Qing Nie

Title(s)Professor, Mathematics
SchoolSchool of Physical Sciences
Address540F Rowland Hall
Zot 3875
Irvine CA 92697
Phone(949) 824-5530
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    Other Positions
    Title(s)Professor, Developmental & Cell Biology


    Collapse Research 
    Collapse Research Activities and Funding
    Dissecting single cell dynamics that coordinate neural crest migration and diversification
    NIH R01DE030565Apr 1, 2021 - Mar 31, 2026
    Role: Co-Principal Investigator
    Mathematical, Computational and Systems Biology
    NIH T32GM136624Jul 1, 2020 - Jun 30, 2025
    Role: Co-Principal Investigator
    Multiscale Models of Wound Cell Plasticity for Regeneration
    NIH U01AR073159Sep 1, 2018 - Aug 31, 2023
    Role: Principal Investigator
    Spatial Dynamics of Tissue and Organ Size Control
    NIH R01NS095355Sep 30, 2015 - Jun 30, 2021
    Role: Co-Principal Investigator
    Defining an Integrated Signaling Network That Patterns the Craniofacial Skeleton
    NIH R01DE023050Jul 1, 2014 - Mar 31, 2020
    Role: Co-Principal Investigator
    Stochastic Dynamics and Noise Control in Patterning Systems
    NIH R01GM107264Jul 1, 2014 - Jun 30, 2019
    Role: Principal Investigator
    Mathematical, Computational and Systems Biology
    NIH T32EB009418Apr 1, 2009 - Mar 31, 2020
    Role: Co-Principal Investigator
    Specificity and Spatial Dynamics of Cell Signaling: The*
    NIH R01GM075309Apr 1, 2005 - Mar 31, 2010
    Role: Principal Investigator
    Principles of Robust Developmental Patterning
    NIH R01GM067247Jul 1, 2002 - Dec 31, 2015
    Role: Co-Principal Investigator
    Role of Ovol Genes in Epidermal Development
    NIH R01AR047320Dec 1, 2000 - Jul 31, 2012
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics. Nat Methods. 2024 Aug 26. Almet AA, Tsai YC, Watanabe M, Nie Q. PMID: 39187683.
      View in: PubMed   Mentions:    Fields:    
    2. Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics. Nat Methods. 2024 Aug 26. Almet AA, Tsai YC, Watanabe M, Nie Q. PMID: 39187683.
      View in: PubMed   Mentions:    Fields:    
    3. Small data methods in omics: the power of one. Nat Methods. 2024 Aug 22. Johnston KG, Grieco SF, Nie Q, Theis FJ, Xu X. PMID: 39174710.
      View in: PubMed   Mentions:    Fields:    
    4. Hydrogel crosslinking modulates macrophages, fibroblasts, and their communication, during wound healing. Nat Commun. 2024 Aug 09; 15(1):6820. Butenko S, Nagalla RR, Guerrero-Juarez CF, Palomba F, David LM, Nguyen RQ, Gay D, Almet AA, Digman MA, Nie Q, Scumpia PO, Plikus MV, Liu WF. PMID: 39122702; PMCID: PMC11315930.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    5. Integrated Single-Cell Analysis Reveals Spatially and Temporally Dynamic Heterogeneity in Fibroblast States During Wound Healing. J Invest Dermatol. 2024 Jul 15. Almet AA, Liu Y, Nie Q, Plikus MV. PMID: 39019149.
      View in: PubMed   Mentions:    Fields:    
    6. Polyunsaturated Fatty Acid - mediated Cellular Rejuvenation for Reversing Age-related Vision Decline. bioRxiv. 2024 Jul 02. Gao F, Tom E, Rydz C, Cho W, Kolesnikov AV, Sha Y, Papadam A, Jafari S, Joseph A, Ahanchi A, Saraei NBS, Lyon D, Foik A, Nie Q, Grassmann F, Kefalov VJ, Skowronska-Krawczyk D. PMID: 39005302; PMCID: PMC11244954.
