Omics



The branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.

The related suffix -ome is used to address the objects of study of such fields, such as the genome, proteome or metabolome respectively. The suffix -ome as used in molecular biology refers to a totality of some sort; it is an example of a "neo-suffix" formed by abstraction from various Greek terms in -ωμα, a sequence that does not form an identifiable suffix in Greek.

Functional genomics aims at identifying the functions of as many genes as possible of a given organism. It combines different -omics techniques such as transcriptomics and proteomics with saturated mutant collections.

Origin
The Oxford English Dictionary (OED) distinguishes three different fields of application for the -ome suffix:
 * 1) in medicine, forming nouns with the sense "swelling, tumour"
 * 2) in botany or zoology, forming nouns in the sense "a part of an animal or plant with a specified structure"
 * 3) in cellular and molecular biology, forming nouns with the sense "all constituents considered collectively"

The -ome suffix originated as a variant of -oma, and became productive in the last quarter of the 19th century. It originally appeared in terms like sclerome or rhizome. All of these terms derive from Greek words in -ωμα, a sequence that is not a single suffix, but analyzable as  -ω-μα, the -ω- belonging to the word stem (usually a verb) and the -μα being a genuine Greek suffix forming abstract nouns.

The OED suggests that its third definition originated as a back-formation from mitome, Early attestations include biome (1916) and genome (first coined as German Genom in 1920 ).

The association with chromosome in molecular biology is by false etymology. The word chromosome derives from the Greek stems χρωμ(ατ)- "colour" and σωμ(ατ)- "body". While σωμα "body" genuinely contains the -μα suffix, the preceding  -ω- is not a stem-forming suffix but part of the word's root. Because genome refers to the complete genetic makeup of an organism, a neo-suffix -ome suggested itself as referring to "wholeness" or "completion".

Bioinformaticians and molecular biologists figured amongst the first scientists to apply the "-ome" suffix widely. Early advocates included bioinformaticians in Cambridge, UK, where there were many early bioinformatics labs such as the MRC centre, Sanger centre, and EBI (European Bioinformatics Institute); for example, the MRC centre carried out the first genome and proteome projects.

Current usage
Many "omes" beyond the original "genome" have become useful and have been widely adopted by research scientists. "Proteomics" has become well-established as a term for studying proteins at a large scale. "Omes" can provide an easy shorthand to encapsulate a field; for example, an interactomics study is clearly recognisable as relating to large-scale analyses of gene-gene, protein-protein, or protein-ligand interactions. Researchers are rapidly taking up omes and omics, as shown by the explosion of the use of these terms in PubMed since the mid-1990s.

Genomics

 * Genomics: Study of the genomes of organisms.
 * Cognitive genomics: Study of the changes in cognitive processes associated with genetic profiles.
 * Comparative genomics: Study of the relationship of genome structure and function across different biological species or strains.
 * Functional genomics: Describes gene and protein functions and interactions (often uses transcriptomics).
 * Metagenomics: Study of metagenomes, i.e., genetic material recovered directly from environmental samples.
 * Neurogenomics: Study of genetic influences on the development and function of the nervous system.
 * Pangenomics: Study of the entire collection of genes or genomes found within a given species.
 * Personal genomics: Branch of genomics concerned with the sequencing and analysis of the genome of an individual. Once the genotypes are known, the individual's genotype can be compared with the published literature to determine likelihood of trait expression and disease risk. Helps in Personalized Medicine
 * Electromics: Branch of genomics concerned with the role of exogenous electric fields in potentiating the gene expression profiles of cells, tissues, and organoids.

Epigenomics
The epigenome is the supporting structure of the genome, including protein and RNA binders, alternative DNA structures, and chemical modifications on DNA.


 * Epigenomics: Modern technologies include chromosome conformation by Hi-C, various ChIP-seq and other sequencing methods combined with proteomic fractionations, and sequencing methods that find chemical modification of cytosines, like bisulfite sequencing.
 * Nucleomics: Study of the complete set of genomic components which form "the cell nucleus as a complex, dynamic biological system, referred to as the nucleome". The 4D Nucleome Consortium officially joined the IHEC (International Human Epigenome Consortium) in 2017.

