Genomics
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
In recent years, several machine learning approaches have been proposed to predict gene expression and epigenetic signals from the DNA sequence alone. These models are often used to deduce, and, to some extent, assess putative new…
Understanding the host-specificity of different families of viruses sheds light on the origin of, e.g., SARS-CoV-2, rabies, and other such zoonotic pathogens in humans. It enables epidemiologists, medical professionals, and policymakers to…
Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…
Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats…
Motivation: Microsatellite instability (MSI) is a cancer biomarker associated with cancer prognosis and chemotherapy sensitivity. Since the discovery of MSI, polymerase chain reaction (PCR)-based testing has been considered the gold…
The Cichorium genus offers a unique opportunity to study the sporophytic self incompatibility (SSI) system, being composed of species characterized by highly efficient SI (C. intybus) and complete self compatibility (C. endivia). The…
Buffaloes are farm animals that contribute to food security by providing high quality meat and milk. They can better tolerate the adverse effects of global climate change on their meat and milk production. Despite their advantages,…
The amount of sequencing data for SARS-CoV-2 is several orders of magnitude larger than any virus. This will continue to grow geometrically for SARS-CoV-2, and other viruses, as many countries heavily finance genomic surveillance efforts.…
Genome-Wide Association Studies (GWAS) help identify genetic variations in people with diseases such as Parkinson's disease (PD), which are less common in those without the disease. Thus, GWAS data can be used to identify genetic variations…
In recent years, single cell RNA sequencing has become a widely used technique to study cellular diversity and function. However, accurately annotating cell types from single cell data has been a challenging task, as it requires extensive…
The vast amount of sequencing data presently available allow the scientific community to explore a range of genetic variables that may drive and progress cancer. A myriad of predictive tools has been proposed, allowing researchers and…
In the field of functional genomics, the analysis of gene expression profiles through Machine and Deep Learning is increasingly providing meaningful insight into a number of diseases. The paper proposes a novel algorithm to perform Feature…
Background: Single-cell RNA sequencing (scRNA-seq) yields valuable insights about gene expression and gives critical information about complex tissue cellular composition. In the analysis of single-cell RNA sequencing, the annotations of…
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the…
In this work we present a deep learning approach to conduct hypothesis-free, transcriptomics-based matching of drugs for diseases. Our proposed neural network architecture is trained on approved drug-disease indications, taking as input the…
Understanding the molecular processes that drive cellular life is a fundamental question in biological research. Ambitious programs have gathered a number of molecular datasets on large populations. To decipher the complex cellular…
The first important step in extracting DNA characters is using the output data of MinION devices in the form of electrical current signals. Various cutting-edge base callers use this data to detect the DNA characters based on the input. In…
Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…
Pleurotus ostreatus is a common cultivated edible mushroom worldwide. The fruiting bodies of P. ostreatus is a rich source of a $\beta$-glucans polysaccharide. The current study aimed to investigate the effectiveness of $\beta$-glucans as a…