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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 selected 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. Morphogen-guided neocortical organoids recapitulate regional areal identity and model neurodevelopmental disorder pathology. bioRxiv. 2025 Sep 03. Tsai YC, Ozaki H, Wang X, Almet AA, Fleming I, Shiraiwa K, Noh MJM, Nie C, Trejo S, Sugita BK, Dalal J, Gonzalez RA, De Jesus B, Chen GL, Gandal MJ, Nie Q, Watanabe M. PMID: 40950130; PMCID: PMC12424832.
      View in: PubMed   Mentions:
    2. Analysis of changes in intercellular communications in Alzheimer's disease reveals conserved changes in glutamatergic transmission in mice and humans. Sci Rep. 2025 Jul 19; 15(1):26248. Bartas K, Nguyen M, Zhao W, Hui M, Nie Q, Beier KT. PMID: 40683902; PMCID: PMC12276270.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    3. Invasion mechanisms of Eimeria coccidian and host immune responses in chicken intestine_A review. Poult Sci. 2025 Oct; 104(10):105560. Jebessa E, Zou X, Berihulay H, Ayalew W, He Y, Chuxiao L, Zhao Z, Qu H, Bello SF, Chen P, Ji J, Nie Q, Luo C. PMID: 40752203; PMCID: PMC12341618.
      View in: PubMed   Mentions:    Fields:    
    4. GCRP: Integrated Global Chicken Reference Panel from 11,951 Chicken Genomes. Genomics Proteomics Bioinformatics. 2025 Jul 11; 23(3). Zhu D, Wang Y, Qu H, Feng C, Zhang H, Sheng Z, Jiang Y, Nie Q, Chu S, Shu D, Jiang Z, Zhang D, Fang L, Li H, Xu Z, Zhao Y, Wang Y, Hu X. PMID: 40234734; PMCID: PMC12458076.
      View in: PubMed   Mentions: 2     Fields:    
    5. Elucidating the genetic basis of earlobe color in Qingyuan partridge chickens through genomics and metabolomics. Poult Sci. 2025 Oct; 104(10):105518. Liu X, Wu R, Hao T, Ye H, Zhang Z, Lei Z, Mo Y, Lin D, Nie Q. PMID: 40633321; PMCID: PMC12275115.
      View in: PubMed   Mentions:    Fields:    
    6. G-Quadruplexes in Gene Regulation and Cellular Function. Wiley Interdiscip Rev RNA. 2025 Jul-Aug; 16(4):e70019. Wen Q, Guo L, Bordbar F, Nie Q. PMID: 40653742.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    7. Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data. Nat Commun. 2025 Jul 01; 16(1):5970. Hou J, Zhao W, Nie Q. PMID: 40593827; PMCID: PMC12219092.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    8. Uncovering minimal pathways in melanoma initiation. Nat Commun. 2025 Jun 26; 16(1):5369. Xiao H, Shiu J, Chen CF, Wu J, Zhou P, Telang SS, Ruiz-Vega R, Edwards RA, Nie Q, Lander AD, Ganesan AK. PMID: 40571713; PMCID: PMC12202705.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    9. Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model. Nat Commun. 2025 Jun 03; 16(1):5149. Masters H, Wang S, Tu C, Nguyen Q, Sha Y, Karikomi MK, Fung PSR, Tran B, Martel C, Kwang N, Neel M, Jaime OG, Espericueta V, Johnson BA, Kessenbrock K, Nie Q, Monuki ES. PMID: 40461502; PMCID: PMC12134268.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    10. Dissecting crosstalk induced by cell-cell communication using single-cell transcriptomic data. bioRxiv. 2025 Jun 03. Hou J, Zhao W, Nie Q. PMID: 40501904; PMCID: PMC12157450.
