Related papers: Augmenting transcriptome assembly combinatorially
Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…
High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we…
Collecting and annotating datasets for pixel-level semantic segmentation tasks are highly labor-intensive. Data augmentation provides a viable solution by enhancing model generalization without additional real-world data collection.…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a high-throughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling…
Differential gene expression (DGE) analysis is foundational to transcriptomic research, yet tool selection can substantially influence results. This study presents a comprehensive comparison of two widely used DGE tools, edgeR and DESeq2,…
Urothelial cell carcinoma (UCC) is the ninth most common cancer that accounts for 4.7% of all the new cancer cases globally. UCC development and progression are due to complex and stochastic genetic programmes. To study the cascades of…
A central goal in automatic music transcription is to detect individual note events in music recordings. An important variant is instrument-dependent music transcription where methods can use calibration data for the instruments in use.…
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate statistical power without undue resource…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
An RNA-seq experiment with 48 biological replicates in each of 2 conditions was performed to determine the number of biological replicates ($n_r$) required, and to identify the most effective statistical analysis tools for identifying…
RNA-sequencing has revolutionized biomedical research and, in particular, our ability to study gene alternative splicing. The problem has important implications for human health, as alternative splicing may be involved in malfunctions at…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
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…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…