Intro
Preface
Organization
Contents
Applied Bioinformatics and Computational Biology
Comparative Transcriptome Profiling of Maytenus ilicifolia Root and Leaf
1 Introduction
2 Methods
2.1 Plant Material and Total RNA Isolation
2.2 Library Preparation and Sequencing
2.3 Quality Control and de novo Assembly
2.4 Functional Annotation
2.5 Differential Expression Analysis
2.6 Gene Ontology Enrichment and KEGG Analysis
3 Results and Discussion
3.1 De novo Assembly and Functional Annotation of M. ilicifolia
3.2 Identification of Differentially Expressed Transcripts in Both Tissues
References
Hypusine Plays a Role in the Translation of Short mRNAs and Mediates the Polyamine and Autophagy Pathways in Saccharomyces Cerevisiae
1 Introduction
2 Materials and Methods
2.1 RNA-seq Data Analysis
2.2 Strain and Growth Conditions
2.3 RNA Isolation and qRT-PCR
2.4 Protein Extraction and Western Blot Analysis
3 Results and Discussion
3.1 Translation of Short ORFs is Impaired in dys1-1 Mutant
3.2 Hypusination Modulates Autophagy
References
Topological Characterization of Cancer Driver Genes Using Reactome Super Pathways Networks
1 Introduction
2 Method
2.1 Reactome Functional Iteration
2.2 Super Pathways as Reactome FI Sub-networks
2.3 Super Pathways Sub-networks Enriched with Drivers Information
3 Results
3.1 Centrality Measures
3.2 Network Attack
4 Discussion and Conclusion
References
Bioinformatics and Computational Biology
CellHeap: A Workflow for Optimizing COVID-19 Single-Cell RNA-Seq Data Processing in the Santos Dumont Supercomputer
1 Introduction
2 Description of the CellHeap Workflow
3 Results
3.1 Input Data and Experiment Setup
3.2 Environmental Setup
3.3 Results Discussion
4 Conclusion
References.

Combining Orthology and Xenology Data in a Common Phylogenetic Tree
1 Introduction
2 Preliminaries
3 Tree-Like Pairs of Maps
4 Tree-Like Pairs of Maps with Constraints
5 Concluding Remark
References
ContFree-NGS: Removing Reads from Contaminating Organisms in Next Generation Sequencing Data
1 Introduction
2 Implementation
3 Evaluation
4 Conclusion
References
Deep Learning-Based COVID-19 Diagnostics of Low-Quality CT Images
1 Introduction
2 Dataset
3 Methodology
3.1 Data Preprocessing
3.2 Deep Neural Network Architectures
4 Experimental Evaluation
4.1 Data Preprocessing
4.2 Transfer Learning with ResNet50
4.3 Image- and Exam-Level Classification of the Test Set
4.4 Interpreting Model Decisions
5 Conclusion
References
Feature Importance Analysis of Non-coding DNA/RNA Sequences Based on Machine Learning Approaches
1 Background
2 Pipeline for Machine Learning Classification Task
2.1 Prediction of sRNAs
2.2 Prediction of CircRNA
3 Results and Discussion
3.1 Case Study 1: sRNAs in Bacteria
3.2 Case Study 2: CircRNA in Humans
4 Conclusion
References
Heuristics for Cycle Packing of Adjacency Graphs for Genomes with Repeated Genes
1 Introduction
2 Definitions
3 Random Packings
4 Genetic Algorithm
5 Experimental Results
5.1 Applications with the Reversal Distance
5.2 Experiments with Real Biological Data
6 Conclusion
References
PIMBA: A PIpeline for MetaBarcoding Analysis
1 Introduction
2 Implementation
2.1 Preprocessing
2.2 Taxonomy Assignment
2.3 Plotting
3 Results and Discussion
3.1 16S rRNA Mock Community
3.2 Fungal ITS Mock Community
3.3 Metazoan COI Mock Community
4 Conclusion
References
Short Papers
CEvADA: Co-Evolution Analysis Data Archive
1 Introduction
2 Technical Notes.