Recent publications from CMCF.
CA1-projecting subiculum neurons facilitate object-place learning.
(2019) Nat. Neurosci.. 22, 1857-1870
Pubmed
Nat. Neurosci.
PMC Article
The Influence of Molecular Reach and Diffusivity on the Efficacy of Membrane-Confined Reactions.
(2019) Biophys. J.. 117, 1189-1201
Pubmed
Biophys. J.
PMC Article
Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation.
(2019) Cell Syst. 9, 271-285.e7
Pubmed
Cell Syst
PMC Article
Bidirectional sliding of two parallel microtubules generated by multiple identical motors.
(2019) J Math Biol. 79, 571-594
Pubmed
J Math Biol
Cell lineage and communication network inference via optimization for single-cell transcriptomics.
(2019) Nucleic Acids Res.. 47, e66
Pubmed
Nucleic Acids Res.
PMC Article
Efficient simulation of thermally fluctuating biopolymers immersed in fluids on 1-micron, 1-second scales.
(2019) J Comput Phys. 386, 248-263
Pubmed
J Comput Phys
PMC Article
Hydrodynamics of transient cell-cell contact: The role of membrane permeability and active protrusion length.
(2019) PLoS Comput. Biol.. 15, e1006352
Pubmed
PLoS Comput. Biol.
PMC Article
A multiscale hybrid mathematical model of epidermal-dermal interactions during skin wound healing.
(2019) Exp. Dermatol.. 28, 493-502
Pubmed
Exp. Dermatol.
PMC Article
Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds.
(2019) Nat Commun. 10, 650
Pubmed
Nat Commun
PMC Article
Tumor growth and calcification in evolving microenvironmental geometries.
(2019) J. Theor. Biol.. 463, 138-154
Pubmed
J. Theor. Biol.
PMC Article
An Ovol2-Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation.
(2019) EMBO Rep.. 20,
Pubmed
EMBO Rep.
PMC Article
Intermediate cell states in epithelial-to-mesenchymal transition.
(2019) Phys Biol. 16, 021001
Pubmed
Phys Biol
PMC Article
Transcriptomics reveals complex kinetics of dorsal-ventral patterning gene expression in the mandibular arch.
(2019) Genesis. 57, e23275
Pubmed
Genesis
PMC Article
A Visually Apparent and Quantifiable CT Imaging Feature Identifies Biophysical Subtypes of Pancreatic Ductal Adenocarcinoma.
(2018) Clin. Cancer Res.. 24, 5883-5894
Pubmed
Clin. Cancer Res.
PMC Article
Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch.
(2018) PLoS Comput. Biol.. 14, e1006569
Pubmed
PLoS Comput. Biol.
PMC Article
Nonlinear studies of tumor morphological stability using a two-fluid flow model.
(2018) J Math Biol. 77, 671-709
Pubmed
J Math Biol
Extracting multivalent detachment rates from heterogeneous nanoparticle populations.
(2018) Phys Chem Chem Phys. 20, 21430-21440
Pubmed
Phys Chem Chem Phys
Stem cells: a window of opportunity in low-dimensional EMT space.
(2018) Oncotarget. 9, 31790-31791
Pubmed
Oncotarget
PMC Article
DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation.
(2018) Stem Cell Reports. 10, 1793-1806
Pubmed
Stem Cell Reports
PMC Article
Exploring intermediate cell states through the lens of single cells.
(2018) Curr Opin Syst Biol. 9, 32-41
Pubmed
Curr Opin Syst Biol
PMC Article
Landscape reveals critical network structures for sharpening gene expression boundaries.
(2018) BMC Syst Biol. 12, 67
Pubmed
BMC Syst Biol
PMC Article
scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data.
(2018) Bioinformatics. 34, 2077-2086
Pubmed
Bioinformatics
PMC Article
A single-cell epigenetic model for paternal psychological stress-induced transgenerational reprogramming in offspring.
(2018) Biol. Reprod.. 98, 846-855
Pubmed
Biol. Reprod.
PMC Article
Mean-Independent Noise Control of Cell Fates via Intermediate States.
(2018) iScience. 3, 11-20
Pubmed
iScience
PMC Article
Three-Dimensional Spatiotemporal Modeling of Colon Cancer Organoids Reveals that Multimodal Control of Stem Cell Self-Renewal is a Critical Determinant of Size and Shape in Early Stages of Tumor Growth.
(2018) Bull. Math. Biol.. 80, 1404-1433
Pubmed
Bull. Math. Biol.
PMC Article
Epithelial-to-mesenchymal transition in cutaneous wound healing: Where we are and where we are heading.
