Advances in Bioinformatics, Biostatistics and Omic Sciences / Luigi Donato [and five others].

Format:

Book

Author/Creator:

Donato, Luigi, author.

Language:

English

Subjects (All):

Bioinformatics.

Biometry.

Computational biology.

Physical Description:

1 online resource (ii, 138 pages) : illustrations

Place of Publication:

Singapore, : Bentham Science, 2020.

Summary:

Bioinformatics, and by extension omic sciences - the collective disciplines that are dependent on the use of extensive datasets of biological information - present a challenge of data management for researchers all over the world. Big data collected as part of research projects and experiments can be complex, with several kinds of variables involved. Coupled with continuously changing bioinformatics and information technology tools, there is a need to bring a multidisciplinary approach into these fields. Advances in Bioinformatics, Biostatistics and Omic Sciences attempts to realize an integrated approach between all omic sciences, exploring innovative bioinformatics and biostatistical methodologies which enable researchers to unveil hidden sides of biological phenomena. This volume presents reviews on the following topics which give a glimpse of recent advances in the field: - New Integrated Mitochondrial DNA Bioinformatics Pipeline to Improve Quality Assessment of Putative Pathogenic Variants from NGS Experiments - Variant Calling on RNA Sequencing Data: State of Art and Future Perspectives - An innovative Gene Prioritization Pipeline for WES analyses - New Integrated Differential Expression Approach for RNA-Seq Data Analysis - Innovations in Data Visualization for Straightforward Interpretation of Nucleic Acid Omics Outcomes This volume serves as a guide for graduate students in bioinformatics as well as researchers planning new projects as a part of their professional and academic activities.

Contents:

Cover

Title

Copyright

End User License Agreement

Contents

Foreword

Preface

CONSENT FOR PUBLICATION

CONFLICT OF INTEREST

ACKNOWLEDGEMENTS

New Integrated Mitochondrial DNA Bioinformatics Pipeline to Improve Quality Assessment of Putative Pathogenic Variants from NGS Experiments

INTRODUCTION

MATERIAL AND METHODS

Samples

Mitogenome Assembly/Mapping

Variant Detection by mtDNA-Server

Variant Annotation and Prioritization

In Silico Predictions and Variant Consequences

RESULTS

Alignment and Assembly of mtDNAs

Mitogenome Annotations MtDNA Variant Calling and Annotations

In Silico Functional Consequences and Pathogenicity Predictions

DISCUSSION

CONCLUSION AND PERSPECTIVES

REFERENCES

Variant Calling on RNA Sequencing Data: State of Art and Future Perspectives

NEXT-GENERATION SEQUENCING

Variant Calling

Differential Gene Expression Analysis

VARIANT CALLING FROM RNA-SEQ DATA: WHAT'S THE NEW?

WHERE VARIANT CALLING ON DNA DOES NOT ARRIVE: RNA EDITING AND IMPRINTING PROFILES

CONCLUDING REMARKS

An Innovative Gene Prioritization Pipeline for DNA-Sequencing Analyses INTRODUCTION

MATERIALS AND METHODS

Prioritization of Genes Carrying Variants Obtained From CLC Genomics Workbench

STOP_ (KNO+UNK) _&_NONSYN_(KNOWN)

NEW MUT & SNPS IN NEW GENES

Prioritization of Genes Obtained from DNASTAR Lasergene Suite

Prioritization by ToppGene

Results from CLC Genomics Workbench

Results from DNASTAR Lasergene Suite

Results from ToppGene

New Integrated Differential Expression Approach for RNA-Seq Data Analysis

MATERIAL AND METHODS Software Packages for Detecting Differentially Expressed Genes

DESEeq2

edgeR

Limma

SAMSeq

TweeDESeq

ANOVA

Other Methods

Datasets and Methods

DE Tools and Normalization Methods

ANALYSIS

Validity of DEG Analysis Tools and Concordance Analysis

Integration of DEG Methods and Performances Evaluation

NOTES

Innovations in Data Visualization for Straightforward Interpretation of Nucleic Acid Omics Outcomes

DNA-Sequencing: Circos and VIVA tools RNA-Sequencing: Omics Playground Suite

Pathway Analysis: ClueGO and CluePedia Cytoscape plug-ins

WES Circular Plot by Circos and Heat Maps by VIVA Provide a Strength Summary of Variant Data

Omics Playground Provided a Straightforward Full-featured Output of RNA-Seq Samples

ClueGO and CluePedia Analyses Produced Appealing Graphical Representation of Pathways and Enrichments Involved Clustered Genes

CONCLUSIONS

Subject Index

Back Cover.

Notes:

Includes bibliographical references and index.

Description based on publisher supplied metadata and other sources.

ISBN:

9789811481789

9811481784

9789811481802

9811481806

OCLC:

1226645017