AIMC Topic: Sequence Analysis, RNA
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Diverse regulated cell death patterns and immune traits in kidney allograft with fibrosis: a prediction of renal allograft failure based on machine learning, single-nucleus RNA sequencing and molecular docking.
Renal failure
Dec 4, 2024
Post-transplant allograft fibrosis remains a challenge in prolonging allograft survival. Regulated cell death has been widely implicated in various kidney diseases, including renal fibrosis. However, the role of different regulated cell death (RCD) ...
Deciphering the impact of senescence in kidney transplant rejection: An integrative machine learning and multi-omics analysis via bulk and single-cell RNA sequencing.
PloS one
Nov 27, 2024
BACKGROUND: The demographic shift towards an older population presents significant challenges for kidney transplantation (KTx), particularly due to the vulnerability of aged donor kidneys to ischemic damage, delayed graft function, and reduced graft ...
Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing.
Nature methods
Nov 14, 2024
The rapid growth of single-cell transcriptomic technology has produced an increasing number of datasets for both embryonic development and in vitro pluripotent stem cell-derived models. This avalanche of data surrounding pluripotency and the process ...
A mapping-free natural language processing-based technique for sequence search in nanopore long-reads.
BMC bioinformatics
Nov 13, 2024
BACKGROUND: In unforeseen situations, such as nuclear power plant's or civilian radiation accidents, there is a need for effective and computationally inexpensive methods to determine the expression level of a selected gene panel, allowing for rough ...
DeSide: A unified deep learning approach for cellular deconvolution of tumor microenvironment.
Proceedings of the National Academy of Sciences of the United States of America
Nov 8, 2024
Cellular deconvolution via bulk RNA sequencing (RNA-seq) presents a cost-effective and efficient alternative to experimental methods such as flow cytometry and single-cell RNA-seq (scRNA-seq) for analyzing the complex cellular composition of tumor mi...
Machine learning identification of NK cell immune characteristics in hepatocellular carcinoma based on single-cell sequencing and bulk RNA sequencing.
Genes & genomics
Oct 21, 2024
BACKGROUND: Hepatocellular carcinoma (HCC) is a highly malignant tumor; however, its immune microenvironment and mechanisms remain elusive. Single-cell sequencing allows for the exploration of immune characteristics within tumor at the cellular level...
Identification of novel biomarkers for atherosclerosis using single-cell RNA sequencing and machine learning.
Mammalian genome : official journal of the International Mammalian Genome Society
Oct 14, 2024
Atherosclerosis (AS) is a predominant etiological factor in numerous cardiovascular diseases, with its associated complications such as myocardial infarction and stroke serving as major contributors to worldwide mortality rates. Here, we devised depe...
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites.
IEEE/ACM transactions on computational biology and bioinformatics
Oct 9, 2024
Pseudouridine is a type of abundant RNA modification that is seen in many different animals and is crucial for a variety of biological functions. Accurately identifying pseudouridine sites within the RNA sequence is vital for the subsequent study of ...
TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning.
IEEE/ACM transactions on computational biology and bioinformatics
Oct 9, 2024
N4-acetylcytidine (ac4C) is a post-transcriptional modification in mRNA that is critical in mRNA translation in terms of stability and regulation. In the past few years, numerous approaches employing convolutional neural networks (CNN) and Transforme...
The role of lactylation in plasma cells and its impact on rheumatoid arthritis pathogenesis: insights from single-cell RNA sequencing and machine learning.
Frontiers in immunology
Oct 3, 2024
INTRODUCTION: Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent synovitis, systemic inflammation, and autoantibody production. This study aims to explore the role of lactylation in plasma cells and its impact on R...
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