Related papers: Understanding the physics of oligonucleotide micro…
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 analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human and…
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…
One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities…
The ability of oligonucleotide microarrays to measure gene expression has been hindered by an imperfect understanding of the relationship between input RNA concentrations and output signals. We argue that this relationship can be understood…
The induced-activity investigations in off-line analysis performed in different experiments, concerning pre-actinide and actinide nuclei, are here presented and discussed. Generalized expressions for the determination of independent…
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…
Despite the success and popularity of oligonucleotide arrays as a high-throughput technique for measuring mRNA expression levels, quantitative calibration studies have until now been limited. The main reason is that suitable data was not…
We introduce a new data fusion method that utilizes multiple data sources to estimate a smooth, finite-dimensional parameter. Most existing methods only make use of fully aligned data sources that share common conditional distributions of…
We derive the statistics of the signals generated by shape fluctuations of large molecules studied by feedback tracking microscopy. We account for the influence of intramolecular dynamics on the response of the tracking system, and derive a…
In biology experiments, oligonucleotide microarrays are contacted with a solution of long nucleic acid (NA) targets. The hybridized probes thus carry long tails. When the surface density of the oligonucleotide probes is high enough, the…
The biological behavior and treatment response of meningiomas depend on their grade, making an accurate diagnosis essential for treatment planning and prognosis assessment. We observed that the weighted fusion of spatial-frequency domain…
In a recent paper [Phys. Rev. E 68, 011906 (2003)], Naef and Magnasco suggested that the "bright" mismatches observed in Affymetrix microarray experiments are caused by the fluorescent molecules used to label RNA target sequences, which…
Given the increasing complexity of omics datasets, a key challenge is not only improving classification performance but also enhancing the transparency and reliability of model decisions. Effective model performance and feature selection…
Microscopic optical potentials have been successful in describing nucleon-nucleus and nucleus-nucleus scattering. Some essential ingredients of the framework, however, have not been examined in detail. Applicability of the microscopic…
Non-coding RNA molecules fold into precise base pairing patterns to carry out critical roles in genetic regulation and protein synthesis. We show here that coupling systematic mutagenesis with high-throughput SHAPE chemical mapping enables…
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses…
The tertiary structures of functional RNA molecules remain difficult to decipher. A new generation of automated RNA structure prediction methods may help address these challenges but have not yet been experimentally validated. Here we apply…
Understanding how multiple features are associated and contribute to a specific objective is as important as understanding how each feature contributes to a particular outcome. Interpretability of a single feature in a prediction may be…
Technological advancements have enabled the recording of spiking activities from large neuron ensembles, presenting an exciting yet challenging opportunity for statistical analysis. This project considers the challenges from a common type…