Menu Close

Recent publications from CMCF.


Chen J, Holt JR, Evans EL, Lowengrub JS and Pathak MM. PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration. (2024) PLoS Comput Biol. 20, e1011855 Pubmed PLoS Comput Biol PMC Article
Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD and Calof AL. Gastrulation-stage gene expression in mouse embryos foreshadows the development of syndromic birth defects. (2024) Sci Adv. 10, eadl4239 Pubmed Sci Adv PMC Article
Janakaloti Narayanareddy BR, Allipeta NR, Allard J and Gross SP. A new method to experimentally quantify dynamics of initial protein-protein interactions. (2024) Commun Biol. 7, 311 Pubmed Commun Biol PMC Article
Barcenas M, Bocci F and Nie Q. Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data. (2024) Biophys J. Pubmed Biophys J
Kang TY, Bocci F, Nie Q, Onuchic JN and Levchenko A. Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. (2024) Elife. 12, Pubmed Elife PMC Article
Caldwell MG and Lander AD. The inherent fragility of collective proliferative control. (2024) bioRxiv. Pubmed bioRxiv PMC Article
Johnson MR, Li S, Guerrero-Juarez CF, Miller P, Brack BJ, Mereby SA, Moreno JA, Feigin CY, Gaska J, Rivera-Perez JA, Nie Q, Ploss A, Shvartsman SY and Mallarino R. A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns. (2023) Nat Ecol Evol. 7, 2143-2159 Pubmed Nat Ecol Evol PMC Article
Silkwood K, Dollinger E, Gervin J, Atwood S, Nie Q and Lander AD. Leveraging gene correlations in single cell transcriptomic data. (2023) bioRxiv. Pubmed bioRxiv PMC Article
Wang X, Almet AA and Nie Q. 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
Walker BL and Nie Q. NeST: nested hierarchical structure identification in spatial transcriptomic data. (2023) Nat Commun. 14, 6554 Pubmed Nat Commun PMC Article
Almet AA, Yuan H, Annusver K, Ramos R, Liu Y, Wiedemann J, Sorkin DH, Landén NX, Sonkoly E, Haniffa M, Nie Q, Lichtenberger BM, Luecken MD, Andersen B, Tsoi LC, Watt FM, Gudjonsson JE, Plikus MV and Kasper M. 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
Vu R, Dragan M, Sun P, Werner S and Dai X. 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
Bocci F, Jia D, Nie Q, Jolly MK and Onuchic J. Theoretical and computational tools to model multistable gene regulatory networks. (2023) Rep Prog Phys. 86, Pubmed Rep Prog Phys PMC Article
Coulis G, Jaime D, Guerrero-Juarez C, Kastenschmidt JM, Farahat PK, Nguyen Q, Pervolarakis N, McLinden K, Thurlow L, Movahedi S, Hughes BS, Duarte J, Sorn A, Montoya E, Mozaffar I, Dragan M, Othy S, Joshi T, Hans CP, Kimonis V, MacLean AL, Nie Q, Wallace LM, Harper SQ, Mozaffar T, Hogarth MW, Bhattacharya S, Jaiswal JK, Golann DR, Su Q, Kessenbrock K, Stec M, Spencer MJ, Zamudio JR and Villalta SA. Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis. (2023) Sci Adv. 9, eadd9984 Pubmed Sci Adv PMC Article
Dragan M, Chen Z, Li Y, Le J, Sun P, Haensel D, Sureshchandra S, Pham A, Lu E, Pham KT, Verlande A, Vu R, Gutierrez G, Li W, Jang C, Masri S and Dai X. Ovol1/2 loss-induced epidermal defects elicit skin immune activation and alter global metabolism. (2023) EMBO Rep. 24, e56214 Pubmed EMBO Rep PMC Article
Wang X, Ramos R, Phan AQ, Yamaga K, Flesher JL, Jiang S, Oh JW, Jin S, Jahid S, Kuan CH, Nguyen TK, Liang HY, Shettigar NU, Hou R, Tran KH, Nguyen A, Vu KN, Phung JL, Ingal JP, Levitt KM, Cao X, Liu Y, Deng Z, Taguchi N, Scarfone VM, Wang G, Paolilli KN, Wang X, Guerrero-Juarez CF, Davis RT, Greenberg EN, Ruiz-Vega R, Vasudeva P, Murad R, Widyastuti LHP, Lee HL, McElwee KJ, Gadeau AP, Lawson DA, Andersen B, Mortazavi A, Yu Z, Nie Q, Kunisada T, Karin M, Tuckermann J, Esko JD, Ganesan AK, Li J and Plikus MV. Signalling by senescent melanocytes hyperactivates hair growth. (2023) Nature. 618, 808-817 Pubmed Nature 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. Author Correction: MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. (2023) Sci Data. 10, 420 Pubmed Sci Data PMC Article
He C, Zhou P and Nie Q. exFINDER: identify external communication signals using single-cell transcriptomics data. (2023) Nucleic Acids Res. 51, e58 Pubmed Nucleic Acids Res PMC Article
Hachey SJ, Sobrino A, Lee JG, Jafari MD, Klempner SJ, Puttock EJ, Edwards RA, Lowengrub JS, Waterman ML, Zell JA and Hughes CCW. A human vascularized microtumor model of patient-derived colorectal cancer recapitulates clinical disease. (2023) Transl Res. 255, 97-108 Pubmed Transl Res PMC Article
