Obtaining genetics insights from deep learning via explainable artificial intelligence

G Novakovsky, N Dexter, MW Libbrecht… - Nature Reviews …, 2023 - nature.com
Artificial intelligence (AI) models based on deep learning now represent the state of the art
for making functional predictions in genomics research. However, the underlying basis on …

Artificial intelligence: A powerful paradigm for scientific research

Y Xu, X Liu, X Cao, C Huang, E Liu, S Qian, X Liu… - The Innovation, 2021 - cell.com
Artificial intelligence (AI) coupled with promising machine learning (ML) techniques well
known from computer science is broadly affecting many aspects of various fields including …

Identification of mobile genetic elements with geNomad

AP Camargo, S Roux, F Schulz, M Babinski, Y Xu… - Nature …, 2024 - nature.com
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …

Predicting transcriptional outcomes of novel multigene perturbations with GEARS

Y Roohani, K Huang, J Leskovec - Nature Biotechnology, 2024 - nature.com
Understanding cellular responses to genetic perturbation is central to numerous biomedical
applications, from identifying genetic interactions involved in cancer to developing methods …

Identification of neoantigens for individualized therapeutic cancer vaccines

F Lang, B Schrörs, M Löwer, Ö Türeci… - Nature reviews Drug …, 2022 - nature.com
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are
recognized by autologous T cells in the host. As neoepitopes are not subject to central …

Deep learning in cancer diagnosis, prognosis and treatment selection

KA Tran, O Kondrashova, A Bradley, ED Williams… - Genome Medicine, 2021 - Springer
Deep learning is a subdiscipline of artificial intelligence that uses a machine learning
technique called artificial neural networks to extract patterns and make predictions from …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Effective gene expression prediction from sequence by integrating long-range interactions

Ž Avsec, V Agarwal, D Visentin, JR Ledsam… - Nature …, 2021 - nature.com
How noncoding DNA determines gene expression in different cell types is a major unsolved
problem, and critical downstream applications in human genetics depend on improved …

Navigating the pitfalls of applying machine learning in genomics

S Whalen, J Schreiber, WS Noble… - Nature Reviews Genetics, 2022 - nature.com
The scale of genetic, epigenomic, transcriptomic, cheminformatic and proteomic data
available today, coupled with easy-to-use machine learning (ML) toolkits, has propelled the …

Direct cell reprogramming: approaches, mechanisms and progress

H Wang, Y Yang, J Liu, L Qian - Nature Reviews Molecular Cell Biology, 2021 - nature.com
The reprogramming of somatic cells with defined factors, which converts cells from one
lineage into cells of another, has greatly reshaped our traditional views on cell identity and …