Xuanping Zhang
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View article: TMBocelot: an omnibus statistical control model optimizing the TMB thresholds with systematic measurement errors
TMBocelot: an omnibus statistical control model optimizing the TMB thresholds with systematic measurement errors Open
Tumor mutation burden (TMB), defined as the number of somatic mutations of tumor DNA, is a well-recognized immunotherapy biomarker endorsed by regulatory agencies and pivotal in stratifying patients for clinical decision-making. However, m…
View article: scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum
scMSI: Accurately inferring the sub-clonal Micro-Satellite status by an integrated deconvolution model on length spectrum Open
Microsatellite instability (MSI) is an important genomic biomarker for cancer diagnosis and treatment, and sequencing-based approaches are often applied to identify MSI because of its fastness and efficiency. These approaches, however, may…
View article: TCRcost: a deep learning model utilizing TCR 3D structure for enhanced of TCR–peptide binding
TCRcost: a deep learning model utilizing TCR 3D structure for enhanced of TCR–peptide binding Open
Introduction Predicting TCR–peptide binding is a complex and significant computational problem in systems immunology. During the past decade, a series of computational methods have been developed for better predicting TCR–peptide binding f…
View article: Improved diagnostic efficiency of CRC subgroups revealed using machine learning based on intestinal microbes
Improved diagnostic efficiency of CRC subgroups revealed using machine learning based on intestinal microbes Open
View article: SPAJoint: A Multivariate Saddlepoint Approximation for Time-to- Event and Response Joint Analysis
SPAJoint: A Multivariate Saddlepoint Approximation for Time-to- Event and Response Joint Analysis Open
Time-to-event and response endpoints are typical phenotypes in association studies that often exhibit stochastic correlation within the same individual. However, current analytic methods do not take the inherent correlation into account. S…
View article: DeepLION2: deep multi-instance contrastive learning framework enhancing the prediction of cancer-associated T cell receptors by attention strategy on motifs
DeepLION2: deep multi-instance contrastive learning framework enhancing the prediction of cancer-associated T cell receptors by attention strategy on motifs Open
Introduction T cell receptor (TCR) repertoires provide valuable insights into complex human diseases, including cancers. Recent advancements in immune sequencing technology have significantly improved our understanding of TCR repertoire. S…
View article: An independent evaluation in a CRC patient cohort of microbiome 16S rRNA sequence analysis methods: OTU clustering, DADA2, and Deblur
An independent evaluation in a CRC patient cohort of microbiome 16S rRNA sequence analysis methods: OTU clustering, DADA2, and Deblur Open
16S rRNA is the universal gene of microbes, and it is often used as a target gene to obtain profiles of microbial communities via next-generation sequencing (NGS) technology. Traditionally, sequences are clustered into operational taxonomi…
View article: OCRFinder: a noise-tolerance machine learning method for accurately estimating open chromatin regions
OCRFinder: a noise-tolerance machine learning method for accurately estimating open chromatin regions Open
Open chromatin regions are the genomic regions associated with basic cellular physiological activities, while chromatin accessibility is reported to affect gene expressions and functions. A basic computational problem is to efficiently est…
View article: What makes TMB an ambivalent biomarker for immunotherapy? A subtle mismatch between the sample-based design of variant callers and real clinical cohort
What makes TMB an ambivalent biomarker for immunotherapy? A subtle mismatch between the sample-based design of variant callers and real clinical cohort Open
Tumor mutation burden (TMB) is a widely recognized biomarker for predicting the efficacy of immunotherapy. However, its use still remains highly controversial. In this study, we examine the underlying causes of this controversy based on cl…
View article: DelInsCaller: An Efficient Algorithm for Identifying Delins and Estimating Haplotypes from Long Reads with High Level of Sequencing Errors
DelInsCaller: An Efficient Algorithm for Identifying Delins and Estimating Haplotypes from Long Reads with High Level of Sequencing Errors Open
Delins, as known as complex indel, is a combined genomic structural variation formed by deleting and inserting DNA fragments at a common genomic location. Recent studies emphasized the importance of delins in cancer diagnosis and treatment…
View article: Clinicopathological differences of high Fusobacterium nucleatum levels in colorectal cancer: A review and meta-analysis
Clinicopathological differences of high Fusobacterium nucleatum levels in colorectal cancer: A review and meta-analysis Open
Objective To systematically evaluate the significance of Fusobacterium nucleatum (Fn) levels the clinicopathological impacts of cancer. Methods Literature from Pubmed, Embase, and Web of Science was retrieved to collect all English literat…
View article: HRD-MILN: Accurately estimate tumor homologous recombination deficiency status from targeted panel sequencing data
HRD-MILN: Accurately estimate tumor homologous recombination deficiency status from targeted panel sequencing data Open
Homologous recombination deficiency (HRD) is a critical feature guiding drug and treatment selection, mainly for ovarian and breast cancers. As it cannot be directly observed, HRD status is estimated on a small set of genomic instability f…
View article: TMBcat: A multi-endpoint p-value criterion on different discrepancy metrics for superiorly inferring tumor mutation burden thresholds
TMBcat: A multi-endpoint p-value criterion on different discrepancy metrics for superiorly inferring tumor mutation burden thresholds Open