      View in: PubMed   Mentions:
    11. Dissecting multilayer cell-cell communications with signaling feedback loops from spatial transcriptomics data. Genome Res. 2025 Jun 02; 35(6):1400-1414. Yan L, Cheng J, Nie Q, Sun X. PMID: 40262896; PMCID: PMC12129024.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    12. Indigenous broilers in crossbreeding: impacts on meat quality and candidate gene screening. Poult Sci. 2025 Jul; 104(7):105245. Li J, Zhou Z, Zhang Z, Zheng X, Sun Y, Guo S, Li Y, Yang X, Kong S, Cai D, Lin D, Mo Y, Cai B, Nie Q. PMID: 40344706; PMCID: PMC12138444.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    13. Fecal microbiota transplantation improves growth performance of chickens by increasing the intestinal Lactobacillus and glutamine. Poult Sci. 2025 Aug; 104(8):105243. Xu Y, Chen K, Huang Y, Yan Y, Zhang W, Tian J, Zhang D, Liu M, Nie Q. PMID: 40398303; PMCID: PMC12149609.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    14. Genetic regulation of gene expression across multiple tissues in chickens. Nat Genet. 2025 May; 57(5):1298-1308. Guan D, Bai Z, Zhu X, Zhong C, Hou Y, Zhu D, ChickenGTEx Consortium, Li H, Lan F, Diao S, Yao Y, Zhao B, Li X, Pan Z, Gao Y, Wang Y, Zou D, Wang R, Xu T, Sun C, Yin H, Teng J, Xu Z, Lin Q, Shi S, Shao D, Degalez F, Lagarrigue S, Wang Y, Wang M, Peng M, Rocha D, Charles M, Smith J, Watson K, Buitenhuis AJ, Sahana G, Lund MS, Warren W, Frantz L, Larson G, Lamont SJ, Si W, Zhao X, Li B, Zhang H, Luo C, Shu D, Qu H, Luo W, Li Z, Nie Q, Zhang X, Xiang R, Liu S, Zhang Z, Zhang Z, Liu GE, Cheng H, Yang N, Hu X, Zhou H, Fang L. PMID: 40200121.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    15. Genomic and transcriptomic analyses unveil the genetic basis of green shank trait in small white-feather chickens. Poult Sci. 2025 Apr; 104(4):104912. Kong S, Cai X, Cai B, Xian Y, Zhou Z, Cai D, Yang X, Lin D, Nie Q. PMID: 39985900; PMCID: PMC11904536.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    16. Cell signaling pathways discovery from multi-modal data. bioRxiv. 2025 Feb 08. He C, Simpson C, Cossentino I, Zhang B, Tkachev S, Eddins DJ, Kosters A, Yang J, Sheth S, Levy T, Possemato A, Huang L, Tabatsky E, Gregoretti I, Ariss M, Dandekar D, Ausekar A, Ghosn EEB, Colonna M, Rikova K, Nie Q, Orlova D. PMID: 39975141; PMCID: PMC11839107.
      View in: PubMed   Mentions: 1  
    17. Changes in gut microbiota affect DNA methylation levels and development of chicken muscle tissue. Poult Sci. 2025 Mar; 104(3):104869. Xu Y, Huang Y, Wei S, Tian J, Huang Y, Nie Q, Zhang D. PMID: 39952142; PMCID: PMC11874558.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    18. Combination adjuvant improves influenza virus immunity by downregulation of immune homeostasis genes in lymphocytes. Immunohorizons. 2025 01 24; 9(2). Dollinger E, Hernandez-Davies J, Felgner J, Jain A, Hwang M, Strahsburger E, Nakajima R, Jasinskas A, Nie Q, Pone EJ, Othy S, Davies DH. PMID: 39849993; PMCID: PMC11841980.