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Big Mechanisms in Systems Biology

Big Mechanisms in Systems Biology Book
Author : Bor-Sen Chen,Cheng-Wei Li
Publisher : Academic Press
Release : 2016-10-25
ISBN : 0128097078
Language : En, Es, Fr & De

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Book Description :

Big Mechanisms in Systems Biology: Big Data Mining, Network Modeling, and Genome-Wide Data Identification explains big mechanisms of systems biology by system identification and big data mining methods using models of biological systems. Systems biology is currently undergoing revolutionary changes in response to the integration of powerful technologies. Faced with a large volume of available literature, complicated mechanisms, small prior knowledge, few classes on the topics, and causal and mechanistic language, this is an ideal resource. This book addresses system immunity, regulation, infection, aging, evolution, and carcinogenesis, which are complicated biological systems with inconsistent findings in existing resources. These inconsistencies may reflect the underlying biology time-varying systems and signal transduction events that are often context-dependent, which raises a significant problem for mechanistic modeling since it is not clear which genes/proteins to include in models or experimental measurements. The book is a valuable resource for bioinformaticians and members of several areas of the biomedical field who are interested in an in-depth understanding on how to process and apply great amounts of biological data to improve research. Written in a didactic manner in order to explain how to investigate Big Mechanisms by big data mining and system identification Provides more than 140 diagrams to illustrate Big Mechanism in systems biology Presents worked examples in each chapter

Investigation of Genetic and Epigenetic Networks for Differential Cellular Mechanisms Between Normal Developing and Regenerating Livers Via Systems Biology Method and Big Data Mining

Investigation of Genetic and Epigenetic Networks for Differential Cellular Mechanisms Between Normal  Developing and Regenerating Livers Via Systems Biology Method and Big Data Mining Book
Author : Shang-Wen Wong
Publisher : Unknown
Release : 2017
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Investigation of Genetic and Epigenetic Networks for Differential Cellular Mechanisms Between Normal Developing and Regenerating Livers Via Systems Biology Method and Big Data Mining book written by Shang-Wen Wong, available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Systems Biology

Systems Biology Book
Author : Dimitrios Vlachakis
Publisher : BoD – Books on Demand
Release : 2019-06-19
ISBN : 1838808035
Language : En, Es, Fr & De

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Book Description :

Systems biology is the inevitable outcome of long years of knowledge acquisition and data accumulation. The aim of systems biology is to integrate in a seamless way all existing knowledge in interconnected disciplines, stretching from modern biomedical research to physics, chemistry, and mathematics. The main integration tool of such complex biomedical systems is via computational and mathematical modeling. In this direction, a series of state-of-the-art computer science techniques are used, namely, data mining and fusion, machine learning, and deep learning all under the prism of big data. All in all, systems biology is at the arrowhead of modern and state-of-the-art biomedical research by attempting to address key biological questions describing holistically complex biological systems.

Molecular Mechanisms of Autonomy in Biological Systems

Molecular Mechanisms of Autonomy in Biological Systems Book
Author : Tara Karimi
Publisher : Springer
Release : 2018-07-28
ISBN : 3319918249
Language : En, Es, Fr & De

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Book Description :

This book presents a novel molecular description for understanding the regulatory mechanisms behind the autonomy and self-organization in biological systems. Chapters focus on defining and explaining the regulatory molecular mechanisms behind different aspects of autonomy and self-organization in the sense of autonomous coding, data processing, structure (mass) formation and energy production in a biological system. Subsequent chapters discuss the cross-talk among mechanisms of energy, and mass and information, transformation in biological systems. Other chapters focus on applications regarding therapeutic approaches in regenerative medicine. Molecular Mechanisms of Autonomy in Biological Systems is an indispensable resource for scientists and researchers in regenerative medicine, stem cell biology, molecular biology, tissue engineering, developmental biology, biochemistry, biophysics, bioinformatics, as well as big data sciences, complexity and soft computing.

Philosophy of Systems Biology

Philosophy of Systems Biology Book
Author : Sara Green
Publisher : Springer
Release : 2016-12-15
ISBN : 3319470000
Language : En, Es, Fr & De

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Book Description :

The emergence of systems biology raises many fascinating questions: What does it mean to take a systems approach to problems in biology? To what extent is the use of mathematical and computational modelling changing the life sciences? How does the availability of big data influence research practices? What are the major challenges for biomedical research in the years to come? This book addresses such questions of relevance not only to philosophers and biologists but also to readers interested in the broader implications of systems biology for science and society. The book features reflections and original work by experts from across the disciplines including systems biologists, philosophers, and interdisciplinary scholars investigating the social and educational aspects of systems biology. In response to the same set of questions, the experts develop and defend their personal perspectives on the distinctive character of systems biology and the challenges that lie ahead. Readers are invited to engage with different views on the questions addressed, and may explore numerous themes relating to the philosophy of systems biology. This edited work will appeal to scholars and all levels, from undergraduates to researchers, and to those interested in a variety of scholarly approaches such as systems biology, mathematical and computational modelling, cell and molecular biology, genomics, systems theory, and of course, philosophy of biology.

