson, John W. Weisel, Mark S. Alber, Jeremiah J. Zartman. Whole Blood Clot Optical Clearing for Nondestructive 3D Imaging and Quantitative Analysis. Biomedical Optics Express, 8(8): 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. [Link]
Aranda R. Duan, Erin M. Jonasson, Emily O. Alberico, Chunlei Li, Jared P. Scripture, Rachel A. Miller, Mark S. Alber, 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, M.S. Alber (2017). Compression-induced structural and mechanical changes of fibrin-collagen composites. Matrix Biology, 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, Mark Alber (2017). Multi-component model of intramural hematoma. Journal of Biomechanics, 50: 42–49.
O. Kim, X. Liang, R.I. Litvinov, J.W. Weisel, M.S. Alber, P.K. Purohit (2016). Foam-like compression behavior of fibrin networks. Biomechanics and Modeling in Mechanobiology, 15: 213–228.
J. Chen, M.S. Alber, D.Z. Chen (2016). A Hybrid Approach for Segmentation and Tracking of Myxococcus xanthus Swarms. IEEE Transactions on Medical Imaging, 35(9): 2074–2084.

Interdisciplinary Center for Quantitative Modeling in Biology

Mark Alber

William Cannon

Weitao Chen

Heyrim Cho

Yat Tin Chow

Jia Gou

Jim Kelliher

Amir Moradifam

Mykhailo Potomkin

Russell Rockne

Qixuan Wang

Other Publications

College of Natural and Agricultural Sciences