Related papers: Augmenting transcriptome assembly combinatorially
High-throughput sequencing is now regularly used for studies of the transcriptome (RNA-seq), particularly for comparisons among experimental conditions. For the time being, a limited number of biological replicates are typically considered…
One of the main challenges in current research on segmentation in cardiac ultrasound is the lack of large and varied labeled datasets and the differences in annotation conventions between datasets. This makes it difficult to design robust…
High-throughput RNA sequencing (RNA-seq) is now the standard method to determine differential gene expression. Identifying differentially expressed genes crucially depends on estimates of read count variability. These estimates are…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
RNA-Seq is a widely-used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
Contrastive learning has emerged as a premier method for learning representations with or without supervision. Recent studies have shown its utility in graph representation learning for pre-training. Despite successes, the understanding of…
Ultra high-throughput sequencing of transcriptomes (RNA-Seq) has enabled the accurate estimation of gene expression at individual isoform level. However, systematic biases introduced during the sequencing and mapping processes as well as…
Multi-instrument music transcription aims to convert polyphonic music recordings into musical scores assigned to each instrument. This task is challenging for modeling as it requires simultaneously identifying multiple instruments and…
RNAs are essential molecules that carry genetic information vital for life, with profound implications for drug development and biotechnology. Despite this importance, RNA research is often hindered by the vast literature available on the…
Antigen-specific T cells play an essential role in immunoregulation and diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of…
In the face of rapidly accumulating genomic data, our understanding of the RNA regulatory code remains incomplete. Recent self-supervised methods in other domains have demonstrated the ability to learn rules underlying the data-generating…
Sequence discriminative training is a great tool to improve the performance of an automatic speech recognition system. It does, however, necessitate a sum over all possible word sequences, which is intractable to compute in practice.…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
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…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic…
Accurate and comprehensive clinical documentation is crucial for delivering high-quality healthcare, facilitating effective communication among providers, and ensuring compliance with regulatory requirements. However, manual transcription…
Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer…
Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cells without sample pooling or RNA extraction. Currently, there is no algorithm optimized…