相关论文: Identification and Measurement of Neighbor Depende…

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…

Methylation of CpG dinucleotides is a prevalent epigenetic modification that is required for proper development in vertebrates, and changes in CpG methylation are essential to cellular differentiation. Genome-wide DNA methylation assays…

We consider models of nucleotidic substitution processes where the rate of substitution at a given site depends on the state of its neighbours. For a wide class of such nonreversible models, we show how to compute consistent, mathematically…

We prove that a wide class of models of Markov neighbor-dependent substitution processes on the integer line is solvable. This class contains some models of nucleotide substitutions recently introduced and studied empirically by molecular…

Understanding the high-pressure phase behavior of carbon dioxide-hydrocarbon mixtures is of considerable interest owing to their wide range of applications. Under certain conditions, these systems are not amenable to direct visual…

This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…

For molecular dynamics simulations of hard particles, we define dynamic neighbors as the distinct particles that collide with a given reference one during a specific time interval. This definition allows us to determine the distribution of…

Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (Austin…

DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…

We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG…

Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores we develop a maximum…

We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…

Stick insect stepping patterns have been studied for insights about locomotor rhythm generation and control, because the underlying neural system is relatively accessible experimentally and produces a variety of rhythmic outputs. Harnessing…

The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…

Cells constantly need to monitor the state of the environment to detect changes and timely respond. The detection of concentration changes of a ligand by a set of receptors can be cast as a problem of hypothesis testing, and the cell viewed…

Background: Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype. Computational prediction of CpG site-specific…

To establish the relationship between locomotory behavior and dynamics of neural circuits in the nematode C. elegans we combined molecular and theoretical approaches. In particular, we quantitatively analyzed the motion of C. elegans with…

DNA methylation datasets in cancer studies are comprised of measurements on a large number of genomic locations called cytosine-phosphate-guanine (CpG) sites with complex correlation structures. A fundamental goal of these studies is the…

Change-point analysis is thriving in this big data era to address problems arising in many fields where massive data sequences are collected to study complicated phenomena over time. It plays an important role in processing these data by…

The transmission or reception of packets passing between computers can be represented in terms of time-stamped events and the resulting activity understood in terms of point-processes. Interestingly, in the disparate domain of neuroscience,…