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Computational Analysis and Integration of MeDIP-seq Methylome Data (Book chapter)

Authors: ---
ISBN: 9789535122401 Year: DOI: 10.5772/61207 Language: Undetermined
Publisher: IntechOpen Grant: Wellcome Trust - 99148
Subject: Biology
Added to DOAB on : 2019-01-17 11:47:01
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The combinatorial number of possible methylomes in biological time and space is astronomical. Consequently, the computational analysis of methylomes needs to cater for a variety of data, throughput and resolution. Here, we review recent advances in 2nd generation sequencing (2GS) with a focus on the different methods used for the analysis of MeDIP-seq data. The challenges and opportunities presented by the integration of methylation data with other genomic data types are discussed as is the potential impact of emerging 3rd generation sequencing (3GS) based technologies on methylation analysis.

Keywords

sequencing --- biochemistry

Game Changer - Next Generation Sequencing and its Impact on Food Microbiology

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889454631 Year: Pages: 302 DOI: 10.3389/978-2-88945-463-1 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Microbiology
Added to DOAB on : 2018-11-16 17:17:57
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Advances in next-generation sequencing technologies (NGS) are revolutionizing the field of food microbiology. Microbial whole genome sequencing (WGS) can provide identification, characterization, and subtyping of pathogens for epidemiological investigations at a level of precision previously not possible. This allows for connections and source attribution to be inferred between related isolates that may be overlooked by traditional techniques. The archiving and global sharing of genome sequences allow for retrospective analysis of virulence genes, antimicrobial resistance markers, mobile genetic elements and other novel genes. The advent of high-throughput 16S rRNA amplicon sequencing, in combination with the advantages offered by massively parallel second-generation sequencing for metagenomics, enable intensive studies on the microbiomes of food products and the impact of foods on the human microbiome. These studies may one day lead to the development of reliable culture-independent methods for food monitoring and surveillance. Similarly, RNA-seq has provided insights into the transcriptomes and hence the behaviour of bacterial pathogens in food, food processing environments, and in interaction with the host at a resolution previously not achieved through the use of microarrays and/or RT-PCR. The vast un-tapped potential applications of NGS along with its rapidly declining costs, give this technology the ability to contribute significantly to consumer protection, global trade facilitation, and increased food safety and security. Despite the rapid advances, challenges remain. How will NGS data be incorporated into our existing global food safety infrastructure? How will massive NGS data be stored and shared globally? What bioinformatics solutions will be used to analyse and optimise these large data sets? This Research Topic discusses recent advances in the field of food microbiology made possible through the use of NGS.

From Genes to Species: Novel Insights from Metagenomics

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199754 Year: Pages: 229 DOI: 10.3389/978-2-88919-975-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Microbiology
Added to DOAB on : 2016-01-19 14:05:46
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The majority of microbes in many environments are considered “as yet uncultured” and were traditionally considered inaccessible for study through the microbiological gold standard of pure culture. The emergence of metagenomic approaches has allowed researchers to access and study these microbes in a culture-independent manner through DNA sequencing and functional expression of metagenomic DNA in a heterologous host. Metagenomics has revealed an extraordinary degree of diversity and novelty, not only among microbial communities themselves, but also within the genomes of these microbes. This Research Topic aims to showcase the utility of metagenomics to gain insights on the microbial and genomic diversity in different environments by revealing the breadth of novelty that was in the past, largely untapped.

