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Genomics categories & taxonomy
<%end if%> Genomic applications map: Guide to terms in these glossaries Site Map Broader categories include Genomics Related categories include Proteomics, Structural genomics Narrower categories include Molecular Medicine Pharmacogenomics agricultural genomics: Agricultural biotechnology continues to benefit from the insights being developed during the era of the Human Genome Project. The proliferation of mapping, genotyping, and diagnostic methodologies has rapidly expanded the analytical tools available to crop scientists for the analysis and utilization of plant genomes. Google = about 2,580 July 24, 2002; about 4,470 Sept. 8, 2003, about 6,480 Jan. 14, 2005; about 27,700 Nov 17, 2006 Related terms: crop genomics, environmental genomics, food genomics, nutritional genomics, plant genomics; Model & other organisms glossary Arabidopsis Agricultural genomics links: applied genomics: Applications are at varying stages of development and include clinical genomics, pharmacogenomics, plant and animal breeding, drug discovery and development and microbial genomics. Google = about 2,860 July 24, 2002; about 7,460 Sept. 8, 2003, about 22,100 Jan. 14, 2005; about 112, 000 Nov. 17, 2006 Commercial Opportunities from Applied Genomics, Noubar Afeyan, NewcoGen Group, AGTC Funds, CHI, GenomeLink 12.1 http://www.chidb.com/newsarticles/issue12_1.asp behavior genomics: Molecular
Medicine glossary Google = about 46 Sept.
8, 2003, about 172 Jan. 14, 2005; about 444 Nov 17, 2006 combinatorial genomics: Similar in concept to required for recognition of all items in long- term memory combinatorial chemistry, this technology shuffles portions of genes to give a vast number of new combinations, which are then screened for a desired function. Enhanced function, or even new functions, can be generated by repeating the cycle circuits many times to "evolve" optimized recombinants in vitro. [Department of Defense Critical Technologies Part III: Developing Critical Technologies Section 3: Biological Technology, July 1999] Google = about 34 July 24, 2002; about 51 Sept. 8, 2003, about 84 Jan. 14, 2005; about 207 Nov 17, 2006 Related terms: Combinatorial libraries & synthesis glossary combinatorial chemistry; comparative genomics: Functional
genomics glossary. Google = about 11,600 July 24, 2002;
about 107,000 Sept. 8, 2003, about 180,000 Jan. 14, 2005; about 702,000 Nov 17,
2006 crop genomics: Molecular technologies, techniques and breeding strategies associated with plants of agricultural importance. Google = about 273 July 24, 2002; about 707 Sept. 8, 2003, about 888 Jan. 14, 2005; about 17,300 July 24, 2007 Related terms: agricultural genomics, plant genomics, nutritional genomics deductive genomics: Functional Genomics glossary. Google = about 35 July 24, 2002; about 145 Sept. 8, 2003, about 395 Jan. 14, 2005; about 260 July 24, 2007 ecological genomics:
New genomic technologies are used in traditional ecological
approaches to learn more about an organism's metabolic and nutritional needs,
thus learning more about its role within a given ecosystem. "One thing
leads to another" Virtue Newsletter: Science, Univ. of Bergen, Norway, Nov.
