SNOMAD

SNOMAD is a program for the standardization and normalization of gene expression datasets. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed across the range of microarray element signal intensities: local mean normalization and local variance correction (Z-score generation using a locally calculated standard deviation).

The SNOMAD gene expression data analysis tools were developed by Carlo Colantuoni and George W. Henry in the laboratory of Jonathan Pevsner (Johns Hopkins School of Medicine, Department of Neuroscience and Kennedy Krieger Research Institute, Department of Neurology) and Scott Zeger (Johns Hopkins School of Public Health).

SNOMAD is Copyrighted (C) 2000 by Carlo Colantuoni, George Henry, Jonathan Pevsner and is distributed under the terms of the GNU General Public License and comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions.

Genetic algorithm, in artificial intelligence, a type of evolutionary computer algorithm in which symbols (often called “genes” or “chromosomes”) representing possible solutions are “bred.” This “breeding” of symbols typically includes the use of a mechanism analogous to the crossing-over process in genetic recombionation and an adjustable mutation rate. A fitness function is used on each generation of algorithms to gradually improve the solutions in analogy to the process of natural selection. The process of evolving the genetic algorithms and automating the selection is known as  genetic programming. In addition to general software, genetic algorithms are sometimes used in research with artificial life, cellular automatons and neural networks.

Although not the first to experiment with genetic algorithms, John Holland did much to develop and popularize the field with his work in the early 1970s at the University of Michigan. As described in his book, Adaptation in Natural and Artificial Systems (1975; revised and expanded 1992), he devised a method, or schema theorem, for evaluating each generation of genetic algorithms. John Koza, one of Holland’s doctoral students and a holder of more than a dozen patents related to genetic programming, was one of the first to develop commercial applications of the field, as a founder of a company known as Scientific Games. Koza shared his programming experiences in a sequence of books beginning with Genetic Programming: On the Programming of Computers by Means of Natural Selection (1992).

Genetic engineering is the artificial manipulation, modification, and recombination of DNA or other nucleic acid  molecules in order to modify an organism or population of organisms.

The term genetic engineering initially meant any of a wide range of techniques for the modification or manipulation of organisms through the processes of heredity and reproduction. As such, the term embraced both artificial selection and all the interventions of biomedical techniques, among them artificial insemination, in vitro fertilization (e.g., “test-tube” babies),sperm banks, cloning, and gene manipulation. But the term now denotes the narrower field of recombinant DNA technology, or gene cloning (see Figure), in which DNA molecules from two or more sources are combined either within cells or in vitro and are then inserted into host organisms in which they are able to propagate. Gene cloning is used to produce new genetic combinations that are of value to science, medicine, agriculture, or industry.

DNA is the carrier of genetic information; it achieves its effects by directing the synthesis of proteins. Most recombinant DNA technology involves the insertion of foreign genes into the plasmids of common laboratory strains of bacteria. Plasmids are small rings of DNA; they are not part of the bacterium’s chromosomes (the main repository of the organism’s genetic information). Nonetheless, they are capable of directing protein synthesis, and, like chromosomal DNA, they are reproduced and passed on to the bacterium’s progeny. Thus, by incorporating foreign DNA (for example, a mammalian gene) into a bacterium, researchers can obtain an almost limitless number of copies of the inserted gene. Furthermore, if the inserted gene is operative (i.e., if it directs protein synthesis), the modified bacterium will produce the protein specified by the foreign DNA.

Human genetic disease, any of the diseases and disorders that are caused by mutations in one or more genes.

With the increasing ability to control infectious and nutritional diseases in developed countries, there has come the realization that genetic diseases are a major cause of disability, death, and human tragedy. Rare, indeed, is the family that is entirely free of any known genetic disorder. Many thousands of different genetic disorders with defined clinical symptoms have been identified. Of the 3 to 6 percent of newborns with a recognized birth defect, at least half involve a predominantly genetic contribution. Furthermore, genetic defects are the major known cause of pregnancy loss in developed nations, and almost half of all spontaneous abortions involve a chromosomally abnormal fetus. About 30 percent of all postnatal infant mortality in developed countries is due to genetic disease; 30 percent of pediatric and 10 percent of adult hospital admissions can be traced to a predominantly genetic cause. Finally, medical investigators estimate that genetic defects—however minor—are present in at least 10 percent of all adults. Thus, these are not rare events.

A congenital defect is any biochemical, functional, or structural abnormality that originates prior to or shortly after birth. It must be emphasized that birth defects do not all have the same basis, and it is even possible for apparently identical defects in different individuals to reflect different underlying causes. Though the genetic and biochemical bases for most recognized defects are still uncertain, it is evident that many of these disorders result from a combination of genetic and environmental factors.