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Recent publications from CMCF.

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
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. Pubmed Biophys J
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
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
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
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
Bovyn M, Reddy B, Gross S and Allard J. Diffusion of kinesin motors on cargo can enhance binding and run lengths during intracellular transport. (2021) Mol Biol Cell. mbcE20100658 Pubmed Mol Biol Cell
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
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. (2020) J Invest Dermatol. Pubmed J Invest Dermatol
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
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. (2020) Brief Bioinform. Pubmed Brief Bioinform
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
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
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
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
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
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
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
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
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
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
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
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
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
Chen Y and Lowengrub JS. Tumor growth and calcification in evolving microenvironmental geometries. (2019) J Theor Biol. 463, 138-154 Pubmed J Theor Biol PMC Article
Sha Y, Haensel D, Gutierrez G, Du H, Dai X and Nie Q. Intermediate cell states in epithelial-to-mesenchymal transition. (2019) Phys Biol. 16, 021001 Pubmed Phys Biol PMC Article
Haensel D, Sun P, MacLean AL, Ma X, Zhou Y, Stemmler MP, Brabletz S, Berx G, Plikus MV, Nie Q, Brabletz T and Dai X. An Ovol2-Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation. (2019) EMBO Rep. 20, Pubmed EMBO Rep PMC Article
Sharma PP, MacLean AL, Meinecke L, Clouthier DE, Nie Q and Schilling TF. Transcriptomics reveals complex kinetics of dorsal-ventral patterning gene expression in the mandibular arch. (2019) Genesis. 57, e23275 Pubmed Genesis PMC Article
Koay EJ, Lee Y, Cristini V, Lowengrub JS, Kang Y, Lucas FAS, Hobbs BP, Ye R, Elganainy D, Almahariq M, Amer AM, Chatterjee D, Yan H, Park PC, Rios Perez MV, Li D, Garg N, Reiss KA, Yu S, Chauhan A, Zaid M, Nikzad N, Wolff RA, Javle M, Varadhachary GR, Shroff RT, Das P, Lee JE, Ferrari M, Maitra A, Taniguchi CM, Kim MP, Crane CH, Katz MH, Wang H, Bhosale P, Tamm EP and Fleming JB. 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
Meinecke L, Sharma PP, Du H, Zhang L, Nie Q and Schilling TF. 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
Pham K, Turian E, Liu K, Li S and Lowengrub J. Nonlinear studies of tumor morphological stability using a two-fluid flow model. (2018) J Math Biol. 77, 671-709 Pubmed J Math Biol
Wang M, Allard J and Haun JB. Extracting multivalent detachment rates from heterogeneous nanoparticle populations. (2018) Phys Chem Chem Phys. 20, 21430-21440 Pubmed Phys Chem Chem Phys
Nie Q. Stem cells: a window of opportunity in low-dimensional EMT space. (2018) Oncotarget. 9, 31790-31791 Pubmed Oncotarget PMC Article
Li C, Zhang L and Nie Q. Landscape reveals critical network structures for sharpening gene expression boundaries. (2018) BMC Syst Biol. 12, 67 Pubmed BMC Syst Biol PMC Article
MacLean AL, Hong T and Nie Q. 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
Jin S, MacLean AL, Peng T and Nie Q. 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
Lei J, Nie Q and Chen DB. 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
He Y, Zuo Q, Edwards J, Zhao K, Lei J, Cai W, Nie Q, Li B and Song J. DNA Methylation and Regulatory Elements during Chicken Germline Stem Cell Differentiation. (2018) Stem Cell Reports. 10, 1793-1806 Pubmed Stem Cell Reports PMC Article
Rackauckas C, Schilling T and Nie Q. Mean-Independent Noise Control of Cell Fates via Intermediate States. (2018) iScience. 3, 11-20 Pubmed iScience PMC Article
Yan H, Konstorum A and Lowengrub JS. 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
Haensel D and Dai X. 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
Yan H, Romero-López M, Benitez LI, Di K, Frieboes HB, Hughes CCW, Bota DA and Lowengrub JS. Multiscale modeling of glioblastoma. (2018) Transl Cancer Res. 7, S96-S98 Pubmed Transl Cancer Res PMC Article
Du H, Wang Y, Haensel D, Lee B, Dai X and Nie Q. Multiscale modeling of layer formation in epidermis. (2018) PLoS Comput Biol. 14, e1006006 Pubmed PLoS Comput Biol PMC Article
Yu P, Nie Q, Tang C and Zhang L. Nanog induced intermediate state in regulating stem cell differentiation and reprogramming. (2018) BMC Syst Biol. 12, 22 Pubmed BMC Syst Biol PMC Article
Xie J, Lu D, Li J, Wang J, Zhang Y, Li Y and Nie Q. Kernel differential subgraph reveals dynamic changes in biomolecular networks. (2018) J Bioinform Comput Biol. 16, 1750027 Pubmed J Bioinform Comput Biol
