Tools

Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell. Epigenetic modifications are reversible modifications on a cell’s DNA or histones that affect gene expression without altering the DNA sequence. Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair.

Genomics is an interdisciplinary field of molecular biology focusing on the DNA content of living organisms. High-throughput sequencing technologies and bioinformatics have transformed genome analysis by mapping and decrypting coding and non-coding DNA sequences, their evolution and inter-relationships. Software tools are proposed here for genome annotation, phylogenomics studies, comparative genomics, genome editing, genome variant and DNA structure analysis, personal and population genomics, as well as epigenomic modifications which include DNA methylation, histone modifications and nucleosome positioning.

Metabolomics is the scientific study of chemical processes involving metabolites, the small molelcule intermediates and products of metabolism. Specifically, metabolomics is the “systematic study of the unique chemical fingerprints that specific cellular processes leave behind”, the study of their small-molecule metabolite profiles. Metabolomics can generally be defined as the study of global metabolite profiles in a system (cell, tissue or organism) under a given set of conditions. Source Citation Metabolic Profiles:

Phenomics is an area of biology concerned with the measurement of phenomes (a phenome is the set of physical and biochemical traits belonging to a given organism) as they change in response to genetic mutation and environmental influences. It is used in functional genomics, pharmaceutical research, metabolic engineering and increasingly in phylogenetics. A key goal of biology is to understand phenotypic characteristics, such as health, disease and evolutionary fitness. Phenotypic variation is produced through a complex web of interactions between genotype and environment, and such a ‘genotype–phenotype’ map is inaccessible without the detailed phenotypic data that allow these interactions to be studied.

The proteome is the entire set of proteins that are produced or modified by an organism or system. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain that has benefitted greatly from the genetic information of the Human Genome Project; it also covers emerging scientific research and the exploration of proteomes from the overall level of intracellular protein composition, structure, and its own unique activity patterns.

The transcriptome is the set of all RNA molecules in one cell or a population of cells. It is sometimes used to refer to all RNAs, or just mRNA, depending on the particular experiment. It differs from the exome in that it includes only those RNA molecules found in a specified cell population, and usually includes the amount or concentration of each RNA molecule in addition to the molecular identities.