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Recent publications from CMCF.

Cao Y, Fu L, Wu J, Peng Q, Nie Q, Zhang J and Xie X. Integrated analysis of multimodal single-cell data with structural similarity. (2022) Nucleic Acids Res. Pubmed Nucleic Acids Res
Yu Z, Yu Q, Xu H, Dai X, Yu Y, Cui L, Chen Y, Gu J, Zhang X, Guo C and Shi Y. 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
Vu R, Jin S, Sun P, Haensel D, Nguyen QH, Dragan M, Kessenbrock K, Nie Q and Dai X. Wound healing in aged skin exhibits systems-level alterations in cellular composition and cell-cell communication. (2022) Cell Rep. 40, 111155 Pubmed Cell Rep
Shiu J, Zhang L, Lentsch G, Flesher JL, Jin S, Polleys C, Jo SJ, Mizzoni C, Mobasher P, Kwan J, Rius-Diaz F, Tromberg BJ, Georgakoudi I, Nie Q, Balu M and Ganesan AK. Multimodal analyses of vitiligo skin identify tissue characteristics of stable disease. (2022) JCI Insight. 7, Pubmed JCI Insight PMC Article
Karikomi M, Zhou P and Nie Q. 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
Liu Y, Guerrero-Juarez CF, Xiao F, Shettigar NU, Ramos R, Kuan CH, Lin YC, de Jesus Martinez Lomeli L, Park JM, Oh JW, Liu R, Lin SJ, Tartaglia M, Yang RB, Yu Z, Nie Q, Li J and Plikus MV. Hedgehog signaling reprograms hair follicle niche fibroblasts to a hyper-activated state. (2022) Dev Cell. 57, 1758-1775.e7 Pubmed Dev Cell PMC Article
Zheng X, Zhao K, Jackson T and Lowengrub J. 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
Ren H, Walker BL, Cang Z and Nie Q. Identifying multicellular spatiotemporal organization of cells with SpaceFlow. (2022) Nat Commun. 13, 4076 Pubmed Nat Commun PMC Article
Deng M, Guerrero-Juarez CF, Sheng X, Xu J, Wu X, Yao K, Li M, Yang X, Li G, Xiao J, Liu X, Wu K, Ren F, Nie Q, Plikus MV, Yu Z and Lv C. 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
Hernandez-Davies JE, Dollinger EP, Pone EJ, Felgner J, Liang L, Strohmeier S, Jan S, Albin TJ, Jain A, Nakajima R, Jasinskas A, Krammer F, Esser-Kahn A, Felgner PL, Nie Q and Davies DH. 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
Guerrero-Juarez CF, Lee GH, Liu Y, Wang S, Karikomi M, Sha Y, Chow RY, Nguyen TTL, Iglesias VS, Aasi S, Drummond ML, Nie Q, Sarin K and Atwood SX. 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
Zhang L, Zhang J and Nie Q. 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
Taylor R, Allard J and Read EL. 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
Uhl P, Lowengrub J, Komarova N and Wodarz D. Spatial dynamics of feedback and feedforward regulation in cell lineages. (2022) PLoS Comput Biol. 18, e1010039 Pubmed PLoS Comput Biol PMC Article
Johnston KG, Grieco SF, Zhang H, Jin S, Xu X and Nie Q. Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT. (2022) Cell Rep Methods. 2, 100207 Pubmed Cell Rep Methods PMC Article
Devine J, Vidal-García M, Liu W, Neves A, Lo Vercio LD, Green RM, Richbourg HA, Marchini M, Unger CM, Nickle AC, Radford B, Young NM, Gonzalez PN, Schuler RE, Bugacov A, Rolian C, Percival CJ, Williams T, Niswander L, Calof AL, Lander AD, Visel A, Jirik FR, Cheverud JM, Klein OD, Birnbaum RY, Merrill AE, Ackermann RR, Graf D, Hemberger M, Dean W, Forkert ND, Murray SA, Westerberg H, Marcucio RS and Hallgrímsson B. MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. (2022) Sci Data. 9, 230 Pubmed Sci Data PMC Article
Park S, Kim H, Wang Y, Eom DS and Allard J. Zebrafish airinemes optimize their shape between ballistic and diffusive search. (2022) Elife. 11, Pubmed Elife PMC Article
