Bioinformatics communities

Ebook "Prokaryotic antimicrobial peptides: From genes to applications" will provide an overview of the advancement of fundamental knowledge and applications of antimicrobial peptides in biomedical, agricultural, veterinary, food, and cosmetic products. Antimicrobial peptides stand as potentially great alternatives to current antibiotics, and most research in this newly-created area has been published in journals and other periodicals. It is the editors’ opinion that it is timely to sum up the most important achievements in the field and provide the scientific community in a reference book.

451p manmanthanhla0201 26-02-2024 3 1   Download

Ebook Nursing informatics and the foundation of knowledge (Fourth edition): Part 2 includes content: Patient engagement and connected health, using informatics to promote community/population health, data mining as a research tool, bioinformatics, biomedical informatics, and computational biology,… and other contents.

995p longtimenosee03 01-02-2024 1 0   Download

Ebook "Geomicrobiology: Molecular and environmental perspective" covers the interaction of microorganisms with geological activities resulting in processes influencing development of the Earth's geo- and biospheres. Addresses environmental proteomics, functional gene arrays, isotope labelling, bioinformatics & related techniques to analyze relationships & functions of microbes in complex, natural communities.

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Part 1 book "Farm animal proteomics 2013" includes content: Mining deeper into the proteome - pros and cons of pre-fractionation and depletion; detection and annotation of common posttranslational modifications in mass spectrometry data, applied bioinformatics in the structural, postgenomic era, PTMomics – a potpourri of experimental approaches; gel-free quantitative proteomics approaches, current status; new proteomics strategies applied to clinical studies,... and other contents.

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The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case.

11p spiritedaway36 25-11-2021 8 1   Download

Long-read sequencing has great promise in enabling portable, rapid molecular-assisted cancer diagnoses. A key challenge in democratizing long-read sequencing technology in the biomedical and clinical community is the lack of graphical bioinformatics software tools which can efficiently process the raw nanopore reads, support graphical output and interactive visualizations for interpretations of results.

8p vitzuyu2711 29-09-2021 12 1   Download

Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi.

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The interest of the scientific community in investigating the impact of rare variants on complex traits has stimulated the development of novel statistical methodologies for association studies.

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Along with the improvement of high throughput sequencing technologies, the genetics community is showing marked interest for the rare variants/common diseases hypothesis. While sequencing can still be prohibitive for large studies, commercially available genotyping arrays targeting rare variants prove to be a reasonable alternative.

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Evidence suggests that common complex diseases may be partially due to SNP-SNP interactions, but such detection is yet to be fully established in a high-dimensional small-sample (small-n-large-p) study. A number of penalized regression techniques are gaining popularity within the statistical community, and are now being applied to detect interactions.

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Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities.

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These models focus on how sets of independent substitutions between amino acids or codons derive one protein sequence from its ancestral sequence during evolution. In this paper, we regard the Empirical Codon Mutation (ECM) Matrix as a communication channel and compute the corresponding channel capacity.

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Social behavior has long been known to influence patterns of genetic diversity, but the effect of social processes on population genetics remains poorly quantified – partly due to limited community-level genetic sampling (which is increasingly being remedied), and partly to a lack of fast simulation software to jointly model genetic evolution and complex social behavior, such as marriage rules.

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Community structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a system’s functional components and the impact of local structures on dynamics at a global scale.

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Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.

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UniFrac is a well-known tool for comparing microbial communities and assessing statistically significant differences between communities. In this paper we identify a discrepancy in the UniFrac methodology that causes semantically equivalent inputs to produce different outputs in tests of statistical significance.

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DNA methylation is a widely studied epigenetic phenomenon; alterations in methylation patterns influence human phenotypes and risk of disease. As part of the Atherosclerosis Risk in Communities (ARIC) study, the Illumina Infinium HumanMethylation450 (HM450) BeadChip was used to measure DNA methylation in peripheral blood obtained from ~3000 African American study participants.

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Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples.

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Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established there is no consensus on how to treat T-RFLP data to achieve the highest possible accuracy and reproducibility.

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Microbiome studies incorporate next-generation sequencing to obtain profiles of microbial communities. Data generated from these experiments are high-dimensional with a rich correlation structure but modest sample sizes.

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