(2018) Dev. Dyn.. 247, 473-480
Pubmed
Dev. Dyn.
PMC Article
Multiscale modeling of layer formation in epidermis.
(2018) PLoS Comput. Biol.. 14, e1006006
Pubmed
PLoS Comput. Biol.
PMC Article
Nanog induced intermediate state in regulating stem cell differentiation and reprogramming.
(2018) BMC Syst Biol. 12, 22
Pubmed
BMC Syst Biol
PMC Article
Kernel differential subgraph reveals dynamic changes in biomolecular networks.
(2018) J Bioinform Comput Biol. 16, 1750027
Pubmed
J Bioinform Comput Biol
Multiscale modeling of glioblastoma.
(2018) Transl Cancer Res. 7, S96-S98
Pubmed
Transl Cancer Res
PMC Article
Activation of the HGF/c-Met axis in the tumor microenvironment: A multispecies model.
(2018) J. Theor. Biol.. 439, 86-99
Pubmed
J. Theor. Biol.
PMC Article
Cargo navigation across 3D microtubule intersections.
(2018) Proc. Natl. Acad. Sci. U.S.A.. 115, 537-542
Pubmed
Proc. Natl. Acad. Sci. U.S.A.
PMC Article
Mathematical modeling of tumor-associated macrophage interactions with the cancer microenvironment.
(2018) J Immunother Cancer. 6, 10
Pubmed
J Immunother Cancer
PMC Article
Multiscale Modeling of Inflammation-Induced Tumorigenesis Reveals Competing Oncogenic and Oncoprotective Roles for Inflammation.
(2017) Cancer Res.. 77, 6429-6441
Pubmed
Cancer Res.
Actin Turnover in Lamellipodial Fragments.
(2017) Curr. Biol.. 27, 2963-2973.e14
Pubmed
Curr. Biol.
PMC Article
MiR-31 promotes mammary stem cell expansion and breast tumorigenesis by suppressing Wnt signaling antagonists.
(2017) Nat Commun. 8, 1036
Pubmed
Nat Commun
PMC Article
Overexpression of Transcription Factor Ovol2 in Epidermal Progenitor Cells Results in Skin Blistering.
(2017) J. Invest. Dermatol.. 137, 1805-1808
Pubmed
J. Invest. Dermatol.
3D Mathematical Modeling of Glioblastoma Suggests That Transdifferentiated Vascular Endothelial Cells Mediate Resistance to Current Standard-of-Care Therapy.
(2017) Cancer Res.. 77, 4171-4184
Pubmed
Cancer Res.
PMC Article
A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning.
(2017) Elife. 6,
Pubmed
Elife
PMC Article
Expanding signaling-molecule wavefront model of cell polarization in the Drosophila wing primordium.
(2017) PLoS Comput. Biol.. 13, e1005610
Pubmed
PLoS Comput. Biol.
PMC Article
A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions.
(2017) BMC Syst Biol. 11, 55
Pubmed
BMC Syst Biol
PMC Article
Dynamics of a multicomponent vesicle in shear flow.
(2017) Soft Matter. 13, 3521-3531
Pubmed
Soft Matter
PMC Article
Spatial pattern formation in microtubule post-translational modifications and the tight localization of motor-driven cargo.
(2017) J Math Biol. 74, 1059-1080
Pubmed
J Math Biol
PMC Article
MicroRNA filters Hox temporal transcription noise to confer boundary formation in the spinal cord.
(2017) Nat Commun. 8, 14685
Pubmed
Nat Commun
PMC Article
Biophysical assay for tethered signaling reactions reveals tether-controlled activity for the phosphatase SHP-1.
(2017) Sci Adv. 3, e1601692
Pubmed
Sci Adv
PMC Article
Mathematical modeling links Wnt signaling to emergent patterns of metabolism in colon cancer.
(2017) Mol. Syst. Biol.. 13, 912
Pubmed
Mol. Syst. Biol.
PMC Article
Recapitulating the human tumor microenvironment: Colon tumor-derived extracellular matrix promotes angiogenesis and tumor cell growth.
(2017) Biomaterials. 116, 118-129
Pubmed
Biomaterials
PMC Article
Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst.
(2017) PLoS Comput. Biol.. 13, e1005320
Pubmed
PLoS Comput. Biol.
PMC Article
Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains.
(2017) PLoS Comput. Biol.. 13, e1005307
Pubmed
PLoS Comput. Biol.
PMC Article
Computational simulation of formin-mediated actin polymerization predicts homologue-dependent mechanosensitivity.
(2017) Cytoskeleton (Hoboken). 74, 29-39
Pubmed
Cytoskeleton (Hoboken)
Diverse feather shape evolution enabled by coupling anisotropic signalling modules with self-organizing branching programme.
