08090nam 22008055 450 991051058570332120260206114200.03-030-91814-910.1007/978-3-030-91814-9(MiAaPQ)EBC6810927(Au-PeEL)EBL6810927(CKB)19919642600041(OCoLC)1286660273(PPN)258838876(DE-He213)978-3-030-91814-9(EXLCZ)991991964260004120211120d2021 u| 0engurcnu||||||||txtrdacontentcrdamediacrrdacarrierAdvances 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. Brigido1st ed. 2021.Cham :Springer International Publishing :Imprint: Springer,2021.1 online resource (159 pages)Lecture Notes in Bioinformatics,2366-6331 ;13063Print version: Stadler, Peter F. Advances in Bioinformatics and Computational Biology Cham : Springer International Publishing AG,c2021 9783030918132 Includes bibliographical references and index.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.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.Lecture Notes in Bioinformatics,2366-6331 ;13063BioinformaticsArtificial intelligenceApplication softwareComputer networksBioinformaticsComputational and Systems BiologyArtificial IntelligenceComputer and Information Systems ApplicationsComputer Communication NetworksBioinformàticathubIntel·ligència artificialthubProgramari d'aplicacióthubXarxes d'ordinadorsthubLlibres electrònicsthubBioinformatics.Artificial intelligence.Application software.Computer networks.Bioinformatics.Computational and Systems Biology.Artificial Intelligence.Computer and Information Systems Applications.Computer Communication Networks.BioinformàticaIntel·ligència artificialProgramari d'aplicacióXarxes d'ordinadors572.80285Stadler Peter F.1965-MiAaPQMiAaPQMiAaPQBOOK9910510585703321Advances in Bioinformatics and Computational Biology2998120UNINA