      View in: PubMed   Mentions:
    7. Interruption of the intratumor CD8+ T cell:Treg crosstalk improves the efficacy of PD-1 immunotherapy. Cancer Cell. 2024 Jun 10; 42(6):1051-1066.e7. Geels SN, Moshensky A, Sousa RS, Murat C, Bustos MA, Walker BL, Singh R, Harbour SN, Gutierrez G, Hwang M, Mempel TR, Weaver CT, Nie Q, Hoon DSB, Ganesan AK, Othy S, Marangoni F. PMID: 38861924; PMCID: PMC11285091.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    8. Spatial transition tensor of single cells. Nat Methods. 2024 Jun; 21(6):1053-1062. Zhou P, Bocci F, Li T, Nie Q. PMID: 38755322; PMCID: PMC11166574.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    9. Transcriptome and Metabolome Profiling Provide New Insights into Disuse Muscle Atrophy in Chicken: The Potential Role of Fast-Twitch Muscle Fibers. Int J Mol Sci. 2024 Mar 20; 25(6). Yao Z, Guo L, Zhang L, Nie Q. PMID: 38542488; PMCID: PMC10971063.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    10. Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data. Biophys J. 2024 Mar 19. Barcenas M, Bocci F, Nie Q. PMID: 38504523.
      View in: PubMed   Mentions: 1     Fields:    
    11. Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. Nat Mach Intell. 2024; 6(1):25-39. Sha Y, Qiu Y, Zhou P, Nie Q. PMID: 38274364; PMCID: PMC10805654.
      View in: PubMed   Mentions: 4  
    12. Leveraging gene correlations in single cell transcriptomic data. bioRxiv. 2023 Nov 01. Silkwood K, Dollinger E, Gervin J, Atwood S, Nie Q, Lander AD. PMID: 36993765; PMCID: PMC10055147.
      View in: PubMed   Mentions:
    13. NeST: nested hierarchical structure identification in spatial transcriptomic data. Nat Commun. 2023 10 17; 14(1):6554. Walker BL, Nie Q. PMID: 37848426; PMCID: PMC10582109.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    14. A Roadmap for a Consensus Human Skin Cell Atlas and Single-Cell Data Standardization. J Invest Dermatol. 2023 09; 143(9):1667-1677. 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, Kasper M. PMID: 37612031; PMCID: PMC10610458.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    15. The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics. Semin Cancer Biol. 2023 10; 95:42-51. Wang X, Almet AA, Nie Q. PMID: 37454878; PMCID: PMC10627116.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    16. Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis. Sci Adv. 2023 07 07; 9(27):eadd9984. 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, Villalta SA. PMID: 37418531; PMCID: PMC10328414.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    17. Signalling by senescent melanocytes hyperactivates hair growth. Nature. 2023 Jun; 618(7966):808-817. 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, Plikus MV. PMID: 37344645; PMCID: PMC10284692.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    18. exFINDER: identify external communication signals using single-cell transcriptomics data. Nucleic Acids Res. 2023 06 09; 51(10):e58. He C, Zhou P, Nie Q. PMID: 37026478; PMCID: PMC10250247.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    19. Single-cell transcriptomics of human-skin-equivalent organoids. Cell Rep. 2023 05 30; 42(5):112511. Stabell AR, Lee GE, Jia Y, Wong KN, Wang S, Ling J, Nguyen SD, Sen GL, Nie Q, Atwood SX. PMID: 37195865; PMCID: PMC10348600.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    20. Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis. bioRxiv. 2023 Apr 18. 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, Villalta SA. PMID: 37131694; PMCID: PMC10153153.
      View in: PubMed   Mentions:
    21. exFINDER: identify external communication signals using single-cell transcriptomics data. bioRxiv. 2023 Mar 27. He C, Zhou P, Nie Q. PMID: 37034624; PMCID: PMC10081188.
      View in: PubMed   Mentions:
    22. Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis. Nat Genet. 2023 04; 55(4):595-606. 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, Kessenbrock K. PMID: 36914836; PMCID: PMC10655552.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    23. Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. Nat Commun. 2023 02 28; 14(1):1128. Zhao W, Johnston KG, Ren H, Xu X, Nie Q. PMID: 36854676; PMCID: PMC9974942.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    24. Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin. Cell Rep. 2023 01 31; 42(1):111994. 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, Andersen B. PMID: 36732947; PMCID: PMC9939370.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    25. Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat. bioRxiv. 2023 Jan 16. Zhao W, Johnston KG, Ren H, Xu X, Nie Q. PMID: 36712056; PMCID: PMC9882151.
      View in: PubMed   Mentions:
    26. Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique. Natl Sci Rev. 2023 Apr; 10(4):nwac287. Cao Y, Chen L, Chen H, Cun Y, Dai X, Du H, Gao F, Guo F, Guo Y, Hao P, He S, He S, He X, Hu Z, Hoh BP, Jin X, Jiang Q, Jiang Q, Khan A, Kong HZ, Li J, Li SC, Li Y, Lin Q, Liu J, Liu Q, Lu J, Lu X, Luo S, Nie Q, Qiu Z, Shi T, Song X, Su J, Tao SC, Wang C, Wang CC, Wang GD, Wang J, Wu Q, Wu S, Xu S, Xue Y, Yang W, Yang Z, Ye K, Ye YN, Yu L, Zhao F, Zhao Y, Zhai W, Zhang D, Zhang L, Zheng H, Zhou Q, Zhu T, Zhang YP. PMID: 37089192; PMCID: PMC10116607.
      View in: PubMed   Mentions:
    27. Integrated analysis of multimodal single-cell data with structural similarity. Nucleic Acids Res. 2022 11 28; 50(21):e121. Cao Y, Fu L, Wu J, Peng Q, Nie Q, Zhang J, Xie X. PMID: 36130281; PMCID: PMC9757079.
      View in: PubMed   Mentions: 27     Fields:    
    28. spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data. Mol Syst Biol. 2022 11; 18(11):e11176. Bocci F, Zhou P, Nie Q. PMID: 36321549; PMCID: PMC9627675.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    29. Analyzing network diversity of cell-cell interactions in COVID-19 using single-cell transcriptomics. Front Genet. 2022; 13:948508. Wang X, Almet AA, Nie Q. PMID: 36105110; PMCID: PMC9465179.
      View in: PubMed   Mentions: 2  
    30. Wound healing in aged skin exhibits systems-level alterations in cellular composition and cell-cell communication. Cell Rep. 2022 08 02; 40(5):111155. Vu R, Jin S, Sun P, Haensel D, Nguyen QH, Dragan M, Kessenbrock K, Nie Q, Dai X. PMID: 35926463; PMCID: PMC9901190.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    31. Identifying multicellular spatiotemporal organization of cells with SpaceFlow. Nat Commun. 2022 07 14; 13(1):4076. Ren H, Walker BL, Cang Z, Nie Q. PMID: 35835774; PMCID: PMC9283532.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    32. Multimodal analyses of vitiligo skin identify tissue characteristics of stable disease. JCI Insight. 2022 07 08; 7(13). 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, Ganesan AK. PMID: 35653192; PMCID: PMC9310536.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    33. Hedgehog signaling reprograms hair follicle niche fibroblasts to a hyper-activated state. Dev Cell. 2022 07 25; 57(14):1758-1775.e7. 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, Plikus MV. PMID: 35777353; PMCID: PMC9344965.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    34. Single-cell analysis of human basal cell carcinoma reveals novel regulators of tumor growth and the tumor microenvironment. Sci Adv. 2022 06 10; 8(23):eabm7981. 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, Atwood SX. PMID: 35687691; PMCID: PMC9187229.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimals
    35. Magnitude and breadth of antibody cross-reactivity induced by recombinant influenza hemagglutinin trimer vaccine is enhanced by combination adjuvants. Sci Rep. 2022 06 02; 12(1):9198. 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, Davies DH. PMID: 35654904; PMCID: PMC9163070.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    36. Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT. Cell Rep Methods. 2022 05 23; 2(5):100207. Johnston KG, Grieco SF, Zhang H, Jin S, Xu X, Nie Q. PMID: 35637911; PMCID: PMC9142684.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    37. De Novo Assembly of 20 Chicken Genomes Reveals the Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes and Subtelomeric Regions. Mol Biol Evol. 2022 04 10; 39(4). Li M, Sun C, Xu N, Bian P, Tian X, Wang X, Wang Y, Jia X, Heller R, Wang M, Wang F, Dai X, Luo R, Guo Y, Wang X, Yang P, Hu D, Liu Z, Fu W, Zhang S, Li X, Wen C, Lan F, Siddiki AZ, Suwannapoom C, Zhao X, Nie Q, Hu X, Jiang Y, Yang N. PMID: 35325213; PMCID: PMC9021737.
      View in: PubMed   Mentions: 28     Fields:    Translation:Animals
    38. Deciphering tissue structure and function using spatial transcriptomics. Commun Biol. 2022 03 10; 5(1):220. Walker BL, Cang Z, Ren H, Bourgain-Chang E, Nie Q. PMID: 35273328; PMCID: PMC8913632.
      View in: PubMed   Mentions: 25  Translation:Cells
    39. Machine Learning of Single Cell Transcriptomic Data From anti-PD-1 Responders and Non-responders Reveals Distinct Resistance Mechanisms in Skin Cancers and PDAC. Front Genet. 2021; 12:806457. Liu R, Dollinger E, Nie Q. PMID: 35178072; PMCID: PMC8844526.
      View in: PubMed   Mentions: 1  
    40. Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development. Cell Rep. 2021 12 21; 37(12):110140. Tatarakis D, Cang Z, Wu X, Sharma PP, Karikomi M, MacLean AL, Nie Q, Schilling TF. PMID: 34936864; PMCID: PMC8741273.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    41. Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell-Cell Signaling during EMT Progression. Cancers (Basel). 2021 Nov 16; 13(22). Bocci F, Zhou P, Nie Q. PMID: 34830900; PMCID: PMC8616061.
      View in: PubMed   Mentions: 9  
    42. A Study of Gene Expression, Structure, and Contractility of iPSC-Derived Cardiac Myocytes from a Family with Heart Disease due to LMNA Mutation. Ann Biomed Eng. 2021 Dec; 49(12):3524-3539. Mehrabi M, Morris TA, Cang Z, Nguyen CHH, Sha Y, Asad MN, Khachikyan N, Greene TL, Becker DM, Nie Q, Zaragoza MV, Grosberg A. PMID: 34585335; PMCID: PMC8671287.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    43. Examining age-dependent DNA methylation patterns and gene expression in the male and female mouse hippocampus. Neurobiol Aging. 2021 12; 108:223-235. Chinn CA, Ren H, Morival JLP, Nie Q, Wood MA, Downing TL. PMID: 34598831; PMCID: PMC9186538.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    44. Modeling the effects of EMT-immune dynamics on carcinoma disease progression. Commun Biol. 2021 08 18; 4(1):983. Bergman DR, Karikomi MK, Yu M, Nie Q, MacLean AL. PMID: 34408236; PMCID: PMC8373868.
      View in: PubMed   Mentions: 2  Translation:Humans
    45. Multiple morphogens and rapid elongation promote segmental patterning during development. PLoS Comput Biol. 2021 06; 17(6):e1009077. Qiu Y, Fung L, Schilling TF, Nie Q. PMID: 34161317; PMCID: PMC8259987.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    46. The landscape of cell-cell communication through single-cell transcriptomics. Curr Opin Syst Biol. 2021 Jun; 26:12-23. Almet AA, Cang Z, Jin S, Nie Q. PMID: 33969247; PMCID: PMC8104132.