Metabolome Analyses

Metabolome Analyses  Book
Author : Seetharaman Vaidyanathan,George G. Harrigan,Royston Goodacre
Publisher : Springer Science & Business Media
Release : 2005-04-28
ISBN : 9780387252391
Language : En, Es, Fr & De

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Book Description :

Metabolome analysis is now recognized as a crucial component of functional genomic and systems biology investigations. Innovative approaches to the study of metabolic regulation in microbial, plant and animal systems are increasingly facilitating the emergence of systems approaches in biology. This book highlights analytical and bioinformatics strategies now available for investigating metabolic networks in microbial, plant and animal systems. The contributing authors are world leaders in this field and they present an unambiguous case for pursuing metabolome analysis as a means to attain a systems level understanding of complex biological systems.

Systems Biology of Cancer

Systems Biology of Cancer Book
Author : Sam Thiagalingam
Publisher : Cambridge University Press
Release : 2015-04-09
ISBN : 1316239527
Language : En, Es, Fr & De

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Book Description :

With over two hundred types of cancer diagnosed to date, researchers the world over have been forced to rapidly update their understanding of the biology of cancer. In fact, only the study of the basic cellular processes, and how these are altered in cancer cells, can ultimately provide a background for rational therapies. Bringing together the state-of-the-art contributions of international experts, Systems Biology of Cancer proposes an ultimate research goal for the whole scientific community: exploiting systems biology to generate in-depth knowledge based on blueprints that are unique to each type of cancer. Readers are provided with a realistic view of what is known and what is yet to be uncovered on the aberrations in the fundamental biological processes, deregulation of major signaling networks, alterations in major cancers and the strategies for using the scientific knowledge for effective diagnosis, prognosis and drug discovery to improve public health.

Systems Immunology and Infection Microbiology

Systems Immunology and Infection Microbiology Book
Author : Bor-Sen Chen
Publisher : Academic Press
Release : 2021-03-16
ISBN : 0128173351
Language : En, Es, Fr & De

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Book Description :

Systems Immunology and Infection Microbiology provides a large amount of biological system models, diagrams and flowcharts to illustrate development procedures and help users understand the results of systems immunology and infection microbiology. Chapters discuss systems immunology, systems infection microbiology, systematic inflammation and immune responses in restoration and regeneration process, systems' innate and adaptive immunity in infection process, systematic genetic and epigenetic pathogenic/defensive mechanism during bacterial infection on human cells is introduced, and the systematic genetic and epigenetic pathogenic/defensive mechanisms during viral infection on human cells. This book provides new big data-driven and systems-driven systems immunology and infection microbiology to researchers applying systems biology and bioinformatics in their work. It is also invaluable to several members of biomedical field who are interested in learning more about those approaches. Encompasses one applicable example in every chapter to illustrate the solution procedure from big data mining, network modeling, host/pathogen cross-talk detection, drug target identification and systems drug design Presents flowcharts to represent the development procedure of systematic immunology and infection in a very clear format Contains 100 color diagrams to help readers understand the related biological networks, their corresponding mechanisms, and significant network biomarkers for therapeutic drug design

Systems Cancer Biology

Systems Cancer Biology Book
Author : Bor-Sen Chen
Publisher : Cambridge Scholars Publishing
Release : 2021-07-13
ISBN : 152757234X
Language : En, Es, Fr & De

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Book Description :

Cancer is a complex and heterogeneous (systematic) disease that exhibits high levels of robustness against various therapeutic interventions. Due to the complex, heterogeneous, and evolving nature of cancer, it is essential for a system-oriented view to be adopted in order to understand the pathogenic mechanism of cancer which will eventually lead to the drug discovery and treatment of patients. This book not only provides new insights from system modeling and large scale experimental data, but also will allow the reader to perceive the systematic characteristics of cancer under some micro-environments. Based on the systems biology method and genome-wide high throughput data, the book presents the PPI network, gene regulatory network and epigenetic network as an integrated genetic and epigenetic cellular network of lung cancer, bladder cancer, thyroid cancer, colorectal cancer, and liver cancer to investigate their core signaling pathways of the carcinogenesis process to identify their corresponding significant carcinogenic biomarkers as drug targets for systems drug discovery and design. Consequently, the book presents the design of a multiple-molecule drug that can target these biomarkers for the therapeutic treatment of cancer with fewer side effects.

