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Bioinformatics is an interdisciplinary field that develops and improves on methods for storing, retrieving, organizing and analyzing biological data. A major activity in bioinformatics is to develop software tools to generate useful biological knowledge.

Bioinformatics has become an important part of many areas of biology. In experimental molecular biology, bioinformatics techniques such as image and signal processing allow extraction of useful results from large amounts of raw data. In the field of genetics and genomics, it aids in sequencing and annotating genomes and their observed mutations. It plays a role in the textual mining of biological literature and the development of biological and gene ontologies to organize and query biological data. It plays a role in the analysis of gene and protein expression and regulation. Bioinformatics tools aid in the comparison of genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of systems biology. In structural biology, it aids in the simulation and modeling of DNA, RNA, and protein structures as well as molecular interactions. Researchers affiliated with our program conduct research in systems biology, genomics, and proteomics.

Systems Biology

Systems biology is an emerging approach applied to biomedical and biological scientific research. Systems biology is a biology-based inter-disciplinary field of study that focuses on complex interactions within biological systems, using a more holistic perspective (holism instead of the more traditional reductionism) approach to biological and biomedical research. Particularly from year 2000 onwards, the concept has been used widely in the biosciences in a variety of contexts. One of the outreaching aims of systems biology is to model and discover emergent properties, properties of cells, tissues and organisms functioning as a system whose theoretical description is only possible using techniques which fall under the remit of systems biology.

Associated Faculty:

  • Robert Zeller (SDSU Biology)
  • Alan Calvitti (VA Hospital)

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Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism). The field includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome’s networks.


Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use “shotgun” Sanger sequencing or massively parallel pyrosequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world.

Associated Faculty:

  • Liz Dinsdale (SDSU Biology)
  • Forest Rohwer (SDSU Biology)
  • Anca Segall (SDSU Biology)
  • Robert Edwards (SDSU Computer Science)

Population Genomics

Population genomics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow on a genome-wide level. It also takes into account the factors of recombination, population subdivision and population structure. It attempts to explain such phenomena as adaptation and speciation.

Associated Faculty:

  • Andrew Bohonak

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Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. Proteomics, formed on the basis of the research and development of the Human Genome Project, is also an emerging scientific research, involving exploration of the proteome from the overall level of intracellular protein composition, structure, and its own unique activity patterns. It is an important component of functional genomics.

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