      View in: PubMed   Mentions: 63  
    47. DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data. Front Genet. 2021; 12:636743. Maseda F, Cang Z, Nie Q. PMID: 33833776; PMCID: PMC8021700.
      View in: PubMed   Mentions: 14  
    48. A multiscale model via single-cell transcriptomics reveals robust patterning mechanisms during early mammalian embryo development. PLoS Comput Biol. 2021 03; 17(3):e1008571. Cang Z, Wang Y, Wang Q, Cho KWY, Holmes W, Nie Q. PMID: 33684098; PMCID: PMC7971879.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    49. Single-cell RNA sequencing of preadipocytes reveals the cell fate heterogeneity induced by melatonin. J Pineal Res. 2021 Apr; 70(3):e12725. Li Z, Zheng M, Mo J, Li K, Yang X, Guo L, Zhang X, Abdalla BA, Nie Q. PMID: 33621367.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    50. Inference and analysis of cell-cell communication using CellChat. Nat Commun. 2021 02 17; 12(1):1088. Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH, Myung P, Plikus MV, Nie Q. PMID: 33597522; PMCID: PMC7889871.
      View in: PubMed   Mentions: 1633     Fields:    Translation:HumansAnimalsCells
    51. Transcriptome Response of Liver and Muscle in Heat-Stressed Laying Hens. Genes (Basel). 2021 02 10; 12(2). Wang Y, Jia X, Hsieh JCF, Monson MS, Zhang J, Shu D, Nie Q, Persia ME, Rothschild MF, Lamont SJ. PMID: 33578825; PMCID: PMC7916550.
      View in: PubMed   Mentions: 8     Fields:    Translation:AnimalsCells
    52. Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial-Mesenchymal Transition From Single-Cell Transcriptomic Data. Front Genet. 2020; 11:604585. Sha Y, Wang S, Bocci F, Zhou P, Nie Q. PMID: 33488673; PMCID: PMC7820899.
      View in: PubMed   Mentions: 15  
    53. scMC learns biological variation through the alignment of multiple single-cell genomics datasets. Genome Biol. 2021 01 04; 22(1):10. Zhang L, Nie Q. PMID: 33397454; PMCID: PMC7784288.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    54. miR-429-3p/LPIN1 Axis Promotes Chicken Abdominal Fat Deposition via PPARγ Pathway. Front Cell Dev Biol. 2020; 8:595637. Chao X, Guo L, Wang Q, Huang W, Liu M, Luan K, Jiang J, Lin S, Nie Q, Luo W, Zhang X, Luo Q. PMID: 33425901; PMCID: PMC7793751.
      View in: PubMed   Mentions: 9  
    55. Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states. Nat Commun. 2020 10 28; 11(1):5434. Lin Z, Jin S, Chen J, Li Z, Lin Z, Tang L, Nie Q, Andersen B. PMID: 33116143; PMCID: PMC7595230.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    56. Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers. Cancers (Basel). 2020 Oct 13; 12(10). Dollinger E, Bergman D, Zhou P, Atwood SX, Nie Q. PMID: 33065980; PMCID: PMC7599806.
