دانلود کتاب Analysis and Control of Cellular Ensembles: Exploiting Dimensionality Reduction in Single-cell Data and Models

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Table of Contents
1 Introduction
1.1 Motivation and focus
1.2 Contributions and Outline
2 Reconstructing temporal and spatial dynamics from single-cell pseudotime
2.1 Background and problem formulation
2.2 MAPiT - MAP of pseudotime into real-Time
2.3 Reconstructing spheroids with MAPiT
2.4 Analysing cell cycle progression with MAPiT
2.5 Summary and discussion
3 Cell cycle analysis with ergodic principles and age-structured population models
3.1 Background and problem formulation
3.2 Age-structured population models
3.3 Relationship between ergodic analysis and age-structure population models
3.4 Cell cycle-dependent expression of Cyclin B1
3.5 Summary and discussion
4 Cell cycle progression inference
4.1 Background and problem formulation
4.2 Cell cycle progression inference with sensitivities
4.3 Evaluation with in silico data
4.4 Analysis of cell cycle progression
4.5 Summary and discussion
5 Passivity-based ensemble control for cell cycle synchronization
5.1 Background and problem formulation
5.2 Theoretical foundation
5.3 Ensemble control for cell cycle synchronization
5.4 Computational studies
5.5 Summary and discussion
6 Ensemble control for cellular oscillators
6.1 Background and problem formulation
6.2 Ensemble control for oscillator moments
6.3 Computational studies
6.4 Summary and discussion
7 Conclusions
7.1 Summary and discussion
7.2 Outlook
Appendices
A Technical background
A.1 Dynamical systems and control theory
A.2 Weakly connected oscillators
A.3 Fourier coefficients and circular moments
B Experimental protocols and data preprocessing
B.1 Ordering cells in pseudotime
B.2 Establishment of NCI-H460/geminin cell line
B.3 Live cell microscopy
B.4 Flow cytometric analysis
B.5 Construction of the average cell cycle trajectory
B.6 Estimation of constant speed and noise from cell cycle lengths
C Spheroid growth model
D Cell cycle model
E Technical computations and proofs
E.1 Speed equation
E.2 Derivation of ODE for j : s 7! x
E.3 Calculation of division rate from cell cycle length distribution
E.4 Proof of Lemma 6.1
Bibliography
Publications of the Author