Menu Close

Recent publications from CMCF.

Yan L, Cheng J, Nie Q and Sun X. Dissecting multilayer cell-cell communications with signaling feedback loops from spatial transcriptomics data. (2025) Genome Res. 35, 1400-1414 Pubmed Genome Res PMC Article
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 and Monuki ES. Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model. (2025) Nat Commun. 16, 5149 Pubmed Nat Commun PMC Article
Ramirez CB, Ahn IS, Rubtsova VI, Cely I, Le J, Kim J, Jung S, Kelly ME, Kim Y, Bae H, Song WS, Alam YH, Zhang G, Diamante G, Chao A, Hoffner L, Anica A, Le I, Lopez ML, Tamburini IJ, Moyer EM, Tsai A, Yang Q, Dai X, Piomelli D, Lee G, Yang X and Jang C. Circulating glycerate predicts resilience to fructose-induced hepatic steatosis. (2025) Cell Metab. 37, 1223-1234.e5 Pubmed Cell Metab PMC Article
Yen YP, Lung TH, Liau ES, Wu CC, Huang GL, Hsu FY, Chang M, Yang ZD, Huang CY, Zheng Z, Zhao W, Hung JH, He C, Nie Q and Chen JA. The motor neuron m6A repertoire governs neuronal homeostasis and FTO inhibition mitigates ALS symptom manifestation. (2025) Nat Commun. 16, 4063 Pubmed Nat Commun PMC Article
Zhang RZ, Ezhov I, Balcerak M, Zhu A, Wiestler B, Menze B and Lowengrub JS. Personalized predictions of Glioblastoma infiltration: Mathematical models, Physics-Informed Neural Networks and multimodal scans. (2025) Med Image Anal. 101, 103423 Pubmed Med Image Anal
Lo Vercio LD, Green RM, Dauter A, Barretto EC, Vidal-García M, Devine J, Marchini M, Robertson S, Zhao X, Mahika A, Shakir MB, Guo S, Boughner JC, Szabo-Rogers H, Dean W, Lander AD, Marcucio RS, Forkert ND and Hallgrímsson B. Quantifying the relationship between cell proliferation and morphology during development of the face. (2025) Development. 152, Pubmed Development PMC Article
Zhu Y, Wunderlich Z and Lander AD. Epithelial cell competition is promoted by signaling from immune cells. (2025) Nat Commun. 16, 3710 Pubmed Nat Commun PMC Article
Tan Y, Wang A, Wang Z, Lin W, Yan Y, Nie Q and Shi J. Transfer learning of multicellular organization via single-cell and spatial transcriptomics. (2025) PLoS Comput Biol. 21, e1012991 Pubmed PLoS Comput Biol PMC Article
Almet AA, Liu Y, Nie Q and Plikus MV. Integrated Single-Cell Analysis Reveals Spatially and Temporally Dynamic Heterogeneity in Fibroblast States during Wound Healing. (2025) J Invest Dermatol. 145, 645-659.e25 Pubmed J Invest Dermatol
Chen Z, Dragan M, Sun P, Haensel D, Vu R, Cui L, Zhu P, Yang N, Shi Y and Dai X. The AhR-Ovol1-Id1 regulatory axis in keratinocytes promotes epidermal and immune homeostasis in atopic dermatitis-like skin inflammation. (2025) Cell Mol Immunol. 22, 300-315 Pubmed Cell Mol Immunol PMC Article
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 and Orlova D. Cell signaling pathways discovery from multi-modal data. (2025) bioRxiv. Pubmed bioRxiv PMC Article
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 and Plikus MV. Superstable lipid vacuoles endow cartilage with its shape and biomechanics. (2025) Science. 387, eads9960 Pubmed Science
Dollinger E, Hernandez-Davies J, Felgner J, Jain A, Hwang M, Strahsburger E, Nakajima R, Jasinskas A, Nie Q, Pone EJ, Othy S and Davies DH. Combination adjuvant improves influenza virus immunity by downregulation of immune homeostasis genes in lymphocytes. (2025) Immunohorizons. 9, Pubmed Immunohorizons PMC Article
Jin S, Plikus MV and Nie Q. CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics. (2025) Nat Protoc. 20, 180-219 Pubmed Nat Protoc
Olaranont N, Wei C, Lowengrub J and Wu M. Chemomechanical regulation of growing tissues from a thermodynamically-consistent framework and its application to tumor spheroid growth. (2024) ArXiv. Pubmed ArXiv PMC Article
Wang X, Almet AA and Nie Q. Detecting global and local hierarchical structures in cell-cell communication using CrossChat. (2024) Nat Commun. 15, 10542 Pubmed Nat Commun PMC Article
Reyes R, Lander AD and Nahmad M. Dynamic readout of the Hh gradient in the wing disc reveals pattern-specific tradeoffs between robustness and precision. (2024) Elife. 13, Pubmed Elife PMC Article
Almet AA, Tsai YC, Watanabe M and Nie Q. Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics. (2024) Nat Methods. 21, 1806-1817 Pubmed Nat Methods PMC Article
Dollinger E, Silkwood K, Atwood S, Nie Q and Lander AD. Statistically principled feature selection for single cell transcriptomics. (2024) bioRxiv. Pubmed bioRxiv PMC Article
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 and Li J. Single-cell transcriptomics reveals aberrant skin-resident cell populations and identifies fibroblasts as a determinant in rosacea. (2024) Nat Commun. 15, 8737 Pubmed Nat Commun PMC Article
