Publications

We have developed GCAP, a machine-learning-based method for the identification ecDNA from the WES dataset. With GCAP, we profiled ecDNA features in more than 13000 tumor samples. We further provide evidence that ecDNA can be promising biomarker for ICI treatment in GI cancers.

In this study, we introduce BioTreasury (http://biotreasury.rjmart.cn), an integrated community-based repository that provides an interactive platform for users and developers to share their experiences in various bioinformatics tools. BioTreasury offers a comprehensive collection of well-indexed bioinformatics software, tools, and databases, totaling over 10,000 entries. In the past two years, we have continuously improved and maintained BioTreasury, adding several exciting features, including creating structured homepages for every tool and user, a hierarchical category of bioinformatics tools and classifying tools using large language model (LLM). BioTreasury streamlines the tool submission process with intelligent auto-completion. Additionally, BioTreasury provides a wide range of social features, for example, enabling users to participate in interactive discussions, rate tools, build and share tool collections for the public.

We performed whole-exome sequencing on tumor samples from 486 patients of the JUPITER-06 study and develop a copy number alteration-corrected tumor mutational burden that depicts immunogenicity more precisely and predicts chemo+anti-PD-1 efficacy. An esophageal cancer genome-based immuno-oncology classification (EGIC) scheme incorporating these immunogenic features and oncogenic alterations is established. EGIC may guide future individualized treatment strategies and inform mechanistic biomarker research for chemo+anti-PD-1 treatment in patients with advanced ESCC.

VSOLassoBag is a variable-selection oriented LASSO bagging algorithm for biomarker development in omic-based translational research, providing a bagging LASSO framework for selecting important variables from multiple models. In this package, we introduced several methods, namely (1) curve elbow point detection, (2) parametrical statistical test and (3) permutation test to help determine the cut-off point for variables selection.

We developed a practical computational framework for comprehensively exploring the MPT from multiregion sequencing (MRS) experiments.To verify the utility of MPTevol, we performed whole-exome MRS for 33 samples of a rare patient with triple-primary tumors and three metastatic sites and systematically investigated clonal dynamics and metastatic routines.

We perform ultradeep whole-exome sequencing on 1015 patients with CRC as part of the ChangKang Project. we find that mitochondrial DNA copy number is an independent factor for predicting the survival outcome of CRCs. Overall, our results provide CRC-related molecular features for clinical practice and a valuable resource for translational research.

We present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS.

In this work, through transcriptomic profiling analysis of 21 paired tumor and normal samples, we identified a novel colorectal cancer–related lncRNA, MNX1-AS1.

In this work, we reviewed current Genetic and Epigenetic Biomarkers of Prognostic and Predictive Significance in Stage II/III Colorectal Cancer"

In this study, transcriptomic aberrance and immune microenvironment of small‐cell carcinoma of the esophagus (SCCE) was comprehensively characterized with transcriptome and immunohistochemistry analysis. Assessment of immune checkpoint blockade (ICB) treatment biomarkers provides a rationale for use of ICB treatment in patients with SCCE.