Stabell AR, Lee GE, Jia Y, Wong KN, Wang S, Ling J, Nguyen SD, Sen GL, Nie Q and Atwood SX. Single-cell transcriptomics of human-skin-equivalent organoids. (2023) Cell Rep. 42, 112511 Pubmed Cell Rep PMC Article
Green RM, Lo Vercio LD, Dauter A, Barretto EC, Devine J, Vidal-García M, Marchini M, Robertson S, Zhao X, Mahika A, Shakir MB, Guo S, Boughner JC, Dean W, Lander AD, Marcucio RS, Forkert ND and Hallgrímsson B. Quantifying the relationship between cell proliferation and morphology during development of the face. (2023) bioRxiv. Pubmed bioRxiv PMC Article
Tang X, Li S, Lowengrub JS and Wise SM. Phase field modeling and computation of vesicle growth or shrinkage. (2023) J Math Biol. 86, 97 Pubmed J Math Biol PMC Article
Nee K, Ma D, Nguyen QH, Pein M, Pervolarakis N, Insua-Rodríguez J, Gong Y, Hernandez G, Alshetaiwi H, Williams J, Rauf M, Dave KR, Boyapati K, Hasnain A, Calderon C, Markaryan A, Edwards R, Lin E, Parajuli R, Zhou P, Nie Q, Shalabi S, LaBarge MA and Kessenbrock K. Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis. (2023) Nat Genet. 55, 595-606 Pubmed Nat Genet PMC Article
Adler FR, Anderson ARA, Bhushan A, Bogdan P, Bravo-Cordero JJ, Brock A, Chen Y, Cukierman E, DelGiorno KE, Denis GV, Ferrall-Fairbanks MC, Gartner ZJ, Germain RN, Gordon DM, Hunter G, Jolly MK, Karacosta LG, Mythreye K, Katira P, Kulkarni RP, Kutys ML, Lander AD, Laughney AM, Levine H, Lou E, Lowenstein PR, Masters KS, Pe'er D, Peyton SR, Platt MO, Purvis JE, Quon G, Richer JK, Riddle NC, Rodriguez A, Snyder JC, Lee Szeto G, Tomlin CJ, Yanai I, Zervantonakis IK and Dueck H. Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation. (2023) Cell Syst. 14, 252-257 Pubmed Cell Syst PMC Article
Rodriguez J, Iniguez A, Jena N, Tata P, Liu ZY, Lander AD, Lowengrub J and Van Etten RA. Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy. (2023) Elife. 12, Pubmed Elife PMC Article
Coulis G, Jaime D, Guerrero-Juarez C, Kastenschmidt JM, Farahat PK, Nguyen Q, Pervolarakis N, McLinden K, Thurlow L, Movahedi S, Duarte J, Sorn A, Montoya E, Mozaffar I, Dragan M, Othy S, Joshi T, Hans CP, Kimonis V, MacLean AL, Nie Q, Wallace LM, Harper SQ, Mozaffar T, Hogarth MW, Bhattacharya S, Jaiswal JK, Golann DR, Su Q, Kessenbrock K, Stec M, Spencer MJ, Zamudio JR and Villalta SA. Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis. (2023) bioRxiv. Pubmed bioRxiv PMC Article
Zhu Y, Zhao Y, Wen J, Liu S, Huang T, Hatial I, Peng X, Al Janabi H, Huang G, Mittlesteadt J, Cheng M, Bhardwaj A, Ashfeld BL, Kao KR, Maeda DY, Dai X, Wiest O, Blagg BSJ, Lu X, Cheng L, Wan J and Lu X. 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
Xiao W, Liu K, Lowengrub J, Li S and Zhao M. 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
He C, Zhou P and Nie Q. exFINDER: identify external communication signals using single-cell transcriptomics data. (2023) bioRxiv. Pubmed bioRxiv PMC Article
Cang Z, Zhao Y, Almet AA, Stabell A, Ramos R, Plikus MV, Atwood SX and Nie Q. Screening cell-cell communication in spatial transcriptomics via collective optimal transport. (2023) Nat Methods. 20, 218-228 Pubmed Nat Methods PMC Article
Bilic P, Christ P, Li HB, Vorontsov E, Ben-Cohen A, Kaissis G, Szeskin A, Jacobs C, Mamani GEH, Chartrand G, Lohöfer F, Holch JW, Sommer W, Hofmann F, Hostettler A, Lev-Cohain N, Drozdzal M, Amitai MM, Vivanti R, Sosna J, Ezhov I, Sekuboyina A, Navarro F, Kofler F, Paetzold JC, Shit S, Hu X, Lipková J, Rempfler M, Piraud M, Kirschke J, Wiestler B, Zhang Z, Hülsemeyer C, Beetz M, Ettlinger F, Antonelli M, Bae W, Bellver M, Bi L, Chen H, Chlebus G, Dam EB, Dou Q, Fu CW, Georgescu B, Giró-I-Nieto X, Gruen F, Han X, Heng PA, Hesser J, Moltz JH, Igel C, Isensee F, Jäger P, Jia F, Kaluva KC, Khened M, Kim I, Kim JH, Kim S, Kohl S, Konopczynski T, Kori A, Krishnamurthi G, Li F, Li H, Li J, Li X, Lowengrub J, Ma J, Maier-Hein K, Maninis KK, Meine H, Merhof D, Pai A, Perslev M, Petersen J, Pont-Tuset J, Qi J, Qi X, Rippel O, Roth K, Sarasua I, Schenk A, Shen Z, Torres J, Wachinger C, Wang C, Weninger L, Wu J, Xu D, Yang X, Yu SC, Yuan Y, Yue M, Zhang L, Cardoso J, Bakas S, Braren R, Heinemann V, Pal C, Tang A, Kadoury S, Soler L, van Ginneken B, Greenspan H, Joskowicz L and Menze B. The Liver Tumor Segmentation Benchmark (LiTS). (2023) Med Image Anal. 84, 102680 Pubmed Med Image Anal PMC Article
