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A chord diagram refers to a set of chords with distinct endpoints on a circle. The intersection graph of a chord diagram $\cal C$ is defined by substituting the chords of $\cal C$ with vertices and by adding edges between two vertices…
Single particle tracking allows probing how biomolecules interact physically with their natural environments. A fundamental challenge when analysing recorded single particle trajectories is the inverse problem of inferring the physical…
Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu}) across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and found substantial variation among genes in the density of synonymous polymorphisms. They…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…
In this paper, we study the connectivity of a one-dimensional soft random geometric graph (RGG). The graph is generated by placing points at random on a bounded line segment and connecting pairs of points with a probability that depends on…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
Gene/pathway-based methods are drawing significant attention due to their usefulness in detecting rare and common variants that affect disease susceptibility. The biological mechanism of drug responses indicates that a gene-based analysis…
Random graphs are more and more used for modeling real world networks such as evolutionary networks of proteins. For this purpose we look at two different models and analyze how properties like connectedness and degree distributions are…
Devising and analyzing learning models for spatiotemporal network data is of importance for tasks including forecasting, anomaly detection, and multi-agent coordination, among others. Graph Convolutional Neural Networks (GCNNs) are an…
Genomic variants, including copy number variants (CNVs) and genome-wide associa-tion study (GWAS) single nucleotide polymorphisms (SNPs), represent structural alterations that influence genomic diversity and disease susceptibility. While…
The article derives multivariate Generalized Gram-Charlier (GGC) series that expands an unknown joint probability density function (\textit{pdf}) of a random vector in terms of the differentiations of the joint \textit{pdf} of a reference…
The functions of proteins and RNAs are determined by a myriad of interactions between their constituent residues, but most quantitative models of how molecular phenotype depends on genotype must approximate this by simple additive effects.…
It is of great interest to quantify the contributions of genetic variation to brain structure and function, which are usually measured by high-dimensional imaging data (e.g., magnetic resonance imaging). In addition to the variance, the…
The Gaussian graphical model (GGM) has become a popular tool for analyzing networks of psychological variables. In a recent paper in this journal, Forbes, Wright, Markon, and Krueger (FWMK) voiced the concern that GGMs that are estimated…
In our earlier work, we introduced the concept of Gene Regulatory Neural Network (GRNN), which utilizes natural neural network-like structures inherent in biological cells to perform computing tasks using chemical inputs. We define this…
A generalization of the random geometric graph (RGG) model is proposed by considering a set of points uniformly and independently distributed on a rectangle of unit area instead of on a unit square [0,1]^2. The topological properties of the…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
An essential problem in domain adaptation is to understand and make use of distribution changes across domains. For this purpose, we first propose a flexible Generative Domain Adaptation Network (G-DAN) with specific latent variables to…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded…