Advances in Bioinformatics and Computational Biology : 14th Brazilian Symposium on Bioinformatics, BSB 2021, Virtual Event, November 22–26, 2021, Proceedings / edited by Peter F. Stadler, Maria Emilia M. T. Walter, Maribel Hernandez-Rosales, Marcelo M. Brigido.

Format:

Book

Contributor:

Stadler, Peter F., 1965- editor.

Series:

Lecture Notes in Bioinformatics, 2366-6331 ; 13063

Language:

English

Subjects (All):

Bioinformatics.

Artificial intelligence.

Application software.

Computer networks.

Computational and Systems Biology.

Artificial Intelligence.

Computer and Information Systems Applications.

Computer Communication Networks.

Local Subjects:

Bioinformatics.

Computational and Systems Biology.

Artificial Intelligence.

Computer and Information Systems Applications.

Computer Communication Networks.

Physical Description:

1 online resource (159 pages)

Edition:

1st ed. 2021.

Place of Publication:

Cham : Springer International Publishing : Imprint: Springer, 2021.

Summary:

This book constitutes the refereed proceedings of the Brazilian Symposium on Bioinformatics, BSB 2021, held in November 2021. Due to COVID-19 pandemic the conference was held virtually The 10 revised full papers and 5 short papers were carefully reviewed and selected from 28 submissions. The papers address a broad range of current topics in computational biology and bioinformatics.

Contents:

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

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

3.1 Translation of Short ORFs is Impaired in dys1-1 Mutant

3.2 Hypusination Modulates Autophagy

Topological Characterization of Cancer Driver Genes Using Reactome Super Pathways Networks

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

Bioinformatics and Computational Biology

CellHeap: A Workflow for Optimizing COVID-19 Single-Cell RNA-Seq Data Processing in the Santos Dumont Supercomputer

2 Description of the CellHeap Workflow

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

2 Preliminaries

3 Tree-Like Pairs of Maps

4 Tree-Like Pairs of Maps with Constraints

5 Concluding Remark

ContFree-NGS: Removing Reads from Contaminating Organisms in Next Generation Sequencing Data

2 Implementation

3 Evaluation

Deep Learning-Based COVID-19 Diagnostics of Low-Quality CT Images

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

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

3.1 Case Study 1: sRNAs in Bacteria

3.2 Case Study 2: CircRNA in Humans

Heuristics for Cycle Packing of Adjacency Graphs for Genomes with Repeated Genes

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

PIMBA: A PIpeline for MetaBarcoding Analysis

2.1 Preprocessing

2.2 Taxonomy Assignment

2.3 Plotting

3.1 16S rRNA Mock Community

3.2 Fungal ITS Mock Community

3.3 Metazoan COI Mock Community

Short Papers

CEvADA: Co-Evolution Analysis Data Archive

2 Technical Notes.

References

FluxPRT: An Adaptable and Extensible Proteomics LIMS

2 Proteomics Lab Operations

3.1 Proteomics Workflow Construction and the Flux LIMS

3.2 Proteomics Guide

4 Results and Discussion

4.1 FluxPRT Workflow

4.2 Proteomics Guide

4.3 FluxPRT Interface

5 Concluding Remarks

6 Availability

MathPIP: Classification of Proinflammatory Peptides Using Mathematical Descriptors

2.1 Data Selection

2.2 Feature Engineering

2.3 Experimental Setting

Metagenomic Insights of the Microbial Community from a Polluted River in Brazil 2020

Mesoscopic Evaluation of DNA Mismatches in PCR Primer-Target Hybridisation to Detect SARS-CoV-2 Variants of Concern

Author Index.

Notes:

Includes bibliographical references and index.

Other Format:

Print version: Stadler, Peter F. Advances in Bioinformatics and Computational Biology

ISBN:

3-030-91814-9

OCLC:

1286660273