Zhao W, Johnston KG, Ren H, Xu X and Nie Q. Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. (2023) Nat Commun. 14, 1128 Pubmed Nat Commun PMC Article
Liau ES, Jin S, Chen YC, Liu WS, Calon M, Nedelec S, Nie Q and Chen JA. Single-cell transcriptomic analysis reveals diversity within mammalian spinal motor neurons. (2023) Nat Commun. 14, 46 Pubmed Nat Commun PMC Article
Zhao W, Johnston KG, Ren H, Xu X and Nie Q. Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. (2023) bioRxiv. Pubmed bioRxiv PMC Article
Wiedemann J, Billi AC, Bocci F, Kashgari G, Xing E, Tsoi LC, Meller L, Swindell WR, Wasikowski R, Xing X, Ma F, Gharaee-Kermani M, Kahlenberg JM, Harms PW, Maverakis E, Nie Q, Gudjonsson JE and Andersen B. Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin. (2023) Cell Rep. 42, 111994 Pubmed Cell Rep PMC Article
Kean CM, Tracy CJ, Mitra A, Rahat B, Van Winkle MT, Gebert CM, Noeker JA, Calof AL, Lander AD, Kassis JA and Pfeifer K. Decreasing dosage partially corrects embryonic growth and brain transcriptome phenotypes in embryos. (2022) Sci Adv. 8, eadd4136 Pubmed Sci Adv PMC Article
Butner JD, Dogra P, Chung C, Pasqualini R, Arap W, Lowengrub J, Cristini V and Wang Z. Mathematical modeling of cancer immunotherapy for personalized clinical translation. (2022) Nat Comput Sci. 2, 785-796 Pubmed Nat Comput Sci PMC Article
Bocci F, Zhou P and Nie Q. 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
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. 50, e121 Pubmed Nucleic Acids Res PMC Article
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 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 PMC Article
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
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
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
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
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
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
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 PMC Article
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
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
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
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 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
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
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 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
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
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
Shiu J and Lander AD. When oncogenes do not cause cancer. (2021) Elife. 10, Pubmed Elife 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
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
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
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
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
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
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
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
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
MacLean AL and Nie Q. The diverse landscape of modeling in single-cell biology. (2021) Phys Biol. 18, Pubmed Phys Biol
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
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
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
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
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
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 (Amst). 410, 202-210 Pubmed Neurocomputing (Amst) 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
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
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
Liang G, Yin H, Allard J and Ding F. 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
Sha Y, Qiu Y, Zhou P and Nie Q. Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. (2024) Nat Mach Intell. 6, 25-39 Pubmed Nat Mach Intell 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
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