Machine learning in drug discovery: a review

S Dara, S Dhamercherla, SS Jadav, CHM Babu… - Artificial intelligence …, 2022 - Springer
This review provides the feasible literature on drug discovery through ML tools and
techniques that are enforced in every phase of drug development to accelerate the research …

Single-cell multiomics: technologies and data analysis methods

J Lee, DY Hyeon, D Hwang - Experimental & Molecular Medicine, 2020 - nature.com
Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …

Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

The triumphs and limitations of computational methods for scRNA-seq

PV Kharchenko - Nature methods, 2021 - nature.com
The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …

Alignment of spatial genomics data using deep Gaussian processes

A Jones, FW Townes, D Li, BE Engelhardt - Nature Methods, 2023 - nature.com
Spatially resolved genomic technologies have allowed us to study the physical organization
of cells and tissues, and promise an understanding of local interactions between cells …

Applications of machine learning in drug discovery and development

J Vamathevan, D Clark, P Czodrowski… - Nature reviews Drug …, 2019 - nature.com
Drug discovery and development pipelines are long, complex and depend on numerous
factors. Machine learning (ML) approaches provide a set of tools that can improve discovery …

Single-cell RNA-seq technologies and related computational data analysis

G Chen, B Ning, T Shi - Frontiers in genetics, 2019 - frontiersin.org
Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …

Deep generative modeling for single-cell transcriptomics

R Lopez, J Regier, MB Cole, MI Jordan, N Yosef - Nature methods, 2018 - nature.com
Single-cell transcriptome measurements can reveal unexplored biological diversity, but they
suffer from technical noise and bias that must be modeled to account for the resulting …

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

R Argelaguet, D Arnol, D Bredikhin, Y Deloro, B Velten… - Genome biology, 2020 - Springer
Technological advances have enabled the profiling of multiple molecular layers at single-
cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a …

Multi-omics integration in the age of million single-cell data

Z Miao, BD Humphreys, AP McMahon… - Nature Reviews …, 2021 - nature.com
An explosion in single-cell technologies has revealed a previously underappreciated
heterogeneity of cell types and novel cell-state associations with sex, disease, development …