2001 http://www.miljolare.no/virtue/newsletter/science/background/ Google = about 78 July 24, 2002; about 343 Sept. 8, 2003, about 590 Jan. 14, 2005; about 23,900 Nov 17, 2006 Related terms: environmental genomics, plant genomics ecotoxicogenomics, ecotoxicology: Drug safety, pharmacovigilance and toxicology environmental genomics: This programme will apply genomics to the natural environment, using sequence data to advance and test evolutionary and ecological theory, and so provide a better understanding of ecosystem function in the context of biodiversity (intraspecific genetic variation, species richness and perceived redundancy). The programme aims to advance our understanding of how organisms perceive
change (at the molecular and genetic level) and make functional responses within
their local environment, and to what extent variation in these responses is
adaptive. These measures may be short- term adaptations, quorum sensing,
regulated gene expression, survival, reproduction etc. Alternatively, they may
be longer- term adaptations in respect to horizontal gene flow, community
diversity, species abundance and the evolution of speciation. Genomics also
allows investigation of adaptation at the level of individual versus community
diversity. Current advances in molecular techniques allow the development of
predictive studies of evolutionary biology and ecology. [Natural Environmental Research Council
UK, Environmental Genomics Programme Summary 2001] http://www.nerc.ac.uk/funding/thematics/envgen/
Google = about 722 July 24, 2002,
about 2,270 Sept. 8, 2003, about 11,100 Jan. 14, 2005; about 77,900 Nov 17, 2006
Related terms: ecological genomics, plant genomics;
Pharmacogenomics glossary
toxicogenomics evolutionary genomics: Functional Genomics glossary Google = about 1,440 July 24, 2002; about 4,830 Sept. 8, 2003, about 25,200 Jan. 14, 2005 food genomics: The genomics of crops, livestock and microbes. Genomics will give us new insights to how our food grows. These insights will generate new opportunities for improving how our food grows, tastes, and nourishes us. Tom Zinnen, Genomics of Food, Biotechnology Center, Univ. of Wisconsin- Madison Extension, 2004 http://www.biotech.wisc.edu/education/genomicsoffood.html Google = about 82 July 24, 2002; about 197 Sept. 8, 2003, about 406 Dec. 28, 2004 forward genetics, forward genomics: Genetic manipulation & disruption glossary Related terms: agricultural genomics, crop genomics, nutritional genomics function, functional genomics: Functional Genomics glossary. Google = "functional genomics" about 72,400 July 24, 2002; about 217,000 Sept. 8, 2003, about 649,000 Jan. 14, 2004 fungal genomics: The fungal genomics project uses functional genomics approaches to identify fungal enzymes for industrial and environmental applications. It is a large-scale, gene discovery program on evolutionarily diverse fungal species chosen for their ability to grow at environmental extremes and their known ability in biodegradation, bioremediation and biocatalysis. Fungal Genomics Project, Centre for Structural and Functional Genomics, Concordia University, Canada, 2003- 2005 https://fungalgenomics.concordia.ca/home/index.php Google = about 22,600 Nov. 7, 2005 genome: Coined by Thomas H. Roderick [of the Jackson Laboratory, Maine, US] in 1986 in Bethesda, MD during a discussion of a name for a planned new journal (Genomics) that was to include sequencing data, discovery of new genes, gene mapping, and new genetic technologies. According to Roderick, the term genomics "also had the comparative aspect of genomes of various species, their evolution, and how they related to each other. Although we didnt come up with the term functional genomics we thought of the genome as a functioning whole beyond just single genes of sequences spread around a chromosome." B Kuska "Beer, Bethesda, and Biology" JNCI 90(2): 93 Jan 21, 1998 More under genome: Genomics glossary genomics: The systematic study of the complete DNA sequences (GENOME) of organisms. [MeSH, 2001] More under genomics: Genomics glossary Basic genetics & genomics (tries to) answer the question of what the difference between genetics and genomics is. Google = about 619,000 July 24, 2002; about 1,480,000 Sept. 8. 