Related papers: Applied Category Theory for Genomics -- An Initiat…
Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…
This work is motivated by the necessity to automate the discovery of structure in vast and evergrowing collection of relational data commonly represented as graphs, for example genomic networks. A novel algorithm, dubbed Graphitour, for…
The topology of any complex system is key to understanding its structure and function. Fundamentally, algebraic topology guarantees that any system represented by a network can be understood through its closed paths. The length of each path…
The loop quantum theory, which constitutes a very small discontinuous space, as new method is applied to biology. The model of protein folding and lungs is proposed. In the model, some known results are used, and four approximate…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described.…
The goal of this paper is to demystify the role played by the Reedy category axioms in homotopy theory. With no assumed prerequisites beyond a healthy appetite for category theoretic arguments, we present streamlined proofs of a number of…
Routing information through networks is a universal phenomenon in both natural and manmade complex systems. When each node has full knowledge of the global network connectivity, finding short communication paths is merely a matter of…
The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing…
Network theory has proven to be a powerful tool in describing and analyzing systems by modelling the relations between their constituent objects. In recent years great progress has been made by augmenting `traditional' network theory.…
Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data…
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However,…
Category theory provides a powerful tool to organize mathematics. A sample of this descriptive power is given by the categorical analysis of the practice of "classes as shorthands" in ZF set theory. In this case category theory provides a…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in…
We show that a number of results on abstract elementary classes (AECs) hold in accessible categories with concrete directed colimits. In particular, we prove a generalization of a recent result of Boney on tameness under a large cardinal…
This article presents results of experimental studies the effectiveness of the genetic algorithm that was applied to effective queries creation and relevant document selection. Studies were carried out to the comparative analysis of the…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…