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:
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.
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.
Table of Contents
PrefaceChapter 1 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
Chapter 2 Variant Calling on Rna Sequencing Data: State of Art And
- Future Perspectives
- Introduction
- 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
- References
Chapter 3 an Innovative Gene Prioritization Pipeline for Dnasequencing
- 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
- Results from Clc Genomics Workbench
- Results from Dnastar Lasergene Suite
- Results from Toppgene
- Discussion
- References
Chapter 4 New Integrated Differential Expression Approach for Rnaseq
- Data Analysis
- Introduction
- 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
- Results
- Validity of Deg Analysis Tools and Concordance Analysis
- Integration of Deg Methods and Performances Evaluation
- Discussion
- Concluding Remarks
- Notes
- References
Chapter 5 Innovations in Data Visualization for Straightforward
- Interpretation of Nucleic Acid Omics Outcomes
- Introduction
- Materials and Methods
- Dna-Sequencing: Circos and Viva Tools
- Rna-Sequencing: Omics Playground Suite
- Pathway Analysis: Cluego and Cluepedia Cytoscape Plug-Ins
- Results
- 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
- Discussion
- Conclusions
- References
- Subject Index
Author
- Luigi Donato
- Simona Alibrandi
- Rosalia D’Angelo
- Concetta Scimone
