Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica

D Baisya, A Ramesh, C Schwartz, S Lonardi… - Nature …, 2022 - nature.com
Genome-wide functional genetic screens have been successful in discovering genotype-
phenotype relationships and in engineering new phenotypes. While broadly applied in …

Superior target genes and pathways for RNAi‐mediated pest control revealed by genome‐wide analysis in the beetle Tribolium castaneum

B Buer, J Dönitz, M Milner, S Mehlhorn… - Pest Management …, 2024 - Wiley Online Library
BACKGROUND An increasing human population, the emergence of resistances against
pesticides and their potential impact on the environment call for the development of new eco …

iEssLnc: quantitative estimation of lncRNA gene essentialities with meta-path-guided random walks on the lncRNA-protein interaction network

YY Zhang, DM Liang, PF Du - Briefings in Bioinformatics, 2023 - academic.oup.com
Gene essentiality is defined as the extent to which a gene is required for the survival and
reproductive success of a living system. It can vary between genetic backgrounds and …

Untangling the Context-Specificity of Essential Genes by Means of Machine Learning: A Constructive Experience

M Giordano, E Falbo, L Maddalena, M Piccirillo… - Biomolecules, 2023 - mdpi.com
Gene essentiality is a genetic concept crucial for a comprehensive understanding of life and
evolution. In the last decade, many essential genes (EGs) have been determined using …

'Bingo'—a large language model-and graph neural network-based workflow for the prediction of essential genes from protein data

J Ma, J Song, ND Young, BCH Chang… - Briefings in …, 2024 - academic.oup.com
The identification and characterization of essential genes are central to our understanding of
the core biological functions in eukaryotic organisms, and has important implications for the …

Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning

TL Campos, PK Korhonen, ND Young, T Wang… - International Journal of …, 2024 - mdpi.com
Over the years, comprehensive explorations of the model organisms Caenorhabditis
elegans (elegant worm) and Drosophila melanogaster (vinegar fly) have contributed …

HELP: A computational framework for labelling and predicting human common and context-specific essential genes

I Granata, L Maddalena, M Manzo… - PLOS Computational …, 2024 - journals.plos.org
Machine learning-based approaches are particularly suitable for identifying essential genes
as they allow the generation of predictive models trained on features from multi-source data …

Combination of computational techniques and RNAi reveal targets in Anopheles gambiae for malaria vector control

EO Adedeji, T Beder, C Damiani, A Cappelli, A Accoti… - Plos one, 2024 - journals.plos.org
Increasing reports of insecticide resistance continue to hamper the gains of vector control
strategies in curbing malaria transmission. This makes identifying new insecticide targets or …

[HTML][HTML] Inference of essential genes in Brugia malayi and Onchocerca volvulus by machine learning and the implications for discovering new interventions

TL Campos, PK Korhonen, ND Young… - Computational and …, 2024 - Elsevier
Detailed explorations of the model organisms Caenorhabditis elegans (elegant worm) and
Drosophila melanogaster (vinegar fly) have substantially improved our knowledge and …

Machine learning on large scale perturbation screens for SARS-CoV-2 host factors identifies β-catenin/CBP inhibitor PRI-724 as a potent antiviral

MA Kelch, A Vera-Guapi, T Beder, M Oswald… - Frontiers in …, 2023 - frontiersin.org
Expanding antiviral treatment options against SARS-CoV-2 remains crucial as the virus
evolves under selection pressure which already led to the emergence of several drug …