      View in: PubMed   Mentions: 5  
    57. Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data. Nucleic Acids Res. 2020 09 25; 48(17):9505-9520. Sha Y, Wang S, Zhou P, Nie Q. PMID: 32870263; PMCID: PMC7515733.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    58. Single cell transcriptomics of human epidermis identifies basal stem cell transition states. Nat Commun. 2020 08 25; 11(1):4239. Wang S, Drummond ML, Guerrero-Juarez CF, Tarapore E, MacLean AL, Stabell AR, Wu SC, Gutierrez G, That BT, Benavente CA, Nie Q, Atwood SX. PMID: 32843640; PMCID: PMC7447770.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansCells
    59. Scaling a Dpp Morphogen Gradient through Feedback Control of Receptors and Co-receptors. Dev Cell. 2020 06 22; 53(6):724-739.e14. Zhu Y, Qiu Y, Chen W, Nie Q, Lander AD. PMID: 32574592; PMCID: PMC7437929.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    60. Inferring spatial and signaling relationships between cells from single cell transcriptomic data. Nat Commun. 2020 04 29; 11(1):2084. Cang Z, Nie Q. PMID: 32350282; PMCID: PMC7190659.
      View in: PubMed   Mentions: 131     Fields:    Translation:AnimalsCells
    61. Defining Epidermal Basal Cell States during Skin Homeostasis and Wound Healing Using Single-Cell Transcriptomics. Cell Rep. 2020 03 17; 30(11):3932-3947.e6. 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, Dai X. PMID: 32187560; PMCID: PMC7218802.
      View in: PubMed   Mentions: 88     Fields:    Translation:AnimalsCells
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    138. The measure of success: constraints, objectives, and tradeoffs in morphogen-mediated patterning. Cold Spring Harb Perspect Biol. 2009 Jul; 1(1):a002022. Lander AD, Lo WC, Nie Q, Wan FY. PMID: 20066078; PMCID: PMC2742077.
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    139. Multi-scale Modelling for Threshold Dependent Differentiation. Math Model Nat Phenom. 2009 Jun 01; 4(4):103-117. Cai AQ, Peng Y, Wells J, Dai X, Nie Q. PMID: 20622931; PMCID: PMC2900806.
      View in: PubMed   Mentions:
    140. Down-regulation of CXCR4 expression by SDF-KDEL in CD34(+) hematopoietic stem cells: An anti-human immunodeficiency virus strategy. J Virol Methods. 2009 Oct; 161(1):30-7. Zhang JC, Sun L, Nie QH, Huang CX, Jia ZS, Wang JP, Lian JQ, Li XH, Wang PZ, Zhang Y, Zhuang Y, Sun YT, Bai X. PMID: 19463855.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    141. Cell lineages and the logic of proliferative control. PLoS Biol. 2009 Jan 20; 7(1):e15. Lander AD, Gokoffski KK, Wan FY, Nie Q, Calof AL. PMID: 19166268; PMCID: PMC2628408.
      View in: PubMed   Mentions: 147     Fields:    Translation:AnimalsCells
    142. Feedback regulation in multistage cell lineages. Math Biosci Eng. 2009 Jan; 6(1):59-82. Lo WC, Chou CS, Gokoffski KK, Wan FY, Lander AD, Calof AL, Nie Q. PMID: 19292508; PMCID: PMC2756546.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    143. Robust spatial sensing of mating pheromone gradients by yeast cells. PLoS One. 2008; 3(12):e3865. Moore TI, Chou CS, Nie Q, Jeon NL, Yi TM. PMID: 19052645; PMCID: PMC2586657.
      View in: PubMed   Mentions: 59     Fields:    Translation:AnimalsCells
    144. Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients. PLoS One. 2008 Sep 01; 3(9):e3103. Chou CS, Nie Q, Yi TM. PMID: 21267054; PMCID: PMC3021495.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    145. Fus3-triggered Tec1 degradation modulates mating transcriptional output during the pheromone response. Mol Syst Biol. 2008; 4:212. Chou S, Zhao S, Song Y, Liu H, Nie Q. PMID: 18682702; PMCID: PMC2538907.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    146. Compact integration factor methods in high spatial dimensions. J Comput Phys. 2008; 227(10):5238-5255. Nie Q, Wan FY, Zhang YT, Liu XF. PMID: 19809596; PMCID: PMC2756762.