(2017) Nat Commun. 8, ncomms14139
Pubmed
Nat Commun
PMC Article
Adhesion-Dependent Wave Generation in Crawling Cells.
(2017) Curr. Biol.. 27, 27-38
Pubmed
Curr. Biol.
PMC Article
Lgr4 is crucial for skin carcinogenesis by regulating MEK/ERK and Wnt/β-catenin signaling pathways.
(2016) Cancer Lett.. 383, 161-170
Pubmed
Cancer Lett.
Conditional Creation and Rescue of Nipbl-Deficiency in Mice Reveals Multiple Determinants of Risk for Congenital Heart Defects.
(2016) PLoS Biol.. 14, e2000197
Pubmed
PLoS Biol.
PMC Article
Controlling Stochasticity in Epithelial-Mesenchymal Transition Through Multiple Intermediate Cellular States.
(2016) Discrete Continuous Dyn Syst Ser B. 21, 2275-2291
Pubmed
Discrete Continuous Dyn Syst Ser B
PMC Article
A hybrid continuous-discrete method for stochastic reaction-diffusion processes.
(2016) R Soc Open Sci. 3, 160485
Pubmed
R Soc Open Sci
PMC Article
A self-enhanced transport mechanism through long noncoding RNAs for X chromosome inactivation.
(2016) Sci Rep. 6, 31517
Pubmed
Sci Rep
PMC Article
Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions.
(2016) PLoS Comput. Biol.. 12, e1004988
Pubmed
PLoS Comput. Biol.
PMC Article
Quantifying the landscape and kinetic paths for epithelial-mesenchymal transition from a core circuit.
(2016) Phys Chem Chem Phys. 18, 17949-56
Pubmed
Phys Chem Chem Phys
PMC Article
Wrinkling dynamics of fluctuating vesicles in time-dependent viscous flow.
(2016) Soft Matter. 12, 5663-75
Pubmed
Soft Matter
PMC Article
A moment-convergence method for stochastic analysis of biochemical reaction networks.
(2016) J Chem Phys. 144, 194109
Pubmed
J Chem Phys
PMC Article
Primary visual cortex shows laminar-specific and balanced circuit organization of excitatory and inhibitory synaptic connectivity.
(2016) J. Physiol. (Lond.). 594, 1891-910
Pubmed
J. Physiol. (Lond.)
PMC Article
Multisite Phosphorylation Modulates the T Cell Receptor ζ-Chain Potency but not the Switchlike Response.
(2016) Biophys. J.. 110, 1896-1906
Pubmed
Biophys. J.
PMC Article
Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the embryonic zebrafish hindbrain.
(2016) Elife. 5, e14034
Pubmed
Elife
PMC Article
Survival of the Curviest: Noise-Driven Selection for Synergistic Epistasis.
(2016) PLoS Genet.. 12, e1006003
Pubmed
PLoS Genet.
PMC Article
Cell Surface Mechanochemistry and the Determinants of Bleb Formation, Healing, and Travel Velocity.
(2016) Biophys. J.. 110, 1636-1647
Pubmed
Biophys. J.
PMC Article
Feedback Regulation in a Cancer Stem Cell Model can Cause an Allee Effect.
(2016) Bull. Math. Biol.. 78, 754-785
Pubmed
Bull. Math. Biol.
PMC Article
Numerical simulation of endocytosis: Viscous flow driven by membranes with non-uniformly distributed curvature-inducing molecules.
(2016) J Comput Phys. 309, 112-128
Pubmed
J Comput Phys
PMC Article
First-Passage Time to Clear the Way for Receptor-Ligand Binding in a Crowded Environment.
(2016) Phys. Rev. Lett.. 116, 128101
Pubmed
Phys. Rev. Lett.
Feedback, Lineages and Self-Organizing Morphogenesis.
(2016) PLoS Comput. Biol.. 12, e1004814
Pubmed
PLoS Comput. Biol.
PMC Article
An interdisciplinary computational/experimental approach to evaluate drug-loaded gold nanoparticle tumor cytotoxicity.
(2016) Nanomedicine (Lond). 11, 197-216
Pubmed
Nanomedicine (Lond)
PMC Article
Collective Properties of a Transcription Initiation Model Under Varying Environment.
(2016) J. Comput. Biol.. 23, 56-66
Pubmed
J. Comput. Biol.
PMC Article
An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States.
(2015) PLoS Comput. Biol.. 11, e1004569
Pubmed
PLoS Comput. Biol.
PMC Article
Semi-permeable Diffusion Barriers Enhance Patterning Robustness in the C. elegans Germline.
