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Boolean modeling in systems biology: an overview of methodology and applications.
Wang RS, Saadatpour A, Albert R. Wang RS, et al. Phys Biol. 2012 Oct;9(5):055001. doi: 10.1088/1478-3975/9/5/055001. Epub 2012 Sep 25. Phys Biol. 2012. PMID: 23011283 Review.
On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the experimental literature and high-throughput technologies, making qualitative approaches such as Boolean network modeling extremely useful. In …
On the other hand, a wealth of molecular level qualitative data on individual components and interactions can be obtained from the ex …
Discrete dynamic modeling of signal transduction networks.
Saadatpour A, Albert R. Saadatpour A, et al. Methods Mol Biol. 2012;880:255-72. doi: 10.1007/978-1-61779-833-7_12. Methods Mol Biol. 2012. PMID: 23361989 Review.
To address this issue, discrete dynamic models, based on a qualitative description of a system's variables, have been applied for the analysis of biological systems with many unknown parameters. ...This is followed by practical examples of a Boolean dynamic f …
To address this issue, discrete dynamic models, based on a qualitative description of a system's variables, have been applied …
Boolean modeling of biological regulatory networks: a methodology tutorial.
Saadatpour A, Albert R. Saadatpour A, et al. Methods. 2013 Jul 15;62(1):3-12. doi: 10.1016/j.ymeth.2012.10.012. Epub 2012 Nov 9. Methods. 2013. PMID: 23142247
In this paper, we present a tutorial on the fundamental steps of Boolean modeling of biological regulatory networks. We demonstrate how to infer a Boolean network model from the available experimental data, analyze the network using graph-theoretical measures, and c …
In this paper, we present a tutorial on the fundamental steps of Boolean modeling of biological regulatory networks. We demonstrate h …
Attractor analysis of asynchronous Boolean models of signal transduction networks.
Saadatpour A, Albert I, Albert R. Saadatpour A, et al. J Theor Biol. 2010 Oct 21;266(4):641-56. doi: 10.1016/j.jtbi.2010.07.022. Epub 2010 Jul 24. J Theor Biol. 2010. PMID: 20659480
Here we fill this gap by combining theoretical analysis such as solution of scalar equations and Markov chain techniques, as well as numerical simulations to carry out a thorough comparative study on the dynamic behavior of a previously proposed Boolean model of …
Here we fill this gap by combining theoretical analysis such as solution of scalar equations and Markov chain techniques, as well as numeric …
Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia.
Saadatpour A, Wang RS, Liao A, Liu X, Loughran TP, Albert I, Albert R. Saadatpour A, et al. PLoS Comput Biol. 2011 Nov;7(11):e1002267. doi: 10.1371/journal.pcbi.1002267. Epub 2011 Nov 10. PLoS Comput Biol. 2011. PMID: 22102804 Free PMC article.
The blood cancer T cell large granular lymphocyte (T-LGL) leukemia is a chronic disease characterized by a clonal proliferation of cytotoxic T cells. ...In this paper, we perform a comprehensive dynamical and structural analysis of a network model of t …
The blood cancer T cell large granular lymphocyte (T-LGL) leukemia is a chronic disease characterized by a clonal proliferatio …
Challenges and emerging directions in single-cell analysis.
Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Yuan GC, et al. Among authors: saadatpour a. Genome Biol. 2017 May 8;18(1):84. doi: 10.1186/s13059-017-1218-y. Genome Biol. 2017. PMID: 28482897 Free PMC article. Review.
Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis.
Saadatpour A, Guo G, Orkin SH, Yuan GC. Saadatpour A, et al. Genome Biol. 2014 Dec 3;15(12):525. doi: 10.1186/s13059-014-0525-9. Genome Biol. 2014. PMID: 25517911 Free PMC article.
BACKGROUND: A fundamental challenge for cancer therapy is that each tumor contains a highly heterogeneous cell population whose structure and mechanistic underpinnings remain incompletely understood. ...We start with fluorescence-activated cell sorting analysis with …
BACKGROUND: A fundamental challenge for cancer therapy is that each tumor contains a highly heterogeneous cell population whos …
Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas.
Suo S, Zhu Q, Saadatpour A, Fei L, Guo G, Yuan GC. Suo S, et al. Among authors: saadatpour a. Cell Rep. 2018 Nov 6;25(6):1436-1445.e3. doi: 10.1016/j.celrep.2018.10.045. Cell Rep. 2018. PMID: 30404000 Free PMC article.
A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations.
Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G. Han X, et al. Cell Res. 2017 Mar;27(3):386-401. doi: 10.1038/cr.2017.17. Epub 2017 Jan 27. Cell Res. 2017. PMID: 28128194 Free PMC article.
Through functional screening assays, we find that mouse embryonic fibroblast cells can be induced to trans-differentiate into a wide range of somatic lineages simultaneously by treatment with a combination of four chemicals. ...Our study describes a cell fate …
Through functional screening assays, we find that mouse embryonic fibroblast cells can be induced to trans-differentiate into a wide …
Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors.
Riddell J, Gazit R, Garrison BS, Guo G, Saadatpour A, Mandal PK, Ebina W, Volchkov P, Yuan GC, Orkin SH, Rossi DJ. Riddell J, et al. Cell. 2014 Apr 24;157(3):549-64. doi: 10.1016/j.cell.2014.04.006. Cell. 2014. PMID: 24766805 Free PMC article.
Single-cell analysis revealed that iHSCs derived under optimal conditions exhibit a gene expression profile that is highly similar to endogenous HSCs. ...Our results raise the prospect that blood cell reprogramming may be a strategy for derivation of transplantable …
Single-cell analysis revealed that iHSCs derived under optimal conditions exhibit a gene expression profile that is highly similar to …
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