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Today, a single laboratory can generate a vast amount of biological data. There is a wealth of data already available in public databases, which makes the modern life sciences almost dependent on bioinformatics. This book brings together an international team of experts to discuss the state-of-the-art from several fields of bioinformatics, from the automatic identification and classification of viruses to the analysis of the transcriptome of single cells and plants, including artificial intelligence algorithms to discover biomarkers and text mining approaches to help in the interpretation of the findings. Machine learning, pattern discovery and analysis, error correction, Bayesian inference and novel computational techniques to discover chromosomal rearrangements continue to play crucial roles in biological discovery, and all of them are explored in chapters of this book. In sum, this book contains high-quality chapters that provide excellent views into key topics of current bioinformatics research, topics that should remain important for the next several years.

Bioinformatics. --- Text Mining Gene Selection; Biological Big Data; Single-Cell RNA Sequencing; Large-Scale Structural Rearrangements in Chromosomes; Machine Learning Approaches; Biomarker Discovery; Gene Expression Data; Bayesian Inference of Gene Expression; Error-Correction Methodologies; Genome Sequencing Data; Plant Transcriptome Assembly; Aligned Pattern Clustering System; Pattern Analysis; Hidden Markov Models; Viral Classification and Discovery; Pattern Discovery and Disentanglement; Aligned Pattern Cluster Analysis; Protein Binding Complexes Detection

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This book includes a collection of eight original research articles and three reviews covering a wide range of topics in the field of kinetoplastids. In addition, readers can find a compendium of molecular biology procedures and bioinformatics tools.

Research & information: general --- Biology, life sciences --- trypanosomatids --- yeasts --- trypanosomatids genome --- cell cycle phases --- S-phase duration --- DNA replication --- replication origins --- neglected tropical diseases --- Leishmania --- Trypanosoma cruzi --- Trypanosoma brucei --- drug discovery --- in vitro models --- in vivo models --- genomics --- drug resistance --- Leishmania infantum --- proteome --- post-translational modifications (PTMs) --- proteogenomics --- mass spectrometry --- Retrotransposon Hot Spot (RHS) multigene family --- chromosome distribution --- recombination --- gene mosaic structure --- evolution --- nuclear protein --- Leishmania braziliensis --- reverse genetics --- CRISPR–Cas9 --- gene targeting --- phenotyping --- heat shock proteins --- Trypanosoma cruzi strain --- sequencing methods --- genome plasticity --- gene expression --- trans-sialidases --- mucins --- SENP --- Ulp2 --- SUMO --- CRISPR --- protease --- genome --- repeats --- 3′UTR --- multigenic family --- Leishmania donovani --- whole-genome sequencing (WGS) --- transcriptome --- artemisinin drug resistance --- Leishmania viruses --- phylogeny --- coevolution --- endosymbiont protozoan viruses --- transcriptome assembly --- transcriptional regulation --- ontology network --- co-expression network --- taxonomic analysis --- database contamination --- kleptoplastidy

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This book includes a collection of eight original research articles and three reviews covering a wide range of topics in the field of kinetoplastids. In addition, readers can find a compendium of molecular biology procedures and bioinformatics tools.

trypanosomatids --- yeasts --- trypanosomatids genome --- cell cycle phases --- S-phase duration --- DNA replication --- replication origins --- neglected tropical diseases --- Leishmania --- Trypanosoma cruzi --- Trypanosoma brucei --- drug discovery --- in vitro models --- in vivo models --- genomics --- drug resistance --- Leishmania infantum --- proteome --- post-translational modifications (PTMs) --- proteogenomics --- mass spectrometry --- Retrotransposon Hot Spot (RHS) multigene family --- chromosome distribution --- recombination --- gene mosaic structure --- evolution --- nuclear protein --- Leishmania braziliensis --- reverse genetics --- CRISPR–Cas9 --- gene targeting --- phenotyping --- heat shock proteins --- Trypanosoma cruzi strain --- sequencing methods --- genome plasticity --- gene expression --- trans-sialidases --- mucins --- SENP --- Ulp2 --- SUMO --- CRISPR --- protease --- genome --- repeats --- 3′UTR --- multigenic family --- Leishmania donovani --- whole-genome sequencing (WGS) --- transcriptome --- artemisinin drug resistance --- Leishmania viruses --- phylogeny --- coevolution --- endosymbiont protozoan viruses --- transcriptome assembly --- transcriptional regulation --- ontology network --- co-expression network --- taxonomic analysis --- database contamination --- kleptoplastidy

