Cultural Imports
The exchanges between genomics and other disciplines are not limited to methods and techniques, but also include cultural practices.
As a discipline, protein-structure prediction pioneered concepts such as the Critical Assessment of protein Structure Prediction (CASP) competition format.
CASP is a community-wide effort to evaluate predictions.
Ever.
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How do researchers share human genomic data?
Researchers are expected to share human genomic data according to the consent provided by the research participants.
Genomic data are typically shared with the scientific community through data resources, which can be accessed in three ways:
- Infographic:
- Types of genomic data access
Credit:Harry Wedel, NHGRI.
See text-only version.
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How many exabytes of data will genomics research generate?
Estimates predict that genomics research will generate between 2 and 40 exabytes of data within the next decade.
Our ability to sequence DNA has far outpaced our ability to decipher the information it contains, so genomic data science will be a vibrant field of research for many years to come.
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Technical Exports
A few methods exported from genomics to other fields were initially developed to address specific biological problems.
However, these methods were later generalized for a broader set of applications.
A notable example of such an export is the latent Dirichlet allocation (LDA) model.
Pritchard et al. [71] initially proposed this unsupervised generat.
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Technical Imports
A central aspect of genomics—the process of mapping reads to the human reference genome—relies on a foundational technique within data science: fast and memory-efficient string-processing algorithms.
Protein pairwise alignment predates DNA sequence alignment.
One of the first successful implementations of sequence alignment was based on Smith–Water.
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What is genomic data science?
Genomic data science is a field of study that enables researchers to use powerful computational and statistical methods to decode the functional information hidden in DNA sequence.
Applied in the context of genomic medicine, these data science tools help researchers and clinicians uncover how differences in DNA affect human health and disease.
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What is the Human Genome Project?
The Human Genome Project has inspired subsequent large-scale data acquisition initiatives such as:
- the International HapMap Project
- 1000 Genomes
- The Cancer Genome Atlas
- as well as the recently announced Human Brain Project and the emerging Human Proteome Project
Concept in genetics
The minimal genome is a concept which can be defined as the set of genes sufficient for life to exist and propagate under nutrient-rich and stress-free conditions.
Alternatively, it can also be defined as the gene set supporting life on an axenic cell culture in rich media, and it is thought what makes up the minimal genome will depend on the environmental conditions that the organism inhabits.
By one early investigation, the minimal genome of a bacterium should include a virtually complete set of proteins for replication and translation, a transcription apparatus including four subunits of RNA polymerase including the sigma factor rudimentary proteins sufficient for recombination and repair, several chaperone proteins, the capacity for anaerobic metabolism through glycolysis and substrate-level phosphorylation, transamination of glutamyl-tRNA to glutaminyl-tRNA, lipid biosynthesis, eight cofactor enzymes, protein export machinery, and a limited metabolite transport network including membrane ATPases.
Proteins involved in the minimum bacterial genome tend to be substantially more related to proteins found in archaea and eukaryotes compared to the average gene in the bacterial genome more generally indicating a substantial number of universally conserved proteins.
The minimal genomes reconstructed on the basis of existing genes does not preclude simpler systems in more primitive cells, such as an RNA world genome which does not have the need for DNA replication machinery, which is otherwise part of the minimal genome of current cells.