High Confidence Network Predictions from Big Biological Data

High Confidence Network Predictions from Big Biological Data Book
Author : Rasmus Magnusson
Publisher : Linköping University Electronic Press
Release : 2020-05-04
ISBN : 9179298877
Language : En, Es, Fr & De

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Book Description :

Biology functions in a most intriguing fashion, with human cells being regulated by multiplex networks of proteins and their dependent systems that control everything from proliferation to cell death. Notably, there are cases when these networks fail to function properly. In some diseases there are multiple small perturbations that push the otherwise healthy cells into a state of malfunction. These maladies are referred to as complex diseases, and include common disorders such as allergy, diabetes type II, and multiple sclerosis, and due to their complexity there is no universally defined approach to fully understand their pathogenesis or pathophysiology. While these perturbations can be measured using high-throughput technologies, the interplay of these perturbations is generally to complex to understand without any structured mathematical analysis. There is today numerous such methods that put the small perturbations of complex diseases into relation of interactions among each other. However, the methods have historically struggled with notable uncertainty in their predictions. This uncertainty can be addressed by at least two different approaches. First, mechanistically realistic mathematical modelling is an approach that has the capacity to accurately describe almost any biological system, but such models can to-date only describe small systems and networks. Secondly, large-scale mathematical modelling approaches exist, but the faithfulness of the models to the underlying biology has been compromised to achieve algorithms that are computationally effective. In this Ph.D. thesis, I suggest how high confidence predictions of network interactions can be extracted from big biological. First, I show how large-scale data can be used when building high-quality ODE models (Paper I). Secondly, by developing the software LASSIM, I show how ODE models can be expanded to the size of entire cell systems (Paper II). However, while LASSIM showed that powerful non-linear ODE-modelling can be applied to understand big biological data, it still remained a machine learning-based approach in contrast to hypothesis-driven model development. Instead, two more studies revolving around large-scale modelling approaches were initiated. The third study suggested that ambiguities in model selection and interaction identification greatly compromise the accuracy of available tools, and that the novel software of Paper III, LiPLike, can be used to remove such predictions. Intriguingly, while LiPLike was able to effectively discard false identifications, the accuracy of predictions remained relatively low. This low accuracy was thought to arise from model simplifications, and therefore the next study aimed at finding methods that come closer to the true biological system (Paper IV). In particular, the study aimed at predicting protein abundance -the true mediators of biological functionality- from the much more easily accessible mRNA levels, and found that such models could be used to get several new insights on protein mechanisms, which was exemplified by the identification of important biomarkers of autoimmune diseases. The analysis of big biological data and the underlying networks is a centrepiece of understanding both diseases and how cell functionality is orchestrated. The work that is presented in this Ph.D. thesis represents a journey between fields with different views on how these networks should be inferred. In particular, it aimed to combine the accuracy of small-scale mechanistic modelling with the system-spanning potential of large-scale linear system modelling, and this thesis thus provides a tool-bench of methods and insights on how knowledge can be extracted from big biological data, and in extension it is a small step towards a generation of new comprehensions of biological systems and complex diseases. Biologiska system är komplexa att förstå och det är först relativt nyligen man på ett strukturerat sätt börjat att analysera biologiska data genom matematisk analys. Ett av de tydligaste områden där en matematisk analys av biologiska system behövs är vid studier av komplexa sjukdomar. Sådana sjukdomar, till vilka åkommor som multipel skleros, diabetes typ II och allergi hör, uppstår genom en komplicerad kombination av arv och miljö som inte är helt förstådd. Studier av komplexa sjukdomar har dock kunnat identifiera många små potentiella störningar över hela det biologiska systemet, men ingen av dessa störningar är individuellt avgörande för att utveckla en komplex sjukdom. Denna svåröverskådlighet förhindrar traditionella analyser för att finna ursprunget till sjukdomen, och går det inte förstå en sjukdom försämras möjligheterna att till exempel hitta nya läkemedel eller att ställa diagnos. För att förstå hur systemen bakom komplexa sjukdomar fungerar, eller inte fungerar, tas olika prover vilka ofta resulterar i enorma mängder data. Dessa datamängder är oftast så stora att vi människor inte kan tolka dem genom att bara läsa talen, utan vi måste använda olika typer av matematiska modeller och datorprogram för att sådan data ska berätta något för oss. Inom två överlappande fält som kommit att kallas systembiologi och bioinformatik har metoder för att analysera biologiska data haft en snabb utveckling de senaste 50 åren. Dessa metoder har haft som mål att svara på flertalet frågor, och ett framträdande mål har varit att identifiera skillnader mellan hur friska och sjuka celler fungerar. En stor del av cellens funktioner regleras av olika nätverk av proteiner, och ett annat mål har varit att förstå hur dessa nätverk regleras. Ytterligare ett mål har varit att identifiera mätbara värden, så kallade biomarkörer, som kan användas för att identifiera sjukdom hos patienter. De metoder som används för att svara på dessa frågor kan grovt delas in i två grupper, mekanistisk modellering och storskalig modellering, med respektive styrkor och svagheter. Mekanistisk modellering har potentialen att ge mycket träffsäkra prediktioner, men kräver mycket manuellt arbete och har därför varit en alltför tidskrävande metod för att applicera på stora biologiska datamängder. Storskalig modellering klarar enkelt av stora datamängder, men har i stället haft en så låg tillförlitlighet