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    19. Improvement of the accuracy of breeding value prediction for egg production traits in Muscovy duck using low-coverage whole-genome sequence data. Poult Sci. 2025 Feb; 104(2):104812. Ye H, Ji C, Liu X, Bello SF, Guo L, Fang X, Lin D, Mo Y, Lei Z, Cai B, Nie Q. PMID: 39817986; PMCID: PMC11786738.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    20. Superstable lipid vacuoles endow cartilage with its shape and biomechanics. Science. 2025 01 10; 387(6730):eads9960. Ramos R, Pham KT, Prince RC, Leiser-Miller LB, Prasad MS, Wang X, Nordberg RC, Bielajew BJ, Hu JC, Yamaga K, Oh JW, Peng T, Datta R, Astrowskaja A, Almet AA, Burns JT, Liu Y, Guerrero-Juarez CF, Tran BQ, Chu YL, Nguyen AM, Hsi TC, Lim NT, Schoeniger S, Liu R, Pai YL, Vadivel CK, Ingleby S, McKechnie AE, van Breukelen F, Hoehn KL, Rasweiler JJ, Kohara M, Loughry WJ, Weldy SH, Cosper R, Yang CC, Lin SJ, Cooper KL, Santana SE, Bradley JE, Kiebish MA, Digman M, James DE, Merrill AE, Nie Q, Schilling TF, Astrowski AA, Potma EO, García-Castro MI, Athanasiou KA, Behringer RR, Plikus MV. PMID: 39787221.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    21. Exploring variances in meat quality between Qingyuan partridge chicken and Cobb broiler: Insights from combined multi-omics analysis. Poult Sci. 2025 Feb; 104(2):104666. Yang X, Cai B, Zhang Z, Mo Y, Zhou Z, Wu R, Kong S, Cai D, Zhang R, Li Z, Nie Q. PMID: 39721276; PMCID: PMC11732453.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    22. Detecting global and local hierarchical structures in cell-cell communication using CrossChat. Nat Commun. 2024 12 03; 15(1):10542. Wang X, Almet AA, Nie Q. PMID: 39627184; PMCID: PMC11615294.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    23. Cross-species single-cell analysis reveals divergence and conservation of peripheral blood mononuclear cells. BMC Genomics. 2024 Dec 02; 25(1):1169. Zhang S, Fang X, Chang M, Zheng M, Guo L, Xu Y, Shu J, Nie Q, Li Z. PMID: 39623297; PMCID: PMC11613757.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    24. Statistically principled feature selection for single cell transcriptomics. bioRxiv. 2024 Oct 15. Dollinger E, Silkwood K, Atwood S, Nie Q, Lander AD. PMID: 39463971; PMCID: PMC11507810.
      View in: PubMed   Mentions:
    25. Single-cell transcriptomics reveals aberrant skin-resident cell populations and identifies fibroblasts as a determinant in rosacea. Nat Commun. 2024 10 09; 15(1):8737. Chen M, Yang L, Zhou P, Jin S, Wu Z, Tan Z, Xiao W, Xu S, Zhu Y, Wang M, Jian D, Liu F, Tang Y, Zhao Z, Huang Y, Shi W, Xie H, Nie Q, Wang B, Deng Z, Li J. PMID: 39384741; PMCID: PMC11464544.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    26. Leveraging gene correlations in single cell transcriptomic data. BMC Bioinformatics. 2024 Sep 18; 25(1):305. Silkwood K, Dollinger E, Gervin J, Atwood S, Nie Q, Lander AD. PMID: 39294560; PMCID: PMC11411778.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    27. CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics. Nat Protoc. 2025 Jan; 20(1):180-219. Jin S, Plikus MV, Nie Q. PMID: 39289562.
