Award Abstract # 1763272
NSF-Simons Center for Multiscale Cell Fate Research
NSF Org: |
DMS
Division Of Mathematical Sciences
|
Recipient: |
UNIVERSITY OF CALIFORNIA IRVINE
|
Initial Amendment Date:
|
May 24, 2018 |
Latest Amendment Date:
|
May 4, 2022 |
Award Number: |
1763272 |
Award Instrument: |
Continuing Grant |
Program Manager: |
Zhilan Feng
zfeng@nsf.gov
(703)292-7523
DMS
Division Of Mathematical Sciences
MPS
Directorate for Mathematical and Physical Sciences
|
Start Date: |
July 1, 2018 |
End Date: |
June 30, 2025 (Estimated) |
Total Intended Award
Amount: |
$5,000,000.00 |
Total Awarded Amount to
Date: |
$5,000,000.00 |
Funds Obligated to Date:
|
FY 2018 = $2,750,000.00
FY 2019 = $1,050,000.00
FY 2020 = $400,000.00
FY 2021 = $411,946.00
FY 2022 = $388,054.00
|
History of Investigator:
|
-
Qing
Nie
(Principal Investigator)
qnie@uci.edu
-
Arthur
Lander
(Co-Principal Investigator)
-
John
Lowengrub
(Co-Principal Investigator)
-
Xing
Dai
(Co-Principal Investigator)
-
Jun
Allard
(Co-Principal Investigator)
|
Recipient Sponsored Research
Office: |
University of California-Irvine
160 ALDRICH HALL
IRVINE
CA
US
92697-0001
(949)824-7295
|
Sponsor Congressional
District: |
47
|
Primary Place of
Performance: |
University of California-Irvine
540F Rowland Hall
Irvine
CA
US
92697-3875
|
Primary Place of
Performance Congressional District: |
47
|
Unique Entity Identifier
(UEI): |
MJC5FCYQTPE6
|
Parent UEI: |
MJC5FCYQTPE6
|
NSF Program(s): |
Genetic Mechanisms, OFFICE OF MULTIDISCIPLINARY AC, Cross-BIO Activities, MATHEMATICAL SCIENCES RES INST, Physiol Mechs & Biomechanics
|
Primary Program Source:
|
01001819DB NSF RESEARCH & RELATED ACTIVIT
01001920DB NSF RESEARCH & RELATED ACTIVIT
01002021DB NSF RESEARCH & RELATED ACTIVIT
01002122DB NSF RESEARCH & RELATED ACTIVIT
01002223DB NSF RESEARCH & RELATED ACTIVIT
01002122DB NSF RESEARCH & RELATED ACTIVIT
|
Program Reference
Code(s): |
068Z,
7465
|
Program Element Code(s):
|
111200,
125300,
727500,
733300,
765800
|
Award Agency Code: |
4900
|
Fund Agency Code: |
4900
|
Assistance Listing
Number(s): |
47.049, 47.074
|
ABSTRACT

The NSF-Simons Center for Multiscale Cell Fate Research at the University of California, Irvine will provide a stimulating and empowering intellectual and physical environment for innovative team research at the interface between mathematics and biology. A cell's fate -- differentiation into a specific biological cell type -- is determined by several interlinked factors: cell-intrinsic mechanisms, signals from the local environment outside the cell, and messages the cell receives from other cells. Despite unprecedented amounts of experimental data at single-cell resolution, how cell fate is determined remains not fully understood. Challenges to development of a theory arise from information crosstalk at multiple temporal and spatial scales, as well as from the need to mine, integrate, and model the new single-cell "big data" derived from experimental measurements. To address these challenges and to establish a founding paradigm for multiscale cell fate research, a team of mathematical scientists and biologists will develop novel mathematical, computational, and statistical tools to analyze cell fate through a multiscale lens. The Center will carry out a coherent program for community building, interdisciplinary training and workforce development, and diversity enhancement to expand the mathematics-biology interface and to promote the convergence of mathematical and biological sciences. The Center will produce cohorts of interconnected young researchers and will nationally seed the next generation's laboratories. The knowledge gained will create new multiscale mathematics for analyzing big data and modeling complex systems, with broader applications to regenerative medicine, embryonic development, and birth defects.