2003, about 4,780,000 Jan. 14, 2005 genome transplantation: As a step toward propagation of synthetic genomes, we completely replaced the genome of a bacterial cell with one from another species by transplanting a whole genome as naked DNA. Carole Lartigue 1, John I. Glass 1*, Nina Alperovich 1, Rembert Pieper 1, Prashanth P. Parmar 1, Clyde A. Hutchison III 1, Hamilton O. Smith 1, J. Craig Venter , Genome Transplantation in Bacteria: Changing One Species to Another, Science Published Online June 28, 2007, Science DOI: 10.1126/science.1144622 Google = about 28,200 July 24, 2007 high-throughput genomics: Genomic studies are now approaching "industrial" speed and scale, thanks to advances in gene sequencing and the increasing availability of high- throughput methods for studying genes, the proteins they encode, and the pathways in which they are involved. Data can now be acquired on many genes at once, either sequentially or in parallel. It is also possible to expand the range of genomic effects being examined. The abundance of new data available means that more targets should now be identifiable, but the key to finding such new targets will be to use the right combination of technologies and have them ideally integrated. Related terms: Bioinformatics high throughput Drug discovery & development target validation. Google = about 1,250 July 24, 2002; about 2,390 Sept. 8, 2003, about 6,710 Jan. 14, 2005 industrial genomics: Genomics scaled up to industrial strength and throughput. Google = about 303 July 24, 2002; about 442 Sept. 8, 2003, about 564 Jan. 14, 2005 Related term: high throughput genomics integrative genomics: The journal Functional & Integrative Genomics is devoted to large- scale studies of genomes and their functions, including systems analyses of biological processes. Topics covered include: Whole genome analysis, Comparative genomics, Genetic variation, Human disease genes and loci, Proteomics, Bioinformatics, Expression profiling, Behavioral genomics, Structural genomics, Chemical genomics, Pharmacogenomics, Integrative genomics, Large- scale analysis of biological systems. [Springer website, Functional & Integrative Genomics - Aims & scope, 1999] http://link.springer.de/link/service/journals/10142/aims.htm Google = about 1,550 July 24, 2002; about 1,970 Aug. 29, 2002; about 5,870 Sept. 8, 2003, about 21,100 Jan. 14, 2005 intergenomics: The bioinformatics competence center "Intergenomics" in Braunschweig has the scientific goal to develop bioinformatic tools for modeling of the interactivity of genome- driven bacterial infection processes in mammals and plants. [Bioinformatics research and education in Germany. Dietmar Schomburg, Martin Vingron, In Silico Biology 2, 0015, 2002] http://www.bioinfo.de/isb/2002/02/0015/main.html Google = about 22 July 24, 2002; about 246 Sept. 8, 2003, about 305 Jan. 14, 2005 medical genomics: Molecular Medicine glossary Google = about 4,090 Sept. 8, 2003, about 15,300 Jan. 14, 2005 metagenome: Historically, biotechnology has missed up to 99% of existing microbial resources by using traditional screening techniques. Strategies of directly cloning 'environmental DNA' comprising the genetic blueprints of entire microbial consortia (the so-called 'metagenome') provide molecular sequence space that along with ingenious in vitro evolution technologies will act synergistically to bring a maximum of available sequence- space into biocatalytic application. Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Lorenz P, Liebeton K, Niehaus F, Eck J. Curr Opin Biotechnol 2002 Dec;13(6): 572- 577 Google = about 43 May 8, 2003, about 970 Jan. 14, 2005 Related terms: microbiome metagenomics: Wikipedia http://en.wikipedia.org/wiki/Metagenomics The committee will convene a workshop and other appropriate information gathering activities in order to define the scope of metagenomics, understand how it is being used now in various disciplines, the technical approaches being used by different groups, and how metagenomics may develop in the future. