Recent publications from CMCF.
CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics.
(2024) Nat Protoc.
Pubmed
Nat Protoc
-Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-Derived iPSC Differentiation Support Cell Type and Lineage-Specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency.
(2024) Cells. 13,
Pubmed
Cells
PMC Article
Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data.
(2024) Biophys J. 123, 2849-2859
Pubmed
Biophys J
PMC Article
Leveraging gene correlations in single cell transcriptomic data.
(2024) BMC Bioinformatics. 25, 305
Pubmed
BMC Bioinformatics
PMC Article
The inherent fragility of collective proliferative control.
(2024) bioRxiv.
Pubmed
bioRxiv
PMC Article
Cohesin prevents cross-domain gene coactivation.
(2024) Nat Genet. 56, 1654-1664
Pubmed
Nat Genet
PMC Article
Hydrogel crosslinking modulates macrophages, fibroblasts, and their communication, during wound healing.
(2024) Nat Commun. 15, 6820
Pubmed
Nat Commun
PMC Article
Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics.
(2024) Nat Methods.
Pubmed
Nat Methods
Polyunsaturated Fatty Acid - mediated Cellular Rejuvenation for Reversing Age-related Vision Decline.
(2024) bioRxiv.
Pubmed
bioRxiv
PMC Article
Integrated Single-Cell Analysis Reveals Spatially and Temporally Dynamic Heterogeneity in Fibroblast States during Wound Healing.
(2024) J Invest Dermatol.
Pubmed
J Invest Dermatol
DRML-Ensemble: drug repurposing method based on feature construction of multi-layer ensemble.
(2024) J Mol Model. 30, 296
Pubmed
J Mol Model
Spatial transition tensor of single cells.
(2024) Nat Methods. 21, 1053-1062
Pubmed
Nat Methods
PMC Article
Parsing patterns: Emerging roles of tissue self-organization in health and disease.
(2024) Cell. 187, 3165-3186
Pubmed
Cell
PMC Article
Interruption of the intratumor CD8 T cell:Treg crosstalk improves the efficacy of PD-1 immunotherapy.
(2024) Cancer Cell. 42, 1051-1066.e7
Pubmed
Cancer Cell
PMC Article
tauFisher predicts circadian time from a single sample of bulk and single-cell pseudobulk transcriptomic data.
(2024) Nat Commun. 15, 3840
Pubmed
Nat Commun
PMC Article
Emx2 underlies the development and evolution of marsupial gliding membranes.
(2024) Nature. 629, 127-135
Pubmed
Nature
PMC Article
PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration.
(2024) PLoS Comput Biol. 20, e1011855
Pubmed
PLoS Comput Biol
PMC Article
A new method to experimentally quantify dynamics of initial protein-protein interactions.
(2024) Commun Biol. 7, 311
Pubmed
Commun Biol
PMC Article
Gastrulation-stage gene expression in mouse embryos foreshadows the development of syndromic birth defects.
(2024) Sci Adv. 10, eadl4239
Pubmed
Sci Adv
PMC Article
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification.
(2024) Elife. 12,
Pubmed
Elife
PMC Article
A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns.
(2023) Nat Ecol Evol. 7, 2143-2159
Pubmed
Nat Ecol Evol
PMC Article
Leveraging gene correlations in single cell transcriptomic data.
(2023) bioRxiv.
Pubmed
bioRxiv
PMC Article
NeST: nested hierarchical structure identification in spatial transcriptomic data.
(2023) Nat Commun. 14, 6554
Pubmed
Nat Commun
PMC Article
The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics.
(2023) Semin Cancer Biol. 95, 42-51
Pubmed
Semin Cancer Biol
PMC Article
A Roadmap for a Consensus Human Skin Cell Atlas and Single-Cell Data Standardization.
(2023) J Invest Dermatol. 143, 1667-1677
Pubmed
J Invest Dermatol
PMC Article
Theoretical and computational tools to model multistable gene regulatory networks.
(2023) Rep Prog Phys. 86,
Pubmed
Rep Prog Phys
PMC Article
Epithelial-Mesenchymal Plasticity and Endothelial-Mesenchymal Transition in Cutaneous Wound Healing.
