Wanjun Gu
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View article: Baseline metabolomic profile as potential biomarker for weight change after Roux-en-Y gastric bypass (RYGB) surgery
Baseline metabolomic profile as potential biomarker for weight change after Roux-en-Y gastric bypass (RYGB) surgery Open
Metabolic and bariatric surgery (MBS) is the most effective intervention for sustained weight loss and cardiometabolic improvement in individuals with severe obesity. However, long-term outcomes vary, with many patients experiencing weight…
View article: Integrative taxonomic revision of the Camellia rhytidocarpa complex (Theaceae) synonymous status of C. lipingensis and C. zengii supported by morphological, anatomical, palynological, and molecular evidence
Integrative taxonomic revision of the Camellia rhytidocarpa complex (Theaceae) synonymous status of C. lipingensis and C. zengii supported by morphological, anatomical, palynological, and molecular evidence Open
Background The section Tuberculata (Camellia L.), as a monophyletic group characterized by tuberculate fruits, exhibits persistent taxonomic ambiguities among its constituent species, exemplified by the unresolved delimitation of Camellia …
View article: The identification of a blood circular RNA signature that differentiates Chikungunya virus infection
The identification of a blood circular RNA signature that differentiates Chikungunya virus infection Open
Objective Chikungunya virus (CHIKV) is a re-emerging mosquito-borne human pathogen, which poses critical threats to the public health. However, an effective diagnostic method for early CHIKV infection remains scarce. Circular RNAs (CircRNA…
View article: Mitochondrial genome assembly of the Chinese endemic species of Camellia luteoflora and revealing its repetitive sequence mediated recombination, codon preferences and MTPTs
Mitochondrial genome assembly of the Chinese endemic species of Camellia luteoflora and revealing its repetitive sequence mediated recombination, codon preferences and MTPTs Open
Camellia luteoflora Y.K. Li ex Hung T. Chang & F.A. Zeng belongs to the Camellia L. genus (Theaceae Mirb.). As an endemic, rare, and critically endangered species in China, it holds significant ornamental and economic value, garnering glob…
View article: Distribution Prediction and Adaptability Analysis of Section <i>Camellia</i> Plants (<i>Camellia</i> Genus) in China Based on the <scp>MaxEnt</scp> Model
Distribution Prediction and Adaptability Analysis of Section <i>Camellia</i> Plants (<i>Camellia</i> Genus) in China Based on the <span>MaxEnt</span> Model Open
Sect. Camellia plants, widely distributed across southern China, hold significant economic value through their dual applications in landscape greening, ornamental horticulture, and oilseed production. However, with rapid changes in the glo…
View article: Learning Strategic Language Agents in the Werewolf Game with Iterative Latent Space Policy Optimization
Learning Strategic Language Agents in the Werewolf Game with Iterative Latent Space Policy Optimization Open
Large language model (LLM) agents have recently demonstrated impressive capabilities in various domains like open-ended conversation and multi-step decision-making. However, it remains challenging for these agents to solve strategic langua…
View article: BloodCircR: A Comprehensive Database for Human Peripheral Blood Circular RNAs
BloodCircR: A Comprehensive Database for Human Peripheral Blood Circular RNAs Open
Background: Blood circular RNAs (circRNAs) are stable, noncoding RNAs with diverse functional roles. However, a comprehensive resource for blood-derived circRNAs is lacking. We developed BloodCircR, a database of circRNAs from human periph…
View article: AQUARIUM_HB: a bioinformatics pipeline for human blood circular RNA analysis
AQUARIUM_HB: a bioinformatics pipeline for human blood circular RNA analysis Open
Accurately identifying and quantifying human blood circular RNAs (circRNAs) from RNA-seq data is a critical bioinformatics challenge in biomarker discovery for human diseases. In this study, we present AQUARIUM-HB, a comprehensive bioinfor…
View article: Peripheral blood cellular dynamics during the progression of human tuberculosis
Peripheral blood cellular dynamics during the progression of human tuberculosis Open
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global health challenge. The composition of peripheral blood immune cells offers valuable insights into the progression and management of TB. In this stud…
View article: Predicting the complexity and mortality of polytrauma patients with machine learning models
Predicting the complexity and mortality of polytrauma patients with machine learning models Open
We aim to develop machine learning (ML) models for predicting the complexity and mortality of polytrauma patients using clinical features, including physician diagnoses and physiological data. We conducted a retrospective analysis of a coh…
View article: Identifying Associations between DCE-MRI Radiomic Features and Expression Heterogeneity of Hallmark Pathways in Breast Cancer: A Multi-Center Radiogenomic Study
Identifying Associations between DCE-MRI Radiomic Features and Expression Heterogeneity of Hallmark Pathways in Breast Cancer: A Multi-Center Radiogenomic Study Open
Background: To investigate the relationship between dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) radiomic features and the expression activity of hallmark pathways and to develop prediction models of pathway-level heterog…
View article: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision
Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision Open
The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed by computational detection tools. During the last decade, a plethora of such tools have been developed, but a systematic comp…
View article: Unsupervised Analysis Based on DCE-MRI Radiomics Features Revealed Three Novel Breast Cancer Subtypes with Distinct Clinical Outcomes and Biological Characteristics
Unsupervised Analysis Based on DCE-MRI Radiomics Features Revealed Three Novel Breast Cancer Subtypes with Distinct Clinical Outcomes and Biological Characteristics Open
Background: This study aimed to reveal the heterogeneity of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) of breast cancer (BC) and identify its prognosis values and molecular characteristics. Methods: Two radiogenomics co…
View article: Predicting hormone receptors and PAM50 subtypes of breast cancer from multi-scale lesion images of DCE-MRI with transfer learning technique
Predicting hormone receptors and PAM50 subtypes of breast cancer from multi-scale lesion images of DCE-MRI with transfer learning technique Open
Transfer learning analysis based on DCE-MRI data of tumor and peri-tumor regions was helpful to the non-invasive assessment of molecular characteristics of BC.
View article: Circular <scp>RNAs</scp> in peripheral blood mononuclear cells are more stable than linear <scp>RNAs</scp> upon sample processing delay
Circular <span>RNAs</span> in peripheral blood mononuclear cells are more stable than linear <span>RNAs</span> upon sample processing delay Open
Circular RNAs (circRNAs) are a novel class of RNAs with closed loop structure. Blood circRNAs are widely acknowledged to be more stable than linear mRNAs, which show promising prospect to be liquid biopsy biomarkers for clinical applicatio…
View article: Radiogenomics analysis reveals the associations of dynamic contrast-enhanced–MRI features with gene expression characteristics, PAM50 subtypes, and prognosis of breast cancer
Radiogenomics analysis reveals the associations of dynamic contrast-enhanced–MRI features with gene expression characteristics, PAM50 subtypes, and prognosis of breast cancer Open
Background To investigate reliable associations between dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) features and gene expression characteristics in breast cancer (BC) and to develop and validate classifiers for predictin…
View article: Evolutionary selection on synonymous codons in RNA G-quadruplex structural region
Evolutionary selection on synonymous codons in RNA G-quadruplex structural region Open
In addition to the amino acid sequence information, synonymous codons can encode multiple regulatory and structural signals in protein coding region. In this study, we investigated how synonymous codons have been adapted to the formation o…
View article: The Evolution of G-quadruplex Structure in mRNA Untranslated Region
The Evolution of G-quadruplex Structure in mRNA Untranslated Region Open
The RNA G-quadruplex (rG4) is a kind of non-canonical high-order secondary structure with important biological functions and is enriched in untranslated regions (UTRs) of protein-coding genes. However, how rG4 structures evolve is largely …
View article: The potential of using blood circular RNA as liquid biopsy biomarker for human diseases
The potential of using blood circular RNA as liquid biopsy biomarker for human diseases Open
Circular RNA (circRNA) is a novel class of single-stranded RNAs with a closed loop structure. The majority of circRNAs are formed by a back-splicing process in pre-mRNA splicing. Their expression is dynamically regulated and shows spatiote…
View article: Peer Review #1 of "Identifying disease-associated signaling pathways through a novel effector gene analysis (v0.2)"
Peer Review #1 of "Identifying disease-associated signaling pathways through a novel effector gene analysis (v0.2)" Open
Signaling pathway analysis methods are commonly used to explain biological behaviors of disease cells .Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal signals they r…
View article: Identifying disease-associated signaling pathways through a novel effector gene analysis
Identifying disease-associated signaling pathways through a novel effector gene analysis Open
Background Signaling pathway analysis methods are commonly used to explain biological behaviors of disease cells. Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal sig…
View article: Peer Review #1 of "Identifying disease-associated signaling pathways through a novel effector gene analysis (v0.1)"
Peer Review #1 of "Identifying disease-associated signaling pathways through a novel effector gene analysis (v0.1)" Open
Signaling pathway analysis methods are commonly used to explain biological behaviors of disease cells .Effector genes typically decide functional attributes (associated with biological behaviors of disease cells) by abnormal signals they r…
View article: Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma
Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma Open
Precise biomarker development is a key step in disease management. However, most of the published biomarkers were derived from a relatively small number of samples with supervised approaches. Recent advances in unsupervised machine learnin…
View article: Signaling Pathway Analysis Combined With the Strength Variations of Interactions Between Genes Under Different Conditions
Signaling Pathway Analysis Combined With the Strength Variations of Interactions Between Genes Under Different Conditions Open
Signaling pathway analysis has become a routine task after differentially expressed gene (DEG) studies across disease conditions, drug treatments, or developmental stages. A signaling pathway can be represented by a graph that consists of …