Repetitive Structures in Biological Sequences: Algorithms and Applications

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450183 Year: Pages: 93 DOI: 10.3389/978-2-88945-018-3 Language: English
Publisher: Frontiers Media SA
Subject: General and Civil Engineering --- Biotechnology
Added to DOAB on : 2018-02-27 16:16:44
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Repetitive structures in biological sequences are emerging as an active focus of research and the unifying concept of "repeatome" (the ensemble of knowledge associated with repeating structures in genomic/proteomic sequences) has been recently proposed in order to highlight several converging trends. One main trend is the ongoing discovery that genomic repetitions are linked to many biological significant events and functions. Diseases (e.g. Huntington's disease) have been causally linked with abnormal expansion of certain repeating sequences in the human genome. Deletions or multiple copy duplications of genes (Copy Number Variations) are important in the aetiology of cancer, Alzheimer, and Parkinson diseases. A second converging trend has been the emergence of many different models and algorithms for detecting non-obvious repeating patterns in strings with applications to in genomic data.Borrowing methodologies from combinatorial pattern, matching, string algorithms, data structures, data mining and machine learning these new approaches break the limitations of the current approaches and offer a new way to design better trans-disciplinary research. The articles collected in this book provides a glance into the rich emerging area of repeatome research, addressing some of its pressing challenges. We believe that these contributions are valuable resources for repeatome research and will stimulate further research from bioinformatic, statistical, and biological points of view.

The Least Cost Path From Landscape Genetics to Landscape Genomics

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889455485 Year: Pages: 116 DOI: 10.3389/978-2-88945-548-5 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Ecology --- Genetics --- Botany
Added to DOAB on : 2019-01-23 14:53:42
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Ecosystems are the stage on which the play of evolution is acted, and ecosystems are complex, spatially structured and temporally varying. The purpose of this Research Topic is to explore critical challenges and opportunities for the transition from landscape genetics to landscape genomics. Landscape genetics has focused on the spatial analysis of small genetic datasets, typically comprised of less than 20 microsatellite markers, taken from clusters of individuals in putative populations or distributed individuals across landscapes. The recent emergence of large scale genomic datasets produced by next generation sequencing methods poses tremendous challenge and opportunity to the field. Perhaps the greatest is to produce, process, curate, archive and analyze spatially referenced genomic datasets in a way such that research is led by a priori hypotheses regarding how environmental heterogeneity and temporal dynamics interact to affect gene flow and selection. The papers in the Research Topic cover a broad range of topics under this area of focus, from reviews of the emergence of landscape genetics, to best practices in spatial analysis of genetic data. The compilation, like the emerging field itself, is eclectic and illustrates the scope of both the challenges and opportunities of this emerging field.

DNA Polymerases in Biotechnology

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889194551 Year: Pages: 146 DOI: 10.3389/978-2-88919-455-1 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-02-05 17:24:33
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DNA polymerases are core tools for molecular biology including PCR, whole genome amplification, DNA sequencing and genotyping. Research has focused on discovery of novel DNA polymerases, characterization of DNA polymerase biochemistry and development of new replication assays. These studies have accelerated DNA polymerase engineering for biotechnology. For example, DNA polymerases have been engineered for increased speed and fidelity in PCR while lowering amplification sequence bias. Inhibitor resistant DNA polymerase variants enable PCR directly from tissue (i.e. blood). Design of DNA polymerases that efficiently incorporate modified nucleotide have been critical for development of next generation DNA sequencing, synthetic biology and other labeling and detection technologies. The Frontiers in Microbiology Research Topic on DNA polymerases in Biotechnology aims to capture current research on DNA polymerases and their use in emerging technologies.

Natural Diversity in the New Millennium

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199525 Year: Pages: 173 DOI: 10.3389/978-2-88919-952-5 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2016-01-19 14:05:46
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Natural diversity has been extensively used to understand plant biology and improve crops. However, studies were commonly based on visual phenotypes or on a few measurable parameters. Nowadays, a large number of parameters can be measured thanks to next generation sequencing, metabolomics, proteomics, and transcriptomics thus providing an unprecedented resolution in the detection of natural diversity. This enhanced resolution offers new possibilities in terms of understanding plant biology. Technology advances also contribute to a better assessment of the biodiversity loss currently taking place. Hence, the topic presents an overview on efforts for maintaining biological diversity in crops, on possibilities offered by recent technologies in the assessment of natural variation, and ends with examples of the diversity found even at the cellular level.