      View in: PubMed   Mentions: 213     Fields:    Translation:HumansAnimalsCells
    28. The first embryonic landscape of G-quadruplexes related to myogenesis. BMC Biol. 2024 Sep 11; 22(1):194. Guo L, Huang W, Wen Q, Zhang S, Bordbar F, Xiao Z, Nie Q. PMID: 39256800; PMCID: PMC11389323.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    29. LMNA-Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-Derived iPSC Differentiation Support Cell Type and Lineage-Specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency. Cells. 2024 09 03; 13(17). Zaragoza MV, Bui TA, Widyastuti HP, Mehrabi M, Cang Z, Sha Y, Grosberg A, Nie Q. PMID: 39273049; PMCID: PMC11394257.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    30. Expression profiling and single nucleotide polymorphism of mitogen-activated protein kinase kinase kinase 8 MAP3K8 in white muscovy ducks (Cairina moschata). Gene. 2025 Jan 10; 932:148901. Bello SF, Xu H, Bolaji UO, Aloryi KD, Adeola AC, Gibril BAA, Popoola MA, Zhu W, Zhang D, Zhang X, Ji C, Nie Q. PMID: 39209181.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    31. 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: 9     Fields:    Translation:HumansAnimalsCells
    32. Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics. Nat Methods. 2024 Oct; 21(10):1806-1817. Almet AA, Tsai YC, Watanabe M, Nie Q. PMID: 39187683; PMCID: PMC11466815.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    33. Small data methods in omics: the power of one. Nat Methods. 2024 Sep; 21(9):1597-1602. Johnston KG, Grieco SF, Nie Q, Theis FJ, Xu X. PMID: 39174710; PMCID: PMC12067744.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    34. 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: 25     Fields:    Translation:AnimalsCells
    35. DRML-Ensemble: drug repurposing method based on feature construction of multi-layer ensemble. J Mol Model. 2024 Jul 31; 30(8):296. Zhang M, He H, Xie J, Nie Q. PMID: 39083073.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    36. Effects of long-time and short-time heat stress on the meat quality of geese. Poult Sci. 2024 Oct; 103(10):104112. Yang Y, Zhang S, Peng H, Chen G, Nie Q, Zhang X, Luo W. PMID: 39106699; PMCID: PMC11343063.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    37. Integrated Single-Cell Analysis Reveals Spatially and Temporally Dynamic Heterogeneity in Fibroblast States during Wound Healing. J Invest Dermatol. 2025 Mar; 145(3):645-659.e25. Almet AA, Liu Y, Nie Q, Plikus MV. PMID: 39019149; PMCID: PMC12324929.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    38. Genome-wide mapping of the binding sites of myocyte enhancer factor 2A in chicken primary myoblasts. Poult Sci. 2024 Oct; 103(10):104097. Wang X, Zhang J, Su J, Huang T, Lian L, Nie Q, Zhang X, Li J, Wang Y. PMID: 39094502; PMCID: PMC11345569.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    39. 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:
    40. VNN1 Gene Expression and Polymorphisms Associated with Chicken Carcass Traits. Animals (Basel). 2024 Jun 26; 14(13). Zhang S, Fang X, Wu R, Nie Q, Li Z. PMID: 38998000; PMCID: PMC11240768.
      View in: PubMed   Mentions:
    41. 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: 31     Fields:    Translation:HumansAnimalsCells
    42. 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: 6     Fields:    Translation:AnimalsCells
    43. Metabolomics reveals the reasons for the occurrence of Pendulous-comb related to egg production performance. Poult Sci. 2024 Aug; 103(8):103867. Cai D, Zhou Z, Cai B, Wang Z, Ju X, Kong S, Yang X, Lin D, Nie Q. PMID: 38820880; PMCID: PMC11167520.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    44. Genetic characteristics and selection signatures between Southern Chinese local and commercial chickens. Poult Sci. 2024 Jul; 103(7):103863. Qi L, Xiao L, Fu R, Nie Q, Zhang X, Luo W. PMID: 38810566; PMCID: PMC11166977.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    45. Using multiomics to explore the weight differences between genders in Muscovy ducks. Poult Sci. 2024 Jul; 103(7):103787. Tian J, Tan L, Wei S, Zhu W, Ji C, Yao Z, Xu Y, Nie Q. PMID: 38743967; PMCID: PMC11108995.