Tumor mutation burden (TMB) is a widely recognized stratification biomarker for predicting the efficacy of immunotherapy; however, the number and universal definition of the categorizing thresholds remain debatable due to the multifaceted …
View article: PEcnv: accurate and efficient detection of copy number variations of various lengths
PEcnv: accurate and efficient detection of copy number variations of various lengths Open
Copy number variation (CNV) is a class of key biomarkers in many complex traits and diseases. Detecting CNV from sequencing data is a substantial bioinformatics problem and a standard requirement in clinical practice. Although many propose…
View article: AttnTAP: A Dual-input Framework Incorporating the Attention Mechanism for Accurately Predicting TCR-peptide Binding
AttnTAP: A Dual-input Framework Incorporating the Attention Mechanism for Accurately Predicting TCR-peptide Binding Open
T-cell receptors (TCRs) are formed by random recombination of genomic precursor elements, some of which mediate the recognition of cancer-associated antigens. Due to the complicated process of T-cell immune response and limited biological …
View article: A Joint Model Considering Measurement Errors for Optimally Identifying Tumor Mutation Burden Threshold
A Joint Model Considering Measurement Errors for Optimally Identifying Tumor Mutation Burden Threshold Open
Tumor mutation burden (TMB) is a recognized stratification biomarker for immunotherapy. Nevertheless, the general TMB-high threshold is unstandardized due to severe clinical controversies, with the underlying cause being inconsistency betw…
View article: Integration of Protein-Protein Interaction Networks and Gene Expression Profiles Helps Detect Pancreatic Adenocarcinoma Candidate Genes
Integration of Protein-Protein Interaction Networks and Gene Expression Profiles Helps Detect Pancreatic Adenocarcinoma Candidate Genes Open
More and more cancer-associated genes (CAGs) are being identified with the development of biological mechanism research. Integrative analysis of protein-protein interaction (PPI) networks and co-expression patterns of these genes can help …
View article: DeepLION: Deep Multi-Instance Learning Improves the Prediction of Cancer-Associated T Cell Receptors for Accurate Cancer Detection
DeepLION: Deep Multi-Instance Learning Improves the Prediction of Cancer-Associated T Cell Receptors for Accurate Cancer Detection Open
Recent studies highlight the potential of T cell receptor (TCR) repertoires in accurately detecting cancers via noninvasive sampling. Unfortunately, due to the complicated associations among cancer antigens and the possible induced T cell …
View article: Health improvements of type 2 diabetic patients through diet and diet plus fecal microbiota transplantation
Health improvements of type 2 diabetic patients through diet and diet plus fecal microbiota transplantation Open
Type 2 diabetes (T2D) is a major public health problem, and gut microbiota dysbiosis has been implicated in the emergence of T2D in humans. Dietary interventions can indirectly influence the health status of patients with type 2 diabetes t…
View article: Robust Prognostic Subtyping of Muscle-Invasive Bladder Cancer Revealed by Deep Learning-Based Multi-Omics Data Integration
Robust Prognostic Subtyping of Muscle-Invasive Bladder Cancer Revealed by Deep Learning-Based Multi-Omics Data Integration Open
Muscle-invasive bladder cancer (MIBC) is the most common urinary system carcinoma associated with poor outcomes. It is necessary to develop a robust classification system for prognostic prediction of MIBC. Recently, increasing omics data a…
View article: A non-linear ensemble model-based surgical risk calculator for mixed data from multiple surgical fields
A non-linear ensemble model-based surgical risk calculator for mixed data from multiple surgical fields Open
View article: Risk-adjusted zero-inflated Poisson CUSUM charts for monitoring influenza surveillance data
Risk-adjusted zero-inflated Poisson CUSUM charts for monitoring influenza surveillance data Open
View article: OCRDetector: Accurately Detecting Open Chromatin Regions via Plasma Cell-Free DNA Sequencing Data
OCRDetector: Accurately Detecting Open Chromatin Regions via Plasma Cell-Free DNA Sequencing Data Open
Open chromatin regions (OCRs) are special regions of the human genome that can be accessed by DNA regulatory elements. Several studies have reported that a series of OCRs are associated with mechanisms involved in human diseases, such as c…
View article: A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model
A hybrid correcting method considering heterozygous variations by a comprehensive probabilistic model Open
View article: A machine learning framework for genotyping the structural variations with copy number variant
A machine learning framework for genotyping the structural variations with copy number variant Open
View article: A machine learning framework for accurately recognizing circular RNAs for clinical decision-supporting
A machine learning framework for accurately recognizing circular RNAs for clinical decision-supporting Open
View article: A prognostic index based on a fourteen long non-coding RNA signature to predict the recurrence-free survival for muscle-invasive bladder cancer patients
A prognostic index based on a fourteen long non-coding RNA signature to predict the recurrence-free survival for muscle-invasive bladder cancer patients Open
View article: Deep sequencing of circulating tumor DNA detects molecular residual disease and predicts recurrence in gastric cancer
Deep sequencing of circulating tumor DNA detects molecular residual disease and predicts recurrence in gastric cancer Open
View article: Accurately estimating the length distributions of genomic micro-satellites by tumor purity deconvolution
Accurately estimating the length distributions of genomic micro-satellites by tumor purity deconvolution Open
View article: A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data
A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data Open