Children: Bioinformatics
A Nexus file typically refers to a data file format used in various scientific fields, particularly in the context of imaging and data management. The term "Nexus" can be specifically associated with different disciplines, so its meaning may vary depending on the context.
Nikos Kyrpides is a prominent scientist and researcher known for his work in the fields of microbiology, bioinformatics, and systems biology. He has contributed significantly to the understanding of microbiome research and environmental genomics. One of his notable roles was as a program director at the U.S. Department of Energy's Joint Genome Institute, where he has been involved in various projects related to microbial ecology and the analysis of genome sequences.
The OBO Foundry (Open Biomedical Ontologies Foundry) is a collaborative initiative aimed at developing, maintaining, and promoting a suite of interoperable biomedical ontologies. Established to facilitate the sharing and integration of biological and medical data, the OBO Foundry provides a framework for ontology developers to create ontologies in a standardized manner, ensuring consistency, reuse, and interoperability across various domains of biomedical research.
Ontology engineering is a field of study and practice focused on the development and formal representation of ontologies, which are explicit specifications of concepts, categories, and relationships within a specific domain of knowledge. It involves creating, refining, and maintaining ontologies to facilitate effective information sharing, retrieval, and interoperability across systems. Key aspects of ontology engineering include: 1. **Ontology Development**: This involves defining the classes, properties, and relationships within a domain.
Ontology for Biomedical Investigations (OBI) is a standardized framework used to facilitate the representation, sharing, and analysis of data related to biomedical research and investigations. It provides a controlled vocabulary and a set of terms that describe various aspects of biomedical studies, including: 1. **Experimental Design:** Terms related to the design of experiments, such as study types, protocols, and methodologies. 2. **Sample Information:** Definitions of different types of biological samples (e.g.
An open reading frame (ORF) is a sequence of DNA that has the potential to be translated into a protein. It is defined as a continuous stretch of nucleotides that begins with a start codon (usually AUG) and ends with a stop codon (either UAA, UAG, or UGA) without any intervening stop codons. The presence of an ORF suggests that the corresponding RNA transcript can be translated into a polypeptide chain.
The Overton Prize is awarded by the Society for the Study of Reproduction (SSR) to recognize significant contributions to the field of reproductive biology. This prestigious award honors researchers who have made outstanding advancements in understanding reproductive processes, including aspects of fertility, development, and reproductive health. The prize typically highlights the work of scientists early in their careers, promoting continued innovative research in the field. It serves to promote and celebrate achievements that enhance our understanding of reproduction and related areas.
PathoPhenoDB is a specialized database designed to facilitate the study and analysis of phenotypes associated with various pathogenic conditions. It typically aggregates and curates information regarding genetic variants, phenotypic traits, and their relationships to diseases, allowing researchers and clinicians to explore the genetic underpinnings of various disorders. The database may include detailed entries on specific diseases, related genetic information, patient records (in anonymized forms), and data derived from clinical studies and literature.
The term "Patrocladogram" does not appear to be a widely recognized term in scientific literature, biology, or related fields as of my last knowledge update in October 2023. It may be a typographical error or a combination of terms that could refer to two concepts: 1. **Cladogram**: A cladogram is a diagram used in cladistics to represent a hypothesis about the evolutionary relationships among various species (or other taxonomic groups).
Peak calling refers to a bioinformatics process used primarily in the analysis of high-throughput sequencing data, particularly in studies involving ChIP-sequencing (ChIP-seq), RNA-sequencing (RNA-seq), and other types of genomic assays. The main goal of peak calling is to identify regions of the genome where there is a significant enrichment of reads that indicate the presence of biological features, such as protein-DNA interactions, transcription factor binding sites, or open chromatin regions.
Peptide mass fingerprinting (PMF) is a technique used in proteomics for the identification of proteins based on the mass-to-charge ratios of peptide fragments. The primary steps involved in peptide mass fingerprinting are as follows: 1. **Protein Isolation and Digestion**: Proteins of interest are isolated from biological samples (such as cells or tissues) and then enzymatically digested, usually with trypsin, which cleaves proteins into smaller peptides at specific amino acid residues.
Perturb-seq is a high-throughput technique that combines genetic perturbations (such as CRISPR-based gene editing) with single-cell RNA sequencing to study gene function and cellular responses at a single-cell level. This method allows researchers to systematically investigate how perturbations in specific genes or regulatory elements affect gene expression, cellular behavior, and phenotypic traits.
Pfam is a comprehensive database of protein families that provides information about their sequences and functional characteristics. It is widely used in bioinformatics and molecular biology for the identification of protein domains and families based on sequence alignments. Key features of Pfam include: 1. **Protein Domains**: Pfam focuses on identifying and categorizing protein domains, which are distinct and conserved parts of proteins that can evolve, function, and exist independently of the rest of the protein chain.
Pharmaceutical bioinformatics is an interdisciplinary field that combines the principles and techniques of bioinformatics with pharmaceutical sciences to facilitate the discovery, development, and optimization of drugs and therapeutic agents. It involves the application of computational tools and methodologies to manage and analyze biological data related to drug discovery and development processes. Key aspects of pharmaceutical bioinformatics include: 1. **Data Integration and Analysis**: Pharmaceutical research generates vast amounts of biological and chemical data, such as genomic, proteomic, metabolomic, and chemical information.
Phylogenetic profiling is a computational method used in the field of bioinformatics to predict the function of genes or proteins based on their evolutionary relationships. The basic premise involves analyzing the presence or absence of a particular gene across different species or organisms to infer functional associations.
Phylomedicine is an interdisciplinary field that integrates evolutionary principles with medical research and practice. It involves the use of phylogenetic methods to understand the evolutionary relationships among organisms, which can provide insights into various medical questions, including disease mechanisms, drug development, and vaccination strategies. Key components of phylomedicine include: 1. **Evolutionary Insights in Disease**: Researchers study how pathogens (like viruses and bacteria) evolve and mutate within host organisms.
Phyloscan is a bioinformatics tool designed for the analysis of genetic sequences, particularly in the context of understanding evolutionary relationships and phylogenetic trees. Its primary application is in the study of viral genomes, allowing researchers to identify and track the evolution of viruses over time. Phyloscan analyzes the phylogenetic patterns present in sequence data, helping scientists understand how different strains of a virus are related, how they spread, and potentially how they mutate.
The Pileup format is a file format used primarily in bioinformatics to represent aligned sequence data from high-throughput sequencing technologies. It is commonly utilized in the context of variant calling and visualization of genomic data. Pileup files condense information from several aligned reads at specific positions across one or more reference sequences (like a genome), allowing for a compact representation of sequence coverage and variation.
Plant genome assembly is the process of reconstructing the complete genomic sequence of a plant species from the DNA sequences obtained through various sequencing technologies. This process is crucial for understanding the genetic makeup of plants, which can have important implications for agriculture, biodiversity, conservation, and research into plant biology.
Planted motif search is a computational problem in bioinformatics and computer science, particularly focused on the analysis of biological sequences such as DNA, RNA, or protein sequences. It involves identifying specific patterns or motifs that are "planted" or embedded within a larger set of sequences, which may contain noise or irrelevant data. ### Key Concepts: 1. **Motifs**: A motif is a recurring sequence pattern that has some biological significance.