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Preprints


21. Modeling the competing effects of the immune system and EMT on tumor development
DR Bergman, MK Karikomi, Q Nie, AL MacLean
bioRvix; doi:10.1101/168922   bioRxiv

20. Single cell transcriptomics of human epidermis reveals basal stem cell transition states
S Wang, ML Drummond, CF Guerrero-Juarez, E Tarapore, AL MacLean, AR Stabell, SC Wu, G Gutierrez, BT That, CA Benavente, Q Nie, SX Atwood
bioRvix; doi:10.1101/784579   bioRxiv

Publications


2020

19. Defining epidermal basal cell states during skin homeostasis and wound healing using single-cell transcriptomics
D Haensel, S Jin, R Cinco, P Sun, Q Nguyen, Z Cang, M Dragan, Y Gong, AL MacLean, K Kessenbrock, E Gratton, Q Nie, X Dai
Cell Reports, 2020; 30(11):3932-3947 Pubmed    Cell Rep

2019

18. Cell lineage and communication network inference via optimization for single-cell transcriptomics
S Wang, MK Karikomi, AL MacLean, Q Nie
18. Cell lineage and communication network inference via optimization […]
S Wang et al.

Nucleic Acids Res, 2019. gkz204  Pubmed    Nucleic Acids Res

17. Transcriptomics reveals complex kinetics of dorsal‐ventral patterning gene expression in the mandibular arch
P Sharma, AL MacLean, L Meinecke, D Clouthier, Q Nie, TF Schilling
17. Transcriptomics reveals complex kinetics of dorsal‐ventral patterning […]
P Sharma, AL MacLean, L Meinecke et al.

genesis, 2018. dvg.23275    Pubmed    genesis

2018

16. An Ovol2‐Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation
D Haensel, P Sun, AL MacLean, X Ma, Y Zhou, MP Stemmler, S Brabletz, G Berx, MV Plikus, Q Nie, T Brabletz, X Dai
16. An Ovol2‐Zeb1 transcriptional circuit regulates […]
D Haensel, P Sun, AL MacLean, et al.

EMBO Rep, 2018. 20:e46273    Pubmed    EMBO Rep

15. Exploring intermediate cell states through the lens of single cells
AL MacLean*, T Hong*, Q Nie
Curr Opin Sys Biol, 2018. 9:32-41    Curr Opin Sys Biol

14. Energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data
14. Energy landscape-based inference of transition probabilities and cellular […]

S Jin, AL MacLean, T Peng, Q Nie
Bioinformatics, 2018. 34(12):2077-2086    Pubmed    Bioinformatics

13. Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis
Ben Lambert*, AL MacLean*, AG Fletcher, AN Coombes, MH Little, HM Byrne
13. Bayesian inference of agent-based models: a tool for studying kidney […]
Ben Lambert*, AL MacLean*, AG Fletcher, et al.

J Math Biol, 2018. 76(7):1673-1697   Pubmed   J Math Biol

2017

12. An agent-based model reveals evolutionary dynamics of inflammation-induced cancer
Y Guo, Q Nie, AL MacLean, Y Li, J Lei, and S Li
Cancer Research, 2017. 77(22):6429–41   Pubmed   Cancer Res

11. Single Cell Phenotyping Reveals Heterogeneity among Haematopoietic Stem Cells
AL MacLean*, MA Smith*, J Liepe, A Sim, R Khorshed, NM Rashidi, N Scherf, A Krinner, I Roeder, C Lo Celso, MPH Stumpf
11. Single Cell Phenotyping Reveals Heterogeneity among Haematopoietic […]
AL MacLean*, MA Smith*, J Liepe, et al.

Stem Cells, 2017. 35(11):2292-2304   Pubmed   Stem Cells

10. A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions
T Peng*, L Liu*, AL MacLean, CW Wong, W Zhao, Q Nie
10. A mathematical model of mechanotransduction reveals […]
T Peng*, L Liu*, AL MacLean, et al.

BMC Sys Bio, 2017. 11(1):55   Pubmed   BMC Syst Biol

9. Stem Cell Population Biology: Insights from Haematopoiesis
AL MacLean, C Lo Celso, MPH Stumpf
Stem Cells, 2017. 35(1):80-88   Pubmed   Stem Cells

2013 – 2016

8. Systematic tracking of altered haematopoiesis during sporozoite-mediated malaria development reveals multiple response points
M Vainieri, A Blagborough, AL MacLean, N Ruivo, H Fletcher, MPH Stumpf, R Sinden, C Lo Celso
8. Systematic tracking of altered haematopoiesis during […]
M Vainieri, A Blagborough, AL MacLean, et al.

Open Biology, 2016. 6(6):160038   Pubmed   Open Biol

7. Feedback mechanisms control coexistence in a stem cell model of acute myeloid leukaemia
7. Feedback mechanisms control coexistence in a stem cell model of acute […]

HL Crowell*, AL MacLean*, MPH Stumpf
J Theor Biol, 2016. 401:43-53   Pubmed   J Theor Biol

6. Cellular Population Dynamics Control the Robustness of the Stem Cell Niche
AL MacLean*, P Kirk*, MPH Stumpf
Biol Open, 2015. 4:1420-1426   Pubmed   Biol Open

5. Conditional Random Matrix Ensembles and the Stability of Dynamical Systems
P Kirk*, DMY Rolando*, AL MacLean, MPH Stumpf
New J Phys, 2015, 17(8)   New J Phys

4. Parameter-free methods distinguish Wnt pathway models and guide design of experiments
AL MacLean, Z Rosen, HM Byrne, HA Harrington
4. Parameter-free methods distinguish Wnt pathway models and guide design […]
AL MacLean, Z Rosen, HM Byrne, et al.

Proc Natl Acad Sci USA 2015, 112(9):2652-57   Pubmed   PNAS

3. Epithelial-mesenchymal transition in metastases affects tumor dormancy in a simple mathematical model
3. Epithelial-mesenchymal transition in metastases affects tumor dormancy

AL MacLean, HA Harrington, MPH Stumpf, MDH Hansen
Biomedicines, 2014. 2(4):384-402   Pubmed   Biomedicines

2. Ecology in the hematopoietic stem cell niche determines the clinical outcome in chronic myeloid leukemia
2. Ecology in the hematopoietic stem cell niche determines the clinical outcome in […]

AL MacLean*, S Filippi*, MPH Stumpf
Proc Natl Acad Sci USA, 2014. 111(10):3882-88   Pubmed   PNAS

1. Population dynamics of normal and leukaemia stem cells in the haematopoietic stem cell niche show distinct regimes where leukaemia will be controlled
1. Population dynamics of normal and leukaemia stem cells in the […]

AL MacLean, C Lo Celso, MPH Stumpf
J R Soc Interface, 2013. 10(81):20120968   Pubmed   J R Soc Interface

Peer-reviewed Book Chapters


Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study
AL MacLean, HA Harrington, MPH Stumpf, HM Byrne
Mathematical and Statistical Techniques for Systems Medicine
AL MacLean, HA Harrington, MPH Stumpf, et al.

Systems Medicine: Meth Molecular Biology: Springer, 2016   Springer   Chapter