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Plants provide the foundation for the structure and function, as well as interactions, among organisms in both tropical and temperate zone habitats. To date, many investigations have revealed patterns and mechanisms generating plant diversity at various scales and from diverse ecological perspectives. However, in the era of climate change, anthropogenic disturbance, and rapid urbanization, new insights are needed to understand how plant species in these forest habitats are changing and adapting. Investigations of plants in both little-disturbed, more natural environments, as well as in urban areas in which crucial green infrastructure is ever more important for sustaining complex human societies are needed. This Special Issue of Forests will focus on plant variation from the perspectives of morphology, genetics, and function, especially plant interactions with biotic and abiotic factors. Research articles may address any aspect of plant evolution and community phylogenetics (explorations of patterns and mechanisms from diverse organismal levels, e.g., molecular, population, species, community, landscape, and ecosystem), plant functional traits (e.g., nutrient traits of leaf, stem, root; reproductive traits of flower, fruit, seed), and/or responses of plant species to changing environments (e.g., water, atmosphere, soil, human activities). Studies providing quantitative evaluation or description of interactions of plants with animals and microbes, both in natural and urban environments, including terrestrial and aquatic systems, are also welcome.

Hevea brasiliensis Müll. Arg. --- HbMad-box genes --- conserved domains --- gene structures --- expression profiles --- stress treatments --- microsatellite locus --- Hardy-Weinberg equilibrium --- genetic differentiation --- breeding population --- artificial selection --- Aegle marmelos (L.) Corr. --- transcripts --- transcriptome assembly --- simple sequence repeats --- transcription factors --- cytochrome p450 --- glycotransferases --- metabolic pathway --- grafting --- pecan --- miRNA --- graft union --- sequencing --- edible forest product --- forest biology --- macro-fungi --- non-timber forest products (NTFPs) --- Pan-Pearl River Delta --- allometry --- anatomy --- Polygonatum odoratum --- Polygonatum multiflorum --- shape --- shoot --- endophytes --- medicinal plants --- pathogen --- molecular identification --- plant-microbe interaction --- gas exchange --- chlorophyll fluorescence --- growth trait --- genetic variation --- early selection --- pedunculate oak --- drought --- stress --- memory --- flushing --- autumn leaf senescence --- phenological shift --- carry-over effect --- mangroves --- DNA barcoding --- species identification --- phylogenetic relation --- moso bamboo --- heat shock factor gene --- abiotic stresses --- co-expression --- yellow-green leaf mutant --- transcriptome --- antenna protein --- photosynthesis --- birch --- Dalbergia odorifera T. Chen --- genetic diversity --- population structure --- EST-SSR marker --- microsatellite marker --- rosewood --- conservation --- Pinus massoniana --- introgression hybrid --- RNA sequencing --- DEGs --- reproduction --- phenology --- leafing out --- flowering --- senescence --- cumulative logistic regression --- hawthorn --- provenance trial --- non-local populations --- variance analysis --- lime application --- understory removal --- microbial community --- forest management --- Eucalyptus --- protogyny (PG) --- protandry (PA) --- pollen viability --- seed success --- polyploidy --- phosphate solubilizing bacteria --- nutrition --- oil tea --- Lagerstroemia species --- simple sequence repeat markers --- bulked segregant analysis --- creeping trait --- plant architecture --- climate change --- forest biodiversity --- plant–environment interactions --- plant traits --- urbanization