Related papers: RNA-Seq Mapping Errors When Using Incomplete Refer…
Historical documents frequently suffer from damage and inconsistencies, including missing or illegible text resulting from issues such as holes, ink problems, and storage damage. These missing portions or gaps are referred to as lacunae. In…
Spatial Transcriptomics is a novel technology that aligns histology images with spatially resolved gene expression profiles. Although groundbreaking, it struggles with gene capture yielding high corruption in acquired data. Given potential…
Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…
regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal…
With recent advances in speech synthesis, synthetic data is becoming a viable alternative to real data for training speech recognition models. However, machine learning with synthetic data is not trivial due to the gap between the synthetic…
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…
Automatic drum transcription is a critical tool in Music Information Retrieval for extracting and analyzing the rhythm of a music track, but it is limited by the size of the datasets available for training. A popular method used to increase…
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However,…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…
In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
Protein synthesis rates are determined, at the translational level, by properties of the transcript's sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or…
Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for…
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…
In differential expression (DE) analysis of RNA-seq count data, it is known that genes with a larger read number are more likely to be differentially expressed. This bias has a profound effect on the subsequent Gene Ontology (GO) analysis…
Background and Objective: The massive parallel sequencing technology facilitates new discoveries in terms of transcript differential analysis; however, all the new findings must be validated, since the diversity of transcript expression may…
The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a greater length increases the chance for reads being…
Most of the state-of-the-art automatic music transcription (AMT) models break down the main transcription task into sub-tasks such as onset prediction and offset prediction and train them with onset and offset labels. These predictions are…
Huge numbers of short reads are being generated for mapping back to the genome to discover the frequency of transcripts, miRNAs, DNAase hypersensitive sites, FAIRE regions, nucleosome occupancy, etc. Since these reads are typically short…