Related papers: Extending the Overlap Graph for Gene Assembly in C…
Multiplex networks describe a large number of systems ranging from social networks to the brain. These multilayer structure encode information in their structure. This information can be extracted by measuring the correlations present in…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Graphs and networks are a key research tool for a variety of science fields, most notably chemistry, biology, engineering and social sciences. Modeling and generation of graphs with efficient sampling is a key challenge for graphs. In…
Overlap is a common phenomenon seen when structural components of a digital object are neither disjoint nor nested inside each other. Overlapping components resist reduction to a structural hierarchy, and tree-based indexing and query…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Current applications have produced graphs on the order of hundreds of thousands of nodes and millions of edges. To take advantage of such graphs, one must be able to find patterns, outliers and communities. These tasks are better performed…
We introduce a statistical method that can reconstruct nonlinear genetic models (i.e., including epistasis, or gene-gene interactions) from phenotype-genotype (GWAS) data. The computational and data resource requirements are similar to…
In this paper we examine a number of term rewriting system for integer number representations, building further upon the datatype defining systems described in [2]. In particular, we look at automated methods for proving confluence and…
E-graphs are a data structure for equational reasoning and optimization over ground terms. One of the benefits of e-graph rewriting is that it can declaratively handle useful but difficult to orient identities like associativity and…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
Universal cycles are generalizations of de Bruijn cycles and Gray codes that were introduced originally by Chung, Diaconis, and Graham in 1992. They have been developed by many authors since, for various combinatorial objects such as…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
We analyse the statistical properties of genealogical trees in a neutral model of a closed population with sexual reproduction and non-overlapping generations. By reconstructing the genealogy of an individual from the population evolution,…
Inferring gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is a complex challenge that requires capturing the intricate relationships between genes and their regulatory interactions. In this study, we tackle…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
Increased biological complexity is generally associated with the addition of new genetic information, which must be integrated into the existing regulatory network that operates within the cell. General arguments on network control, as well…
One of the theoretical models proposed for the mechanism of gene unscrambling in some species of ciliates is the template-guided recombination (TGR) system by Prescott, Ehrenfeucht and Rozenberg which has been generalized by Daley and…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
The reassembling of a simple connected graph G = (V,E) is an abstraction of a problem arising in earlier studies of network analysis. Its simplest formulation is in two steps: (1) We cut every edge of G into two halves, thus obtaining a…
Interpreting graph neural networks (GNNs) is difficult because message passing mixes signals and internal channels rarely align with human concepts. We study superposition, the sharing of directions by multiple features, directly in the…