What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1004706
Download full text from publisher
References listed on IDEAS
- David G. Spiller & Christopher D. Wood & David A. Rand & Michael R. H. White, 2010. "Measurement of single-cell dynamics," Nature, Nature, vol. 465(7299), pages 736-745, June.
- Sabrina L. Spencer & Suzanne Gaudet & John G. Albeck & John M. Burke & Peter K. Sorger, 2009. "Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis," Nature, Nature, vol. 459(7245), pages 428-432, May.
- Bonassi Fernando V. & You Lingchong & West Mike, 2011. "Bayesian Learning from Marginal Data in Bionetwork Models," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-27, October.
- Jan Hasenauer & Christine Hasenauer & Tim Hucho & Fabian J Theis, 2014. "ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics," PLOS Computational Biology, Public Library of Science, vol. 10(7), pages 1-17, July.
- Filippo Menolascina & Gianfranco Fiore & Emanuele Orabona & Luca De Stefano & Mike Ferry & Jeff Hasty & Mario di Bernardo & Diego di Bernardo, 2014. "In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-14, May.
- Joachim Almquist & Loubna Bendrioua & Caroline Beck Adiels & Mattias Goksör & Stefan Hohmann & Mats Jirstrand, 2015. "A Nonlinear Mixed Effects Approach for Modeling the Cell-To-Cell Variability of Mig1 Dynamics in Yeast," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-32, April.
- Alejandro Colman-Lerner & Andrew Gordon & Eduard Serra & Tina Chin & Orna Resnekov & Drew Endy & C. Gustavo Pesce & Roger Brent, 2005. "Regulated cell-to-cell variation in a cell-fate decision system," Nature, Nature, vol. 437(7059), pages 699-706, September.
- Kuhn, E. & Lavielle, M., 2005. "Maximum likelihood estimation in nonlinear mixed effects models," Computational Statistics & Data Analysis, Elsevier, vol. 49(4), pages 1020-1038, June.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Kazunari Iwamoto & Yuki Shindo & Koichi Takahashi, 2016. "Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway," PLOS Computational Biology, Public Library of Science, vol. 12(11), pages 1-18, November.
- Lucy Ham & Megan A. Coomer & Kaan Öcal & Ramon Grima & Michael P. H. Stumpf, 2024. "A stochastic vs deterministic perspective on the timing of cellular events," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
- Ibirénoyé Romaric Sodjahin & Fabienne Femenia & Obafemi Philippe Koutchade & A. Carpentier, 2022.
"On the economic value of the agronomic effects of crop diversification for farmers: estimation based on farm cost accounting data [Valeur économique des effets agronomiques de la diversification de,"
Working Papers
hal-03639951, HAL.
- Ibirénoyé Honoré Romaric Sodjahin & Fabienne Femenia & Obafémi Philippe Koutchade & Alain Carpentier, 2022. "On the economic value of the agronomic effects of crop diversification for farmers: estimation based on farm cost accounting data," Working Papers SMART 22-02, INRAE UMR SMART.
- Sodjahin, Ibirénoyé Honoré Romaric & Féménia, Fabienne & Koutchade, Obafémi Philippe & Carpentier, Alain, 2022. "On the economic value of the agronomic effects of crop diversification for farmers: estimation based on farm cost accounting data," Working Papers 320398, Institut National de la recherche Agronomique (INRA), Departement Sciences Sociales, Agriculture et Alimentation, Espace et Environnement (SAE2).
- Ibirénoyé Honoré Romaric Sodjahin & Fabienne Femenia & Obafémi, Philippe Koutchadé & Alain Carpentier, 2023. "On the economic value of the agronomic effects of crop diversification for farmers: estimation based on farm cost accounting data," Post-Print hal-04667088, HAL.
- Baey, Charlotte & Didier, Anne & Lemaire, Sébastien & Maupas, Fabienne & Cournède, Paul-Henry, 2013. "Modelling the interindividual variability of organogenesis in sugar beet populations using a hierarchical segmented model," Ecological Modelling, Elsevier, vol. 263(C), pages 56-63.
- Espen Bernton & Pierre E. Jacob & Mathieu Gerber & Christian P. Robert, 2019. "Approximate Bayesian computation with the Wasserstein distance," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 81(2), pages 235-269, April.