Microbiomics

 * The microbiome is defined as a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The microbiome not only refers to the microorganisms involved but also encompass their theatre of activity, which results in the formation of specific ecological niches. The microbiome, which forms a dynamic and interactive micro-ecosystem prone to change in time and scale, is integrated in macro-ecosystems including eukaryotic hosts, and here crucial for their functioning and health.
 * Culturomics (microbiology) is the high-throughput cell culture of bacteria that aims to comprehensively identify strains or species in samples obtained from tissues such as the human gut or from the environment.

Lipidomics
The lipidome is the entire complement of cellular lipids, including the modifications made to a particular set of lipids, produced by an organism or system.
 * Lipidomics: Large-scale study of pathways and networks of lipids. Mass spectrometry techniques are used.

Proteomics
The proteome is the entire complement of proteins, including the modifications made to a particular set of proteins, produced by an organism or system.
 * Proteomics: Large-scale study of proteins, particularly their structures and functions. Mass spectrometry techniques are used.
 * Chemoproteomics: An array of techniques used to study protein-small molecule interactions
 * Immunoproteomics: Study of large sets of proteins (proteomics) involved in the immune response
 * Nutriproteomics: Identifying the molecular targets of nutritive and non-nutritive components of the diet. Uses proteomics mass spectrometry data for protein expression studies
 * Proteogenomics: An emerging field of biological research at the intersection of proteomics and genomics. Proteomics data used for gene annotations.
 * Structural genomics: Study of the three-dimensional structure of every protein encoded by a given genome using a combination of experimental and modeling approaches.

Glycomics
Glycomics is the comprehensive study of the glycome i.e. sugars and carbohydrates.

Foodomics
Foodomics was defined by Alejandro Cifuentes in 2009 as "a discipline that studies the food and nutrition domains through the application and integration of advanced omics technologies to improve consumer’s well-being, health, and knowledge."

Transcriptomics
Transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA, produced in one or a population of cells.
 * Transcriptomics: Study of transcriptomes, their structures and functions.

Metabolomics
The metabolome is the ensemble of small molecules found within a biological matrix.


 * Metabolomics: Scientific study of chemical processes involving metabolites. It is a "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles
 * Metabonomics: The quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification

Nutrition, pharmacology, and toxicology

 * Nutritional genomics: A science studying the relationship between human genome, nutrition and health.
 * Nutrigenetics studies the effect of genetic variations on the interaction between diet and health with implications to susceptible subgroups
 * Nutrigenomics: Study of the effects of foods and food constituents on gene expression. Studies the effect of nutrients on the genome, proteome, and metabolome
 * Pharmacogenomics investigates the effect of the sum of variations within the human genome on drugs;
 * Pharmacomicrobiomics investigates the effect of variations within the human microbiome on drugs and vice versa.
 * Toxicogenomics: a field of science that deals with the collection, interpretation, and storage of information about gene and protein activity within particular cell or tissue of an organism in response to toxic substances.

Culture
Inspired by foundational questions in evolutionary biology, a Harvard team around Jean-Baptiste Michel and Erez Lieberman Aiden created the American neologism culturomics for the application of big data collection and analysis to cultural studies.

Miscellaneous

 * Mitointeractome
 * Psychogenomics: Process of applying the powerful tools of genomics and proteomics to achieve a better understanding of the biological substrates of normal behavior and of diseases of the brain that manifest themselves as behavioral abnormalities. Applying psychogenomics to the study of drug addiction, the ultimate goal is to develop more effective treatments for these disorders as well as objective diagnostic tools, preventive measures, and eventually cures.
 * Stem cell genomics: Helps in stem cell biology. Aim is to establish stem cells as a leading model system for understanding human biology and disease states and ultimately to accelerate progress toward clinical translation.
 * Connectomics: The study of the connectome, the totality of the neural connections in the brain.
 * Microbiomics: The study of the genomes of the communities of microorganisms that live in a specific environmental niche.
 * Cellomics: The quantitative cell analysis and study using bioimaging methods and bioinformatics.
 * Tomomics: A combination of tomography and omics methods to understand tissue or cell biochemistry at high spatial resolution, typically using imaging mass spectrometry data.
 * Viral metagenomics: Using omics methods in soil, ocean water, and humans to study the Virome and Human virome.
 * Ethomics: The high-throughput machine measurement of animal behaviour.
 * Videomics (or vide-omics): A video analysis paradigm inspired by genomics principles, where a continuous image sequence (or video) can be interpreted as the capture of a single image evolving through time through mutations revealing 'a scene'.
 * Multiomics: Integration of different omics in a single study or analysis pipeline.

