Analysis And Control Of Cellular Ensembles Exploiting Dimensionality Reduction In Single Cell Data And Models
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Analysis And Control Of Cellular Ensembles Exploiting Dimensionality Reduction In Single Cell Data And Models
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Author : Karsten Kuritz
language : en
Publisher: Logos Verlag Berlin GmbH
Release Date : 2020-11-20
Analysis And Control Of Cellular Ensembles Exploiting Dimensionality Reduction In Single Cell Data And Models written by Karsten Kuritz and has been published by Logos Verlag Berlin GmbH this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-11-20 with Language Arts & Disciplines categories.
An ensemble system is a collection of nearly identical dynamical systems which admit a certain degree of heterogeneity, and which are subject to the restriction that they may only be manipulated or observed as a whole. This thesis presents analysis and control methods for cellular ensembles by considering reduced 1-dimensional dynamics of biological processes in high-dimensional single-cell data and models. To be more specific, we address the quest for real-time analysis of biological processes within single-cell data by introducing the measure-preserving map of pseudotime into real-time, in short MAPiT. MAPiT enables the reconstruction of temporal and spatial dynamics from single-cell snapshot experiments. In addition, we propose a PDE-constrained learning algorithm which allows for efficient inference of changes in cell cycle progression from time series single-cell snapshot data. The second part of this thesis, is devoted to controlling a heterogeneous cell population, in the sense, that we aim at achieving a desired distribution of cellular oscillators on their periodic orbit. A systems theoretic approach to the ensemble control problem provides novel necessary and sufficient conditions for the control of phase distributions in terms of the Fourier coefficients of the phase response curve. This thesis establishes a connection between the previously separate areas of single cell analysis and ensemble control. Our holistic view opens new perspectives for theoretic concepts in basic research and therapeutic strategies in precision medicine.
Computational Methods For Single Cell Data Analysis
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Author : Guo-Cheng Yuan
language : en
Publisher: Humana Press
Release Date : 2019-02-14
Computational Methods For Single Cell Data Analysis written by Guo-Cheng Yuan and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-02-14 with Science categories.
This detailed book provides state-of-art computational approaches to further explore the exciting opportunities presented by single-cell technologies. Chapters each detail a computational toolbox aimed to overcome a specific challenge in single-cell analysis, such as data normalization, rare cell-type identification, and spatial transcriptomics analysis, all with a focus on hands-on implementation of computational methods for analyzing experimental data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Methods for Single-Cell Data Analysis aims to cover a wide range of tasks and serves as a vital handbook for single-cell data analysis.
Probabilistic Boolean Networks
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Author : Ilya Shmulevich
language : en
Publisher: SIAM
Release Date : 2010-01-01
Probabilistic Boolean Networks written by Ilya Shmulevich and has been published by SIAM this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-01-01 with Mathematics categories.
This is the first comprehensive treatment of probabilistic Boolean networks (PBNs), an important model class for studying genetic regulatory networks. This book covers basic model properties, including the relationships between network structure and dynamics, steady-state analysis, and relationships to other model classes." "Researchers in mathematics, computer science, and engineering are exposed to important applications in systems biology and presented with ample opportunities for developing new approaches and methods. The book is also appropriate for advanced undergraduates, graduate students, and scientists working in the fields of computational biology, genomic signal processing, control and systems theory, and computer science.
Ensemble Machine Learning
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Author : Cha Zhang
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-02-17
Ensemble Machine Learning written by Cha Zhang and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-02-17 with Computers categories.
It is common wisdom that gathering a variety of views and inputs improves the process of decision making, and, indeed, underpins a democratic society. Dubbed “ensemble learning” by researchers in computational intelligence and machine learning, it is known to improve a decision system’s robustness and accuracy. Now, fresh developments are allowing researchers to unleash the power of ensemble learning in an increasing range of real-world applications. Ensemble learning algorithms such as “boosting” and “random forest” facilitate solutions to key computational issues such as face recognition and are now being applied in areas as diverse as object tracking and bioinformatics. Responding to a shortage of literature dedicated to the topic, this volume offers comprehensive coverage of state-of-the-art ensemble learning techniques, including the random forest skeleton tracking algorithm in the Xbox Kinect sensor, which bypasses the need for game controllers. At once a solid theoretical study and a practical guide, the volume is a windfall for researchers and practitioners alike.
Fundamentals Of Wireless Communication
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Author : David Tse
language : en
Publisher: Cambridge University Press
Release Date : 2005-05-26
Fundamentals Of Wireless Communication written by David Tse and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-05-26 with Computers categories.
