相关论文: Solving the riddle of the bright mismatches: hybri…

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…

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…

Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences than the…

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…

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…

Microarray-based genotyping is based on the high discrimination capability of oligonucleotide probes. For detection of Single Nucleotide Polymorphisms (SNPs) single-base discrimination is required. We investigate how various…

Analysis of data from an Affymetrix Latin Square spike-in experiment indicates that measured fluorescence intensities of features on an oligonucleotide microarray are related to spike-in RNA target concentrations via a hyperbolic response…

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…

Variability in illumination is a primary factor limiting deep learning robustness for field-based plant disease detection. This study evaluates Histogram Matching (HM), a technique that transforms the pixel intensity distribution of an…

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…

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…

We study the problem of selecting control clones in DNA array hybridization experiments. The problem arises in the OFRG method for analyzing microbial communities. The OFRG method performs classification of rRNA gene clones using binary…

This paper investigates the hybrid precoding design for millimeter wave (mmWave) multiple-input multiple-output (MIMO) systems with finite-alphabet inputs. The precoding problem is a joint optimization of analog and digital precoders, and…

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…

In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…

Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…

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…

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…

. Genechip oligonucleotide microarrays have been used widely for transcriptional profiling of a large number of genes in a given paradigm. Gene expression estimation precedes biological inference and is given as a complex combination of…

We discuss a technique that allows blind recovery of signals or blind identification of mixtures in instances where such recovery or identification were previously thought to be impossible: (i) closely located or highly correlated sources…