相关论文: Effective affinities in microarray data
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…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…
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…
Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called…
In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free…
Background: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild type DNA. This excess can give rise to false positives due to competitive hybridization of…
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…
Competitve hybridization, at the surface and in the bulk, lowers the sensitivity of DNA chips. Competitive surface hybridization occurs when different targets can hybridize with the same probe. Competitive bulk hybridization takes place…
The lack of specificity in microarray experiments due to non-specific hybridization raises a serious problem for the analysis of microarray data because the residual chemical background intensity is not related to the expression degree of…
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
Affinity propagation is an exemplar-based clustering algorithm that finds a set of data-points that best exemplify the data, and associates each datapoint with one exemplar. We extend affinity propagation in a principled way to solve the…
A goodness-of-fit test for the fitting of a parametric model to data obtained from a detector with finite resolution and limited acceptance is proposed. The parameters of the model are found by minimization of a statistic that is used for…
A general method for obtaining highly efficient factorial designs of relatively small sizes is developed for cDNA microarray experiments. The method allows the main effects and interactions of successive orders to be of possibly unequal…
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…
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…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…
Recent advances in acquisition equipment is providing experiments with growing amounts of precise yet affordable sensors. At the same time an improved computational power, coming from new hardware resources (GPU, FPGA, ACAP), has been made…
While designing oligonucleotide-based microarrays, cross-hybridization between surface-bound oligos and non-intended labeled targets is probably the most difficult parameter to predict. Although literature describes rules-of-thumb…
The joint utilization of diverse data sources for medical imaging segmentation has emerged as a crucial area of research, aiming to address challenges such as data heterogeneity, domain shift, and data quality discrepancies. Integrating…