The NSF-Simons Center for Multiscale Cell Fate Research will establish new understanding of mechanisms and principles of cell fate control through investigation of emerging behavior of cells across scales. The study aims for transformative insight into cell fate, with a focus on three biological themes: cellular complexity and plasticity in skin, stochastic dynamics and migration of neural crest cells, and epigenetic control of stem cell specification. While each theme addresses different gaps in understanding of cell fate, they all emphasize emergent complexity arising from multiscale interactions, and they share several mathematical aspects. The Center aims to develop new mathematical methods driven by these specific cell-fate questions as well as broader biological applications. Data-driven and principle-based multiscale models of cell fate will guide experiments, with subsequent feedback to the modeling efforts. Three concerted efforts will be made to enhance overall capacity of research and training at the interface between mathematics and biology: 1) expanding mathematical sciences proximal to the biology interface, 2) connecting mathematical scientists across the spectrum, and 3) fostering mathematical scientists' ability to connect directly to experiments. A wide range of new and closely interconnected community-building and outreach programs, including community-initiated Interdisciplinary Opportunity Awards, a Convergence Accelerator Team program with national reach, a BioBridge Clinic on experimental techniques, and a Mathematical Experience through Learning Research program for high school students, will be developed and implemented to achieve the Center's ambitious goals.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Walker, Benjamin L. and Nie, Qing
"NeST: nested hierarchical structure identification in spatial transcriptomic data"
Nature Communications
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, 2023
https://doi.org/10.1038/s41467-023-42343-x
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Walker B, Q. Nie.
"NeST: Nested hierarchical structure identification in spatial transcriptomics data"
Nature communications
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Wan, Biao and Yu, Jin
"Two-phase dynamics of DNA supercoiling based on DNA polymer physics"
Biophysical Journal
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https://doi.org/10.1016/j.bpj.2022.01.001
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Wang, Lingyan and Song, Kaiyuan and Yu, Jin and Da, Lin-Tai
"Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process"
Acta Biochimica et Biophysica Sinica
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Wang, Shuxiong and Drummond, Michael L. and Guerrero-Juarez, Christian F. and Tarapore, Eric and MacLean, Adam L. and Stabell, Adam R. and Wu, Stephanie C. and Gutierrez, Guadalupe and That, Bao T. and Benavente, Claudia A. and Nie, Qing and Atwood, Scott
"Single cell transcriptomics of human epidermis identifies basal stem cell transition states"
Nature Communications
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https://doi.org/10.1038/s41467-020-18075-7
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Wang, Shuxiong and Karikomi, Matthew and MacLean, Adam L and Nie, Qing
"Cell lineage and communication network inference via optimization for single-cell transcriptomics"
Nucleic Acids Research
, 2019
10.1093/nar/gkz204
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Wang, Xiaojie and Ramos, Raul and Phan, Anne Q. and Yamaga, Kosuke and Flesher, Jessica L. and Jiang, Shan and Oh, Ji Won and Jin, Suoqin and Jahid, Sohail and Kuan, Chen-Hsiang and Nguyen, Truman Kt and Liang, Heidi Y. and Shettigar, Nitish Udupi and Hou
"Signalling by senescent melanocytes hyperactivates hair growth"
Nature
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Wang, Xinyi and Almet, Axel A. and Nie, Qing
"Analyzing network diversity of cellcell interactions in COVID-19 using single-cell transcriptomics"
Frontiers in Genetics
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https://doi.org/10.3389/fgene.2022.948508
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Wang, Xinyi and Almet, Axel A. and Nie, Qing
"The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics"
Seminars in cancer biology
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https://doi.org/10.1016/j.semcancer.2023.07.001
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Wang, Yangyang and GuerreroJuarez, Christian F. and Qiu, Yuchi and Du, Huijing and Chen, Weitao and Figueroa, Seth and Plikus, Maksim V. and Nie, Qing
"A multiscale hybrid mathematical model of epidermaldermal interactions during skin wound healing"
Experimental Dermatology
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https://doi.org/10.1111/exd.13909
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Waymack, Rachel and Fletcher, Alvaro and Enciso, German and Wunderlich, Zeba
"Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic"
eLife
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Weiss, Lora D. and van den Driessche, P. and Lowengrub, John S. and Wodarz, Dominik and Komarova, Natalia L.
"Effect of feedback regulation on stem cell fractions in tissues and tumors: Understanding chemoresistance in cancer"
Journal of Theoretical Biology
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https://doi.org/10.1016/j.jtbi.2020.110499
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Wiedemann, Julie and Billi, Allison C. and Bocci, Federico and Kashgari, Ghaidaa and Xing, Enze and Tsoi, Lam C. and Meller, Leo and Swindell, William R. and Wasikowski, Rachael and Xing, Xianying and Ma, Feiyang and Gharaee-Kermani, Mehrnaz and Kahlenber
"Differential cell composition and split epidermal differentiation in human palm, sole, and hip skin"
Cell Reports
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Wodarz, Dominik and Komarova, Natalia L. and Schang, Luis M.
"Role of high-dose exposure in transmission hot zones as a driver of SARS-CoV-2 dynamics"
Journal of The Royal Society Interface
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Xie, Jiang and Yang, Fuzhang and Wang, Jiao and Karikomi, Mathew and Yin, Yiting and Sun, Jiamin and Wen, Tieqiao and Nie, Qing
"DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks"
Neurocomputing
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Xie, Jiang and Zhao, Chang and Sun, Jiamin and Li, Jiaxin and Yang, Fuzhang and Wang, Jiao and Nie, Qing
"Prediction of Essential Genes in Comparison States Using Machine Learning"
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, 2020
https://doi.org/10.1109/TCBB.2020.3027392
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Yan, Huaming and Ramirez-Guerrero, Daniel and Lowengrub, John and Wu, Min
"Stress generation, relaxation and size control in confined tumor growth"
PLOS Computational Biology
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https://doi.org/10.1371/journal.pcbi.1009701
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Ying, Xiong and Leng, Si-Yang and Ma, Huan-Fei and Nie, Qing and Lai, Ying-Cheng and Lin, Wei
"Continuity Scaling: A Rigorous Framework for Detecting and Quantifying Causality Accurately"
Research
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https://doi.org/10.34133/2022/9870149
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Zhang, Jiajun and Nie, Qing and Zhou, Tianshou
"Revealing Dynamic Mechanisms of Cell Fate Decisions From Single-Cell Transcriptomic Data"
Frontiers in Genetics
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10.3389/fgene.2019.01280
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Zhang, Lihua and Nie, Qing
"scMC learns biological variation through the alignment of multiple single-cell genomics datasets"
Genome Biology
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, 2021
https://doi.org/10.1186/s13059-020-02238-2
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Zhang, Lihua and Zhang, Jing and Nie, Qing
"DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data"
Science Advances
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https://doi.org/10.1126/sciadv.abl7393
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Zhang, Ling-juan and Chen, Stella Xiang and Guerrero-Juarez, Christian F. and Li, Fengwu and Tong, Yun and Liang, Yuqiong and Liggins, Marc and Chen, Xu and Chen, Hao and Li, Min and Hata, Tissa and Zheng, Ye and Plikus, Maksim V. and Gallo, Richard L.
"Age-Related Loss of Innate Immune Antimicrobial Function of Dermal Fat Is Mediated by Transforming Growth Factor Beta"
Immunity
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10.1016/j.immuni.2018.11.003
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Zhang, Ling-juan and Guerrero-Juarez, Christian F. and Chen, Stella X. and Zhang, Xiaowei and Yin, Meimei and Li, Fengwu and Wu, Shuai and Chen, Joyce and Li, Min and Liu, Yingzi and Jiang, Shang I. and Hata, Tissa and Plikus, Maksim V. and Gallo, Richard
"Diet-induced obesity promotes infection by impairment of the innate antimicrobial defense function of dermal adipocyte progenitors"
Science Translational Medicine
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, 2021
https://doi.org/10.1126/scitranslmed.abb5280
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Zhao, Meng and Niroobakhsh, Zahra and Lowengrub, John and Li, Shuwang
"Nonlinear limiting dynamics of a shrinking interface in a Hele-Shaw cell"
Journal of Fluid Mechanics
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https://doi.org/10.1017/jfm.2020.983
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Zhao, Wei and Johnston, Kevin G. and Ren, Honglei and Xu, Xiangmin and Nie, Qing
"Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat"
Nature Communications
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https://doi.org/10.1038/s41467-023-36800-w
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Zhao, Wei and Qiao, Lingxia and Yan, Shiyu and Nie, Qing and Zhang, Lei
"Mathematical modeling of histone modifications reveals the formation mechanism and function of bivalent chromatin"
iScience
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https://doi.org/10.1016/j.isci.2021.102732
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Zheng, Xiaoying and Jin, Suoqin and Nie, Qing and Zou, Xiufen
"scRCMF: Identification of Cell Subpopulations and Transition States From Single-Cell Transcriptomes"
IEEE Transactions on Biomedical Engineering
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https://doi.org/10.1109/tbme.2019.2937228
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Zhou, Peijie and Wang, Shuxiong and Li, Tiejun and Nie, Qing
"Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics"
Nature Communications
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https://doi.org/10.1038/s41467-021-25548-w
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Zhu, Yilun and Qiu, Yuchi and Chen, Weitao and Nie, Qing and Lander, Arthur D.
"Scaling a Dpp Morphogen Gradient through Feedback Control of Receptors and Co-receptors"
Developmental Cell
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https://doi.org/10.1016/j.devcel.2020.05.029
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Zixuan Cang, Qing Nie
"Supervised Optimal Transport"
SIAM journal on applied mathematics
, 2022
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