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet, Board on Life Sciences , National Academies Press, 2007 http://books.nap.edu/openbook.php?record_id=11902&page=151 Recent advances in genomics of bacteria in water and soil have confirmed the utility of metagenomics, a technique for studying the genomes of all microbes, regardless of their ability to be cultured, using a whole-genome shotgun sequencing approach. Metagenomics is a cost-effective, culture-independent approach to identify microbes and analyze microbial genomes. Metagenomics treats the microbial community as a single dynamic entity. It explores the genome content of the community and leads to analysis of changes in content and expression as a function of site, time, and various states of perturbation, e.g., progression towards and regression from disease following treatment. National Institute of Dental and Craniofacial Research NIDCR, Metagenomic Analyses of the Oral Microbiome (R01) Program Announcement (PA) Number: PA-07-170, 2007 This is a reissue of PA-04-131, which was previously released July 22, 2004. http://grants.nih.gov/grants/guide/pa-files/PA-07-170.html Google = about 195 May 8, 2003, about 872 Jan. 14, 2005, about 166,000 July 24, 2007 microbial genomics:
The Microbial Genome Program and the closely linked Genomics:GTL
program are generating novel insights into both the biological underpinnings of
climate change and the role of microbes in the overall processing of metals,
carbon, radionuclides, and nitrogen. Scientists are only beginning to appreciate
the power of microbial sequencing for generating new and testable hypotheses and
advancing science. http://microbialgenomics.energy.gov/
Google = about 9,050
Sept. 8, 2003, about 25,000 Jan. 14, 2005; abour 141,000 June 14, 2007
Related terms: Genomics categories Beowulf Genomics; Omes &
omics glossary microbiome
nanogenomics: Nanoscience
& Miniaturization
glossary Google = about 13 July 24, 2002;
about 12 Sept. 8, 2003, about 50 Jan .14, 2005 paleogenomics: The complete sequence of the human and other vertebrate and nonvertebrate genomes provide a wealth of information on the organization, relationships and evolution of the metazoans. In the absence of fossil DNA, this knowledge will forever remain a yearning for dreamy molecular biologists. And yet, will not the power of deduction and reconstitution of information gained through man's sophisticated technologies one day recreate a "virtual" metazoan ancestor? D Birnbaum, F Coulier, MJ Pebusque, P Pontarotti "Paleogenomics": looking in the past to the future, J Exp Zool. 288(1): 21- 22, April 15, 2000 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10750049&query_hl=8 Large-scale sequencing of mammoth DNA. "We sequenced 28 million base pairs of DNA in a metagenomics approach using a woolly mammoth (Mammuthus primigenius) sample from Siberia The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics." Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA, Hendrik N. Poinar 1*, Carsten Schwarz 2, Ji Qi 3, Beth Shapiro 4, Ross D. E. MacPhee 5, Bernard Buigues 6, Alexei Tikhonov 7, Daniel Huson 8, Lynn P. Tomsho 3, Alexander Auch 3, Markus Rampp 9, Webb Miller 3, Stephan C. Schuster 3* Google = about 234 Nov 6, 2005, about 576 Oct. 25, 2006 phage genomics: The Age of Genomics dawned only gradually for bacteriophages. It was 1977 when the genome of phage phi X174 was published and 1983 when the "large" genome of phage lambda hit the streets. More recently, the pace has quickened, so that we now have over 100 complete phage genomes and can expect thousands in a very few years. These sequences have been marvelously informative for the biology of the individual phages, but with the advent of high volume sequencing technology, the real excitement for phage biology is that it is now possible to analyze the sequences together and thereby address -- for the first time at whole genome resolution -- a set of fundamental biological questions related to populations. [H. Brussow, RW Hendrix, Phage genomics: small is beautiful, Cell 108 (1) : 13- 16, Jan. 11, 2002] Google = about 58 July 24, 2002; about 158 Sept. 8, 2003, about 590 Jan. 14, 2005 Related terms: Functional genomics glossary bacteriophage, phage, phage display? pharmacogenomics: Pharmacogenomics
glossary Google = about 22,200 July 24, 2002;
about 63,000 Sept. 8, 2003, about 262,000 Jan. 14, 2005 plant genomics: Plant biotechnology, molecular biology,
and related technologies relevant to plants (agricultural, forests,