1. Genomics: Study of the genome, the complete set of genes in an organism.

2. Proteomics: Study of the proteome, the entire collection of proteins in an organism's cells.

3. Metabolomics: Study of metabolism and the function and interactions of metabolic breakdown products, or metabolites.

4. Transcriptomics: Study of the full complement of RNA in an organism's cells.

5. Lipidomics: Study of lipids and pathways involved in lipid signaling.

6. Epigenomics: Study of the chemical modifications to DNA and histone proteins that regulate gene expression without changing the DNA sequence.

7. Glycomics: Study of the glycome, the complete set of sugars, or glycans, in an organism.

8. Phenomics: Study of phenomes, the physical and biochemical traits of organisms.

9. harmacogenomics: Study of how genes affect a person's response to drugs.

10. Toxicogenomics: Study of the effects of toxic chemicals on the genome and gene expression.

11. Nutrigenomics: Study of the interactions between nutrition and genes.

12. Microbiomics: Study of microbial communities (microbiota) and their collective genomes (microbiome).

13. Viromics: Study of the viral community and their interactions within a host organism.

14. Exposomics: Study of the totality of human environmental exposures and their effects on health.

15. Connectomics: Study of neural connections in the brain.

16. Immunomics: Study of the immune system on an omic scale.

17. Interactomics: Study of the relationships and interactions between proteins and other molecules.

18. Fluxomics: Study of the rates of metabolic reactions in a biological system.

19. *Phosphoproteomics: Study of phosphorylated proteins and their roles in cell signaling and function.

20. Splicomics: Study of RNA splicing and its variations across different tissues or conditions.

21. Secretomics: Study of the secretome, the entire set of proteins secreted by a cell, tissue, or organism.

22. Degradomics: Study of the proteolytic enzymes (proteases) and their substrates.

23. Ubiquitinomics: Study of ubiquitin and ubiquitin-like protein modifications on other proteins.

24. Metallomics: Study of the role of metal ions in biological systems.

25. Redoxomics**: Study of redox states and the roles of reactive oxygen species in cellular processes.

26. Volatilomics**: Study of volatile organic compounds produced by living organisms.

27. Theranostics**: A combination of therapeutics and diagnostics, often studied at an omics level.

28. Cytomics**: Study of the cell and its functions at a molecular level.

29. Sensomics**: Study of sensory perception and the associated molecules and pathways.

30. Foodomics**: Application of omics technologies in food and nutrition research.

31. Chronomics**: Study of biological rhythms and their molecular mechanisms.

32. Peptidomics**: Study of peptides, their structures, functions, and roles in biology.

33. Ecogenomics**: Study of the genetic composition of ecological communities and their interactions with the environment.

34. Pathogenomics**: Study of the genomes of pathogens to understand their biology and interaction with hosts.

35. Nucleomics**: Study of the nuclear components of cells, including chromatin and nuclear bodies.

36. Single-cell omics**: Study of the omics data at the single-cell level to understand cellular heterogeneity.

37. Oncomics**: Study of cancer-related genes, proteins, and pathways.

38. Biomechanics omics**: Study of the mechanical properties of biological molecules and structures.

39. Symbiomics**: Study of symbiotic relationships at the molecular level.

40. Interactomics**: Study of molecular interactions in biological systems, including protein-protein, protein-DNA, and protein-RNA interactions.