Barcenas M, Bocci F and Nie Q. Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data. (2024) Biophys J. 123, 2849-2859 Pubmed Biophys J PMC Article
Johnston KG, Grieco SF, Nie Q, Theis FJ and Xu X. Small data methods in omics: the power of one. (2024) Nat Methods. 21, 1597-1602 Pubmed Nat Methods PMC Article
Zaragoza MV, Bui TA, Widyastuti HP, Mehrabi M, Cang Z, Sha Y, Grosberg A and Nie Q. -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. (2024) Cells. 13, Pubmed Cells PMC Article
Silkwood K, Dollinger E, Gervin J, Atwood S, Nie Q and Lander AD. Leveraging gene correlations in single cell transcriptomic data. (2024) BMC Bioinformatics. 25, 305 Pubmed BMC Bioinformatics PMC Article
Corrette J, Li J, Shao H, Veerasubramanian PK, Spakowitz A, Downing TL and Allard J. Nucleosome placement and polymer mechanics explain genomic contacts on 100kbp scales. (2024) bioRxiv. Pubmed bioRxiv PMC Article
Dong P, Zhang S, Gandin V, Xie L, Wang L, Lemire AL, Li W, Otsuna H, Kawase T, Lander AD, Chang HY and Liu ZJ. Cohesin prevents cross-domain gene coactivation. (2024) Nat Genet. 56, 1654-1664 Pubmed Nat Genet PMC Article
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 and Liu WF. Hydrogel crosslinking modulates macrophages, fibroblasts, and their communication, during wound healing. (2024) Nat Commun. 15, 6820 Pubmed Nat Commun PMC Article
Caldwell MG and Lander AD. The inherent fragility of collective proliferative control. (2024) bioRxiv. Pubmed bioRxiv PMC Article
Zhang M, He H, Xie J and Nie Q. DRML-Ensemble: drug repurposing method based on feature construction of multi-layer ensemble. (2024) J Mol Model. 30, 296 Pubmed J Mol Model
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 and Skowronska-Krawczyk D. Polyunsaturated Fatty Acid - mediated Cellular Rejuvenation for Reversing Age-related Vision Decline. (2024) bioRxiv. Pubmed bioRxiv PMC Article
Zhou P, Bocci F, Li T and Nie Q. Spatial transition tensor of single cells. (2024) Nat Methods. 21, 1053-1062 Pubmed Nat Methods PMC Article
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 and Marangoni F. Interruption of the intratumor CD8 T cell:Treg crosstalk improves the efficacy of PD-1 immunotherapy. (2024) Cancer Cell. 42, 1051-1066.e7 Pubmed Cancer Cell PMC Article
Ramos R, Swedlund B, Ganesan AK, Morsut L, Maini PK, Monuki ES, Lander AD, Chuong CM and Plikus MV. Parsing patterns: Emerging roles of tissue self-organization in health and disease. (2024) Cell. 187, 3165-3186 Pubmed Cell PMC Article
Moreno JA, Dudchenko O, Feigin CY, Mereby SA, Chen Z, Ramos R, Almet AA, Sen H, Brack BJ, Johnson MR, Li S, Wang W, Gaska JM, Ploss A, Weisz D, Omer AD, Yao W, Colaric Z, Kaur P, Leger JS, Nie Q, Mena A, Flanagan JP, Keller G, Sanger T, Ostrow B, Plikus MV, Kvon EZ, Aiden EL and Mallarino R. Emx2 underlies the development and evolution of marsupial gliding membranes. (2024) Nature. 629, 127-135 Pubmed Nature PMC Article
Duan J, Ngo MN, Karri SS, Tsoi LC, Gudjonsson JE, Shahbaba B, Lowengrub J and Andersen B. tauFisher predicts circadian time from a single sample of bulk and single-cell pseudobulk transcriptomic data. (2024) Nat Commun. 15, 3840 Pubmed Nat Commun PMC Article
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
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
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
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
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
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
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
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
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
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
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
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
He C, Zhou P and Nie Q. exFINDER: identify external communication signals using single-cell transcriptomics data. (2023) bioRxiv. Pubmed bioRxiv 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Liu R, Dollinger E and Nie Q. Machine Learning of Single Cell Transcriptomic Data From anti-PD-1 Responders and Non-responders Reveals Distinct Resistance Mechanisms in Skin Cancers and PDAC. (2021) Front Genet. 12, 806457 Pubmed Front Genet PMC Article
Wang H, Zhao J, Nie Q, Zheng C and Sun X. Dissecting Spatiotemporal Structures in Spatial Transcriptomics via Diffusion-Based Adversarial Learning. (2024) Research (Wash D C). 7, 0390 Pubmed Research (Wash D C) PMC Article