Center for Cancer Systems Biology
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Publications Supported by U54 CA217378, "Complexity, Cooperation and Community in Cancer"
Vu T, Vallmitjana A, Gu J, La K, Xu Q, Flores J, Zimak J, Shiu J, Hosohama L, Wu J, Douglas C, Waterman ML, Ganesan A, Hedde PN, Gratton E, Zhao W. Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis. Nat Commun. 2022 Jan 10;13(1):169. doi: 10.1038/s41467-021-27787-0.
Yan H, Ramirez-Guerrero D, Lowengrub J, Wu M. Stress generation, relaxation and size control in confined tumor growth. PLoS Comput Biol. 2021 Dec 21;17(12):e1009701. doi: 10.1371/journal.pcbi.1009701.
Chen GT, Tifrea DF, Murad R, Habowski AN, Lyou Y, Duong MR, Hosohama L, Mortazavi A, Edwards RA, Waterman ML. Disruption of β-Catenin-Dependent Wnt Signaling in Colon Cancer Cells Remodels the Microenvironment to Promote Tumor Invasion. Mol Cancer Res. 2021 Nov 19. doi: 10.1158/1541-7786.MCR-21-0349.
Fu L, Cao Y, Wu J, Peng Q, Nie Q, Xie X. UFold: fast and accurate RNA secondary structure prediction with deep learning. Nucleic Acids Res. 2021 Nov 18:gkab1074. doi: 10.1093/nar/gkab1074.
Bocci F, Zhou P, Nie Q. Single-Cell RNA-seq Analysis Reveals the Acquition of Cancer Stem Cell Traits and Increase of Cell-Cell Signaling during EMT Progression. Cancers (Basel). 2021 Nov 16;13(22):5726. doi: 10.3390/cancers13225726.
Paul D, Komarova NL. Multi-scale network targeting: A holistic systems-biology approach to cancer treatment. Prog Biophys Mol Biol. 2021 Oct;165:72-79. doi: 10.1016/j.pbiomolbio.2021.08.004.
Ewald ML, Chen YH, Lee AP, Hughes CCW. The vascular niche in next generation microphysiological systems. Lab Chip. 2021 Sep 7;21(17):3244-3262. doi: 10.1039/d1lc00530h.
Wang MX, Lander A, Lai PY. Regulatory feedback effects on tissue growth dynamics in a two-stage cell lineage model. Phys Rev E. 2021 Sep;104(3-1):034405. doi: 10.1103/PhysRevE.104.034405.
Bergman DR, Karikomi MK, Yu M, Nie Q, MacLean AL. Modeling the effects of EMT-immune dynamics on carcinoma disease progression. Commun Biol. 2021 Aug 18;4(1):983. doi: 10.1038/s42003-021-02499-y.
Shirure VS, Hughes CCW, George SC. Engineering Vascularized Organoid-on-a-Chip Models. Annu Rev Biomed Eng. 2021 Jul 13;23:141-167. doi: 10.1146/annurev-bioeng-090120-094330.
Cao Y, Fu L, Wu J, Peng Q, Nie Q, Zhang J, Xie X. SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration. Bioinformatics. 2021 Jul 12;37(Suppl_1):i317-i326. doi: 10.1093/bioinformatics/btab303.
Hachey SJ, Movsesyan S, Nguyen QH, Burton-Sojo G, Tankanzyan A, Wu J, Hoang T, Hatch MM, Celaya E, Gomez S, Chen GT, Davis RT, Nee K, Pervolarakis N, Lawson DA, Kessenbrock K, Lee AP, Waterman ML, Hughes CCW. An In Vitro Vascularized Micro-Tumor Model of Human Colorectal Cancer Recapitulates In Vivo Drug Responses. Lab Chip. 2021 Apr 7;21(7):1333-1351. doi: 10.1039/d0lc01216e.
Sun X, Zhang J, Nie Q. Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples. PLoS Comput Biol. 2021 Mar 5;17(3):e1008379. doi: 10.1371/journal.pcbi.1008379.
Habowski AN, Habowski TJ, Waterman ML. GECO: gene expression clustering optimization app for non-linear data visualization of patterns. BMC Bioinformatics. 2021 Jan 25;22(1):29. doi: 10.1186/s12859-020-03951-2.
Weiss L, Van den Driessche P, Lowengrub J, Wodarz D, Komarova NL. Effect of feedback regulation on stem cell fractions in tissues and tumors: understanding chemo-resistance in cancer. J. Theo Biol. 2021 Jan 21; 509:110499. doi: 10.1016/j.jtbi.2020.110499
Lomeli LM, Iniguez A, Tata P, Jena N, Liu ZY, Van Etten R, Lander AD, Shahbaba B, Lowengrub JS, Minin VN. Optimal experimental design for mathematical models of haematopoiesis. J R Soc Interface. 2021 Jan;18(174):20200729. doi: 10.1098/rsif.2020.0729.
Fu L, Zhang L, Dollinger E, Peng Q, Nie Q, Xie X. Predicting transcription factor binding in single cells through deep learning. Sci Adv. 2020 Dec 18;6(51):eaba9031. doi: 10.1126/sciadv.aba9031.
