Jean Yang
YOU?
Author Swipe
View article: Circulating tumor cells predict relapse in head and neck mucosal squamous cell carcinoma
Circulating tumor cells predict relapse in head and neck mucosal squamous cell carcinoma Open
CTCs detected using the AccuCyte-CyteFinder platform demonstrate independent prognostic value in HNmSCC patients, complementing conventional pathologic assessment, particularly margin involvement. This proof-of-concept study provides preli…
View article: Longitudinal Assessment of Health-Related Quality of Life in Adult with CKD
Longitudinal Assessment of Health-Related Quality of Life in Adult with CKD Open
Background: There is sparse data about the change in HRQoL with the temporal progression of CKD. In this study, we assessed the association between change in CKD stages, overall and domain-specific QoL and determined the factors that were …
View article: Circulating IFNγ-associated protein signatures predict response to neoadjuvant immunotherapy in patients with stage III melanoma
Circulating IFNγ-associated protein signatures predict response to neoadjuvant immunotherapy in patients with stage III melanoma Open
Background Immune checkpoint inhibitors (ICIs), such as anti-programmed cell death protein 1 (PD-1) and anti-cytotoxic T-lymphocyte associated protein 4 (CTLA-4), have transformed the management of stage III melanoma in the neoadjuvant set…
View article: BenchHub enables an inclusive and transparent ecosystem for community-focused benchmarking in computational biology
BenchHub enables an inclusive and transparent ecosystem for community-focused benchmarking in computational biology Open
The rapid growth of computational methods for the computational biology field highlights the critical role of benchmarking in guiding method selection. However, there is no standardised data structure that effectively links and stores data…
View article: CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data
CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data Open
Motivation Clustering is a fundamental task in single-cell omics data analysis and can significantly impact downstream analyses and biological interpretations. The standard approach involves grouping cells based on their gene expression pr…
View article: dioscRi enables transferable prediction of clinical outcomes in multi-parameter cytometry data
dioscRi enables transferable prediction of clinical outcomes in multi-parameter cytometry data Open
Multi-parameter cytometry technologies enable high-dimensional analysis of immune cell populations at single-cell resolution. Deep learning has emerged as a transformative tool for analyzing these datasets, but existing methods often strug…
View article: Spatial gene expression at single-cell resolution from histology using deep learning with GHIST
Spatial gene expression at single-cell resolution from histology using deep learning with GHIST Open
The increased use of spatially resolved transcriptomics provides new biological insights into disease mechanisms. However, the high cost and complexity of these methods are barriers to broader application. Consequently, methods have been c…
View article: Multi-view gene panel characterization for spatially resolved omics
Multi-view gene panel characterization for spatially resolved omics Open
Spatially resolved transcriptomics has revolutionized the study of complex tissues by enabling cellular and subcellular resolution. However, targeted spatial technologies depend on pre-selected gene panels, which are typically curated base…
View article: The current landscape and emerging challenges of benchmarking single-cell methods
The current landscape and emerging challenges of benchmarking single-cell methods Open
With the rapid development of computational methods for single-cell sequencing data, benchmarking serves as a valuable resource. As the number of benchmarking studies surges, it is timely to assess the current state of the field. We conduc…
View article: Endothelial Colony-Forming Cell Transcriptomic Profiling in CT-defined Coronary Artery Disease from the BioHEART-CT Study Implicate CCBE1 in Mitochondrial Dysfunction-associated Atherosclerosis
Endothelial Colony-Forming Cell Transcriptomic Profiling in CT-defined Coronary Artery Disease from the BioHEART-CT Study Implicate CCBE1 in Mitochondrial Dysfunction-associated Atherosclerosis Open
Background Endothelial dysfunction is an early contributor to atherosclerosis. This study combined CT imaging of coronary artery disease (CAD) and patient-dervied endothelial colony-forming cells (ECFCs) transcriptional profiling to invest…
View article: SEC61B regulates calcium flux and platelet hyperreactivity in diabetes
SEC61B regulates calcium flux and platelet hyperreactivity in diabetes Open
Platelet hyperreactivity increases the risk of cardiovascular thrombosis in diabetes and failure of antiplatelet drug therapies. Elevated basal and agonist-induced calcium flux is a fundamental cause of platelet hyperreactivity in diabetes…
View article: Integration of Whole-Genome Sequencing Analysis with Unique Patient-Derived Models Reveals Clinically Relevant Drug Targets in <i>TFCP2</i> Fusion–Defined Rhabdomyosarcoma
Integration of Whole-Genome Sequencing Analysis with Unique Patient-Derived Models Reveals Clinically Relevant Drug Targets in <i>TFCP2</i> Fusion–Defined Rhabdomyosarcoma Open
Precision medicine is a likely future for all cancer treatment but may have its greatest impact on less common, high-mortality, and molecularly heterogeneous cancers. TFCP2-rearranged rhabdomyosarcoma (RMS) is a rare, aggressive cancer wit…
View article: [Prevalence characteristics of autoimmune thyroid disease in women aged 10-59 years in Qingdao City from 2022 to 2024].