Microbial responses to environmental changes

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197231 Year: Pages: 261 DOI: 10.3389/978-2-88919-723-1 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
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Advances in next generation sequencing technologies, omics, and bioinformatics are revealing a tremendous and unsuspected diversity of microbes, both at a compositional and functional level. Moreover, the expansion of ecological concepts into microbial ecology has greatly advanced our comprehension of the role microbes play in the functioning of ecosystems across a wide range of biomes. Super-imposed on this new information about microbes, their functions and how they are organized, environmental gradients are changing rapidly, largely driven by direct and indirect human activities. In the context of global change, understanding the mechanisms that shape microbial communities is pivotal to predict microbial responses to novel selective forces and their implications at the local as well as global scale. One of the main features of microbial communities is their ability to react to changes in the environment. Thus, many studies have reported changes in the performance and composition of communities along environmental gradients. However, the mechanisms underlying these responses remain unclear. It is assumed that the response of microbes to changes in the environment is mediated by a complex combination of shifts in the physiological properties, single-cell activities, or composition of communities: it may occur by means of physiological adjustments of the taxa present in a community or selecting towards more tolerant/better adapted phylotypes. Knowing whether certain factors trigger one, many, or all mechanisms would greatly increase confidence in predictions of future microbial composition and processes. This Research Topic brings together studies that applied the latest molecular techniques for studying microbial composition and functioning and integrated ecological, biogeochemical and/or modeling approaches to provide a comprehensive and mechanistic perspective of the responses of micro-organisms to environmental changes. This Research Topic presents new findings on environmental parameters influencing microbial communities, the type and magnitude of response and differences in the response among microbial groups, and which collectively deepen our current understanding and knowledge of the underlying mechanisms of microbial structural and functional responses to environmental changes and gradients in both aquatic and terrestrial ecosystems. The body of work has, furthermore, identified many challenges and questions that yet remain to be addressed and new perspectives to follow up on.

Emerging Tools for Emerging Symbioses - Using Genomics Applications to Studying Endophytes

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452194 Year: Pages: 157 DOI: 10.3389/978-2-88945-219-4 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2017-10-13 14:57:01
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Plants are typically colonized by numerous endophyte species symbiotically without any noticeable disease symptoms. These microbes are abundant, diverse and play critical ecological roles across natural and agricultural ecosystems. Endophytes have attracted the attention of researchers due to their various beneficial effects on plants, especially in agricultural crop species. Genomic tools will enhance our understanding on the growth and nutrition requirements of this host-symbiont relationship. Recent advances in DNA sequencing technologies and bioinformatic pipelines have allowed analyzing the plant microbiome and host-endophyte interaction more effectively with limited bias. Furthermore, various studies have employed and utilized transcriptomic and genomic tools to understand the role of endophytes and their interaction with plant hosts. This electronic book covers various research articles highlighting the important developments on endophytes using transcriptomics, next generation sequencing and genomic tools.

The Cognition of Sequences

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453986 Year: Pages: 132 DOI: 10.3389/978-2-88945-398-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Psychology
Added to DOAB on : 2018-11-16 17:17:57
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It is impossible to perceive the innumerable stimuli impinging on our senses, all at once. Out of the myriad stimuli, external and internal, a few are selected for further processing; and even among these, we try to put each in some sort of relation with the others, to be able to make some sense about them all. Time, of course, is an elementary dimension we use to organize our experiences. Thus, the perception of sequences is basic to human cognition. Nevertheless, research addressing sequences is rather sparse. Partly, this is due to difficulty in designing experiments in this area due to huge individual differences. Then, there is the assumption that temporal order has more to do with memory than perception. Another problem is that sequences seem endemic to the auditory world. So much so that some researchers have suggested that sound provides the ‘auditory scaffolding’ for sequencing behavior. Little wonder that research studies addressing sequences in modalities other than audition are extremely rare.This research topic aimed to gather a holistic picture of sequencing behaviour among humans by collecting snapshots of the current research on the topic of sequencing. We particularly sought contributions which addressed sequences beyond the auditory modality. The single unifying criteria for these diverse contributions was that they shed new light on previously unexplored empirical relationships and/or provoked new lines of research with incisive ideas regarding sequencing behavior. Seasoned researchers contributed their views on perception, memory, and production of sequences.

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