(2015) Dev. Cell. 35, 405-17
Pubmed
Dev. Cell
PMC Article
A Mechanistic Collective Cell Model for Epithelial Colony Growth and Contact Inhibition.
(2015) Biophys. J.. 109, 1347-57
Pubmed
Biophys. J.
PMC Article
Akt Phosphorylates Wnt Coactivator and Chromatin Effector Pygo2 at Serine 48 to Antagonize Its Ubiquitin/Proteasome-mediated Degradation.
(2015) J. Biol. Chem.. 290, 21553-67
Pubmed
J. Biol. Chem.
PMC Article
POPE: post optimization posterior evaluation of likelihood free models.
(2015) BMC Bioinformatics. 16, 264
Pubmed
BMC Bioinformatics
PMC Article
Deciphering principles of morphogenesis from temporal and spatial patterns on the integument.
(2015) Dev. Dyn.. 244, 905-20
Pubmed
Dev. Dyn.
PMC Article
Graphics processing unit-based alignment of protein interaction networks.
(2015) IET Syst Biol. 9, 120-7
Pubmed
IET Syst Biol
An Integration Factor Method for Stochastic and Stiff Reaction-Diffusion Systems.
(2015) J Comput Phys. 295, 505-522
Pubmed
J Comput Phys
PMC Article
The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis.
(2015) PLoS Comput. Biol.. 11, e1004285
Pubmed
PLoS Comput. Biol.
PMC Article
Semi-implicit Integration Factor Methods on Sparse Grids for High-Dimensional Systems.
(2015) J Comput Phys. 292, 43-55
Pubmed
J Comput Phys
PMC Article
Clinical, developmental and molecular update on Cornelia de Lange syndrome and the cohesin complex: abstracts from the 2014 Scientific and Educational Symposium.
(2015) Am. J. Med. Genet. A. 167, 1179-92
Pubmed
Am. J. Med. Genet. A
Semi-adaptive response and noise attenuation in bone morphogenetic protein signalling.
(2015) J R Soc Interface. 12,
Pubmed
J R Soc Interface
PMC Article
Organ-level quorum sensing directs regeneration in hair stem cell populations.
(2015) Cell. 161, 277-90
Pubmed
Cell
PMC Article
The effect of spontaneous curvature on a two-phase vesicle.
(2015) Nonlinearity. 28, 773-793
Pubmed
Nonlinearity
PMC Article
Diffuse interface models of locally inextensible vesicles in a viscous fluid.
(2014) J Comput Phys. 277, 32-47
Pubmed
J Comput Phys
PMC Article
Computational modelling of epidermal stratification highlights the importance of asymmetric cell division for predictable and robust layer formation.
(2014) J R Soc Interface. 11,
Pubmed
J R Soc Interface
PMC Article
Nipbl and mediator cooperatively regulate gene expression to control limb development.
(2014) PLoS Genet.. 10, e1004671
Pubmed
PLoS Genet.
PMC Article
Actin-myosin spatial patterns from a simplified isotropic viscoelastic model.
(2014) Biophys. J.. 107, 863-70
Pubmed
Biophys. J.
PMC Article
The protective role of symmetric stem cell division on the accumulation of heritable damage.
(2014) PLoS Comput. Biol.. 10, e1003802
Pubmed
PLoS Comput. Biol.
PMC Article
The co-factor of LIM domains (CLIM/LDB/NLI) maintains basal mammary epithelial stem cells and promotes breast tumorigenesis.
(2014) PLoS Genet.. 10, e1004520
Pubmed
PLoS Genet.
PMC Article
Computational Modeling of Tumor Response to Drug Release from Vasculature-Bound Nanoparticles.
(2015) PLoS ONE. 10, e0144888
Pubmed
PLoS ONE
PMC Article
The effect of Nipped-B-like (Nipbl) haploinsufficiency on genome-wide cohesin binding and target gene expression: modeling Cornelia de Lange syndrome.
(2017) Clin Epigenetics. 9, 89
Pubmed
Clin Epigenetics
PMC Article
Ex Vivo Imaging and Genetic Manipulation of Mouse Hair Follicle Bulge Stem Cells.
(2019) Methods Mol. Biol.. 1879, 15-29
Pubmed
Methods Mol. Biol.
ADAPTIVE METHODS FOR STOCHASTIC DIFFERENTIAL EQUATIONS VIA NATURAL EMBEDDINGS AND REJECTION SAMPLING WITH MEMORY.
(2017) Discrete Continuous Dyn Syst Ser B. 22, 2731-2761
Pubmed
Discrete Continuous Dyn Syst Ser B
PMC Article