Konstorum A and Lowengrub JS. 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
Bergman JP, Bovyn MJ, Doval FF, Sharma A, Gudheti MV, Gross SP, Allard JF and Vershinin MD. 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
Mahlbacher G, Curtis LT, Lowengrub J and Frieboes HB. Mathematical modeling of tumor-associated macrophage interactions with the cancer microenvironment. (2018) J Immunother Cancer. 6, 10 Pubmed J Immunother Cancer PMC Article
Ye H, Zhou J, Er D, Price CC, Yu Z, Liu Y, Lowengrub J, Lou J, Liu Z and Shenoy VB. Toward a Mechanistic Understanding of Vertical Growth of van der Waals Stacked 2D Materials: A Multiscale Model and Experiments. (2017) ACS Nano. 11, 12780-12788 Pubmed ACS Nano
Guo Y, Nie Q, MacLean AL, Li Y, Lei J and Li S. Multiscale Modeling of Inflammation-Induced Tumorigenesis Reveals Competing Oncogenic and Oncoprotective Roles for Inflammation. (2017) Cancer Res. 77, 6429-6441 Pubmed Cancer Res
Raz-Ben Aroush D, Ofer N, Abu-Shah E, Allard J, Krichevsky O, Mogilner A and Keren K. Actin Turnover in Lamellipodial Fragments. (2017) Curr Biol. 27, 2963-2973.e14 Pubmed Curr Biol PMC Article
Dai X and Medzhitov R. Inflammation: Memory beyond immunity. (2017) Nature. 550, 460-461 Pubmed Nature
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. 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
Lee B, Watanabe K, Haensel D, Sui JY and Dai X. Overexpression of Transcription Factor Ovol2 in Epidermal Progenitor Cells Results in Skin Blistering. (2017) J Invest Dermatol. 137, 1805-1808 Pubmed J Invest Dermatol
Yan H, Romero-López M, Benitez LI, Di K, Frieboes HB, Hughes CCW, Bota DA and Lowengrub JS. 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
Wortman JC, Nahmad M, Zhang PC, Lander AD and Yu CC. 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
Wang Q, Oh JW, Lee HL, Dhar A, Peng T, Ramos R, Guerrero-Juarez CF, Wang X, Zhao R, Cao X, Le J, Fuentes MA, Jocoy SC, Rossi AR, Vu B, Pham K, Wang X, Mali NM, Park JM, Choi JH, Lee H, Legrand JMD, Kandyba E, Kim JC, Kim M, Foley J, Yu Z, Kobielak K, Andersen B, Khosrotehrani K, Nie Q and Plikus MV. A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning. (2017) Elife. 6, Pubmed Elife PMC Article
Liu K, Marple GR, Allard J, Li S, Veerapaneni S and Lowengrub J. Dynamics of a multicomponent vesicle in shear flow. (2017) Soft Matter. 13, 3521-3531 Pubmed Soft Matter PMC Article
Peng T, Liu L, MacLean AL, Wong CW, Zhao W and Nie Q. 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
Iniguez A and Allard J. 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
Li CJ, Hong T, Tung YT, Yen YP, Hsu HC, Lu YL, Chang M, Nie Q and Chen JA. MicroRNA filters Hox temporal transcription noise to confer boundary formation in the spinal cord. (2017) Nat Commun. 8, 14685 Pubmed Nat Commun PMC Article
Goyette J, Salas CS, Coker-Gordon N, Bridge M, Isaacson SA, Allard J and Dushek O. 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
Romero-López M, Trinh AL, Sobrino A, Hatch MM, Keating MT, Fimbres C, Lewis DE, Gershon PD, Botvinick EL, Digman M, Lowengrub JS and Hughes CC. 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
Lee M, Chen GT, Puttock E, Wang K, Edwards RA, Waterman ML and Lowengrub J. 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
Bryant D, Clemens L and Allard J. Computational simulation of formin-mediated actin polymerization predicts homologue-dependent mechanosensitivity. (2017) Cytoskeleton (Hoboken). 74, 29-39 Pubmed Cytoskeleton (Hoboken)
Barnhart EL, Allard J, Lou SS, Theriot JA and Mogilner A. Adhesion-Dependent Wave Generation in Crawling Cells. (2017) Curr Biol. 27, 27-38 Pubmed Curr Biol PMC Article
Holmes WR, Reyes de Mochel NS, Wang Q, Du H, Peng T, Chiang M, Cinquin O, Cho K and Nie Q. Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst. (2017) PLoS Comput Biol. 13, e1005320 Pubmed PLoS Comput Biol PMC Article
Wang Q, Holmes WR, Sosnik J, Schilling T and Nie Q. 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
Li A, Figueroa S, Jiang TX, Wu P, Widelitz R, Nie Q and Chuong CM. 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
Xu P, Dang Y, Wang L, Liu X, Ren X, Gu J, Liu M, Dai X and Ye X. 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
Lo WC, Zheng L and Nie Q. A hybrid continuous-discrete method for stochastic reaction-diffusion processes. (2016) R Soc Open Sci. 3, 160485 Pubmed R Soc Open Sci PMC Article
Santos R, Kawauchi S, Jacobs RE, Lopez-Burks ME, Choi H, Wikenheiser J, Hallgrimsson B, Jamniczky HA, Fraser SE, Lander AD and Calof AL. 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
Rackauckas C and Nie Q. 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
Haensel D, McNeil MA and Dai X. Ex Vivo Imaging and Genetic Manipulation of Mouse Hair Follicle Bulge Stem Cells. (2019) Methods Mol Biol. 1879, 15-29 Pubmed Methods Mol Biol
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
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
Newkirk DA, Chen YY, Chien R, Zeng W, Biesinger J, Flowers E, Kawauchi S, Santos R, Calof AL, Lander AD, Xie X and Yokomori K. 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