… a denoising method, dubbed SAMDUDE, which operates on aligned genomic data in order
… setting, we perform denoising and variant calling comparisons on human data sets. We show …

… This eliminates alignment artifacts in the wavelet coefficients that arise from a discrete … rigidly
fixed a priori and hence may not align well with the genomic changes on a chromosome. An …

… We confirmed DAs can effectively extract meaningful genomic features from genomic data …
For gene expression data, the sequencing, alignment, quality control and quantification were …

… that adjusts the error rate by incorporating the degree of alignment. To this end, we define
the relative gain of the number of aligned bases after denoising by a tool over raw data as …

… Spatially resolved genomic technologies … align spatial observations across slices, samples,
scales, individuals and technologies. Here, we propose a probabilistic model that aligns …

… to generate a multiple sequence alignment (MSA) of reads, … data, where the few produced
reads were longer and coverage was lower. With such small data sets, a pairwise alignment of …

… when the datasets were not denoised or trimmed based on quality scores. The magnitude
of difference in the numbers of OTUs between denoised and untrimmed data depended on the …

… Related denoising algorithms have been developed in the microbial … denoising pipeline
was designed as a faster version of the original PyroNoise [15]. The algorithm denoiser aligns …

… Since interaction data for all these genomes are not available, in order to validate this
approach, we aim at high specificity (low number of false positives), and low sensitivity (high …

… To evaluate the utility of network filters for denoising biological data in realistic settings, …
denoise the input expression data before model training, compared to training on unfiltered data…