41. Paleomics**: Study of ancient biological materials through omics technologies.

42. Methylomics**: Study of DNA methylation patterns across the genome.

43. Toxicoepigenomics**: Study of the effects of environmental toxins on epigenetic modifications.

44. Neurogenomics**: Study of the genetic basis of nervous system structure and function.

45. Immunopeptidomics**: Study of peptides presented by the immune system, particularly those bound to MHC molecules.

46. Phytomics**: Study of plant genomes and their interactions with the environment.

47. Autoimmunomics**: Study of the molecular mechanisms underlying autoimmune diseases.

48. Agrigenomics**: Application of genomics in agriculture to improve crop and livestock production.

49. Thermogenomics**: Study of the genetic basis of thermoregulation and heat production in organisms.

50. Biome omics**: Study of the genetic and molecular makeup of whole biomes (large ecological areas).

51. Metagenomics**: Study of genetic material recovered directly from environmental samples, bypassing the need for isolating and culturing individual species.

52. Astrobiomics**: Study of potential life and biological molecules in space environments.

53. Connectomics**: Study of the comprehensive maps of neural connections in the brain.

54. Kinomics**: Study of kinases and their roles in cellular signaling.

55. Phenomics**: Study of phenotypes on an omics scale, capturing the physical and biochemical traits of organisms.

56. Glycoproteomics**: Study of glycoproteins, which are proteins with carbohydrate groups attached.

57. Nutriproteomics**: Study of the effects of nutrients on the proteome.

58. Epitranscriptomics**: Study of chemical modifications on RNA molecules and their impact on gene expression and function.

59. Glycolipidomics**: Study of glycolipids, complex molecules consisting of carbohydrates and lipids.

60. Endocrinomics**: Study of the endocrine system and hormone-related omics data.

61. Psychomics**: Study of the molecular basis of psychological and psychiatric conditions.

62. Interactomics**: Comprehensive study of all molecular interactions in a cell.

63. Distributomics**: Study of the distribution patterns of molecules within cells or organisms.

64. Pangenomics**: Study of the complete set of genes within a species, including core and accessory genes.

65. Adaptomics**: Study of adaptive changes in organisms at the molecular level.

66. Seromics**: Study of serum proteins and metabolites.

67. Neuroproteomics**: Study of the proteome of the nervous system.

68. Phytochemomics**: Study of the complex chemical compounds in plants.

69. Agingomics**: Study of the molecular and genetic factors involved in aging.

70. Radiogenomics**: Study of the relationship between genetic variation and response to radiation therapy.

71. Immunogenomics**: Study of the genetic basis of immune system function and diversity.

72. Biogeomics**: Study of the genomic basis of biodiversity and ecosystem function.

73. Virogenomics**: Study of viral genomes and their interactions with host organisms.

74. Dermomics**: Study of the molecular and genetic aspects of skin biology.

75. Allergomics**: Study of the molecular and genetic basis of allergic reactions.

76. Plantomics**: Comprehensive study of plant biology using omics approaches.

77. Oceanomics**: Study of marine organisms and ecosystems using omics technologies.

78. Parasite genomics**: Study of the genomes of parasitic organisms.

79. Aquaculture omics**: Application of omics technologies to improve aquaculture practices.

80. Epigenomics**: Study of the complete set of epigenetic modifications on the genetic material of a cell.

81. Pathophysiomics**: Study of the molecular and cellular mechanisms of disease processes.

82. Quantum omics**: Study of quantum mechanical properties of biological molecules and their influence on biological functions.

83. Thermogenomics**: Study of the genetic basis of temperature regulation in organisms.

84. Chronomics**: Study of biological rhythms and their molecular bases.

85. Syntheomics**: Study of synthetic biology approaches using omics data to design and construct new biological parts, devices, and systems.

86. Holobiont omics**: Study of the omics data of a host and its associated microbiota as a single ecological unit.

87. Ecophysiomics**: Study of the interactions between the physiological functions of organisms and their environment at an omics level.