horticultural). Google = about 5,240 July 24, 2002;
about 15,600 Sept. 8, 2003, about 45,000 Jan. 14, 2005 Related terms: agricultural genomics, crop genomics; Model
& other organisms: transgenics quantitative genomics: An offshoot of quantitative genetics, includes QTL mapping, gene expression data analysis. ENU-induced mutant mice carry single- base substitutions in their genomic DNA. ENU induces many single- base substitutions; therefore, the mutant mice have the causative point mutation for the mutant phenotype as well as many other silent mutations in the genome. In this sense, ENU- induced mutant mice are very similar to the situation of single nucleotide polymorphisms (SNPs) and will be a good animal model for the human SNP project. ... ENU- induced mutant mice carry single- base substitutions in their genomic DNA. ENU induces many single- base substitutions; therefore, the mutant mice have the causative point mutation for the mutant phenotype as well as many other silent mutations in the genome. In this sense, ENU- induced mutant mice are very similar to the situation of single nucleotide polymorphisms (SNPs) and will be a good animal model for the human SNP project. [Bioinformatics for the Large- Scale Mouse Mutagenesis Project: Data- mining: Population and Quantitative Genomics, RIKEN, Japan, 2001] http://www.gsc.riken.go.jp/Mouse/AboutUs/inform.htm Google = about 111 July 24, 2002; about 321 Sept. 8, 2003, about 527 Jan 14, 2005; about 11,700 Nov 17 2006 Related terms: SNPs & Genetic variations; Model organisms Radgenomics: -Omes
& -omics glossary synthetic genomics: Synthetic genomics is a new field of science that involves the design and assembly of genes and gene pathways and whole chromosomes from chemical components of DNA. As a computer analogy, we view the genome of a cell as the operating system and the cytoplasm of the cell as the hardware. Synthetic Genomics Inc. Science of synthetic genomics, 2007 http://www.syntheticgenomics.com/science.htm Google = about 33,000 July 24, 2007, including references to Synthetic Genomics Inc. Related term: genome transplantation subtractive genomics: One of the recently adopted strategies is based on a subtractive genomics approach, in which the subtraction dataset between the host and pathogen genome provides information for a set of genes that are likely to be essential to the pathogen but absent in the host. This approach has been used successfully in recent times to identify essential genes in Pseudomonas aeruginosa. Anirban Dutta1, Shashi Kr. Singh1, Payel Ghosh1, Runni Mukherjee1, Sayak Mitter1 and Debashis Bandyopadhyay2, In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori, In Silico Biology 6, 0005 (2006); ©2006, Bioinformation Systems e.V. http://www.bioinfo.de/isb/2006/06/0005/main.html Google = about 9, July 3, 2003, about 17 Jan. 14, 2005; about 47 Nov 17, 2006' about 68 July 24, 2007 toxicogenomics: Pharmacogenomics glossary Google = about 2,620 July 24, 2002, about 9,630 Sept. 8, 2003, about 88,200 Jan. 14, 2005; about 584, 000 Nov 17, 2006 translational genomics: This laboratory undertakes translational research on the genetics of human breast and prostate cancer. Our goal is to identify genes and molecular alterations of clinical significance for cancer development and progression. With the availability of virtually the entire human genome sequence, it will be important to identify genetic alterations and molecular mechanisms that may serve as diagnostic or therapeutic targets. Olli-P. Kallioniemi, Head, Translational Genomics Section, National Human Genome Research Institute, NIH, US, 2001 http://www.nhgri.nih.gov/Intramural_research/People/kallioniemio.html Google = about 124 July 24, 2002; about 2,150 Sept. 8, 2003, about 14,100 Jan. 14, 2005; about 84, 000 Nov 17, 2006 Related terms: Expression glossary, Genetic variations glossary virtual genomes: In silico & molecular modeling Google = about 78 July 24, 2002; about 126 Sept. 8, 2003, about 192 Jan. 14, 2005; about 1,390 Nov 17, 2006 virtual genomics: Google = about 397 July 24, 2002; about 1,040 Sept. 8, 2003, about 880 Jan. 14, 2005; about 689 Nov 17, 2006 How to look for other unfamiliar terms IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry. |