Case Studies in Systems Biology

Case Studies in Systems Biology Book
Author : Pavel Kraikivski
Publisher : Springer
Release : 2021-03-26
ISBN : 9783030677411
Language : En, Es, Fr & De

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Book Description :

This book provides case studies that can be used in Systems Biology related classes. Each case study has the same structure which answers the following questions: What is the biological problem and why is it interesting? What are the relevant details with regard to cell physiology and molecular mechanisms? How are the details put together into a mathematical model? How is the model analyzed and simulated? What are the results of the model? How do they compare to the known facts of the cell physiology? Does the model make predictions? What can be done to extend the model? The book presents a summary of results and references to more relevant sources. The volume contains the classic collection of topics and studies that are well established yet novel in the systems biology field.

LabStudio

LabStudio Book
Author : Jenny E. Sabin,Peter Lloyd Jones
Publisher : Unknown
Release : 2017-05
ISBN : 9781138783966
Language : En, Es, Fr & De

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Book Description :

LabStudio: Design Research between Architecture and Biology introduces the concept of the research design laboratory in which funded research and trans-disciplinary participants achieve radical advances in science, design, and applied architectural practice. The book demonstrates to natural scientists and architects alike new approaches to more traditional design studio and hypothesis-led research that are complementary, iterative, experimental, and reciprocal. These originate from 3-D spatial biology and generative design in architecture, creating philosophies and practices that are high-risk, non-linear, and design-driven for often surprising results. Authors Jenny E. Sabin, an architectural designer, and Peter Lloyd Jones, a spatial biologist, present case studies, prototypes, and exercises from their practice, LabStudio, illustrating in hundreds of color images a new model for seemingly unrelated, open-ended, data-, systems- and technology-driven methods that you can adopt for incredible results.

Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer

Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer Book
Author : Osbaldo Resendis-Antonio,Christian Diener
Publisher : Frontiers Media SA
Release : 2017-11-23
ISBN : 2889453332
Language : En, Es, Fr & De

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Book Description :

Since the discovery of the Warburg effect in the 1920s cancer has been tightly associated with the genetic and metabolic state of the cell. One of the hallmarks of cancer is the alteration of the cellular metabolism in order to promote proliferation and undermine cellular defense mechanisms such as apoptosis or detection by the immune system. However, the strategies by which this is achieved in different cancers and sometimes even in different patients of the same cancer is very heterogeneous, which hinders the design of general treatment options. Recently, there has been an ongoing effort to study this phenomenon on a genomic scale in order to understand the causality underlying the disease. Hence, current “omics” technologies have contributed to identify and monitor different biological pieces at different biological levels, such as genes, proteins or metabolites. These technological capacities have provided us with vast amounts of clinical data where a single patient may often give rise to various tissue samples, each of them being characterized in detail by genomescale data on the sequence, expression, proteome and metabolome level. Data with such detail poses the imminent problem of extracting meaningful interpretations and translating them into specific treatment options. To this purpose, Systems Biology provides a set of promising computational tools in order to decipher the mechanisms driving a healthy cell’s metabolism into a cancerous one. However, this enterprise requires bridging the gap between large data resources, mathematical analysis and modeling specifically designed to work with the available data. This is by no means trivial and requires high levels of communication and adaptation between the experimental and theoretical side of research.

Computational Systems Biology

Computational Systems Biology Book
Author : Andres Kriete,Roland Eils
Publisher : Academic Press
Release : 2013-11-26
ISBN : 0124059384
Language : En, Es, Fr & De

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Book Description :

This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.

