Recent publications from CMCF.
Simulation of receptor triggering by kinetic segregation shows role of oligomers and close contacts.
(2022) Biophys J. 121, 1660-1674
Pubmed
Biophys J
PMC Article
Spatial dynamics of feedback and feedforward regulation in cell lineages.
(2022) PLoS Comput Biol. 18, e1010039
Pubmed
PLoS Comput Biol
PMC Article
Zebrafish airinemes optimize their shape between ballistic and diffusive search.
(2022) Elife. 11,
Pubmed
Elife
PMC Article
Harvesting random embedding for high-frequency change-point detection in temporal complex systems.
(2022) Natl Sci Rev. 9, nwab228
Pubmed
Natl Sci Rev
PMC Article
Deciphering tissue structure and function using spatial transcriptomics.
(2022) Commun Biol. 5, 220
Pubmed
Commun Biol
PMC Article
IL-17A Promotes Psoriasis-Associated Keratinocyte Proliferation through ACT1-Dependent Activation of YAP-AREG Axis.
(2022) J Invest Dermatol.
Pubmed
J Invest Dermatol
Dormant reporter-marked basal stem/progenitor cells contribute to mammary lobuloalveoli formation.
(2022) iScience. 25, 103982
Pubmed
iScience
PMC Article
Modelling glioma progression, mass effect and intracranial pressure in patient anatomy.
(2022) J R Soc Interface. 19, 20210922
Pubmed
J R Soc Interface
PMC Article
Defining mammary basal cell transcriptional states using single-cell RNA-sequencing.
(2022) Sci Rep. 12, 4893
Pubmed
Sci Rep
PMC Article
Epidermis-Intrinsic Transcription Factor Ovol1 Coordinately Regulates Barrier Maintenance and Neutrophil Accumulation in Psoriasis-Like Inflammation.
(2022) J Invest Dermatol. 142, 583-593.e5
Pubmed
J Invest Dermatol
Dephosphorylation accelerates the dissociation of ZAP70 from the T cell receptor.
(2022) Proc Natl Acad Sci U S A. 119,
Pubmed
Proc Natl Acad Sci U S A
PMC Article
Modeling of Tumor Growth with Input from Patient-Specific Metabolomic Data.
(2022) Ann Biomed Eng. 50, 314-329
Pubmed
Ann Biomed Eng
NTR 2.0: a rationally engineered prodrug-converting enzyme with substantially enhanced efficacy for targeted cell ablation.
(2022) Nat Methods. 19, 205-215
Pubmed
Nat Methods
PMC Article
UFold: fast and accurate RNA secondary structure prediction with deep learning.
(2022) Nucleic Acids Res. 50, e14
Pubmed
Nucleic Acids Res
PMC Article
Nfatc1's Role in Mammary Epithelial Morphogenesis and Basal Stem/progenitor Cell Self-renewal.
(2021) J Mammary Gland Biol Neoplasia. 26, 357-365
Pubmed
J Mammary Gland Biol Neoplasia
PMC Article
Stress generation, relaxation and size control in confined tumor growth.
(2021) PLoS Comput Biol. 17, e1009701
Pubmed
PLoS Comput Biol
PMC Article
Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development.
(2021) Cell Rep. 37, 110140
Pubmed
Cell Rep
PMC Article
Altered Epithelial-mesenchymal Plasticity as a Result of Ovol2 Deletion Minimally Impacts the Self-renewal of Adult Mammary Basal Epithelial Cells.
(2021) J Mammary Gland Biol Neoplasia. 26, 377-386
Pubmed
J Mammary Gland Biol Neoplasia
PMC Article
Examining age-dependent DNA methylation patterns and gene expression in the male and female mouse hippocampus.
(2021) Neurobiol Aging. 108, 223-235
Pubmed
Neurobiol Aging
A Study of Gene Expression, Structure, and Contractility of iPSC-Derived Cardiac Myocytes from a Family with Heart Disease due to LMNA Mutation.
(2021) Ann Biomed Eng. 49, 3524-3539
Pubmed
Ann Biomed Eng
PMC Article
Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell-Cell Signaling during EMT Progression.
(2021) Cancers (Basel). 13,
Pubmed
Cancers (Basel)
PMC Article
Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition.
(2021) Biophys J. 120, 4484-4500
Pubmed
Biophys J
PMC Article
Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics.
(2021) Nat Commun. 12, 5609
Pubmed
Nat Commun
PMC Article
Regulatory feedback effects on tissue growth dynamics in a two-stage cell lineage model.
(2021) Phys Rev E. 104, 034405
Pubmed
Phys Rev E
PMC Article
Modeling the effects of EMT-immune dynamics on carcinoma disease progression.
(2021) Commun Biol. 4, 983
Pubmed
Commun Biol
PMC Article
Identifying age-specific gene signatures of the human cerebral cortex with joint analysis of transcriptomes and functional connectomes.