This textbook takes a unified view of the fundamentals of wireless communication and explains cutting-edge concepts in a simple and intuitive way. An abundant supply of exercises make it ideal for graduate courses in electrical and computer engineering and it will also be of great interest to practising engineers.
Interactive Web Based Data Visualization With R Plotly And Shiny
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Author : Carson Sievert
language : en
Publisher: CRC Press
Release Date : 2020-01-30
Interactive Web Based Data Visualization With R Plotly And Shiny written by Carson Sievert and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-01-30 with Business & Economics categories.
The richly illustrated Interactive Web-Based Data Visualization with R, plotly, and shiny focuses on the process of programming interactive web graphics for multidimensional data analysis. It is written for the data analyst who wants to leverage the capabilities of interactive web graphics without having to learn web programming. Through many R code examples, you will learn how to tap the extensive functionality of these tools to enhance the presentation and exploration of data. By mastering these concepts and tools, you will impress your colleagues with your ability to quickly generate more informative, engaging, and reproducible interactive graphics using free and open source software that you can share over email, export to pdf, and more. Key Features: Convert static ggplot2 graphics to an interactive web-based form Link, animate, and arrange multiple plots in standalone HTML from R Embed, modify, and respond to plotly graphics in a shiny app Learn best practices for visualizing continuous, discrete, and multivariate data Learn numerous ways to visualize geo-spatial data This book makes heavy use of plotly for graphical rendering, but you will also learn about other R packages that support different phases of a data science workflow, such as tidyr, dplyr, and tidyverse. Along the way, you will gain insight into best practices for visualization of high-dimensional data, statistical graphics, and graphical perception. The printed book is complemented by an interactive website where readers can view movies demonstrating the examples and interact with graphics.
Dynamic Mode Decomposition
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Author : J. Nathan Kutz
language : en
Publisher: SIAM
Release Date : 2016-11-23
Dynamic Mode Decomposition written by J. Nathan Kutz and has been published by SIAM this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-11-23 with Science categories.
Data-driven dynamical systems is a burgeoning field?it connects how measurements of nonlinear dynamical systems and/or complex systems can be used with well-established methods in dynamical systems theory. This is a critically important new direction because the governing equations of many problems under consideration by practitioners in various scientific fields are not typically known. Thus, using data alone to help derive, in an optimal sense, the best dynamical system representation of a given application allows for important new insights. The recently developed dynamic mode decomposition (DMD) is an innovative tool for integrating data with dynamical systems theory. The DMD has deep connections with traditional dynamical systems theory and many recent innovations in compressed sensing and machine learning. Dynamic Mode Decomposition: Data-Driven Modeling of Complex Systems, the first book to address the DMD algorithm, presents a pedagogical and comprehensive approach to all aspects of DMD currently developed or under development; blends theoretical development, example codes, and applications to showcase the theory and its many innovations and uses; highlights the numerous innovations around the DMD algorithm and demonstrates its efficacy using example problems from engineering and the physical and biological sciences; and provides extensive MATLAB code, data for intuitive examples of key methods, and graphical presentations.
A Tale Of Three Next Generation Sequencing Platforms
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Author : Applied Research Press
language : en
Publisher: Createspace Independent Publishing Platform
Release Date : 2015-07-24
A Tale Of Three Next Generation Sequencing Platforms written by Applied Research Press and has been published by Createspace Independent Publishing Platform this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-07-24 with categories.
Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent's PGM, Pacific Biosciences' RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support. Proceeds from the sale of this book go to the support of an elderly disabled person.
Dissertation Abstracts International
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Author :
language : en
Publisher:
Release Date : 2002
Dissertation Abstracts International written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2002 with Dissertations, Academic categories.
Analysis Of Single Cell Data
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Author : Carolin Loos
language : en
Publisher: Springer
Release Date : 2016-03-17
Analysis Of Single Cell Data written by Carolin Loos and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-03-17 with Mathematics categories.
Carolin Loos introduces two novel approaches for the analysis of single-cell data. Both approaches can be used to study cellular heterogeneity and therefore advance a holistic understanding of biological processes. The first method, ODE constrained mixture modeling, enables the identification of subpopulation structures and sources of variability in single-cell snapshot data. The second method estimates parameters of single-cell time-lapse data using approximate Bayesian computation and is able to exploit the temporal cross-correlation of the data as well as lineage information.