Genomics Topic Room

By: Chris Smith, Ph.D. (San Francisco State University) & Michael Goldman, Ph.D. (San Francisco State University) © 2008 Nature Education
Citation: Smith, C. & Goldman, M. Genomics. Nature Education 1(1), (2008)

The age of -omics biology means that scientists examine changes at the level of the genome, not at the level of individual genes or proteins.

The genome is the set of all genes, regulatory sequences, and other information contained within the noncoding regions of an organism's DNA. Thus, genomics is genetics writ large, the culmination of rapidly accumulating information about vast numbers of genes and DNA sequences from scores of organisms.

The content of this topic room describes genomes in intricate and fascinating detail, paying special attention to the methods used to gather and analyze data on a scale never before seen in the biological sciences. Various articles describe different genomics-based methods for the study of genetic variation, including microarrays and array-based comparative genomic hybridization. Other articles examine the value of genomic data in areas as diverse as medicine, systematics, and conservation biology. Like all stories in science, the history of genomics is fraught with conflict, disagreement, and excitement; accordingly, this topic room also tries to relate some of the personalities and ideas that have shaped genomics, including the ongoing face-off between publicly funded and corporate genome sequencing concerns. Finally, this topic room serves as an "-omics" center of sorts, providing information on epigenomics (DNA modification), transcriptomics (cellular RNA content), and proteomics (the constellation of proteins characteristic of a given cell).

This content is currently under construction.

Explore Within Genomics (21)

What do we know?

Ontologies: Scientific Data Sharing Made Easy
Ontologies are formal ways of organizing knowledge that are structured, yet flexible, and computable because of logically defined relationships. When used to describe biology, they accelerate scientific discovery by allowing scientists to find and...
Behavioral Genomics
Are human behaviors controlled by genetics, or is environment the major contributor to behavior? If our genes do in fact control how we act, does this mean that we have single genes for each of our many behaviors, including behaviors such promiscu...
Comparative Methylation Hybridization
The methylation of DNA sequences is an important component of epigenetic control. Methylated sequences can be inherited, as in the case of imprinted genes like IGF2. Epigenetic changes to DNA can also occur over time, thereby playing an important ...
Complex Genomes: Shotgun Sequencing
To the great surprise of researchers, the number of genes in model organisms like mice, flies, and worms turned out to be not that different from the number of genes in humans. The major lesson to be learned from this information is that neither g...
DNA Sequencing Technologies
The Human Genome Project set out to sequence the DNA of every human chromosome, thereby promising to advance knowledge of human biology and improve medicine. This project was huge in scale, as it sought to determine the order of all 3 billion nucl...
DNA Sequencing Technologies Key to the Human Genome Project
The human genome consists of 3.2 billion base pairs of DNA that are distributed among 24 different chromosomes (22 autosomes and the X and Y chromosomes). Researchers now estimate that between 20,000 and 25,000 genes are buried within these billio...
Epigenomics: The New Tool in Studying Complex Diseases
Identical twins often develop different physical characteristics and predispositions to disease, even though they carry the same sequence of DNA nucleotides. How can this be? The field of epigenomics seeks to answer this question by exploring the ...
Genomic Data Resources: Challenges and Promises
The amount of genomic sequence data has risen exponentially over the last decade. Along with this rise, the number and types of genomic databases have also increased. These resources have proved a boon to biological research and discovery. Yet, as...
Human Chromosome Translocations and Cancer
Translocations generate novel chromosomes, but these chromosomes do not have a pairing partner in subsequent meioses. Cytogeneticists have identified thousands of different translocations, may of which have been linked to aneuploidy, infertility, ...
Microarray-based Comparative Genomic Hybridization (aCGH)
Many human genetic disorders result from unbalanced chromosomal abnormalities, in which there is net gain or loss of genetic material. In their attempts to identify such abnormalities, researchers are increasingly employing the technique known as ...
Pharmacogenomics and Personalized Medicine
How might doctors predict which patients will benefit from a particular medicine and which patients will suffer serious side effects? Such questions are at the heart of personalized medicine, which uses an individual’s genetic profile to mak...
Pufferfish and Ancestral Genomes
Comparative genomics tells us a great deal about the evolution of the pufferfish genome, including a potential duplication event, and it also indicates similarities between this genome and that of humans. Such information permits researchers to be...
Sequencing Human Genome: the Contributions of Francis Collins and Craig Venter
The events leading up to the era of genome sequencing took more than a quarter of a century and the combined work of hundreds of scientists. Throughout this period, the practicality of sequencing the 3 billion base pairs in the human genome—...
Simple Viral and Bacterial Genomes
Small genome sequences have shed light on the basic principles of genomics. As a result, researchers now know how few genes are required for self-sufficient life. Moreover, large-scale sequencing efforts, such as the Human Microbiome Project, cont...
The Proteome: Discovering the Structure and Function of Proteins
The proteome is a shape-shifting, ever-changing beast, because proteins are continually being synthesized, modified, and degraded. This means that scientists face significant challenges in seeking to capture and describe the proteome. Moreover, th...
Transcriptome: Connecting the Genome to Gene Function
RNA represents the working copy of the genome, whether it functions as a template for proteins or a noncoding gene product. The transcriptome consists of all of the expressed RNA molecules in a cell at a given time, and it provides information abo...

How do we know it?

Basic Local Alignment Search Tool (BLAST)
How can a scientist identify the function of a newly cloned gene? As gene and protein sequence databases grew exponentially at the end of the twentieth century, scientists turned to computers to help analyze the data. Online resources like the Bas...
DNA Fingerprinting Using Amplified Fragment Length Polymorphisms (AFLP)
Amplified fragment length polymorphism polymerase chain reaction (AFLP-PCR) is a powerful technique often employed by researchers to generate DNA “fingerprints” that are highly specific to particular species. Although this approach req...

Why do we care?

Genomes of Other Organisms: DNA Barcoding and Metagenomics
The Human Genome Project has generated an immense amount of data upon which scientists will focus for years to come, answering fundamental questions about human development, behavior, and evolution. While we dedicate extensive resources to studyi...
Interpreting Shared Characteristics: The Platypus Genome
Despite what the newspapers may say, the recent sequencing of the platypus genome has not revealed that this animal is part bird, part reptile, and part mammal. Rather, this sequence information is valuable in that it allows researchers to compare...
Sustainable Bioenergy: Genomics and Biofuels Development
Genomics is playing a significant role in addressing the global energy crisis by helping researchers better understand and harness various renewable energy sources, such as lignocellulosic biomass, microalgae, and cyanobacteria. Furthermore, genet...