Hou JW, Ma HF, He D, Sun J, Nie Q and Lin W. 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
Lipková J, Menze B, Wiestler B, Koumoutsakos P and Lowengrub JS. 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
Gutierrez G, Sun P, Han Y and Dai X. Defining mammary basal cell transcriptional states using single-cell RNA-sequencing. (2022) Sci Rep. 12, 4893 Pubmed Sci Rep PMC Article
Liu R, Hu H, McNeil M, Xu J, Bi X, Lou P, Guerrero-Juarez CF, Dai X, Plikus MV, Shuai J, Yu Z and Lv C. Dormant reporter-marked basal stem/progenitor cells contribute to mammary lobuloalveoli formation. (2022) iScience. 25, 103982 Pubmed iScience PMC Article
Dragan M, Sun P, Chen Z, Ma X, Vu R, Shi Y, Villalta SA and Dai X. 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
Miller HA, Lowengrub J and Frieboes HB. Modeling of Tumor Growth with Input from Patient-Specific Metabolomic Data. (2022) Ann Biomed Eng. 50, 314-329 Pubmed Ann Biomed Eng
Goyette J, Depoil D, Yang Z, Isaacson SA, Allard J, van der Merwe PA, Gaus K, Dustin ML and Dushek O. 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
Walker BL, Cang Z, Ren H, Bourgain-Chang E and Nie Q. Deciphering tissue structure and function using spatial transcriptomics. (2022) Commun Biol. 5, 220 Pubmed Commun Biol PMC Article
Fu L, Cao Y, Wu J, Peng Q, Nie Q and Xie X. UFold: fast and accurate RNA secondary structure prediction with deep learning. (2022) Nucleic Acids Res. 50, e14 Pubmed Nucleic Acids Res PMC Article
Sharrock AV, Mulligan TS, Hall KR, Williams EM, White DT, Zhang L, Emmerich K, Matthews F, Nimmagadda S, Washington S, Le KD, Meir-Levi D, Cox OL, Saxena MT, Calof AL, Lopez-Burks ME, Lander AD, Ding D, Ji H, Ackerley DF and Mumm JS. 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
Han Y, Villarreal-Ponce A, Gutierrez G, Nguyen Q, Sun P, Wu T, Sui B, Berx G, Brabletz T, Kessenbrock K, Zeng YA, Watanabe K and Dai X. 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
Shiu J and Lander AD. When oncogenes do not cause cancer. (2021) Elife. 10, Pubmed Elife PMC Article
McNeil M, Han Y, Sun P, Watanabe K, Jiang J, Chen N, Yu Z, Zhou B and Dai X. 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
Yan H, Ramirez-Guerrero D, Lowengrub J and Wu M. Stress generation, relaxation and size control in confined tumor growth. (2021) PLoS Comput Biol. 17, e1009701 Pubmed PLoS Comput Biol PMC Article
Mehrabi M, Morris TA, Cang Z, Nguyen CHH, Sha Y, Asad MN, Khachikyan N, Greene TL, Becker DM, Nie Q, Zaragoza MV and Grosberg A. 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
Sun P, Han Y, Plikus M and Dai X. 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
Chinn CA, Ren H, Morival JLP, Nie Q, Wood MA and Downing TL. 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
Tatarakis D, Cang Z, Wu X, Sharma PP, Karikomi M, MacLean AL, Nie Q and Schilling TF. 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
Bocci F, Zhou P and Nie Q. 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
Lang J, Nie Q and Li C. Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition. (2021) Biophys J. 120, 4484-4500 Pubmed Biophys J PMC Article
Zhou P, Wang S, Li T and Nie Q. Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics. (2021) Nat Commun. 12, 5609 Pubmed Nat Commun PMC Article
Wang MX, Lander A and Lai PY. 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
