ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples

A Tampuu, Z Bzhalava, J Dillner, R Vicente - PloS one, 2019 - journals.plos.org
Despite its clinical importance, detection of highly divergent or yet unknown viruses is a
major challenge. When human samples are sequenced, conventional alignments classify …

Explainable deep neural networks for novel viral genome prediction

CM Dasari, R Bhukya - Applied Intelligence, 2022 - Springer
Viral infection causes a wide variety of human diseases including cancer and COVID-19.
Viruses invade host cells and associate with host molecules, potentially disrupting the …

Aeromonas hydrophila ST251 and Aeromonas dhakensis are major emerging pathogens of striped catfish in Vietnam

KL Bartie, TPH Ngô, M Bekaert… - Frontiers in …, 2023 - frontiersin.org
Introduction Aeromonads are ubiquitous in aquatic environments and several species are
opportunistic pathogens of fish. Disease losses caused by motile Aeromonas species …

Machine Learning for detection of viral sequences in human metagenomic datasets

Z Bzhalava, A Tampuu, P Bała, R Vicente, J Dillner - BMC bioinformatics, 2018 - Springer
Background Detection of highly divergent or yet unknown viruses from metagenomics
sequencing datasets is a major bioinformatics challenge. When human samples are …

Impaired mRNA splicing and proteostasis in preadipocytes in obesity-related metabolic disease

J Sánchez-Ceinos, R Guzmán-Ruiz… - Elife, 2021 - elifesciences.org
Preadipocytes are crucial for healthy adipose tissue expansion. Preadipocyte differentiation
is altered in obese individuals, which has been proposed to contribute to obesity-associated …

Allele mining in prolactin receptor gene and its association with some economic traits in Egyptian goat breeds

AM Nowier, HR Darwish, SI Ramadan… - Animal …, 2023 - Taylor & Francis
The objectives of the current study were to identify polymorphism in the prolactin receptor
(PRLR) gene among three Egyptian goat breeds (Zaraibi, Damascus, and Barki) and to …

Genome-wide identification of the MIOX gene family and their expression profile in cotton development and response to abiotic stress

Z Li, Z Liu, Y Wei, Y Liu, L Xing, M Liu, P Li, Q Lu… - PLoS …, 2021 - journals.plos.org
The enzyme myo-inositol oxygenase (MIOX) catalyzes the myo-inositol into glucuronic acid.
In this study, 6 MIOX genes were identified from all of the three diploid cotton species …

Nucleic Transformer: Classifying DNA Sequences with Self-Attention and Convolutions

S He, B Gao, R Sabnis, Q Sun - ACS Synthetic Biology, 2023 - ACS Publications
Much work has been done to apply machine learning and deep learning to genomics tasks,
but these applications usually require extensive domain knowledge, and the resulting …

Comprehensive Genome-Wide Investigation and Transcriptional Regulation of the DHHC Gene Family in Cotton Seed and Fiber Development

S Silaiyiman, Q Zheng, Y Wang, L Ouyang, Z Guo, J Yu… - Agronomy, 2024 - mdpi.com
Protein palmitoylation, the most common and the only reversible post-translational lipid
modification following protein translation, plays a pivotal role in the biochemical and …

PCJ Java library as a solution to integrate HPC, Big Data and Artificial Intelligence workloads

M Nowicki, Ł Górski, P Bała - Journal of Big Data, 2021 - Springer
With the development of peta-and exascale size computational systems there is growing
interest in running Big Data and Artificial Intelligence (AI) applications on them. Big Data and …