Advances in bioinformatics and computational biology : 14th Brazilian Symposium on Bioinformatics, BSB 2021, virtual event, November 22-26, 2021, proceedings / / Peter F. Stadler [and three others], editors

• Record Nr.: UNISA996464531703316
• Pubbl/distr/stampa: Cham, Switzerland : , : Springer, , [2021]; ©2021
• ISBN: 3-030-91814-9
• Descrizione fisica: 1 online resource (159 pages)
• Collana: Lecture notes in computer science, lecture notes in bioinformatics ; ; Volume 13063
• Disciplina: 572.80285
• Soggetti: Bioinformatics; Computational biology
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: 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.; References -- FluxPRT: An Adaptable and Extensible Proteomics LIMS -- 1 Introduction -- 2 Proteomics Lab Operations -- 3 Methodology -- 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 -- References -- MathPIP: Classification of Proinflammatory Peptides Using Mathematical Descriptors -- 1 Background -- 2 Materials and Methods -- 2.1 Data Selection -- 2.2 Feature Engineering -- 2.3 Experimental Setting -- 3 Results and Discussion -- 4 Conclusion -- References -- Metagenomic Insights of the Microbial Community from a Polluted River in Brazil 2020 -- 1 Introduction -- 2 Materials and Methods -- 3 Results -- 4 Conclusion -- References -- Mesoscopic Evaluation of DNA Mismatches in PCR Primer-Target Hybridisation to Detect SARS-CoV-2 Variants of Concern -- 1 Introduction -- 2 Materials and Methods -- 3 Results and Discussion -- 4 Conclusion -- References -- Author Index.