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MARKER UNCERTAINTIES. “Yet most of these variants are in non-coding regions and we are often not even certain of the association of the variant with an actual gene.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

PROBABILITY MARKERS. “We currently lack the capability to evaluate the impact of most sequence variants found and what their functional consequences are. A decade of Genome-Wide Association Studies have revealed a multitude of common variants associated with various traits and diseases, each of which seems to contribute to or at least to increase the probability of a phenotype by a small amount.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

PERSONALIZED MEDICINE. “The rapid availability of ubiquitous sequencing holds great promise for medicine to the extent that genomics empowers the analysis of patient genomes to guide personalized treatment. While we can now sequence an individual's genome and transcriptomes, it remains extremely difficult to use that data to inform treatment.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

NEW TOOLS. “There are now a multitude of implementations based on this concept that introduce additional functional data such as protein interaction data, gene regulatory networks, pathway topology information, metabolic changes or expression kinetics. These methods have been applied not only to understand gene expression changes but also in Genome-Wide Association Studies (GWAS), comparative genomics and gene prioritization.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

RANKED NOT SELECTED. “The first functional enrichment analysis methods identified pathways that were overrepresented within a list of differentially expressed genes and were rapidly followed by the gene set enrichment approach where a ranked, rather than a selected, list of genes was used to find associations between phenotypes and cellular functions.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

STARTING WITH TEASERS on a variety of different time perspectives. When we slip into a different time lens, we see the world completely differently. There are ancient beings on earth who appear to have this perspective, such as viruses, who seem at ease waiting millennia for the right time to animate. View in LinkedIn

THE ASSUMPTION. “These functional assessment methodologies rely on the premise that the expressed components of cellular systems are likely to be functionally coordinated and that genes belonging to the same functional unit should show similar expression profiles.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

SPACE AND TIME, are the two variables that dominate physics. So with biology: dimensional scales and time scales are of considerable importance. The quantum scale is ruled by different forces than the classical scale. Time for a bacteria is on a different scale than for a human. View in LinkedIn

BIOLOGICAL MEANING. “Functional enrichment analysis methods (also referred to as pathway or gene set enrichment) are methodologies that allow us to analyze gene expression data for the biological meaning of particular expression patterns in order to gain additional insight into the actual biology of the system.” https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-S1 View in LinkedIn

FRAGMENT FROM NATURE deals with a scant explored subject, namely biological time scales. With ranges of biological time from nanoseconds for some biochemical reactions to millennia for some types of evolution, and the likelihood that time scale shifts may be subject to some type of emergence, it is curious that we have so ignored this topic. View in LinkedIn