(2021) Brief Bioinform. 22,
Pubmed
Brief Bioinform
Mathematical modeling of histone modifications reveals the formation mechanism and function of bivalent chromatin.
(2021) iScience. 24, 102732
Pubmed
iScience
PMC Article
SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration.
(2021) Bioinformatics. 37, i317-i326
Pubmed
Bioinformatics
PMC Article
OVOL1 Regulates Psoriasis-Like Skin Inflammation and Epidermal Hyperplasia.
(2021) J Invest Dermatol. 141, 1542-1552
Pubmed
J Invest Dermatol
PMC Article
The landscape of cell-cell communication through single-cell transcriptomics.
(2021) Curr Opin Syst Biol. 26, 12-23
Pubmed
Curr Opin Syst Biol
PMC Article
Multiple morphogens and rapid elongation promote segmental patterning during development.
(2021) PLoS Comput Biol. 17, e1009077
Pubmed
PLoS Comput Biol
PMC Article
Controlling fingering instabilities in Hele-Shaw flows in the presence of wetting film effects.
(2021) Phys Rev E. 103, 063105
Pubmed
Phys Rev E
Determination of the molecular reach of the protein tyrosine phosphatase SHP-1.
(2021) Biophys J. 120, 2054-2066
Pubmed
Biophys J
PMC Article
Diffusion of kinesin motors on cargo can enhance binding and run lengths during intracellular transport.
(2021) Mol Biol Cell. 32, 984-994
Pubmed
Mol Biol Cell
PMC Article
An in vitro vascularized micro-tumor model of human colorectal cancer recapitulates in vivo responses to standard-of-care therapy.
(2021) Lab Chip. 21, 1333-1351
Pubmed
Lab Chip
PMC Article
Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples.
(2021) PLoS Comput Biol. 17, e1008379
Pubmed
PLoS Comput Biol
PMC Article
A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development.
(2021) PLoS Comput Biol. 17, e1008571
Pubmed
PLoS Comput Biol
PMC Article
Inference and analysis of cell-cell communication using CellChat.
(2021) Nat Commun. 12, 1088
Pubmed
Nat Commun
PMC Article
Effect of feedback regulation on stem cell fractions in tissues and tumors: Understanding chemoresistance in cancer.
(2021) J Theor Biol. 509, 110499
Pubmed
J Theor Biol
PMC Article
scMC learns biological variation through the alignment of multiple single-cell genomics datasets.
(2021) Genome Biol. 22, 10
Pubmed
Genome Biol
PMC Article
Intrinsic Disorder in the T Cell Receptor Creates Cooperativity and Controls ZAP70 Binding.
(2021) Biophys J. 120, 379-392
Pubmed
Biophys J
PMC Article
Optimal experimental design for mathematical models of haematopoiesis.
(2021) J R Soc Interface. 18, 20200729
Pubmed
J R Soc Interface
PMC Article
Keratinocyte-Macrophage Crosstalk by the Nrf2/Ccl2/EGF Signaling Axis Orchestrates Tissue Repair.
(2020) Cell Rep. 33, 108417
Pubmed
Cell Rep
PMC Article
Author Correction: MiR-31 promotes mammary stem cell expansion and breast tumorigenesis by suppressing Wnt signaling antagonists.
(2020) Nat Commun. 11, 5308
Pubmed
Nat Commun
PMC Article
The Msi1-mTOR pathway drives the pathogenesis of mammary and extramammary Paget's disease.
(2020) Cell Res. 30, 854-872
Pubmed
Cell Res
PMC Article
Dynamics of nevus development implicate cell cooperation in the growth arrest of transformed melanocytes.
(2020) Elife. 9,
Pubmed
Elife
PMC Article
Integrated Single-Cell Transcriptomics and Chromatin Accessibility Analysis Reveals Regulators of Mammary Epithelial Cell Identity.
(2020) Cell Rep. 33, 108273
Pubmed
Cell Rep
PMC Article
Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers.
(2020) Cancers (Basel). 12,
Pubmed
Cancers (Basel)
PMC Article
Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states.
(2020) Nat Commun. 11, 5434
Pubmed
Nat Commun
PMC Article
DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks.
(2020) Neurocomputing. 410, 202-210
Pubmed
Neurocomputing
PMC Article
Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data.
(2020) Nucleic Acids Res. 48, 9505-9520
Pubmed
Nucleic Acids Res
PMC Article
Lgr4 Deletion Delays the Hair Cycle and Inhibits the Activation of Hair Follicle Stem Cells.
(2020) J Invest Dermatol. 140, 1706-1712.e4
Pubmed
J Invest Dermatol
PMC Article
Single cell transcriptomics of human epidermis identifies basal stem cell transition states.