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    46. A large-scale comparison of the meat quality characteristics of different chicken breeds in South China. Poult Sci. 2024 Jun; 103(6):103740. Xiao L, Qi L, Fu R, Nie Q, Zhang X, Luo W. PMID: 38701629; PMCID: PMC11087722.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    47. Comprehensive analysis of differentially expressed mRNA profiles in chicken jejunum and cecum following Eimeria maxima infection. Poult Sci. 2024 Jun; 103(6):103716. Jebessa E, Bello SF, Xu Y, Cai B, Tuli MD, Girma M, Bordbar F, Hanotte O, Nie Q. PMID: 38703453; PMCID: PMC11087723.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    48. MeRIP sequencing reveals the regulation of N6-methyladenosine in muscle development between hypertrophic and leaner broilers. Poult Sci. 2024 Jun; 103(6):103708. Wang Z, Ju X, Li K, Cai D, Zhou Z, Nie Q. PMID: 38631230; PMCID: PMC11040168.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    49. 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
    50. Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data. Biophys J. 2024 09 03; 123(17):2849-2859. Barcenas M, Bocci F, Nie Q. PMID: 38504523; PMCID: PMC11393678.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    51. Assessment of selective breeding effects and selection signatures in Qingyuan partridge chicken and its strains. Poult Sci. 2024 May; 103(5):103626. Kong S, Cai B, Li X, Zhou Z, Fang X, Yang X, Cai D, Luo X, Guo S, Nie Q. PMID: 38513549; PMCID: PMC10966089.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    52. MicroRNA expression profile of chicken jejunum in different time points Eimeria maxima infection. Front Immunol. 2023; 14:1331532. Jebessa E, Bello SF, Guo L, Tuli MD, Hanotte O, Nie Q. PMID: 38288128; PMCID: PMC10823020.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    53. MYH1G-AS is a chromatin-associated lncRNA that regulates skeletal muscle development in chicken. Cell Mol Biol Lett. 2024 Jan 04; 29(1):9. Cai B, Ma M, Yuan R, Zhou Z, Zhang J, Kong S, Lin D, Lian L, Li J, Zhang X, Nie Q. PMID: 38177995; PMCID: PMC10765903.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    54. The transmembrane protein TMEM182 promotes fat deposition and alters metabolomics and lipidomics. Int J Biol Macromol. 2024 Feb; 259(Pt 1):129144. Chen G, Lin Z, Peng H, Zhang S, Zhang Z, Zhang X, Nie Q, Luo W. PMID: 38181918.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    55. LncEDCH1 g.1703613 T>C regulates chicken carcass traits by targeting miR-196-2-3p. Poult Sci. 2024 Mar; 103(3):103412. Yuan R, Cai B, Ma M, Zhao C, Xian Y, Nie Q, Zhang X, Zhang D. PMID: 38198912; PMCID: PMC10825527.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    56. Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population. Poult Sci. 2024 Feb; 103(2):103341. Pan R, Qi L, Xu Z, Zhang D, Nie Q, Zhang X, Luo W. PMID: 38134459; PMCID: PMC10776626.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    57. 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: 27  
    58. Metabolomic, lipidomic, and proteomic profiles provide insights on meat quality differences between Shitou and Wuzong geese. Food Chem. 2024 Apr 16; 438:137967. Chen G, Qi L, Zhang S, Peng H, Lin Z, Zhang X, Nie Q, Luo W. PMID: 37979274.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    59. DNA methylation in poultry: a review. J Anim Sci Biotechnol. 2023 Nov 05; 14(1):138. Ju X, Wang Z, Cai D, Bello SF, Nie Q. PMID: 37925454; PMCID: PMC10625706.
      View in: PubMed   Mentions: 4  
    60. 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:
    61. Chicken muscle antibody array reveals the regulations of LDHA on myoblast differentiation through energy metabolism. Int J Biol Macromol. 2024 Jan; 254(Pt 1):127629. Zhang Z, Luo W, Chen G, Chen J, Lin S, Ren T, Lin Z, Zhao C, Wen H, Nie Q, Meng X, Zhang X. PMID: 37890747.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    62. 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: 7     Fields:    Translation:Cells
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    277. Stem cell niche structure as an inherent cause of undulating epithelial morphologies. Biophys J. 2013 Jan 08; 104(1):237-46. Ovadia J, Nie Q. PMID: 23332076; PMCID: PMC3540249.
