Search results: Found 11

Listing 1 - 10 of 11 << page
of 2
>>
Sort by
Systems Biology and the Challenge of Deciphering the Metabolic Mechanisms Underlying Cancer

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453337 Year: Pages: 142 DOI: 10.3389/978-2-88945-333-7 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Physiology --- Biology
Added to DOAB on : 2018-11-16 17:17:57
License:

Loading...
Export citation

Choose an application

Abstract

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.

New Trends on Genome and Transcriptome Characterizations

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889456109 Year: Pages: 157 DOI: 10.3389/978-2-88945-610-9 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2019-01-23 14:53:43
License:

Loading...
Export citation

Choose an application

Abstract

This Research Topic is devoted to bioinformaticians, geneticists and researchers who study or apply methods and algorithms for genomes and transcriptome analyses, aimed at understanding pathology discriminations and classifications. Papers are encouraged that use unconventional approaches and/or where mathematical and computational concepts are applied to biological and medical contexts in original ways. The contributions presented in the Topic should be of interest also to a wide class of scientists and students involved in the several fields where genomic and transcriptomic approaches are becoming essential for future investigations.

Genome Informatics 2009:Genome Informatics Series Vol. 22

Authors: --- --- --- --- et al.
Book Series: Genome Informatics Series ISBN: 9781848165786 Year: Pages: 228 DOI: 10.1142/p718 Language: ENGLISH
Publisher: World Scientific Publishing Co.
Added to DOAB on : 2019-07-04 04:29:21

Loading...
Export citation

Choose an application

Abstract

This volume contains 17 peer-reviewed papers based on the presentations at the 9th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2009) held at the Life Science Engineering Building of Boston University from July 27 to 29, 2009. This workshop started in 2001 as a platform for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following institutions and programs:Boston University Graduate Program in BioinformaticsCharité – Universitätsmedizin BerlinFreie Universität BerlinGlobal COE Program — Center of Education and Research for Advanced Genome-Based Medicine, University of TokyoThe International Research Training Group (IRTG) Genomics and Systems Biology of Molecular NetworksInternational Research and Training Program on Bioinformatics and Systems Biology, Kyoto University Bioinformatics CenterMax-Delbrück Center for Molecular Medicine in BerlinMax Planck Institute for Molecular Genetics in BerlinMax Planck Institute of Molecular Plant Physiology in Potsdam

Genome Informatics 2009:Genome Informatics Series Vol. 23

Authors: --- ---
Book Series: Genome Informatics Series ISBN: 9781848165632 Year: Pages: 240 DOI: 10.1142/p715 Language: ENGLISH
Publisher: World Scientific Publishing Co.
Added to DOAB on : 2019-07-04 04:35:35

Loading...
Export citation

Choose an application

Abstract

This volume contains papers presented at the 20th International Conference on Genome Informatics (GIW 2009) held at the Pacifico Yokohama, Japan from December 14 to 16, 2009. The GIW Series provides an international forum for the presentation and discussion of original research papers on all aspects of bioinformatics, computational biology and systems biology. Its scope includes biological sequence analysis, protein structure prediction, genetic regulatory networks, bioinformatic algorithms, comparative genomics, and biomolecular data integration and analysis. Boasting a history of 20 years, GIW is the longest-running international bioinformatics conference.A total of 18 contributed papers were selected for presentation at GIW 2009 and for inclusion in this book. In addition, this book contains abstracts from the five invited speakers: Sean Eddy (HHMI's Janelia Farm, USA), Minoru Kanehisa (Kyoto University, Japan), Sang Yup Lee (KAIST, Korea), Hideyuki Okano (Keio University, Japan) and Mark Ragan (University of Queensland, Australia).

Natural Computing and Beyond

Authors: ---
Book Series: Proceedings in Information and Communications Technology ISSN: 18672914 ISBN: 9784431543930 9784431543947 Year: Volume: 6 Pages: 155 DOI: http://dx.doi.org/10.1007/978-4-431-54394-7 Language: English
Publisher: Springer
Subject: Manufactures --- Transportation --- Computer Science --- Biotechnology
Added to DOAB on : 2013-09-04 12:15:49
License:

Loading...
Export citation

Choose an application

Abstract

This book contains the joint proceedings of the Winter School of Hakodate (WSH) 2011 held in Hakodate, Japan, March 15–16, 2011, and the 6th International Workshop on Natural Computing (6th IWNC) held in Tokyo, Japan, March 28–30, 2012, organized by the Special Interest Group of Natural Computing (SIG-NAC), the Japanese Society for Artificial Intelligence (JSAI). This volume compiles refereed contributions to various aspects of natural computing, ranging from computing with slime mold, artificial chemistry, eco-physics, and synthetic biology, to computational aesthetics.