88. Resistomics**: Study of antibiotic resistance genes and their mechanisms.

89. Aptameromics**: Study of aptamers, short DNA or RNA molecules that bind to specific targets, and their applications.

90. Virulomics**: Study of virulence factors and mechanisms of pathogenicity in microbes.

91. Mycomics**: Study of fungal genomes and their biological functions.

92. Photomics**: Study of the interaction between light and biological systems.

93. Nanonics**: Study of nanomaterials and their interactions with biological systems using omics approaches.

94. Allergenomics**: Study of allergens and the molecular basis of allergic responses.

95. Xenobiomics**: Study of the effects of foreign substances (xenobiotics) on biological systems.

96. Physiomics**: Study of the physiological aspects of biological systems at an omics scale.

97. Psychogenomics**: Study of the genetic and molecular basis of psychological traits and disorders.

98. Methylomics**: Study of DNA methylation patterns and their effects on gene expression.

99. Cardiomics**: Study of the molecular and genetic basis of cardiovascular function and diseases.

100. Degradomics**: Study of the proteolytic processes and protein degradation pathways.

101. Astrobiomics**: Study of the potential for life and biological processes in extraterrestrial environments.

102. Geonomics**: Study of the genetic basis of geological and geobiological processes.

103. Radiomics**: Study of the quantifiable features of medical images and their association with clinical outcomes.

104. Biome omics**: Study of the genetic, molecular, and ecological interactions within biomes.

105. Allosteromics**: Study of allosteric sites and their regulatory roles in protein function.

106. Biothermodynamics**: Study of the thermodynamic properties of biological molecules and systems using omics approaches.

107. Anthropomics**: Study of human diversity and evolution using omics data.

108. Connectomics**: Study of neural connections within the brain and nervous system.

109. Autophagomics**: Study of the autophagy process at an omics level.

110. Photogenomics**: Study of the effects of light on gene expression and cellular functions.

111. Aeroomics**: Study of airborne biological particles and their impact on health and environment.

112. Epitranscriptomics**: Study of chemical modifications on RNA molecules and their impact on gene expression and function.

113. Radiogenomics**: Study of the relationship between genomic features and response to radiation therapy.

114. Nephromics**: Study of the kidneys and their functions at a molecular level.

115. Dermatomics**: Study of the skin and its molecular composition and functions.

116. Xenomics**: Study of the effects and interactions of foreign genetic material introduced into an organism.

117. MicroRNAomics**: Study of microRNAs and their roles in regulating gene expression.

118. Synthetic omics**: Study and design of synthetic biological systems using omics data.

119. Environomics**: Study of the interactions between organisms and their environment using omics technologies.

120. Paleomics**: Study of ancient biological materials and their molecular information.

121. Regulomics**: Study of regulatory networks and their roles in gene expression.

122. Pathobiomics**: Study of disease pathways and mechanisms at an omics scale.

123. Evolvomics**: Study of evolutionary processes and patterns using omics data.

124. Thermobiomics**: Study of the effects of temperature on biological molecules and systems.

125. Circadiomics**: Study of circadian rhythms and their molecular underpinnings.

126. Nanomics**: Study of nanoscale biological processes and materials.

127. Metaproteomics**: Study of the collective protein content in environmental samples.

128. Biomechanics omics**: Study of the mechanical properties of biological molecules and systems.

129. Cancer omics**: Study of the molecular basis of cancer, including oncogenomics and cancer proteomics.

130. Synthetic biology omics**: Application of omics technologies to design and construct new biological parts, devices, and systems.