[Prevalence characteristics of autoimmune thyroid disease in women aged 10-59 years in Qingdao City from 2022 to 2024]. Open
The three-year pre-valence of HT and GD in females aged 10-59 years in Qingdao City from 2022 to 2024 is low, but the annual prevalence is on the rise, and the three-year prevalence of HT and GD in females aged 25-39 years is higher than t…
View article: Pathway metabolite ratios reveal distinctive glutamine metabolism in a subset of proliferating cells
Pathway metabolite ratios reveal distinctive glutamine metabolism in a subset of proliferating cells Open
Large-scale metabolomic analyses of pan-cancer cell line panels have provided significant insights into the relationships between metabolism and cancer cell biology. Here, we took a pathway-centric approach by transforming targeted metabol…
View article: Interpretable Differential Abundance Signature (iDAS)
Interpretable Differential Abundance Signature (iDAS) Open
Single‐cell technologies have revolutionized the understanding of cellular dynamics by allowing researchers to investigate individual cell responses under various conditions, such as comparing diseased versus healthy states. Many different…
View article: A Kidney Transplant Support System for Patient-Clinician Shared Decision-Making
A Kidney Transplant Support System for Patient-Clinician Shared Decision-Making Open
An optimal deceased donor allocation program requires a fair, ethical, and transparent algorithm to ensure efficient and effective allocation of deceased donor kidneys to recipients that will benefit most, by maximizing utility of the dono…
View article: Multi-view gene panel characterization for spatially resolved omics
Multi-view gene panel characterization for spatially resolved omics Open
Spatially resolved transcriptomics has transformed our ability to study complex tissues at the cellular and subcellular resolution. However, targeted spatial technologies require pre-selected gene panels, which are typically curated based …
View article: Improving Lesion Segmentation in Medical Images by Global and Regional Feature Compensation
Improving Lesion Segmentation in Medical Images by Global and Regional Feature Compensation Open
Automated lesion segmentation of medical images has made tremendous improvements in recent years due to deep learning advancements. However, accurately capturing fine-grained global and regional feature representations remains a challenge.…
View article: Benchmarking the translational potential of spatial gene expression prediction from histology
Benchmarking the translational potential of spatial gene expression prediction from histology Open
Spatial transcriptomics has enabled the quantification of gene expression at spatial coordinates across a tissue, offering crucial insights into molecular underpinnings of diseases. In light of this, several methods predicting spatial gene…
View article: International Consensus Recommendations of Diagnostic Criteria and Terminologies for Extranodal Extension in Head and Neck Squamous Cell Carcinoma: An HN CLEAR Initiative (Update 1)
International Consensus Recommendations of Diagnostic Criteria and Terminologies for Extranodal Extension in Head and Neck Squamous Cell Carcinoma: An HN CLEAR Initiative (Update 1) Open
Purpose Extranodal extension (ENE) increases the risk of recurrence and death in head and neck squamous cell carcinoma (HNSCC) patients and is an indication for treatment escalation. Histopathology forms the mainstay of diagnosing ENE. The…
View article: Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels
Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels Open
Summary With the recent advancement in single-cell RNA-sequencing technologies and the increased availability of integrative tools, challenges arise in easy and fast access to large collections of cell atlas. Existing cell atlas portals ra…
View article: IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits Open
Motivation The human gut microbiome, consisting of trillions of bacteria, significantly impacts health and disease. High-throughput profiling through the advancement of modern technology provides the potential to enhance our understanding …