(2020) Nat Commun. 11, 4239
Pubmed
Nat Commun
PMC Article
A multiscale model of virus pandemic: Heterogeneous interactive entities in a globally connected world.
(2020) Math Models Methods Appl Sci. 30, 1591-1651
Pubmed
Math Models Methods Appl Sci
PMC Article
Cycling Stem Cells Are Radioresistant and Regenerate the Intestine.
(2020) Cell Rep. 32, 107952
Pubmed
Cell Rep
PMC Article
Scaling a Dpp Morphogen Gradient through Feedback Control of Receptors and Co-receptors.
(2020) Dev Cell. 53, 724-739.e14
Pubmed
Dev Cell
PMC Article
Inferring spatial and signaling relationships between cells from single cell transcriptomic data.
(2020) Nat Commun. 11, 2084
Pubmed
Nat Commun
PMC Article
Molecular flexibility of DNA as a key determinant of RAD51 recruitment.
(2020) EMBO J. 39, e103002
Pubmed
EMBO J
PMC Article
Circadian control of interferon-sensitive gene expression in murine skin.
(2020) Proc Natl Acad Sci U S A. 117, 5761-5771
Pubmed
Proc Natl Acad Sci U S A
PMC Article
Epithelial Migration and Non-adhesive Periderm Are Required for Digit Separation during Mammalian Development.
(2020) Dev Cell. 52, 764-778.e4
Pubmed
Dev Cell
PMC Article
Complex Far-Field Geometries Determine the Stability of Solid Tumor Growth with Chemotaxis.
(2020) Bull Math Biol. 82, 39
Pubmed
Bull Math Biol
PMC Article
Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics.
(2020) Cell Rep. 30, 3932-3947.e6
Pubmed
Cell Rep
PMC Article
scAI: an unsupervised approach for the integrative analysis of parallel single-cell transcriptomic and epigenomic profiles.
(2020) Genome Biol. 21, 25
Pubmed
Genome Biol
PMC Article
Kernel Differential Subgraph Analysis to Reveal the Key Period Affecting Glioblastoma.
(2020) Biomolecules. 10,
Pubmed
Biomolecules
PMC Article
A HYBRID METHOD FOR STIFF REACTION-DIFFUSION EQUATIONS.
(2019) Discrete Continuous Dyn Syst Ser B. 24, 6387-6417
Pubmed
Discrete Continuous Dyn Syst Ser B
PMC Article
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
STOCHASTIC DYNAMICS OF CELL LINEAGE IN TISSUE HOMEOSTASIS.
(2019) Discrete Continuous Dyn Syst Ser B. 24, 3971-3994
Pubmed
Discrete Continuous Dyn Syst Ser B
PMC Article
Bidirectional sliding of two parallel microtubules generated by multiple identical motors.
(2019) J Math Biol. 79, 571-594
Pubmed
J Math Biol
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
Cell lineage and communication network inference via optimization for single-cell transcriptomics.
(2019) Nucleic Acids Res. 47, e66
Pubmed
Nucleic Acids Res
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
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
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
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
An Ovol2-Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation.
(2019) EMBO Rep. 20,
Pubmed
EMBO Rep
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
Stem cells: a window of opportunity in low-dimensional EMT space.
(2018) Oncotarget. 9, 31790-31791
Pubmed
Oncotarget
PMC Article
Extracting multivalent detachment rates from heterogeneous nanoparticle populations.
(2018) Phys Chem Chem Phys. 20, 21430-21440
Pubmed
Phys Chem Chem Phys
DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation.
(2018) Stem Cell Reports. 10, 1793-1806
Pubmed
Stem Cell Reports
PMC Article
Landscape reveals critical network structures for sharpening gene expression boundaries.
(2018) BMC Syst Biol. 12, 67
Pubmed
BMC Syst Biol
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
Mean-Independent Noise Control of Cell Fates via Intermediate States.
(2018) iScience. 3, 11-20
Pubmed
iScience
PMC Article
Multiscale modeling of glioblastoma.
(2018) Transl Cancer Res. 7, S96-S98
Pubmed
Transl Cancer Res
PMC Article
Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial-Mesenchymal Transition From Single-Cell Transcriptomic Data.
(2020) Front Genet. 11, 604585
Pubmed
Front Genet
PMC Article
Machine Learning of Single Cell Transcriptomic Data From anti-PD-1 Responders and Non-responders Reveals Distinct Resistance Mechanisms in Skin Cancers and PDAC.
(2021) Front Genet. 12, 806457
Pubmed
Front Genet
PMC Article
DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data.
(2021) Front Genet. 12, 636743
Pubmed
Front Genet
PMC Article
Revealing Dynamic Mechanisms of Cell Fate Decisions From Single-Cell Transcriptomic Data.
(2019) Front Genet. 10, 1280
Pubmed
Front Genet
PMC Article