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    278. Dynamics and precision in retinoic acid morphogen gradients. Curr Opin Genet Dev. 2012 Dec; 22(6):562-9. Schilling TF, Nie Q, Lander AD. PMID: 23266215; PMCID: PMC3790664.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    279. External noise control in inherently stochastic biological systems. J Math Phys. 2012 Nov; 53(11):115616. Zheng L, Chen M, Nie Q. PMID: 23213267; PMCID: PMC3505197.
      View in: PubMed   Mentions: 6  
    280. A reaction-diffusion mechanism influences cell lineage progression as a basis for formation, regeneration, and stability of intestinal crypts. BMC Syst Biol. 2012 Jul 31; 6:93. Zhang L, Lander AD, Nie Q. PMID: 22849824; PMCID: PMC3434027.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    281. Deep sequencing-based transcriptome analysis of chicken spleen in response to avian pathogenic Escherichia coli (APEC) infection. PLoS One. 2012; 7(7):e41645. Nie Q, Sandford EE, Zhang X, Nolan LK, Lamont SJ. PMID: 22860004; PMCID: PMC3409229.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    282. Protein scaffolds can enhance the bistability of multisite phosphorylation systems. PLoS Comput Biol. 2012; 8(6):e1002551. Chan C, Liu X, Wang L, Bardwell L, Nie Q, Enciso G. PMID: 22737061; PMCID: PMC3380838.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    283. Cellular retinoic acid-binding proteins are essential for hindbrain patterning and signal robustness in zebrafish. Development. 2012 Jun; 139(12):2150-5. Cai AQ, Radtke K, Linville A, Lander AD, Nie Q, Schilling TF. PMID: 22619388; PMCID: PMC3357909.
      View in: PubMed   Mentions: 36     Fields:    Translation:AnimalsCells
    284. A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems. J Comput Phys. 2012 Jun 01; 231(15):5062-5077. Lo WC, Chen L, Wang M, Nie Q. PMID: 22773849; PMCID: PMC3389814.
      View in: PubMed   Mentions: 5  
    285. The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits. PLoS One. 2012; 7(4):e33851. Shen X, Zeng H, Xie L, He J, Li J, Xie X, Luo C, Xu H, Zhou M, Nie Q, Zhang X. PMID: 22496769; PMCID: PMC3322132.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    286. Free extracellular diffusion creates the Dpp morphogen gradient of the Drosophila wing disc. Curr Biol. 2012 Apr 24; 22(8):668-75. Zhou S, Lo WC, Suhalim JL, Digman MA, Gratton E, Nie Q, Lander AD. PMID: 22445299; PMCID: PMC3338872.
      View in: PubMed   Mentions: 78     Fields:    Translation:AnimalsCells
    287. Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain. Mol Syst Biol. 2012; 8:613. Zhang L, Radtke K, Zheng L, Cai AQ, Schilling TF, Nie Q. PMID: 23010996; PMCID: PMC3472692.
      View in: PubMed   Mentions: 45     Fields:    Translation:AnimalsCells
    288. Noise filtering tradeoffs in spatial gradient sensing and cell polarization response. BMC Syst Biol. 2011 Dec 13; 5:196. Chou CS, Bardwell L, Nie Q, Yi TM. PMID: 22166067; PMCID: PMC3268761.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    289. Mathematical analysis of steady-state solutions in compartment and continuum models of cell polarization. Math Biosci Eng. 2011 Oct 01; 8(4):1135-68. Zheng Z, Chou CS, Yi TM, Nie Q. PMID: 21936604; PMCID: PMC3806509.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    290. Analysis of muscle and ovary transcriptome of Sus scrofa: assembly, annotation and marker discovery. DNA Res. 2011 Oct; 18(5):343-51. Nie Q, Fang M, Jia X, Zhang W, Zhou X, He X, Zhang X. PMID: 21729922; PMCID: PMC3190955.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    291. Operator Splitting Implicit Integration Factor Methods for Stiff Reaction-Diffusion-Advection Systems. J Comput Phys. 2011 Jul; 230(15):5996-6009. Zhao S, Ovadia J, Liu X, Zhang YT, Nie Q. PMID: 21666863; PMCID: PMC3109754.
