Computational graph pangenomics: a tutorial on data structures and their applications

JA Baaijens, P Bonizzoni, C Boucher, G Della Vedova… - Natural computing, 2022‏ - Springer
Computational pangenomics is an emerging research field that is changing the way
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

L Denti, R Rizzi, S Beretta, GD Vedova, M Previtali… - BMC …, 2018‏ - Springer
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 …

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 …

Differential quantification of alternative splicing events on spliced pangenome graphs

S Ciccolella, D Cozzi, G Della Vedova… - PLOS Computational …, 2024‏ - journals.plos.org
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 …

Counting pseudoalignments to novel splicing events

L Borozan, F Rojas Ringeling, SY Kao… - …, 2023‏ - academic.oup.com
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 …

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 …

FSG: fast string graph construction for de novo assembly

P Bonizzoni, GD Vedova, Y Pirola… - Journal of …, 2017‏ - liebertpub.com
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 …

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 …

[HTML][HTML] Plant virus interaction mechanism and associated pathways in mosaic disease of small cardamom (Elettaria cardamomum Maton) by RNA-Seq approach

A Khan, KJ George, RS Jasrotia, S Aravind, UB Angadi… - Genomics, 2020‏ - Elsevier
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 …

Manifold de Bruijn graphs

Y Lin, PA Pevzner - International Workshop on Algorithms in …, 2014‏ - Springer
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 …