Advances in Systems Immunology and Cancer

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193134 Year: Pages: 108 DOI: 10.3389/978-2-88919-313-4 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Biology --- Biotechnology --- General and Civil Engineering --- Psychiatry --- Medicine (General) --- Physiology --- Neurology --- Science (General)
Added to DOAB on : 2016-02-05 17:24:33
License:

Loading...
Export citation

Choose an application

Abstract

Aims and Scope: The Research Topic is designed to feature the latest innovative and leading-edge research, reviews and opinions on the study of complex and dynamic processes related to the mammalian immune system and cancer. All papers were meticulously selected to present our readers the multidisciplinary approach to tackle the existing challenges faced in these important fields. From high throughput experimental methodologies to computational and theoretical approaches, the articles are intended to introduce physicists, chemists, computer scientists, biologists and immunologists the idea of systems biology approach to the understanding of mammalian immune system and cancer processes. Attention was given to works that developed more effective approaches to the treatment of proinflammatory disease and cancer. The strong interdisciplinary focus will discuss biological systems at the level from a few molecules to the entire organism. Specific focus domain includes: Innate and adaptive immunity, cancer and cancer stem cell, genomic, proteomic and metabolic analysis, imaging, biophysics of immune and cancer response, computational modeling, non-linear analysis, statistical analysis, translational and disease models Types of articles: Viewpoint, commentaries, research letters, research articles, review and methodologies

Precision Medicine in Oncology

Authors: --- --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889457052 Year: Pages: 163 DOI: 10.3389/978-2-88945-705-2 Language: English
Publisher: Frontiers Media SA
Subject: Medicine (General) --- Oncology
Added to DOAB on : 2019-01-23 14:53:43
License:

Loading...
Export citation

Choose an application

Abstract

The emerging precision medicine approach aims to tailor disease prevention and treatment to each patient on the basis of individual variability, environmental factors and lifestyle. Fundamental achievements in the last few decades have converged to offer nowadays the compelling opportunity to move towards this innovative approach: i) unprecedented improvements in disease modeling in silico, in vitro and in vivo; ii) acquisition of a wide range of biomedical information combined with the development of computational toolsets for flexible and integrative analyses of multi-assay datasets. Our deeper understanding of oncogenic mechanisms has finally begun to have a crucial impact on clinical decisions at several steps, from cancer prevention and diagnosis to therapeutic intervention. However, precision oncology still encounters several unresolved hurdles including tumour heterogeneity and recurrence as well as unexplained drug resistance and lack of effective ways to monitor response to therapeutic treatments. Notably, limitations in biomedical research regulation and governance represent additional debatable issues that need careful consideration.

Systems and Computational Biology - Bioinformatics and Computational Modeling

Author:
ISBN: 9789533078755 Year: Pages: 348 DOI: 10.5772/1866 Language: English
Publisher: IntechOpen
Subject: Biology
Added to DOAB on : 2019-10-03 07:51:48

Loading...
Export citation

Choose an application

Abstract

Whereas some ""microarray"" or ""bioinformatics"" scientists among us may have been criticized as doing ""cataloging research"", the majority of us believe that we are sincerely exploring new scientific and technological systems to benefit human health, human food and animal feed production, and environmental protections. Indeed, we are humbled by the complexity, extent and beauty of cross-talks in various biological systems; on the other hand, we are becoming more educated and are able to start addressing honestly and skillfully the various important issues concerning translational medicine, global agriculture, and the environment. The two volumes of this book present a series of high-quality research or review articles in a timely fashion to this emerging research field of our scientific community.

The Emerging Discipline of Quantitative Systems Pharmacology

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196425 Year: Pages: 97 DOI: 10.3389/978-2-88919-642-5 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Therapeutics
Added to DOAB on : 2016-08-16 10:34:25
License:

