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Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…
Genome-wide association studies (GWAS) have been widely used to examine the association between single nucleotide polymorphisms (SNPs) and complex traits, where both the sample size n and the number of SNPs p can be very large. Recently,…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
We describe a graph reduction operation, generalizing three graph reduction operations related to gene assembly in ciliates. The graph formalization of gene assembly considers three reduction rules, called the positive rule, double rule,…
Accurately reconstructing Gene Regulatory Networks (GRNs) is crucial for understanding gene functions and disease mechanisms. Single-cell RNA sequencing (scRNA-seq) technology provides vast data for computational GRN reconstruction. Since…
A major goal in genomics is to properly capture the complex dynamical behaviors of gene regulatory networks (GRNs). This includes inferring the complex interactions between genes, which can be used for a wide range of genomics analyses,…
Representative Selection (RS) is the problem of finding a small subset of exemplars from a dataset that is representative of the dataset. In this paper, we study RS for attributed graphs, and focus on finding representative nodes that…
In computational genomics, many analyses rely on efficient storage and traversal of $k$-mers, motivating compact representations such as spectrum-preserving string sets (SPSS), which store strings whose $k$-mer spectrum matches that of the…
An overlap representation is an assignment of sets to the vertices of a graph in such a way that two vertices are adjacent if and only if the sets assigned to them overlap. The overlap number of a graph is the minimum number of elements…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…
Gene regulatory network inference (GRNI) aims to discover how genes causally regulate each other from gene expression data. It is well-known that statistical dependencies in observed data do not necessarily imply causation, as spurious…
Introduction The focus of analyzing data from microarray experiments and extracting biological insight from such data has experienced a shift from identification of individual genes in association with a phenotype to that of biological…
Graph coarsening aims to diminish the size of a graph to lighten its memory footprint, and has numerous applications in graph signal processing and machine learning. It is usually defined using a reduction matrix and a lifting matrix,…
Genetic Network Programming (GNP) is an evolutionary algorithm that extends Genetic Programming (GP). It is typically used in agent control problems. In contrast to GP, which employs a tree structure, GNP utilizes a directed graph…
Downsampling produces coarsened, multi-resolution representations of data and it is used, for example, to produce lossy compression and visualization of large images, reduce computational costs, and boost deep neural representation…