- Allassonnière, Stéphanie & Kuhn, Estelle, 2015. "Convergent stochastic Expectation Maximization algorithm with efficient sampling in high dimension. Application to deformable template model estimation," Computational Statistics & Data Analysis, Elsevier, vol. 91(C), pages 4-19.
- Laura Azzimonti & Francesca Ieva & Anna Maria Paganoni, 2013. "Nonlinear nonparametric mixed-effects models for unsupervised classification," Computational Statistics, Springer, vol. 28(4), pages 1549-1570, August.
- Samson, Adeline & Lavielle, Marc & Mentre, France, 2006. "Extension of the SAEM algorithm to left-censored data in nonlinear mixed-effects model: Application to HIV dynamics model," Computational Statistics & Data Analysis, Elsevier, vol. 51(3), pages 1562-1574, December.
- Sébastien Benzekry & Clare Lamont & Afshin Beheshti & Amanda Tracz & John M L Ebos & Lynn Hlatky & Philip Hahnfeldt, 2014. "Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth," PLOS Computational Biology, Public Library of Science, vol. 10(8), pages 1-19, August.
- Andreas Doncic & Umut Eser & Oguzhan Atay & Jan M Skotheim, 2013. "An Algorithm to Automate Yeast Segmentation and Tracking," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-11, March.
- Michael Chevalier & Ophelia Venturelli & Hana El-Samad, 2015. "The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks," PLOS Computational Biology, Public Library of Science, vol. 11(10), pages 1-21, October.
- Trevezas, S. & Malefaki, S. & Cournède, P.-H., 2014. "Parameter estimation via stochastic variants of the ECM algorithm with applications to plant growth modeling," Computational Statistics & Data Analysis, Elsevier, vol. 78(C), pages 82-99.
- Ollier, Edouard & Samson, Adeline & Delavenne, Xavier & Viallon, Vivian, 2016. "A SAEM algorithm for fused lasso penalized NonLinear Mixed Effect Models: Application to group comparison in pharmacokinetics," Computational Statistics & Data Analysis, Elsevier, vol. 95(C), pages 207-221.
- Boubacar Mainassara, Y. & Carbon, M. & Francq, C., 2012.
"Computing and estimating information matrices of weak ARMA models,"
Computational Statistics & Data Analysis, Elsevier, vol. 56(2), pages 345-361.
- Boubacar Mainassara, Yacouba & Carbon, Michel & Francq, Christian, 2010. "Computing and estimating information matrices of weak arma models," MPRA Paper 27685, University Library of Munich, Germany.
- Buzbas, Erkan O. & Rosenberg, Noah A., 2015. "AABC: Approximate approximate Bayesian computation for inference in population-genetic models," Theoretical Population Biology, Elsevier, vol. 99(C), pages 31-42.
- Fu, Eric & Heckman, Nancy, 2019. "Model-based curve registration via stochastic approximation EM algorithm," Computational Statistics & Data Analysis, Elsevier, vol. 131(C), pages 159-175.
- Munch, Jakob R. & Nguyen, Daniel X., 2014.
"Decomposing firm-level sales variation,"
Journal of Economic Behavior & Organization, Elsevier, vol. 106(C), pages 317-334.
- Jakob R. Munch & Daniel X., 2008. "Decomposing Firm-level Sales Variation," EPRU Working Paper Series 2009-05, Economic Policy Research Unit (EPRU), University of Copenhagen. Department of Economics, revised Jun 2009.
- Larissa A. Matos & Víctor H. Lachos & Tsung-I Lin & Luis M. Castro, 2019. "Heavy-tailed longitudinal regression models for censored data: a robust parametric approach," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 28(3), pages 844-878, September.
- Kim, Seong-Joon & Mun, Byeong Min & Bae, Suk Joo, 2019. "A cost-driven reliability demonstration plan based on accelerated degradation tests," Reliability Engineering and System Safety, Elsevier, vol. 183(C), pages 226-239.
- Allassonnière, Stéphanie & Chevallier, Juliette, 2021. "A new class of stochastic EM algorithms. Escaping local maxima and handling intractable sampling," Computational Statistics & Data Analysis, Elsevier, vol. 159(C).
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1004706. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.