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 …

[HTML][HTML] Integration strategies of multi-omics data for machine learning analysis

M Picard, MP Scott-Boyer, A Bodein, O Périn… - Computational and …, 2021 - Elsevier
Increased availability of high-throughput technologies has generated an ever-growing
number of omics data that seek to portray many different but complementary biological …

scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention

R Meng, S Yin, J Sun, H Hu, Q Zhao - Computers in biology and medicine, 2023 - Elsevier
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful
technique for investigating cellular heterogeneity and structure. However, analyzing scRNA …

[HTML][HTML] A Python library for probabilistic analysis of single-cell omics data

A Gayoso, R Lopez, G Xing, P Boyeau… - Nature …, 2022 - nature.com
To the Editor—Methods for analyzing single-cell data 1, 2, 3, 4 perform a core set of
computational tasks. These tasks include dimensionality reduction, cell clustering, cell-state …

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 …

Current best practices in single‐cell RNA‐seq analysis: a tutorial

MD Luecken, FJ Theis - Molecular systems biology, 2019 - embopress.org
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …

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 …

Challenges in unsupervised clustering of single-cell RNA-seq data

VY Kiselev, TS Andrews, M Hemberg - Nature Reviews Genetics, 2019 - nature.com
Single-cell RNA sequencing (scRNA-seq) allows researchers to collect large catalogues
detailing the transcriptomes of individual cells. Unsupervised clustering is of central …

Orchestrating single-cell analysis with Bioconductor

RA Amezquita, ATL Lun, E Becht, VJ Carey… - Nature …, 2020 - nature.com
Recent technological advancements have enabled the profiling of a large number of
genome-wide features in individual cells. However, single-cell data present unique …

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

F Zhang, K Wei, K Slowikowski, CY Fonseka… - Nature …, 2019 - nature.com
To define the cell populations that drive joint inflammation in rheumatoid arthritis (RA), we
applied single-cell RNA sequencing (scRNA-seq), mass cytometry, bulk RNA sequencing …