Bergman DR, Karikomi MK, Yu M, Nie Q and MacLean AL. Modeling the effects of EMT-immune dynamics on carcinoma disease progression. (2021) Commun Biol. 4, 983 Pubmed Commun Biol PMC Article
Cao Y, Fu L, Wu J, Peng Q, Nie Q, Zhang J and Xie X. SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration. (2021) Bioinformatics. 37, i317-i326 Pubmed Bioinformatics PMC Article
Zhao W, Qiao L, Yan S, Nie Q and Zhang L. Mathematical modeling of histone modifications reveals the formation mechanism and function of bivalent chromatin. (2021) iScience. 24, 102732 Pubmed iScience PMC Article
Zhao X, Chen J, Xiao P, Feng J, Nie Q and Zhao XM. 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
MacLean AL and Nie Q. The diverse landscape of modeling in single-cell biology. (2021) Phys Biol. 18, Pubmed Phys Biol
Anjos PHA, Zhao M, Lowengrub J, Bao W and Li S. Controlling fingering instabilities in Hele-Shaw flows in the presence of wetting film effects. (2021) Phys Rev E. 103, 063105 Pubmed Phys Rev E
Sun P, Vu R, Dragan M, Haensel D, Gutierrez G, Nguyen Q, Greenberg E, Chen Z, Wu J, Atwood S, Pearlman E, Shi Y, Han W, Kessenbrock K and Dai X. OVOL1 Regulates Psoriasis-Like Skin Inflammation and Epidermal Hyperplasia. (2021) J Invest Dermatol. 141, 1542-1552 Pubmed J Invest Dermatol PMC Article
Almet AA, Cang Z, Jin S and Nie Q. 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
Qiu Y, Fung L, Schilling TF and Nie Q. Multiple morphogens and rapid elongation promote segmental patterning during development. (2021) PLoS Comput Biol. 17, e1009077 Pubmed PLoS Comput Biol PMC Article
Clemens L, Kutuzov M, Bayer KV, Goyette J, Allard J and Dushek O. Determination of the molecular reach of the protein tyrosine phosphatase SHP-1. (2021) Biophys J. 120, 2054-2066 Pubmed Biophys J PMC Article
Bovyn M, Janakaloti Narayanareddy BR, Gross S and Allard J. 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
Hachey SJ, Movsesyan S, Nguyen QH, Burton-Sojo G, Tankazyan A, Wu J, Hoang T, Zhao D, Wang S, Hatch MM, Celaya E, Gomez S, Chen GT, Davis RT, Nee K, Pervolarakis N, Lawson DA, Kessenbrock K, Lee AP, Lowengrub J, Waterman ML and Hughes CCW. 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
Sun X, Zhang J and Nie Q. 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
Cang Z, Wang Y, Wang Q, Cho KWY, Holmes W and Nie Q. 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
Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH, Myung P, Plikus MV and Nie Q. Inference and analysis of cell-cell communication using CellChat. (2021) Nat Commun. 12, 1088 Pubmed Nat Commun PMC Article
Zhang L and Nie Q. scMC learns biological variation through the alignment of multiple single-cell genomics datasets. (2021) Genome Biol. 22, 10 Pubmed Genome Biol PMC Article
Clemens L, Dushek O and Allard J. Intrinsic Disorder in the T Cell Receptor Creates Cooperativity and Controls ZAP70 Binding. (2021) Biophys J. 120, 379-392 Pubmed Biophys J PMC Article
Lomeli LM, Iniguez A, Tata P, Jena N, Liu ZY, Van Etten R, Lander AD, Shahbaba B, Lowengrub JS and Minin VN. Optimal experimental design for mathematical models of haematopoiesis. (2021) J R Soc Interface. 18, 20200729 Pubmed J R Soc Interface PMC Article
Weiss LD, van den Driessche P, Lowengrub JS, Wodarz D and Komarova NL. 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
Fu L, Zhang L, Dollinger E, Peng Q, Nie Q and Xie X. Predicting transcription factor binding in single cells through deep learning. (2020) Sci Adv. 6, Pubmed Sci Adv