Dollinger E, Bergman D, Zhou P, Atwood SX, Nie Q. Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers. Cancers (Basel). 2020 Oct 13;12(10):2946. doi: 10.3390/cancers12102946.
Ruiz-Vega R, Chen CF, Razzak E, Vasudeva P, Krasieva TB, Shiu J, Caldwell MG, Yan H, Lowengrub J, Ganesan AK, Lander AD. Dynamics of nevus development implicate cell cooperation in the growth arrest of transformed melanocytes. Elife. 2020 Oct 13; 9:e61026. doi: 10.7554/eLife.61026.
Song Y, Guerrero-Juarez CF, Chen Z, Tang Y, Ma X, Lv C, Bi X, Deng M, Bu L, Tian Y, Liu R, Zhao R, Xu J, Sheng X, Du S, Liu Y, Zhu Y, Shan SJ, Chen HD, Zhao Y, Zhou G, Shuai J, Ren F, Xue L, Ying Z, Dai X, Lengner CJ, Andersen B, Plikus MV, Nie Q, Yu Z. The Msi1-mTOR pathway drives the pathogenesis of mammary and extramammary Paget's disease. Cell Res. 2020 Oct;30(10):854-872. doi: 10.1038/s41422-020-0334-5.
Sha Y, Wang S, Zhou P, Nie Q. Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data. Nucleic Acids Res. 2020 Sep 25;48(17):9505-9520. doi: 10.1093/nar/gkaa725.
Habowski AN, Flesher JL, Bates, JM, Tsai CF, Martin K, Zhao R, Ganesan AK, Edwards RA, Shi T, Wiley HS, Shi Y, Hertel KJ, Waterman ML. Transcriptomic and Proteomic Signatures of Stemness and Differentiation in the Colon Crypt. Nature Comm Biol. 2020 Aug 19; 3(1): 453. doi: 10.1038/s42003-020-01181-z.
Butner JD, Fuentes D, Ozpolat B, Calin GA, Zhou X, Lowengrub J, Cristini V, Wang Z. A multiscale Agent-Based Model of Ductal Carcinoma In Situ. IEEE Trans Biomed Eng. 2020 May;67(5):1450-1461. doi: 10.1109/TBME.2019.2938485.
Tran TQ, Hanse EA, Habowski AN, Li H, Gabra MBI, Yang Y, Lowman XH, Ooi AM, Liao SY, Edwards RA, Waterman ML, Kong M. α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer. Nat Cancer. 2020 Mar;1(3):345-358. doi: 10.1038/s43018-020-0035-5.
Davis RT, Blake K, Ma D, Gabra MBI, Hernandez GA, Phung AT, Yang Y, Maurer D, Lefebvre AEYT, Alshetaiwi H, Xiao Z, Liu J, Locasale JW, Digman MA, Mjolsness E, Kong M, Werb Z, Lawson DA. Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing. Nat Cell Biol. 2020 Mar; 22(3):310-320. doi: 10.1038/s41556-020-0477-0.
Flesher JL, Paterson-Coleman EK, Vasudeva P, Ruiz-Vega R, Marshall M, Pearlman E, MacGregor GR, Neumann J, Ganesan AK. Delineating the role of MITF isoforms in pigmentation and tissue homeostasis Pigment Cell Melanoma Res. 2020 Mar;33(2):279-292. doi: 10.1111/pcmr.12828.
Lu MJ, Liu C, Lowengrub J, Li S. Complex Far-Field Geometries Determine the Stability of Solid Tumor Growth with Chemotaxis. Bull Math Biol. 2020 Mar 12; 82(3):39. doi:10.1007/s11538-020-00716-z.
Alshetaiwi H, Pervolarakis N, McIntyre LL, Ma D, Nguyen Q, Rath JA, Nee K, Hernandez G, Evans K, Torosian L, Silva A, Walsh C, Kessenbrock K. Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics.Sci Immunol. 2020 Feb 21;5(44). pii: eaay6017. doi: 10.1126/sciimmunol.aay6017.
Xie J, Sun J, Feng J, Yang F, Wang J, Wen T, Nie Q. Kernel Differential Subgraph Analysis to Reveal the Key Period Affecting Glioblastoma.Biomolecules. 2020 Feb 17;10(2). pii: E318. doi: 10.3390/biom10020318.
Chen Y, Lowengrub JS.
Tumor growth and calcification in evolving microenvironmental geometries. J Theor Biol. 2019 Feb 21;463:138-154. doi: 10.1016/j.jtbi.2018.12.006. Epub 2018 Dec 5. PMID: 30528340
Lipkova J, Angelikopoulos P, Wu S, Alberts E, Wiestler B, Diehl C, Preibisch C, Pyka T, Combs SE, Hadjidoukas P, Van Leemput K, Koumoutsakos P, Lowengrub J, Menze B. Personalized Radiotherapy Design for Glioblastoma: Integrating Mathematical Tumor Models, Multimodal Scans, and Bayesian Inference. IEEE Trans Med Imaging. 2019 Aug;38(8):1875-1884. doi: 10.1109/TMI.2019.2902044. Epub 2019 Feb 27. PMID: 30835219