Loading...
Export citation

Choose an application

Abstract

In 2011, the National Institutes of Health (NIH), in collaboration with leaders from the pharmaceutical industry and the academic community, published a white paper describing the emerging discipline of Quantitative Systems Pharmacology (QSP), and recommended the establishment of NIH-supported interdisciplinary research and training programs for QSP. QSP is still in its infancy, but has tremendous potential to change the way we approach biomedical research. QSP is really the integration of two disciplines that have been increasingly useful in biomedical research; “Systems Biology” and “Quantitative Pharmacology”. Systems Biology is the field of biomedical research that seeks to understand the relationships between genes and biologically active molecules to develop qualitative models of these systems; and Quantitative Pharmacology is the field of biomedical research that seeks to use computer aided modeling and simulation to increase our understanding of the pharmacokinetics (PK) and pharmacodynamics (PD) of drugs, and to aid in the design of pre-clinical and clinical experiments. The purpose of QSP modeling is to develop quantitative computer models of biological systems and disease processes, and the effects of drug PK and PD on those systems. QSP models allow testing of numerous potential experiments “in-silico” to eliminate those associated with a low probability of success, avoiding the potential costs of evaluating all of those failed experiments in the real world. At the same time, QSP models allow us to develop our understanding of the interaction between drugs and biological systems in a more systematic and rigorous manner. As the need to be more cost-efficient in the use of research funding increases, biomedical researchers will be required to gain the maximum insight from each experiment that is conducted. This need is even more acute in the pharmaceutical industry, where there is tremendous competition to develop innovative therapies in a highly regulated environment, combined with very high research and development (R&D) costs for bringing new drugs to market (~$1.3 billion/drug). Analogous modeling & simulation approaches have been successfully integrated into other disciplines to improve the fundamental understanding of the science and to improve the efficiency of R&D (e.g., physics, engineering, economics, etc.). The biomedical research community has been slow to integrate computer aided modeling & simulation for many reasons: including the perception that biology and pharmacology are “too complex” and “too variable” to be modeled with mathematical equations; a lack of adequate graduate training programs; and the lack of support from government agencies that fund biomedical research. However, there is an active community of researchers in the pharmaceutical industry, the academic community, and government agencies that develop QSP and quantitative systems biology models and apply them both to better characterize and predict drug pharmacology and disease processes; as well as to improve efficiency and productivity in pharmaceutical R&D.

Computational Systems Biology of Pathogen-Host Interactions

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198214 Year: Pages: 198 DOI: 10.3389/978-2-88919-821-4 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
License:

Loading...
Export citation

Choose an application

Abstract

A thorough understanding of pathogenic microorganisms and their interactions with host organisms is crucial to prevent infectious threats due to the fact that Pathogen-Host Interactions (PHIs) have critical roles in initiating and sustaining infections. Therefore, the analysis of infection mechanisms through PHIs is indispensable to identify diagnostic biomarkers and next-generation drug targets and then to develop strategic novel solutions against drug-resistance and for personalized therapy. Traditional approaches are limited in capturing mechanisms of infection since they investigate hosts or pathogens individually. On the other hand, the systems biology approach focuses on the whole PHI system, and is more promising in capturing infection mechanisms. Here, we bring together studies on the below listed sections to present the current picture of the research on Computational Systems Biology of Pathogen-Host Interactions:- Computational Inference of PHI Networks using Omics Data- Computational Prediction of PHIs- Text Mining of PHI Data from the Literature- Mathematical Modeling and Bioinformatic Analysis of PHIs Computational Inference of PHI Networks using Omics Data Gene regulatory, metabolic and protein-protein networks of PHI systems are crucial for a thorough understanding of infection mechanisms. Great advances in molecular biology and biotechnology have allowed the production of related omics data experimentally. Many computational methods are emerging to infer molecular interaction networks of PHI systems from the corresponding omics data. Computational Prediction of PHIs Due to the lack of experimentally-found PHI data, many computational methods have been developed for the prediction of pathogen-host protein-protein interactions. Despite being emerging, currently available experimental PHI data are far from complete for a systems view of infection mechanisms through PHIs. Therefore, computational methods are the main tools to predict new PHIs. To this end, the development of new computational methods is of great interest. Text Mining of PHI Data from Literature Despite the recent development of many PHI-specific databases, most data relevant to PHIs are still buried in the biomedical literature, which demands for the use of text mining techniques to unravel PHIs hidden in the literature. Only some rare efforts have been performed to achieve this aim. Therefore, the development of novel text mining methods specific for PHI data retrieval is of key importance for efficient use of the available literature. Mathematical Modeling and Bioinformatic Analysis of PHIs After the reconstruction of PHI networks experimentally and/or computationally, their mathematical modeling and detailed computational analysis is required using bioinformatics tools to get insights on infection mechanisms. Bioinformatics methods are increasingly applied to analyze the increasing amount of experimentally-found and computationally-predicted PHI data. Acknowledgements: We, editors of this e-book, acknowledge Emrah Nikerel (Yeditepe University, Turkey) and Arzucan Özgür (Bogaaziçi University, Turkey) for their contributions during the initiation of the Research Topic.

Listing 1 - 10 of 11 << page
of 2
>>
Sort by