Villarreal-Ponce A, Tiruneh MW, Lee J, Guerrero-Juarez CF, Kuhn J, David JA, Dammeyer K, Mc Kell R, Kwong J, Rabbani PS, Nie Q and Ceradini DJ. Keratinocyte-Macrophage Crosstalk by the Nrf2/Ccl2/EGF Signaling Axis Orchestrates Tissue Repair. (2020) Cell Rep. 33, 108417 Pubmed Cell Rep PMC Article
Xie J, Yang F, Wang J, Karikomi M, Yin Y, Sun J, Wen T and Nie Q. DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks. (2020) Neurocomputing. 410, 202-210 Pubmed Neurocomputing PMC Article
Pervolarakis N, Nguyen QH, Williams J, Gong Y, Gutierrez G, Sun P, Jhutty D, Zheng GXY, Nemec CM, Dai X, Watanabe K and Kessenbrock K. 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
Lv C, Li F, Li X, Tian Y, Zhang Y, Sheng X, Song Y, Meng Q, Yuan S, Luan L, Andl T, Feng X, Jiao B, Xu M, Plikus MV, Dai X, Lengner C, Cui W, Ren F, Shuai J, Millar SE and Yu Z. 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
Ruiz-Vega R, Chen CF, Razzak E, Vasudeva P, Krasieva TB, Shiu J, Caldwell MG, Yan H, Lowengrub J, Ganesan AK and Lander AD. Dynamics of nevus development implicate cell cooperation in the growth arrest of transformed melanocytes. (2020) Elife. 9, Pubmed Elife PMC Article
Lin Z, Jin S, Chen J, Li Z, Lin Z, Tang L, Nie Q and Andersen B. 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
Dollinger E, Bergman D, Zhou P, Atwood SX and Nie Q. Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers. (2020) Cancers (Basel). 12, Pubmed Cancers (Basel) PMC Article
Song Y, Guerrero-Juarez CF, Chen Z, Tang Y, Ma X, Lv C, Bi X, Deng M, Bu L, Tian Y, Liu R, Zhao R, Xu J, Sheng X, Du S, Liu Y, Zhu Y, Shan SJ, Chen HD, Zhao Y, Zhou G, Shuai J, Ren F, Xue L, Ying Z, Dai X, Lengner CJ, Andersen B, Plikus MV, Nie Q and Yu Z. 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
Sha Y, Wang S, Zhou P and Nie Q. 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
Ren X, Xia W, Xu P, Shen H, Dai X, Liu M, Shi Y, Ye X and Dang Y. 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
Wang S, Drummond ML, Guerrero-Juarez CF, Tarapore E, MacLean AL, Stabell AR, Wu SC, Gutierrez G, That BT, Benavente CA, Nie Q and Atwood SX. Single cell transcriptomics of human epidermis identifies basal stem cell transition states. (2020) Nat Commun. 11, 4239 Pubmed Nat Commun PMC Article
Bellomo N, Bingham R, Chaplain MAJ, Dosi G, Forni G, Knopoff DA, Lowengrub J, Twarock R and Virgillito ME. 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
Sheng X, Lin Z, Lv C, Shao C, Bi X, Deng M, Xu J, Guerrero-Juarez CF, Li M, Wu X, Zhao R, Yang X, Li G, Liu X, Wang Q, Nie Q, Cui W, Gao S, Zhang H, Liu Z, Cong Y, Plikus MV, Lengner CJ, Andersen B, Ren F and Yu Z. Cycling Stem Cells Are Radioresistant and Regenerate the Intestine. (2020) Cell Rep. 32, 107952 Pubmed Cell Rep PMC Article
Zhu Y, Qiu Y, Chen W, Nie Q and Lander AD. 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
Cang Z and Nie Q. Inferring spatial and signaling relationships between cells from single cell transcriptomic data. (2020) Nat Commun. 11, 2084 Pubmed Nat Commun PMC Article
Paoletti F, El-Sagheer AH, Allard J, Brown T, Dushek O and Esashi F. Molecular flexibility of DNA as a key determinant of RAD51 recruitment. (2020) EMBO J. 39, e103002 Pubmed EMBO J PMC Article
Lander AD, Nie Q, Sanchez-Tapia C, Simonyan A and Wan FYM. Regulatory feedback on receptor and non-receptor synthesis for robust signaling. (2020) Dev Dyn. 249, 383-409 Pubmed Dev Dyn
