Advances in Bioinformatics and Computational Biology: 13th Brazilian Symposium on Bioinformatics, BSB 2020, São Paulo, Brazil, November 23–27, 2020, Proceedings

Preface
Organization
Contents
A Classification of de Bruijn Graph Approaches for De Novo Fragment Assembly
1 Introduction
2 Genome Assembly
3 The de Bruijn Graph De Novo Assembly Approach
4 de Bruijn Graph Based Assemblers
4.1 Main Classification of Approaches
4.2 General Strategies to Reduce Memory Footprint for DBG Construction
4.3 Specific Strategies to Reduce the Large Memory Consumption
4.4 k-mers Counters
5 Conclusions
References
Redundancy Treatment of NGS Contigs in Microbial Genome Finishing with Hashing-Based Approach
1 Introduction
1.1 DNA Repetitions and Contigs Redundancy
1.2 Computational Methods for Redundancy Detection in Sequences
1.3 Contribution of This Work
2 Biological Dataset and Assembly
3 The Proposed Hybrid Model
4 Results and Discussion
5 Conclusion
References
Efficient Out-of-Core Contig Generation
1 Introduction
2 De Novo Assembly Using de Bruijn Graph
3 Overview of Our Proposed Approach
4 Contig Generation
5 Conclusions
References
In silico Pathogenomic Analysis of Corynebacterium Pseudotuberculosis Biovar Ovis
1 Introduction
1.1 Corynebacterium Pseudotuberculosis
1.2 Comparative Pathogenomics
1.3 Determinants of Pathogenicity
2 Methods
2.1 Pan-Genomic Analysis of C. Pseudotuberculosis Biovar Ovis
2.2 Prediction of Virulence Factors in Corynebacterium
2.3 Composition of Pathogenicity Islands (PAI)
2.4 Synteny in C. Pseudotuberculosis Genomes
2.5 In Silico Prediction of Pathogenicity Potentials
2.6 Protein-Protein Interactions
2.7 Identification of Prophages
3 Results and Discussion
3.1 Identification of Adherence Factors
3.2 Identification of Iron Uptake Factors
3.3 Identification of Regulation Factors
3.4 Identification of Toxin Factors
3.5 Prediction of Pathogenicity Islands
3.6 Prediction of Pathogenicity Potentials
3.7 Identification of Prophages
3.8 Prediction of Protein-Protein Interactions
4 Conclusion
References
Assessing the Sex-Related Genomic Composition Difference Using a k-mer-Based Approach: A Case of Study in Arapaima gigas (Pirarucu)
1 Introduction
2 Materials and Methods
2.1 Sequencing and Data Processing
2.2 k-mer Analysis
3 Results and Discussion
4 Conclusions
References
COVID-19 X-ray Image Diagnostic with Deep Neural Networks
1 Introduction
2 Dataset
3 Methodology
3.1 Data Preparation
3.2 Classification Model
4 Experimental Evaluation
4.1 Model Evaluation
4.2 Multi-class and Binary Classification of the Unbalanced Dataset
4.3 Ensemble of CNNs
4.4 Test Set Evaluation
5 Conclusions and Future Work
References
Classification of Musculoskeletal Abnormalities with Convolutional Neural Networks
1 Introduction
2 Methodology
2.1 Dataset
2.2 Experiments
3 Results and Discussion
4 Conclusion
References
Combining Mutation and Gene Network Data in a Machine Learning Approach for False-Positive Cancer Driver Gene Discovery
1 Introduction
2 Method
2.1 Data Collection and Preprocessing
2.2 Machine Learning Training Process
3 Results
3.1 Model Evaluation
3.2 Concept Application and Validation
4 Discussion and Conclusion
References
Unraveling the Role of Nanobodies Tetrad on Their Folding and Stability Assisted by Machine and Deep Learning Algorithms
1 Introduction
2 Computational Details
2.1 Dataset Preparation
2.2 Classification Methods
3 Results and Discussion
3.1 Features Selection
3.2 Linear Separability of the Data
3.3 Classification Algorithms
4 Conclusions
References
Experiencing DfAnalyzer for Runtime Analysis of Phylogenomic Dataflows
1 Introduction
2 Background
2.1 DfAnalyzer: Runtime Dataflow Analysis of Scientific Applications Using Provenance
2.2 Related Work
3 Evaluating DfAnalyzer for Phylogenomics Experiments
3.1 Specializing DfAnalyzer
3.2 SciPhylomics Workflow
3.3 Setup of the Experiment
3.4 Data Analysis in Practice
4 Conclusion
References
Sorting by Reversals and Transpositions with Proportion Restriction
1 Introduction
2 Basic Definitions
2.1 Breakpoints
2.2 Cycle Graph
3 Approximation Algorithms
3.1 Unsigned Case
3.2 Signed Case
4 Asymptotic Approximation for the Signed Case
5 Conclusion
References
Heuristics for Breakpoint Graph Decomposition with Applications in Genome Rearrangement Problems
1 Introduction
2 Preliminaries
3 Heuristics for Breakpoint Graph Decomposition
3.1 Greedy Algorithm
3.2 Tabu Search
4 Experimental Results
4.1 Applications in Genome Rearrangement Distance
5 Conclusion
References
Center Genome with Respect to the Rank Distance
1 Introduction
2 Definitions
