Related papers: Physics-based analysis of Affymetrix microarray da…
The Affymetrix U95 and U133 Latin Square spike-in datasets are reanalysed, together with a dataset from a version of the U95 spike-in experiment without a complex non-specific background. The approach uses a physico-chemical model which…
DNA microarrays are devices that are able, in principle, to detect and quantify the presence of specific nucleic acid sequences in complex biological mixtures. The measurement consists in detecting fluorescence signals from several spots on…
In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was…
The effect of target molecule depletion from the supernatant solution is incorporated into a physico-chemical model of hybridisation on oligonucleotide microarrays. Two possible regimes are identified: local depletion, in which depletion by…
We quantify if the chemical abundance gradients given by a dynamical model of core collapse including time-dependent changes in density and temperature differ greatly from abundances derived from static models, where the density and…
Identifying relationships between molecular variations and their clinical presentations has been challenged by the heterogeneous causes of a disease. It is imperative to unveil the relationship between the high dimensional molecular…
We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity…
There has been a strong push recently to examine biological scale simulations of neuromorphic algorithms to achieve stronger inference capabilities. This paper presents a set of piecewise linear spiking neuron models, which can reproduce…
Although microarrays are routine analysis tools in biomedical research, they still yield noisy output that often requires experimental confirmation. Many studies have aimed at optimizing probe design and statistical analysis to tackle this…
The presence of different transcripts of a gene across samples can be analysed by whole-transcriptome microarrays. Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large…
A method for dimension reduction with clustering, classification, or discriminant analysis is introduced. This mixture model-based approach is based on fitting generalized hyperbolic mixtures on a reduced subspace within the paradigm of…
The evolution of star-forming core analogues undergoing inside-out collapse is studied with a multi-point chemodynamical model which self-consistently computes the abundance distribution of chemical species in the core. For several collapse…
We have coupled a chemical model with two dynamical models of collapsing low mass star-forming cores to predict abundances across the core of the commonly used infall tracers, CS and HCO$^+$, at various stages of the collapse. The models…
We present PrestaLine: Gorynych, a comprehensive numerical tool designed to model the dynamical, chemical, and spectral evolution of collapsing molecular cores from the prestellar phase to protostellar accretion. The code integrates three…
We investigate differences in the molecular abundances between magnetically super- and sub-critical prestellar cores, performing three-dimensional non-ideal magnetohydrodynamical (MHD) simulations with varying densities and magnetic field…
Elastomeric mechanical metamaterials exhibit unconventional behaviour, emerging from their microstructures often deforming in a highly nonlinear and unstable manner. Such microstructural pattern transformations lead to non-local behaviour…
It is well known that correlations in microarray data represent a serious nuisance deteriorating the performance of gene selection procedures. This paper is intended to demonstrate that the correlation structure of microarray data provides…
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…
We develop analytic approximations to the density evolution of prestellar cores, based on the results of hydrodynamical simulations. We use these approximations as input for a time-dependent gas-grain chemical code to investigate the…
We introduce a random hypergraph model for core-periphery structure. By leveraging our model's sufficient statistics, we develop a novel statistical inference algorithm that is able to scale to large hypergraphs with runtime that is…