Transition paths across the EMT landscape are dictated by network logic
A Dey, AL MacLean
bioRxiv; 10.1101/2024.12.03.626660   bioRxiv

Modeling the dynamics of EMT reveals genes associated with pan-cancer intermediate states and plasticity
M McDermott, R Mehta, ET Roussos Torres, AL MacLean
bioRxiv; 10.1101/2024.10.03.616309   bioRxiv

Data-driven model discovery and model selection for noisy biological systems
X Wu, M McDermott, AL MacLean
bioRxiv; 10.1101/2024.10.03.616508   bioRxiv

Gene regulatory network inference with popInfer reveals dynamic regulation of hematopoietic stem cell quiescence upon diet restriction and aging
MK Rommelfanger, M Behrends, Y Chen, J Martinez, M Bens, L Xiong, KL Rudolph, AL MacLean
bioRxiv; 10.1101/2023.04.18.537360   bioRxiv

Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life
J Kreger, JA Mooney, D Shibata, AL MacLean
Nat Commun (2024); 10.1038/s41467-024-54711-2   PubMed   Nat Commun

Hematopoietic stem cell aging by the niche
AL MacLean, KL Rudolph
Blood (2024); 10.1182/blood.2024024890   PubMed   Blood

Exploring Stem Cells: A Hands-On Approach to Elementary STEM Education
JL Stellman, AE Zambidis, AL MacLean, DJ Kast
Connected Science Learning; In press.

Mimicking the breast metastatic microenvironment: characterization of a novel syngeneic…
AG Baugh, E Gonzalez, VH Narumi, J Kreger, Y Liu, C Rafie, S Castanon, J Jang, LT Kagohara, DP Anastasiadou, J Leatherman, TD Armstrong, I Chan, GS Karagiannis, EM Jaffee, AL MacLean, ET Roussos Torres
Clin Exp Metas (2024); 10.1007/s10585-024-10289-z   PubMed   Clin Exp Metas

Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects
S Chea, J Kreger, ME Lopez-Burks, AL MacLean, AD Lander, AL Calof
Science Advances (2024); 10.1126/sciadv.add9984  PubMed    Science Advances

Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis
G Coulis et al.
Science Advances (2023); 10.1126/sciadv.add9984  PubMed    Science Advances

Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney
L Xiong, J Liu, SY Han, K Koppitch, JJ Guo, MK Rommelfanger, F Gao, IB Hallgrimsdottir, L Pachter, J Kim, AL MacLean, AP McMahon
Dev Cell (2023); 10.1016/j.devcel.2023.08.010   PubMed    Dev Cell

Single-cell Ca2+ parameter inference reveals how transcriptional states inform dynamic cell fates
X Wu, R Wollman, AL MacLean
J R Soc Interface (2023); 10.1098/rsif.2023.0172   PubMed    J R Soc Interface

Myeloid-derived suppressor cell dynamics control outcomes in the metastatic niche
J Kreger, ET Roussos Torres, AL MacLean
Can Immunol Res (2023); 10.1158/2326-6066.CIR-22-0617   PubMed    Can Immunol Res

Julia for Biologists
E Roesch, JG Greener, AL MacLean, H Nassar, C Rackauckas, TE Holy, MPH Stumpf
Nat Meth (2023); 10.1038/s41592-023-01832-z   PubMed    Nat Meth

Stem cells: Voices carry
AL MacLean
Nat Chem Biol (2023); 10.1038/s41589-022-01238-6    Nat Chem Biol

Profiling intermediate cell states in high resolution
AL MacLean
Cell Rep Meth (2022); 10.1016/j.crmeth.2022.100204   PubMed    Cell Rep Meth

Age-dependent effects of Igf2bp2 on gene regulation, function, and aging of hematopoietic stem cells in mice
M Suo, MK Rommelfanger, Y Chen, EM Amro, B Han, Z Chen, K Szafranski, SR Chakkarappan, BO Boehm, AL MacLean, KL Rudolph
Blood (2022); doi.org/10.1182/blood.2021012197   PubMed    Blood

Single-cell transcriptomic analysis of zebrafish cranial neural crest reveals spatiotemporal regulation of lineage decisions during development
D Tatarakis, Z Cang, X Wu, P Sharma, MK Karikomi, AL MacLean, Q Nie, TF Schilling
Cell Reports (2021); 37(12), 110140   PubMed    Cell Rep

A single-cell resolved cell-cell communication model explains lineage commitment in hematopoiesis
MK Rommelfanger, AL MacLean
Development (2021); 148(24), dev199779   PubMed    Development

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure
HM Rando et al.
mSystems (2021); 6(5)   PubMed    mSystems

The diverse landscape of modeling in single-cell biology
AL MacLean, Q Nie
Phys Biol, (2021); 18:050201   PubMed    Phys Biol

RVAgene: Generative modeling of gene expression time series data
R Mitra, AL MacLean
Bioinformatics, (2021); btab260   PubMed    Bioinformatics

Modeling the competing effects of the immune system and EMT on tumor development
DR Bergman, MK Karikomi, Q Nie, AL MacLean
Communications Biol, (2021); 4:983   PubMed    Communications Biol

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

Nat Commun, 2020; 11:4239   PubMed    Nat Commun

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

Cell lineage and communication network inference via optimization for single-cell transcriptomics
S Wang, MK Karikomi, AL MacLean, Q Nie

Nucleic Acids Res, 2019. gkz204  Pubmed    Nucleic Acids Res

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

genesis, 2018. dvg.23275    Pubmed    genesis

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

EMBO Rep, 2018. 20:e46273    Pubmed    EMBO Rep

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

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

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

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

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

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

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

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

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

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

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

Feedback mechanisms control coexistence in a stem cell model of acute myeloid leukaemia

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

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

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

Parameter-free methods distinguish Wnt pathway models and guide design of experiments
AL MacLean, Z Rosen, HM Byrne, HA Harrington

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

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

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

Ecology in the hematopoietic stem cell niche determines the clinical outcome in chronic myeloid leukemia

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

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

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

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

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