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View article: Establishing the Asia & Pacific Bioinformatics Joint Congress: a historic milestone in regional bioinformatics collaboration
Establishing the Asia & Pacific Bioinformatics Joint Congress: a historic milestone in regional bioinformatics collaboration Open
In response to the need for greater cohesion among regional conferences, the Asia Pacific Bioinformatics Network (APBioNET) set out in 2015 to realize a long-held aspiration—a single, unifying bioinformatics “super conference” for the Asia…
View article: Machine Learning‐Based Predictive Modeling Maximizes the Efficacy of <scp>mTOR</scp> /p53 Co‐Targeting Therapy Against <scp>AML</scp>
Machine Learning‐Based Predictive Modeling Maximizes the Efficacy of <span>mTOR</span> /p53 Co‐Targeting Therapy Against <span>AML</span> Open
Although mTOR signaling plays a key role in acute myeloid leukemia (AML), mTOR inhibitors have shown limited efficacy against AML in clinical trials. In this study, we found that the anti‐leukemic effect of mTOR inhibition was mediated in …
View article: Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks
Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks Open
Background Understanding the dynamics of gene regulatory networks (GRNs) across various cellular states is crucial for deciphering the underlying mechanisms governing cell behavior and functionality. However, current comparative analytical…
View article: SCOIGET: Predicting Spatial Tumor Evolution Pattern by Inferring Spatial Copy Number Variation Distributions
SCOIGET: Predicting Spatial Tumor Evolution Pattern by Inferring Spatial Copy Number Variation Distributions Open
Constructing a comprehensive spatiotemporal map of tumor heterogeneity is essential for understanding tumor evolution, with copy number variation (CNV) as a significant feature. Existing studies often rely on tools originally developed for…
View article: SpliceSelectNet: A Hierarchical Transformer-Based Deep Learning Model for Splice Site Prediction
SpliceSelectNet: A Hierarchical Transformer-Based Deep Learning Model for Splice Site Prediction Open
Accurate RNA splicing is essential for gene expression and protein function, yet the mechanisms governing splice site recognition remain incompletely understood. Aberrant splicing caused by mutations can lead to severe diseases, including …
View article: In Silico Analysis Revealed Marco (SR-A6) and Abca1/2 as Potential Regulators of Lipid Metabolism in M1 Macrophage Hysteresis
In Silico Analysis Revealed Marco (SR-A6) and Abca1/2 as Potential Regulators of Lipid Metabolism in M1 Macrophage Hysteresis Open
Macrophages undergo polarization, resulting in distinct phenotypes. These transitions, including de-/repolarization, lead to hysteresis, where cells retain genetic and epigenetic signatures of previous states, influencing macrophage functi…
View article: Computational analysis of the functional impact of MHC-II-expressing triple-negative breast cancer
Computational analysis of the functional impact of MHC-II-expressing triple-negative breast cancer Open
The tumor microenvironment (TME) plays a crucial role in tumor progression and immunoregulation. Major histocompatibility complex class II (MHC-II) is essential for immune surveillance within the TME. While MHC-II genes are typically expre…
View article: Machine Learning-Based Predictive Modeling Maximizes the Efficacy of mTOR/TP53 Co-Targeting Therapy Against Acute Myeloid Leukemia
Machine Learning-Based Predictive Modeling Maximizes the Efficacy of mTOR/TP53 Co-Targeting Therapy Against Acute Myeloid Leukemia Open
The mammalian target of rapamycin (mTOR) is a serine/threonine kinase that plays a critical role in regulating cell growth, proliferation and survival. The mTOR pathway is often hyperactivated in acute myeloid leukemia (AML) and is associa…
View article: Extensive Computational Screening Identifies Marco (SR-A6) and Abca1/2 as Key Regulators of Intracellular Lipid Metabolism to Compensate Low Cholesterol Biosynthesis in M1 Macrophages Hysteresis
Extensive Computational Screening Identifies Marco (SR-A6) and Abca1/2 as Key Regulators of Intracellular Lipid Metabolism to Compensate Low Cholesterol Biosynthesis in M1 Macrophages Hysteresis Open
(1) Background: Macrophages undergo polarization, resulting in distinct phenotypes. These transitions, including de-/repolarization, lead to hysteresis, where cells retain genetic and epigenetic signatures of previous states, influencing m…
View article: Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina
Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina Open
Despite known single-cell expression profiles in vertebrate retinas, understanding of their developmental and evolutionary expression patterns among homologous cell classes remains limited. We examined and compared approximately 240 000 re…
View article: TF-EPI: an interpretable enhancer-promoter interaction detection method based on Transformer
TF-EPI: an interpretable enhancer-promoter interaction detection method based on Transformer Open
The detection of enhancer-promoter interactions (EPIs) is crucial for understanding gene expression regulation, disease mechanisms, and more. In this study, we developed TF-EPI, a deep learning model based on Transformer designed to detect…
View article: Single‐cell transcriptomic analysis of B cells reveals new insights into atypical memory B cells in COVID‐19
Single‐cell transcriptomic analysis of B cells reveals new insights into atypical memory B cells in COVID‐19 Open
Here, we performed single‐cell RNA sequencing of S1 and receptor binding domain protein‐specific B cells from convalescent COVID‐19 patients with different clinical manifestations. This study aimed to evaluate the role and developmental pa…