Kashgari G, Meinecke L, Gordon W, Ruiz B, Yang J, Ma AL, Xie Y, Ho H, Plikus MV, Nie Q, Jester JV and Andersen B. 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
Greenberg EN, Marshall ME, Jin S, Venkatesh S, Dragan M, Tsoi LC, Gudjonsson JE, Nie Q, Takahashi JS and Andersen B. 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
Lu MJ, Liu C, Lowengrub J and Li S. 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
Haensel D, Jin S, Sun P, Cinco R, Dragan M, Nguyen Q, Cang Z, Gong Y, Vu R, MacLean AL, Kessenbrock K, Gratton E, Nie Q and Dai X. 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
Xie J, Sun J, Feng J, Yang F, Wang J, Wen T and Nie Q. Kernel Differential Subgraph Analysis to Reveal the Key Period Affecting Glioblastoma. (2020) Biomolecules. 10, Pubmed Biomolecules PMC Article
Jin S, Zhang L and Nie Q. 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
Qiu Y, Chen W and Nie Q. 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
Sun Y, Jin S, Lin X, Chen L, Qiao X, Jiang L, Zhou P, Johnston KG, Golshani P, Nie Q, Holmes TC, Nitz DA and Xu X. CA1-projecting subiculum neurons facilitate object-place learning. (2019) Nat Neurosci. 22, 1857-1870 Pubmed Nat Neurosci PMC Article
Zhang Y, Clemens L, Goyette J, Allard J, Dushek O and Isaacson SA. 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
Qiao L, Zhao W, Tang C, Nie Q and Zhang L. Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation. (2019) Cell Syst. 9, 271-285.e7 Pubmed Cell Syst PMC Article
Nie Q and Plikus MV. Equal opportunities in stemness. (2019) Nat Cell Biol. 21, 921-923 Pubmed Nat Cell Biol PMC Article
Qiu Y, Chen W and Nie Q. 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
Allard J, Doumic M, Mogilner A and Oelz D. Bidirectional sliding of two parallel microtubules generated by multiple identical motors. (2019) J Math Biol. 79, 571-594 Pubmed J Math Biol
Wang S, Karikomi M, MacLean AL and Nie Q. Cell lineage and communication network inference via optimization for single-cell transcriptomics. (2019) Nucleic Acids Res. 47, e66 Pubmed Nucleic Acids Res PMC Article
Liu K, Lowengrub J and Allard J. 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
Liu K, Chu B, Newby J, Read EL, Lowengrub J and Allard J. 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
Wang Y, Guerrero-Juarez CF, Qiu Y, Du H, Chen W, Figueroa S, Plikus MV and Nie Q. A multiscale hybrid mathematical model of epidermal-dermal interactions during skin wound healing. (2019) Exp Dermatol. 28, 493-502 Pubmed Exp Dermatol PMC Article
Guerrero-Juarez CF, Dedhia PH, Jin S, Ruiz-Vega R, Ma D, Liu Y, Yamaga K, Shestova O, Gay DL, Yang Z, Kessenbrock K, Nie Q, Pear WS, Cotsarelis G and Plikus MV. 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
Maseda F, Cang Z and Nie Q. DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data. (2021) Front Genet. 12, 636743 Pubmed Front Genet PMC Article
Ying X, Leng SY, Ma HF, Nie Q, Lai YC and Lin W. 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
Liu R, Dollinger E and Nie Q. 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
Wang X, Almet AA and Nie Q. Analyzing network diversity of cell-cell interactions in COVID-19 using single-cell transcriptomics. (2022) Front Genet. 13, 948508 Pubmed Front Genet PMC Article
Sha Y, Wang S, Bocci F, Zhou P and Nie Q. 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
Zhang J, Nie Q and Zhou T. Revealing Dynamic Mechanisms of Cell Fate Decisions From Single-Cell Transcriptomic Data. (2019) Front Genet. 10, 1280 Pubmed Front Genet PMC Article