3 Results
3.1 Co-tailed Genomes
3.2 Genomes Not Co-tailed
3.3 Main Result
4 Conclusions
References
ImTeNet: Image-Text Classification Network for Abnormality Detection and Automatic Reporting on Musculoskeletal Radiographs
1 Introduction
2 Related Work
3 Proposed Method
3.1 Caption Generation
3.2 Image-Text Classification Framework
4 Experimental Setup
4.1 Musculoskeletal Radiographs (MURA) for Abnormality Classification
4.2 Implementation Details
5 Results and Discussion
5.1 Analysis
6 Conclusions and Future Work
References
A Scientometric Overview of Bioinformatics Tools in the Pseudomonas Putida Genome Study
1 Introduction
2 Methods
3 Results and Discussion
3.1 Knowledge Areas
3.2 Main Journals
3.3 Sequencing Data
3.4 Assembly
3.5 Annotation
4 Conclusions
References
Polysome-seq as a Measure of Translational Profile from Deoxyhypusine Synthase Mutant in Saccharomyces cerevisiae
1 Introduction
2 Materials and Methods
2.1 Strain and Growth Conditions
2.2 Polysome Profilling
2.3 RNA Isolation
2.4 Library Preparation and Sequencing
2.5 RNA-seq Data Analysis
2.6 Ribo-Seq and Protein Abundance Comparative Analysis
2.7 Differential Expression Analysis
2.8 Enrichment of Gene Ontology and Enrichment Analysis of Transcription Factors
3 Results and Discussion
3.1 RNA-seq and Polysome-Seq Experiments in DYS1 and dys1-1 Strains
3.2 Polysome-seq as a Measure for Translational Profile
3.3 Yeast Hypusination Mutant dys1-1 Responds Transcriptionally for Gene Regulation
References
Anti-CD3 Stimulated T Cell Transcriptome Reveals Novel ncRNAs and Correlates with a Suppressive Profile
1 Introduction
2 Materials and Methods
2.1 Sample Preparation and Sequencing
2.2 Genome Mapping and Transcript Prediction
2.3 Data Mining and Ontology Classification
2.4 cDNA Synthesis Transcript Testing
2.5 Gene Expression Analysis by qPCR Assays
3 Results
3.1 LincRNAs
3.2 Novel Predicted Transcripts
3.3 Testing Novel LncRNA Isoforms
4 Discussion
5 Conclusion
References
A Simplified Complex Network-Based Approach to mRNA and ncRNA Transcript Classification
1 Introduction
2 Graphs and Complex Networks
3 Materials and Methods
3.1 Materials
3.2 Methods
4 Results and Discussion
5 Conclusion
References
A Systems Biology Driven Approach to Map the EP300 Interactors Using Comprehensive Protein Interaction Network
1 Introduction
2 Materials and Method
2.1 Collection of EP300 Interactors
2.2 Protein Class and Subcellular Location Analysis
2.3 Functional Annotation and Pathway Enrichment Analysis
2.4 Construction of EP300 Interactome
3 Results and Discussion
3.1 Analysis of Subcellular Location and Protein Class
3.2 Functional Enrichment Analysis of EP300 Interactors
3.3 Pathway Enrichment Analysis of EP300 Interactors
3.4 EP300 Interactome and Identification of First-Degree Nodes
4 Conclusion
References
Analyzing Switch Regions of Human Rab10 by Molecular Dynamics Simulations
1 Introduction
2 Methodology
2.1 Molecular Docking
2.2 Molecular Dynamics
3 Results and Discussion
3.1 Molecular Docking Study
3.2 Molecular Dynamics Study
4 Conclusions
References
Importance of Meta-analysis in Studies Involving Plant Responses to Climate Change in Brazil
1 Introduction
2 Methodology
2.1 How to Get the Data to Perform the Meta-analysis
2.2 How to Apply a Meta-analysis
3 Results and Discussion
3.1 History of Climate Change Conferences and the Impact on the Meta-analytical Production on the Effect of Elevated CO2 on Plants
3.2 Integrative Analysis of Variables that Are Contemplated in Brazilian Studies Eligible for a Meta-analysis on Plant Responses to Climate Change
4 Conclusion
References
A Brief History of Bioinformatics Told by Data Visualization
1 Introduction
2 Materials and Methods
2.1 Data Collection
2.2 Data Visualizations
3 Results and Discussion
3.1 The History that the Keywords in Papers Tell Us
3.2 Omics
3.3 Keywords in Disuse
3.4 Artificial Intelligence and the Influence of the Pop Culture in Science
3.5 A Promising Future for Molecular Dynamics
3.6 Popular Programming Languages for Bioinformatics
3.7 Limitations of This Study
4 Conclusion
References
Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases
1 Introduction
2 Method
3 Results and Discussion
3.1 Comparison with Related Works
4 Conclusion and Future Work
References
Oncogenic Signaling Pathways in Mucopolysaccharidoses
1 Introduction
2 Methods
3 Results
4 Discussion
5 Concluding Remarks
References
Natural Products as Potential Inhibitors for SARS-CoV-2 Papain-Like Protease: An in Silico Study
1 Introduction
2 Methods
3 Results and Discussion
4 Conclusion
References
Author Index