View article: Integrative analysis of cancer multimodality data identifying COPS5 as a novel biomarker of diffuse large B-cell lymphoma
Integrative analysis of cancer multimodality data identifying COPS5 as a novel biomarker of diffuse large B-cell lymphoma Open
Preventing, diagnosing, and treating diseases requires accurate clinical biomarkers, which remains challenging. Recently, advanced computational approaches have accelerated the discovery of promising biomarkers from high-dimensional multim…
View article: DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics
DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics Open
Spatial transcriptomics provides a unique opportunity for understanding cellular organization and function in a spatial context. However, spatial transcriptome exists the problem of dropout noise, exposing a major challenge for accurate do…
View article: Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks
Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks Open
Motivation Understanding the dynamics of gene regulatory networks (GRNs) across various cellular states is crucial for deciphering the underlying mechanisms governing cell behavior and functionality. However, current comparative analytical…
View article: Characterization of <i>trans</i>-spliced chimeric RNAs: insights into the mechanism of <i>trans</i>-splicing
Characterization of <i>trans</i>-spliced chimeric RNAs: insights into the mechanism of <i>trans</i>-splicing Open
Trans-splicing is a post-transcriptional processing event that joins exons from separate RNAs to produce a chimeric RNA. However, the detailed mechanism of trans-splicing remains poorly understood. Here, we characterize trans-spliced genes…
View article: A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response
A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response Open
Delineating the intricate interplay between promoter-proximal and -distal regulators is crucial for understanding the function of transcriptional mediator complexes implicated in the regulation of gene expression. The present study aimed t…
View article: HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data
HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data Open
Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality…
View article: Resting heart rate and risk of dementia: a Mendelian randomization study in the international genomics of Alzheimer’s Project and UK Biobank
Resting heart rate and risk of dementia: a Mendelian randomization study in the international genomics of Alzheimer’s Project and UK Biobank Open
Background Observational studies have demonstrated that a higher resting heart rate (RHR) is associated with an increased risk of dementia. However, it is not clear whether the association is causal. This study aimed to determine the causa…
View article: DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics
DenoiseST: A dual-channel unsupervised deep learning-based denoising method to identify spatial domains and functionally variable genes in spatial transcriptomics Open
Spatial transcriptomics provides a unique opportunity for understanding cellular organization and function in a spatial context. However, spatial transcriptome exists the problem of dropout noise, exposing a major challenge for accurate do…
View article: Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization
Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization Open
Macrophages display extreme plasticity, and the mechanisms and applications of polarization and de-/repolarization of macrophages have been extensively investigated. However, the regulation of macrophage hysteresis after de-/repolarization…
View article: STAIG: Spatial Transcriptomics Analysis via Image-Aided Graph Contrastive Learning for Domain Exploration and Alignment-Free Integration
STAIG: Spatial Transcriptomics Analysis via Image-Aided Graph Contrastive Learning for Domain Exploration and Alignment-Free Integration Open
Spatial transcriptomics is an essential application for investigating cellular structures and interactions and requires multimodal information to precisely study spatial domains. Here, we propose STAIG, a novel deep-learning model that int…
View article: Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina
Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina Open
Despite known single-cell expression profiles in vertebrate retinas, understanding of their developmental and evolutionary expression patterns among homologous cell classes remains limited. We examined and compared approximately 240,000 re…
View article: HyGAnno: Hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data
HyGAnno: Hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data Open
Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality…
View article: Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression
Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression Open
In this research, we elucidate the presence of around 11,000 housekeeping cis-regulatory elements (HK-CREs) and describe their main characteristics. Besides the trivial promoters of housekeeping genes, most HK-CREs reside in promoter regio…
View article: A computational approach for deciphering the interactions between proximal and distal regulators in B cell differentiation
A computational approach for deciphering the interactions between proximal and distal regulators in B cell differentiation Open
Delineating the intricate interplay between promoter-proximal and -distal regulators is crucial for understanding the function of transcriptional mediator complexes implicated in the regulation of gene expression. The aim of the present st…