Related papers: Effective affinities in microarray data
Biological processes rely on finely tuned homo- and heteromeric interactions between (biomacro)molecules. The strength of an interaction, typically given by the dissociation constant (KD), plays a crucial role in basic research and must be…
Observational studies provide invaluable opportunities to draw causal inference, but they may suffer from biases due to pretreatment difference between treated and control units. Matching is a popular approach to reduce observed covariate…
Highly accurate numerical or physical experiments are often time-consuming or expensive to obtain. When time or budget restrictions prohibit the generation of additional data, the amount of available samples may be too limited to provide…
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…
Magnetic resonance imaging (MRI) is the non-invasive modality of choice for body tissue composition analysis due to its excellent soft tissue contrast and lack of ionizing radiation. However, quantification of body composition requires an…
In finite mixture models, apart from underlying mixing measure, true kernel density function of each subpopulation in the data is, in many scenarios, unknown. Perhaps the most popular approach is to choose some kernel functions that we…
The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
The integration of multi-omics data has emerged as a promising approach for gaining comprehensive insights into complex diseases such as cancer. This paper proposes a novel approach to identify cancer subtypes through the integration of…
Multimodal biometric systems have gained popularity for their enhanced recognition accuracy and resistance to attacks like spoofing. This research explores methods for fusing iris and face feature vectors and implements robust security…
Modern data science applications often involve complex relational data with dynamic structures. An abrupt change in such dynamic relational data is typically observed in systems that undergo regime changes due to interventions. In such a…
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…
Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD),…
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…
Motivation: The discovery of relationships between gene expression measurements and phenotypic responses is hampered by both computational and statistical impediments. Conventional statistical methods are less than ideal because they either…
We present a quantitative, multi-scale coarse-grained model of DNA coated colloids. The parameters of this model are transferable and are solely based on experimental data. As a test case, we focus on nano-sized colloids carrying…
The quality and consistency of training data remain critical bottlenecks for protein-ligand binding prediction. Public affinity datasets, aggregated from thousands of labs and assay formats, introduce biases that limit model generalization…
In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to…
In order to get accurate information about complex systems depending on a lot of parameters, frequently different experimental methods and/or different experimental conditions are used. The evaluation of these data sets is quite often a…
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…