      View in: PubMed   Mentions: 10  
    147. Complex regulation of cyp26a1 creates a robust retinoic acid gradient in the zebrafish embryo. PLoS Biol. 2007 Nov; 5(11):e304. White RJ, Nie Q, Lander AD, Schilling TF. PMID: 18031199; PMCID: PMC2080651.
      View in: PubMed   Mentions: 117     Fields:    Translation:AnimalsCells
    148. Computational analysis of BMP gradients in dorsal-ventral patterning of the zebrafish embryo. J Theor Biol. 2007 Oct 21; 248(4):579-89. Zhang YT, Lander AD, Nie Q. PMID: 17673236; PMCID: PMC4151269.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    149. Toll-like receptor 4 siRNA attenuates LPS-induced secretion of inflammatory cytokines and chemokines by macrophages. J Infect. 2007 Jul; 55(1):e1-9. Xu Z, Huang CX, Li Y, Wang PZ, Ren GL, Chen CS, Shang FJ, Zhang Y, Liu QQ, Jia ZS, Nie QH, Sun YT, Bai XF. PMID: 17336389.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    150. Mathematical models of specificity in cell signaling. Biophys J. 2007 May 15; 92(10):3425-41. Bardwell L, Zou X, Nie Q, Komarova NL. PMID: 17325015; PMCID: PMC1853162.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    151. Wingless directly represses DPP morphogen expression via an armadillo/TCF/Brinker complex. PLoS One. 2007 Jan 03; 2(1):e142. Theisen H, Syed A, Nguyen BT, Lukacsovich T, Purcell J, Srivastava GP, Iron D, Gaudenz K, Nie Q, Wan FY, Waterman ML, Marsh JL. PMID: 17206277; PMCID: PMC1764032.
      View in: PubMed   Mentions: 20     Fields:    Translation:AnimalsCells
    152. Membrane-associated non-receptors and morphogen gradients. Bull Math Biol. 2007 Jan; 69(1):33-54. Lander AD, Nie Q, Wan FY. PMID: 17054000; PMCID: PMC1994248.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    153. A theoretical framework for specificity in cell signaling. Mol Syst Biol. 2005; 1:2005.0023. Komarova NL, Zou X, Nie Q, Bardwell L. PMID: 16729058; PMCID: PMC1681467.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    154. Spatially distributed morphogen production and morphogen gradient formation. Math Biosci Eng. 2005 Apr; 2(2):239-62. Lander AD, Nie Q, Wan FY. PMID: 20369921.
      View in: PubMed   Mentions: 15     Fields:    
    155. Current status of severe acute respiratory syndrome in China. World J Gastroenterol. 2003 Aug; 9(8):1635-45. Nie QH, Luo XD, Zhang JZ, Su Q. PMID: 12918094; PMCID: PMC4611517.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansPHPublic Health
    156. [The present and prospects of clinical diagnosis and treatment of severe acute respiratory syndrome]. Zhongguo Wei Zhong Bing Ji Jiu Yi Xue. 2003 Jul; 15(7):441-4. Cao YZ, Nie QH. PMID: 12857505.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    157. Nonlinear simulation of tumor growth. J Math Biol. 2003 Mar; 46(3):191-224. Cristini V, Lowengrub J, Nie Q. PMID: 12728333.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansAnimals
    158. Do morphogen gradients arise by diffusion? Dev Cell. 2002 Jun; 2(6):785-96. Lander AD, Nie Q, Wan FY. PMID: 12062090.
      View in: PubMed   Mentions: 139     Fields:    Translation:AnimalsCells
    159. Methodologic research on TIMP-1, TIMP-2 detection as a new diagnostic index for hepatic fibrosis and its significance. World J Gastroenterol. 2002 Apr; 8(2):282-7. Nie QH, Cheng YQ, Xie YM, Zhou YX, Bai XG, Cao YZ. PMID: 11925608; PMCID: PMC4658367.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
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