Related papers: Compound Poisson Statistics and Models of Clusteri…
In the framework of the Statistical Multifragmentation Model, the nuclear isoscaling analysis is extended to constrain the ratio between the sizes of the decaying sources formed in a collision between two heavy ions. It is found that the…
Asymmetric damage segregation (ADS) is ubiquitous among unicellular organisms: After a mother cell divides, its two daughter cells receive sometimes slightly, sometimes strongly different fractions of damaged proteins accumulated in the…
Bursting cells lead to ambient RNA that contaminates sequencing data. This process is especially problematic in perturbation experiments where transcription factors are implanted into cells to determine their effects. The presence of…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
Molecular dynamics simulations were employed to investigate the phase separation process of a two-dimensional active Brownian dumbbell model. We evaluated the time dependence of the typical size of the dense component using the scaling…
Identification of local structure in intensive data -- such as time series, images, and higher dimensional processes -- is an important problem in astronomy. Since the data are typically generated by an inhomogeneous Poisson process, an…
The detection of local genomic signals using high-throughput DNA sequencing data can be cast as a problem of scanning a Poisson random field for local changes in the rate of the process. We propose a likelihood-based framework for for such…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A…
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Post-clustering inference in single-cell RNA sequencing (scRNA-seq) analysis presents significant challenges in controlling Type I error during differential expression analysis. Data fission, a promising approach that aims to split data…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
Damage spreading for 2D Ising cluster dynamics is investigated numerically by using random numbers in a way that conforms with the notion of submitting the two evolving replicas to the same thermal noise. Two damage spreading transitions…
In dynamic force spectroscopy, a (bio-)molecular complex is subjected to a steadily increasing force until the chemical bond breaks. Repeating the same experiment many times results in a broad distribution of rupture forces, whose…
A new model that includes the time-dependent dynamics of the single-particle (s.p.) motion in conjunction with the macroscopic evolution of the system is proposed for describing the compound nucleus (CN) formation in fusion of heavy nuclei.…
Intracellular positive ions neutralise negative charges on the phosphates of a DNA strand conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a…
Cancer treatment with radiotherapy aims to kill tumor cells and spare healthy tissue.Thus,the experimentally observed sparing of healthy tissue by the FLASH effect during irradiations with ultra-high dose rates (UHDR) enables clinicians to…
We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant…