In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this pa
Advances in sequencing and high-throughput techniques have provided an unprecedented opportunity to interrogate human diseases on a genome-wide scale. The list of disease-causing mutations is expanding rapidly, and mutations affecting mRNA translation are no exception. Translation (protein synthesis) is ...
In the context of pathway analysis, WRS can be used to compare the ranks or p values (derived from a statistical test, such as a t test) of the DE genes inside and outside a pathway. WRS is available in R via the function wilcox.test, which takes the list of DE genes, their ...
DNA sequencing technologies deviate from the ideal uniform distribution of reads. These biases impair scientific and medical applications. Accordingly, we have developed computational methods for discovering, describing and measuring bias. We applied the
Evolution of the deuterostome lineage was accompanied by an increase in systematic complexity especially with regard to highly specialized tissues and organs. Based on the observation of an increased number of paralogous genes in vertebrates compared wit
R genes are a key component of genetic interactions between plants and biotrophic bacteria and are known to regulate resistance against bacterial invasion. The most common R proteins contain a nucleotide-binding site and a leucine-rich repeat (NBS-LRR) d
Cell proliferation and differentiation require signalling pathways that enforce appropriate and timely gene expression. We find that Tor2, the catalytic subunit of the TORC1 complex in fission yeast, targets a conserved nuclear RNA elimination network, particularly the serine and proline-rich protein Pi...
Meta-analysis is a statistical procedure for analyzing the combined data from different studies, and can be a major source of concise up-to-date information. The overall conclusions of a meta-analysis, however, depend heavily on the quality of the meta-a
Network size is correlated with DEG list size (r = 0.827, P < 0.01). Other factors that influence network size include the proportion of DEGs with fly homologues, and the proportion of these with co-citation information currently available in PubMed. A majority of networks (6 of ...
For each method a list of GO categories ordered by significance was generated. Figure 3 compares the ranks of the GO categories between the GOseq method and hypergeometric method as a function of gene length (Figure 3a) or total read count (Figure 3b) within categories. As expected, ...