A comprehensive overview and comparative analysis on deep learning models: CNN, RNN, LSTM, GRU

FM Shiri, T Perumal, N Mustapha… - arxiv preprint arxiv …, 2023 - arxiv.org
Deep learning (DL) has emerged as a powerful subset of machine learning (ML) and
artificial intelligence (AI), outperforming traditional ML methods, especially in handling …

Deep learning techniques with genomic data in cancer prognosis: a comprehensive review of the 2021–2023 literature

M Lee - Biology, 2023 - mdpi.com
Simple Summary The ongoing advancements in deep learning, notably its use in predicting
cancer survival through genomic data analysis, calls for an up-to-date review. This paper …

[HTML][HTML] scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network

C Li, X Shao, S Zhang, Y Wang, K **, P Yang, X Lu… - Cell Reports …, 2024 - cell.com
Cells respond divergently to drugs due to the heterogeneity among cell populations. Thus, it
is crucial to identify drug-responsive cell populations in order to accurately elucidate the …

1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma

TS Johnson, P Sudha, E Liu, N Becker… - Nature …, 2024 - nature.com
Multiple Myeloma is an incurable plasma cell malignancy with a poor survival rate that is
usually treated with immunomodulatory drugs (iMiDs) and proteosome inhibitors (PIs). The …

CellSTAR: a comprehensive resource for single-cell transcriptomic annotation

Y Zhang, H Sun, W Zhang, T Fu, S Huang… - Nucleic acids …, 2024 - academic.oup.com
Large-scale studies of single-cell sequencing and biological experiments have successfully
revealed expression patterns that distinguish different cell types in tissues, emphasizing the …

Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones

A Ianevski, K Nader, K Driva, W Senkowski… - Nature …, 2024 - nature.com
Intratumoral cellular heterogeneity necessitates multi-targeting therapies for improved
clinical benefits in advanced malignancies. However, systematic identification of patient …

scAB detects multiresolution cell states with clinical significance by integrating single-cell genomics and bulk sequencing data

Q Zhang, S **, X Zou - Nucleic Acids Research, 2022 - academic.oup.com
Although single-cell sequencing has provided a powerful tool to deconvolute cellular
heterogeneity of diseases like cancer, extrapolating clinical significance or identifying …

Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI

C Liu, Y Zhang, X Gao, G Wang - BMC biology, 2023 - Springer
Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the
transcriptomics field by advancing analyses from tissue-level to cell-level resolution. Despite …

Bioinformatics roadmap for therapy selection in cancer genomics

MJ Jiménez‐Santos, S García‐Martín… - Molecular …, 2022 - Wiley Online Library
Tumour heterogeneity is one of the main characteristics of cancer and can be categorised
into inter‐or intratumour heterogeneity. This heterogeneity has been revealed as one of the …

PIPET: predicting relevant subpopulations in single-cell data using phenotypic information from bulk data

X Ruan, Y Cheng, Y Ye, Y Wang, X Chen… - Briefings in …, 2024 - academic.oup.com
Single-cell RNA sequencing has revealed cellular heterogeneity in complex tissues, notably
benefiting research on diseases such as cancer. However, the integration of single-cell data …