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Computational graph pangenomics: a tutorial on data structures and their applications
Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …
computer scientists are facing challenges in biological sequence analysis. In past decades …
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Background While the reconstruction of transcripts from a sample of RNA-Seq data is a
computationally expensive and complicated task, the detection of splicing events from RNA …
computationally expensive and complicated task, the detection of splicing events from RNA …
Identification of a novel human E‐cadherin splice variant and assessment of its effects upon EMT‐related events
ML Matos, L Lapyckyj, M Rosso… - Journal of cellular …, 2017 - Wiley Online Library
Epithelial Cadherin (E‐cadherin) is involved in calcium‐dependent cell–cell adhesion and
signal transduction. The E‐cadherin decrease/loss is a hallmark of Epithelial to …
signal transduction. The E‐cadherin decrease/loss is a hallmark of Epithelial to …
Differential quantification of alternative splicing events on spliced pangenome graphs
Pangenomes are becoming a powerful framework to perform many bioinformatics analyses
taking into account the genetic variability of a population, thus reducing the bias introduced …
taking into account the genetic variability of a population, thus reducing the bias introduced …
Counting pseudoalignments to novel splicing events
Motivation Alternative splicing (AS) of introns from pre-mRNA produces diverse sets of
transcripts across cell types and tissues, but is also dysregulated in many diseases …
transcripts across cell types and tissues, but is also dysregulated in many diseases …
Artificial intelligence and bioinformatics
J Nicolas - A Guided Tour of Artificial Intelligence Research …, 2020 - Springer
The chapter shines a light on the strong links shared by Artificial intelligence and
Bioinformatics since many years. Bioinformatics offers many NP-hard problems that are …
Bioinformatics since many years. Bioinformatics offers many NP-hard problems that are …
FSG: fast string graph construction for de novo assembly
The string graph for a collection of next-generation reads is a lossless data representation
that is fundamental for de novo assemblers based on the overlap-layout-consensus …
that is fundamental for de novo assemblers based on the overlap-layout-consensus …
RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera)
M Yang, L Xu, Y Liu, P Yang - PLoS One, 2015 - journals.plos.org
RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms
(SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we …
(SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we …
[HTML][HTML] Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach
Small cardamom (Elettaria cardamomum), grown in limited coastal tropical countries is one
of the costliest and widely exported agri-produce having global turnover of> 10 billion USD …
of the costliest and widely exported agri-produce having global turnover of> 10 billion USD …
Manifold de Bruijn graphs
Genome assembly is usually abstracted as the problem of reconstructing a string from a set
of its k-mers. This abstraction naturally leads to the classical de Bruijn graph approach—the …
of its k-mers. This abstraction naturally leads to the classical de Bruijn graph approach—the …