Related papers: Augmenting transcriptome assembly combinatorially
Current popular methods in literature of RNA sequencing normalisation do not account for gene length when compared across samples, whilst adjusting for count biases in the data. This creates a gap in the normalisation as bigger genes in RNA…
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…
Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…
An extended aperture has the potential to greatly improve ultrasound imaging performance. This work extends the effective aperture size by coherently compounding the received radio frequency data from multiple transducers. A framework is…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
We consider the problem of data augmentation, i.e., generating artificial samples to extend a given corpus of training data. Specifically, we propose attributed-guided augmentation (AGA) which learns a mapping that allows to synthesize data…
Handwritten text and scene text suffer from various shapes and distorted patterns. Thus training a robust recognition model requires a large amount of data to cover diversity as much as possible. In contrast to data collection and…
Microbiome sample representation to input into LLMs is essential for downstream tasks such as phenotype prediction and environmental classification. While prior studies have explored embedding-based representations of each microbiome…
Many modern biological assays, including RNA sequencing, yield integer-valued counts that reflect the number of molecules detected. These measurements are often not at the desired resolution: while the unit of interest is typically a single…
Isoform quantification is an important goal of RNA-seq experiments, yet it remains prob- lematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology…
Advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions at the single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M…
RNA sequencing techniques, like bulk RNA-seq and Single Cell (sc) RNA-seq, are critical tools for the biologist looking to analyze the genetic activity/transcriptome of a tissue or cell during an experimental procedure. Platforms like…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
CLIP-seq methods are valuable techniques to experimentally determine transcriptome-wide binding sites of RNA-binding proteins. Despite the constant improvement of such techniques (e.g. eCLIP), the results are affected by various types of…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
Network alignment (NA) is the task of discovering node correspondences across different networks. Although NA methods have achieved remarkable success in a myriad of scenarios, their satisfactory performance is not without prior anchor link…