Bioinformatics in the Era of Post Genomics and Big Data

Bioinformatics in the Era of Post Genomics and Big Data Book
Author : Ibrokhim Y. Abdurakhmonov
Publisher : BoD – Books on Demand
Release : 2018-06-20
ISBN : 1789232686
Language : En, Es, Fr & De

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Book Description :

Bioinformatics has evolved significantly in the era of post genomics and big data. Huge advancements were made toward storing, handling, mining, comparing, extracting, clustering and analysis as well as visualization of big macromolecular data using novel computational approaches, machine and deep learning methods, and web-based server tools. There are extensively ongoing world-wide efforts to build the resources for regional hosting, organized and structured access and improving the pre-existing bioinformatics tools to efficiently and meaningfully analyze day-to-day increasing big data. This book intends to provide the reader with updates and progress on genomic data analysis, data modeling and network-based system tools.

Computational Methods in Systems Biology

Computational Methods in Systems Biology Book
Author : Jérôme Feret,Heinz Koeppl
Publisher : Springer
Release : 2017-10-06
ISBN : 3319674714
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 15th International Conference on Computational Methods in Systems Biology, CMSB 2017, held in Darmstadt, Germany, in September 2017. The 15 full papers, 4 tool papers and 4 posters presented together with 1 invited talk were carefully reviewed and selected from 41 regular paper submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verication, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology.

Systems Biology

Systems Biology Book
Author : Lilia Alberghina,Hans V. Westerhoff
Publisher : Springer Science & Business Media
Release : 2007-10-04
ISBN : 9783540742692
Language : En, Es, Fr & De

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Book Description :

For life to be understood and disease to become manageable, the wealth of postgenomic data now needs to be made dynamic. This development requires systems biology, integrating computational models for cells and organisms in health and disease; quantitative experiments (high-throughput, genome-wide, living cell, in silico); and new concepts and principles concerning interactions. This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies. The benefits for industry, such as the new network-based drug-target design validation, and testing, are also presented.

Computational Methods in Systems Biology

Computational Methods in Systems Biology Book
Author : Milan Češka,David Šafránek
Publisher : Springer
Release : 2018-08-27
ISBN : 3319994298
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 16th International Conference on Computational Methods in Systems Biology, CMSB 2018, held in BRNO, Czech Republic, in September 2018. The 15 full and 7 short papers presented together with 5 invited talks were carefully reviewed and selected from 46 submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology; parameter and model inference from experimental data; automated parameter and model synthesis; model integration and biological databases; multi-scale modeling and analysis methods; design, analysis, and verification methods for synthetic biology; methods for biomolecular computing and engineered molecular devices. Chapters 3, 9 and 10 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Data Driven Innovation Big Data for Growth and Well Being

Data Driven Innovation Big Data for Growth and Well Being Book
Author : OECD
Publisher : OECD Publishing
Release : 2015-10-06
ISBN : 9264229353
Language : En, Es, Fr & De

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Book Description :

This report improves the evidence base on the role of Data Driven Innovation for promoting growth and well-being, and provide policy guidance on how to maximise the benefits of DDI and mitigate the associated economic and societal risks.

Plant Single Cell Type Systems Biology

Plant Single Cell Type Systems Biology Book
Author : Marc Libault,Sixue Chen
Publisher : Frontiers Media SA
Release : 2016-09-06
ISBN : 2889199487
Language : En, Es, Fr & De

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Book Description :

The phenotype of a plant in response to a stress condition is the reflection of the molecular responses in different cell-types composing the plant. The multicellular complexity represents a challenge when accessing specific responses of each cell or cell type composing the plant. To overcome this difficulty and allow the clear characterization of the plant cell molecular mechanisms, the research community is now focusing on studying a single cell and single cell-types. The isolation of plant single cells is limited by the cell wall that confers the rigidity of the plant and its overall structure. Various methods have been developed for isolating plant cells (e.g. laser capture microdissection; cell sorting of Green Fluorescent Protein (GFP)-tagged protoplasts, differential protoplastization of cells such as guard cells, isolation of easily accessible cell types such as cotton fiber, pollen cells, trichomes and root hair cells). The development of these innovative approaches to isolate single plant cells or cell-types combined with the application of sensitive and high-throughput technologies allows a better analysis of the developmental processes and response to environmental stresses. Ultimately, single plant cell and cell-type biology will lead to establishment of more reliable and accurate -molecular regulatory networks at the resolution of basic life unit. The goal of this Research Topic is to cover new technological and biological advances in the study of plant single cell, cell-type and systems biology.