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Homologous recombination plays a key role in generating genetic diversity, while maintaining protein functionality. The mechanisms by which RecA enables a single-stranded segment of DNA to recognize a homologous tract within a whole genome…
Nearest neighbor (NN) matching as a tool to align data sampled from different groups is both conceptually natural and practically well-used. In a landmark paper, Abadie and Imbens (2006) provided the first large-sample analysis of NN…
In Cowell et al. (2007), a Bayesian network for analysis of mixed traces of DNA was presented using gamma distributions for modelling peak sizes in the electropherogram. It was demonstrated that the analysis was sensitive to the choice of a…
The presence of neighbor dependencies generated a specific pattern of dinucleotide frequencies in all organisms. Especially, the CpG-methylation-deamination process is the predominant substitution process in vertebrates and needs to be…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
This paper develops a novel unified framework for testing mutual independence among random objects residing in possibly different metric spaces. The framework generalizes existing methodologies and introduces new measures of mutual…
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…
Experiments in online platforms frequently suffer from network interference, in which a treatment applied to a given unit affects outcomes for other units connected via the platform. This SUTVA violation biases naive approaches to…
The analysis of a protein-expression pattern from tissue microarray (TMA) data will not immediately give an answer on synergistic or antagonistic effects between the expression of the observed proteins. But contrary to apparent first…
We develop a model-based methodology for integrating gene-set information with an experimentally-derived gene list. The methodology uses a previously reported sampling model, but takes advantage of natural constraints in the…
This paper studies semiparametric identification of substitution and complementarity patterns between two goods using a panel multinomial choice model with bundles. The model allows the two goods to be either substitutes or complements and…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Metric learning aims at learning a distance which is consistent with the semantic meaning of the samples. The problem is generally solved by learning an embedding for each sample such that the embeddings of samples of the same category are…
Mining large-scale high-throughput tandem mass spectrometry data sets is a very important problem in mass spectrometry based protein identification. One of the fundamental problems in large scale mining of spectra is to design appropriate…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
Cancer development is associated with aberrant DNA methylation, including increased stochastic variability. Statistical tests for discovering cancer methylation biomarkers have focused on changes in mean methylation. To improve the power of…
In molecular dynamics (MD) simulation, force field determines the capability of an individual model in capturing physical and chemistry properties. The method for generating proper parameters of the force field form is the key component for…
Amyloid filaments are associated with neurodegenerative diseases such as Alzheimer's and Parkinson's. Simplified models of amyloid aggregation are crucial because the original mass-action equations involve numerous variables, complicating…