(2023) Cold Spring Harb Perspect Biol. 15,
Pubmed
Cold Spring Harb Perspect Biol
PMC Article
Ovol1/2 loss-induced epidermal defects elicit skin immune activation and alter global metabolism.
(2023) EMBO Rep. 24, e56214
Pubmed
EMBO Rep
PMC Article
Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis.
(2023) Sci Adv. 9, eadd9984
Pubmed
Sci Adv
PMC Article
Signalling by senescent melanocytes hyperactivates hair growth.
(2023) Nature. 618, 808-817
Pubmed
Nature
PMC Article
Author Correction: MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses.
(2023) Sci Data. 10, 420
Pubmed
Sci Data
PMC Article
exFINDER: identify external communication signals using single-cell transcriptomics data.
(2023) Nucleic Acids Res. 51, e58
Pubmed
Nucleic Acids Res
PMC Article
A human vascularized microtumor model of patient-derived colorectal cancer recapitulates clinical disease.
(2023) Transl Res. 255, 97-108
Pubmed
Transl Res
PMC Article
Single-cell transcriptomics of human-skin-equivalent organoids.
(2023) Cell Rep. 42, 112511
Pubmed
Cell Rep
PMC Article
Quantifying the relationship between cell proliferation and morphology during development of the face.
(2023) bioRxiv.
Pubmed
bioRxiv
PMC Article
Phase field modeling and computation of vesicle growth or shrinkage.
(2023) J Math Biol. 86, 97
Pubmed
J Math Biol
PMC Article
Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation.
(2023) Cell Syst. 14, 252-257
Pubmed
Cell Syst
PMC Article
Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy.
(2023) Elife. 12,
Pubmed
Elife
PMC Article
Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis.
(2023) bioRxiv.
Pubmed
bioRxiv
PMC Article
Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis.
(2023) Nat Genet. 55, 595-606
Pubmed
Nat Genet
PMC Article
Targeting the chromatin effector Pygo2 promotes cytotoxic T cell responses and overcomes immunotherapy resistance in prostate cancer.
(2023) Sci Immunol. 8, eade4656
Pubmed
Sci Immunol
PMC Article
Three-dimensional numerical study on wrinkling of vesicles in elongation flow based on the immersed boundary method.
(2023) Phys Rev E. 107, 035103
Pubmed
Phys Rev E
exFINDER: identify external communication signals using single-cell transcriptomics data.
(2023) bioRxiv.
Pubmed
bioRxiv
PMC Article
Screening cell-cell communication in spatial transcriptomics via collective optimal transport.
(2023) Nat Methods. 20, 218-228
Pubmed
Nat Methods
PMC Article
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat.
(2023) Nat Commun. 14, 1128
Pubmed
Nat Commun
PMC Article
The Liver Tumor Segmentation Benchmark (LiTS).
(2023) Med Image Anal. 84, 102680
Pubmed
Med Image Anal
PMC Article
Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat.
(2023) bioRxiv.
Pubmed
bioRxiv
PMC Article
Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin.
(2023) Cell Rep. 42, 111994
Pubmed
Cell Rep
PMC Article
Single-cell transcriptomic analysis reveals diversity within mammalian spinal motor neurons.
(2023) Nat Commun. 14, 46
Pubmed
Nat Commun
PMC Article
Decreasing dosage partially corrects embryonic growth and brain transcriptome phenotypes in embryos.
(2022) Sci Adv. 8, eadd4136
Pubmed
Sci Adv
PMC Article
Mathematical modeling of cancer immunotherapy for personalized clinical translation.
(2022) Nat Comput Sci. 2, 785-796
Pubmed
Nat Comput Sci
PMC Article
Integrated analysis of multimodal single-cell data with structural similarity.
(2022) Nucleic Acids Res. 50, e121
Pubmed
Nucleic Acids Res
PMC Article
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.
(2022) Mol Syst Biol. 18, e11176
Pubmed
Mol Syst Biol
PMC Article
IL-17A Promotes Psoriasis-Associated Keratinocyte Proliferation through ACT1-Dependent Activation of YAP-AREG Axis.
(2022) J Invest Dermatol. 142, 2343-2352
Pubmed
J Invest Dermatol
Wound healing in aged skin exhibits systems-level alterations in cellular composition and cell-cell communication.
(2022) Cell Rep. 40, 111155
Pubmed
Cell Rep
PMC Article
Lepr mesenchymal cells sense diet to modulate intestinal stem/progenitor cells via Leptin-Igf1 axis.
(2022) Cell Res. 32, 670-686
Pubmed
Cell Res
PMC Article
Tumor growth towards lower extracellular matrix conductivity regions under Darcy's Law and steady morphology.
(2022) J Math Biol. 85, 5
Pubmed
J Math Biol
PMC Article
Multimodal analyses of vitiligo skin identify tissue characteristics of stable disease.
(2022) JCI Insight. 7,
Pubmed
JCI Insight
PMC Article
DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data.
(2022) Brief Bioinform. 23,
Pubmed
Brief Bioinform
PMC Article
Hedgehog signaling reprograms hair follicle niche fibroblasts to a hyper-activated state.
(2022) Dev Cell. 57, 1758-1775.e7
Pubmed
Dev Cell
PMC Article
Identifying multicellular spatiotemporal organization of cells with SpaceFlow.
(2022) Nat Commun. 13, 4076
Pubmed
Nat Commun
PMC Article
DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data.
(2022) Sci Adv. 8, eabl7393
Pubmed
Sci Adv
PMC Article
Magnitude and breadth of antibody cross-reactivity induced by recombinant influenza hemagglutinin trimer vaccine is enhanced by combination adjuvants.
(2022) Sci Rep. 12, 9198
Pubmed
Sci Rep
PMC Article
Single-cell analysis of human basal cell carcinoma reveals novel regulators of tumor growth and the tumor microenvironment.
(2022) Sci Adv. 8, eabm7981
Pubmed
Sci Adv
PMC Article
MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses.
(2022) Sci Data. 9, 230
Pubmed
Sci Data
PMC Article
Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT.
(2022) Cell Rep Methods. 2, 100207
Pubmed
Cell Rep Methods
PMC Article
Spatial dynamics of feedback and feedforward regulation in cell lineages.
(2022) PLoS Comput Biol. 18, e1010039
Pubmed
PLoS Comput Biol
PMC Article
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
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
Zebrafish airinemes optimize their shape between ballistic and diffusive search.
(2022) Elife. 11,
Pubmed
Elife
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
Modeling of Tumor Growth with Input from Patient-Specific Metabolomic Data.
(2022) Ann Biomed Eng. 50, 314-329
Pubmed
Ann Biomed Eng
PMC Article
Deciphering tissue structure and function using spatial transcriptomics.
(2022) Commun Biol. 5, 220
Pubmed
Commun Biol
PMC Article
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
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
PMC Article
Dormant reporter-marked basal stem/progenitor cells contribute to mammary lobuloalveoli formation.
(2022) iScience. 25, 103982
Pubmed
iScience
PMC Article
Defining mammary basal cell transcriptional states using single-cell RNA-sequencing.
(2022) Sci Rep. 12, 4893
Pubmed
Sci Rep
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
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
Coordinate control of basal epithelial cell fate and stem cell maintenance by core EMT transcription factor Zeb1.
(2022) Cell Rep. 38, 110240
Pubmed
Cell Rep
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
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
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
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
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
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
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
Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics.
(2021) Nat Commun. 12, 5609
Pubmed
Nat Commun
PMC Article
Modeling the effects of EMT-immune dynamics on carcinoma disease progression.
(2021) Commun Biol. 4, 983
Pubmed
Commun Biol
PMC Article
Continuity Scaling: A Rigorous Framework for Detecting and Quantifying Causality Accurately.
(2022) Research (Wash D C). 2022, 9870149
Pubmed
Research (Wash D C)
PMC Article
Reconstructing growth and dynamic trajectories from single-cell transcriptomics data.
(2024) Nat Mach Intell. 6, 25-39
Pubmed
Nat Mach Intell
PMC Article
Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments.
(2022) PLoS One. 17, e0275804
Pubmed
PLoS One
PMC Article
Dissecting Spatiotemporal Structures in Spatial Transcriptomics via Diffusion-Based Adversarial Learning.
(2024) Research (Wash D C). 7, 0390
Pubmed
Research (Wash D C)
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
Analyzing network diversity of cell-cell interactions in COVID-19 using single-cell transcriptomics.
(2022) Front Genet. 13, 948508
Pubmed
Front Genet
PMC Article