      View in: PubMed   Mentions: 6  
    292. Identification and characterization of the pig ABIN-1 gene and investigation of its association with reproduction traits. J Genet. 2011 Apr 19; 90(1):e10-20. Fang M, Du H, Hu Y, Zhou X, Ouyang H, Zhang W, Jia X, Li J, Wang Y, Nie Q, Zhang X. PMID: 21677409.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    293. Size-normalized Robustness of Dpp Gradient in Drosophila Wing Imaginal Disc. J Mech Mater Struct. 2011 Jan 01; 6(1-4):321-350. Lander AD, Nie Q, Vargas B, Wan FY. PMID: 21841941; PMCID: PMC3154743.
      View in: PubMed   Mentions: 10  
    294. Ultrasensitive responses and specificity in cell signaling. BMC Syst Biol. 2010 Aug 25; 4:119. Haney S, Bardwell L, Nie Q. PMID: 20735856; PMCID: PMC2940771.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    295. Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms. BMC Syst Biol. 2010 Aug 09; 4:107. Christley S, Lee B, Dai X, Nie Q. PMID: 20696053; PMCID: PMC2936904.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    296. A critical quantity for noise attenuation in feedback systems. PLoS Comput Biol. 2010 Apr 29; 6(4):e1000764. Wang L, Xin J, Nie Q. PMID: 20442870; PMCID: PMC2861702.
      View in: PubMed   Mentions: 28     Fields:    Translation:AnimalsCells
    297. Identification and characterization of adipose triglyceride lipase (ATGL) gene in birds. Mol Biol Rep. 2010 Oct; 37(7):3487-93. Nie Q, Hu Y, Xie L, Zhang C, Shen X, Zhang X. PMID: 20091124.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    298. Incorporating existing network information into gene network inference. PLoS One. 2009 Aug 27; 4(8):e6799. Christley S, Nie Q, Xie X. PMID: 19710931; PMCID: PMC2729382.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    299. Ovol2 suppresses cell cycling and terminal differentiation of keratinocytes by directly repressing c-Myc and Notch1. J Biol Chem. 2009 Oct 16; 284(42):29125-35. Wells J, Lee B, Cai AQ, Karapetyan A, Lee WJ, Rugg E, Sinha S, Nie Q, Dai X. PMID: 19700410; PMCID: PMC2781457.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansAnimalsCells
    300. Localized Ectopic Expression of Dpp Receptors in a Drosophila Embryo. Stud Appl Math. 2009 Aug 01; 123(2):175-214. Lander AD, Nie Q, Wan FY, Zhang YT. PMID: 20160891; PMCID: PMC2774827.
      View in: PubMed   Mentions: 5  
    301. 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.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    302. 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:
    303. 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: 10     Fields:    Translation:HumansCells
    304. 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: 156     Fields:    Translation:AnimalsCells
    305. 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: 64     Fields:    Translation:HumansAnimalsCells
    306. 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: 61     Fields:    Translation:AnimalsCells
    307. 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: 23     Fields:    Translation:AnimalsCells
    308. 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
    309. cDNA cloning, characterization, and variation analysis of chicken adipose triglyceride lipase (ATGL) gene. Mol Cell Biochem. 2009 Jan; 320(1-2):67-74. Nie Q, Fang M, Xie L, Shi J, Zhang X. PMID: 18679582.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    310. 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  
    311. 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: 128     Fields:    Translation:AnimalsCells
    312. 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
    313. 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: 12     Fields:    Translation:AnimalsCells
    314. 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: 38     Fields:    Translation:Cells
    315. 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
    316. 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: 17     Fields:    Translation:AnimalsCells
    317. 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: 36     Fields:    Translation:AnimalsCells
    318. 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: 20     Fields:    
    319. 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
    320. [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
    321. 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: 76     Fields:    Translation:HumansAnimals
    322. 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: 153     Fields:    Translation:AnimalsCells
    323. 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: 11     Fields:    Translation:HumansCells
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