Related papers: Applied Category Theory for Genomics -- An Initiat…
In recent years, we have witnessed a dramatic data explosion in genomics, thanks to the improvement in sequencing technologies and the drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
This is a collection of introductory, expository notes on applied category theory, inspired by the 2018 Applied Category Theory Workshop, and in these notes we take a leisurely stroll through two themes (functorial semantics and…
Cryptography is a theory of secret functions. Category theory is a general theory of functions. Cryptography has reached a stage where its structures often take several pages to define, and its formulas sometimes run from page to page.…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
After it was proposed that life on Earth might descend from seeding by an earlier civilization, some authors noted that this alternative offers a testable aspect: the seeds could be supplied with a signature that might be found in extant…
In mathematical applications, category theory remains a contentious issue, with enthusiastic fans and a skeptical majority. In a muted form this split applies to the authors of this note. When we learned that the only mathematically sound…
In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
Quantum computing is a rapidly developing field in the second wave of quantum development, with the potential to revolutionize a wide range of industries and fields of study. As the capabilities of quantum computers continue to advance,…
Component systems - ensembles of realizations built from a shared repertoire of modular parts - are ubiquitous in biological, ecological, technological, and socio-cultural domains. From genomes to texts, cities, and software, these systems…
All living organisms use the same genetic languages in their molecular biology machinery. They can be understood as the optimal solutions to the replication tasks involving DNA and proteins. These solutions perfectly fit the pattern…
Group theory is a particularly fertile field for the design of practical algorithms. Algorithms have been developed across the various branches of the subject and they find wide application. Because of its relative maturity, computational…
This book collects the lectures about graph theory and its applications which were given to students of mathematical departments of Moscow State University and Peking University. Graph theory is a very wide field with a lot of applications…
One of the prime motivation for topology was Homotopy theory, which captures the general idea of a continuous transformation between two entities, which may be spaces or maps. In later decades, an algebraic formulation of topology was…
Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…
Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
We introduce a categorical language in which it is possible to talk about DNA sequencing, alignment methods, CRISPR, homologous recombination, haplotypes, and genetic linkage. This language takes the form of a class of limit-sketches whose…
The origin of life is shrouded in mystery, with few surviving clues, obscured by evolutionary competition. Previous reviews have touched on the complementary approaches of top-down and bottom-up synthetic biology to augment our…