131. Gutomics**: Study of the gut microbiome and its interactions with the host.

132. Nutrigenomics**: Study of the relationship between nutrition and the genome.

133. Plant omics**: Comprehensive study of plant biology using omics approaches.

134. Infectomics**: Study of the molecular mechanisms of infectious diseases.

135. Microbiomics**: Study of microbial communities and their functions.

136. Sexomics**: Study of the molecular basis of sex differences in biology.

137. Biomechanomics**: Study of the interaction between mechanical forces and biological systems.

138. Neurogenomics**: Study of the genetic basis of neurological functions and disorders.

139. Omeomics**: Study of the relationships and interactions between different omes (genome, proteome, etc.).

140. Immunotranscriptomics**: Study of the transcriptome of immune cells.

141. Nervomics**: Study of the nervous system and its molecular components.

142. Embryomics**: Study of the molecular and genetic processes during embryonic development.

143. Agingomics**: Study of the molecular basis of aging.

144. Photoproteomics**: Study of proteins involved in light sensing and response.

145. Hematomics**: Study of the molecular composition and function of blood.

146. Biophotonics omics**: Study of the interaction of light with biological materials at an omics level.

147. Anatomics**: Study of the molecular basis of anatomical structures.

148. Mycobiomics**: Study of fungal communities and their interactions with the host or environment.

149. Pathogenomics**: Study of the genomes of pathogens.

150. Symbiomics**: Study of symbiotic relationships at the molecular level.

151. Aquomics**: Study of aquatic organisms and their molecular biology.

152. Bacteriomics**: Study of bacteria and their genomes.

153. Biomarkeromics**: Study of biomarkers using omics technologies for disease detection and monitoring.

154. Cardiomics**: Study of the cardiovascular system at a molecular level.

155. Cellomics**: Study of cell structure, function, and behavior using high-throughput methods.

156. Chemogenomics**: Study of the genomic response to chemical compounds.

157. Cryomics**: Study of biological molecules and systems under low-temperature conditions.

158. Distributomics**: Study of the spatial distribution of molecules within cells or tissues.

159. Ecosystem omics**: Study of entire ecosystems using omics approaches.

160. Energetics omics**: Study of the energy flow and metabolism in biological systems.

161. Gastroomics**: Study of the gastrointestinal system and its microbiota.

162. Genetherapeutics omics**: Study of gene therapy approaches and their effects at an omics level.

163. Hormonomics**: Study of hormones and their molecular pathways.

164. Hydratomics**: Study of the hydration state of biological molecules and systems.

165. Inflamomics**: Study of inflammation and its molecular pathways.

166. Metalloproteomics**: Study of metalloproteins and their roles in biology.

167. Morphomics**: Study of the shape and structure of organisms and their molecular basis.

168. Nervomics**: Study of the nervous system and its molecular composition.

169. Neurochemomics**: Study of the chemical processes in the nervous system.

170. Nutriomics**: Study of the interactions between nutrients and the genome.

171. Ocularomics**: Study of the eye and its molecular biology.

172. Optogenomics**: Study of the genetic basis of light perception and response.

173. Organomics**: Study of specific organs at a molecular level.

174. Parasitomics**: Study of parasites and their interactions with hosts.

175. Pathophenomics**: Study of disease phenotypes and their molecular basis.

176. Pharmacomics**: Study of drugs and their effects on the genome and proteome.

177. Polyomics**: Study of the complex interactions between multiple omes (genome, proteome, etc.).

178. Psychomics**: Study of the molecular basis of psychological traits and disorders.

179. Pulmonomics**: Study of the lungs and respiratory system at a molecular level.

180. Reproductomics**: Study of reproductive systems and their molecular biology.

181. Respiromics**: Study of the respiratory system and its molecular functions.

182. Selenomics**: Study of the role of selenium in biology.

183. Sexomics**: Study of the molecular basis of sex differences and sexual development.

184. Spatiomics**: Study of the spatial distribution of molecules within biological systems.

185. Sportomics**: Study of the molecular basis of sports performance and physical activity.

186. Stemcellomics**: Study of stem cells and their molecular properties.

187. Stromomics**: Study of the stroma, the supportive tissue in organs, and its molecular components.

188. Subcellomics**: Study of the molecular composition of subcellular compartments.

189. Synaptomics**: Study of synapses and their molecular components.

190. Toxinomics**: Study of toxins and their effects on the genome and proteome.

191. Traumomics**: Study of the molecular basis of trauma and injury.

192. Vascularomics**: Study of the vascular system and its molecular biology.

193. Virosomomics**: Study of the structure and function of viral particles.

194. Zoonomics**: Study of zoonotic diseases and their molecular basis.

Unrelated words in -omics
The word "comic" does not use the "omics" suffix; it derives from Greek "κωμ(ο)-" (merriment) + "-ικ(ο)-" (an adjectival suffix), rather than presenting a truncation of "σωμ(ατ)-".

Similarly, the word "economy" is assembled from Greek "οικ(ο)-" (household) + "νομ(ο)-" (law or custom), and "economic(s)" from "οικ(ο)-" + "νομ(ο)-" + "-ικ(ο)-". The suffix -omics is sometimes used to create names for schools of economics, such as Reaganomics.