A5003337805- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Monoclonal and Polyclonal Antibodies Research
- Single-cell and spatial transcriptomics
- T-cell and B-cell Immunology
- Quantum and electron transport phenomena
- vaccines and immunoinformatics approaches
- Cancer Immunotherapy and Biomarkers
- Genomics and Rare Diseases
- Cancer-related molecular mechanisms research
- Physics of Superconductivity and Magnetism
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Glycosylation and Glycoproteins Research
- Ferroptosis and cancer prognosis
- Quantum Computing Algorithms and Architecture
- Immunotherapy and Immune Responses
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Quantum Information and Cryptography
- Genetic factors in colorectal cancer
- Prostate Cancer Treatment and Research
- Semiconductor Quantum Structures and Devices
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
ShanghaiTech University
2020-2025
Obstetrics and Gynecology Hospital of Fudan University
2023-2024
Center for Excellence in Molecular Cell Science
2020-2023
Chinese Academy of Sciences
2020-2023
University of Chinese Academy of Sciences
2020-2023
UCSC Xena platform provides huge amounts of processed cancer omics data from large research projects (e.g. TCGA, CCLE and PCAWG) or individual groups enables unprecedented opportunities. However, a graphical user interface-based tool for interactively analyzing generating elegant plots is still lacking, especially researchers clinicians with limited programming experience. Here, we present UCSCXenaShiny, an R Shiny package quickly searching, downloading, exploring, visualizing hubs. This...
Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures single base substitution (SBS) have been extensively studied in different types Copy number alterations are important drivers for progression multiple However, practical tools studying copy still lacking. Here, a user-friendly open source bioinformatics tool "sigminer" has constructed signature extraction, analysis and visualization....
Extrachromosomal DNA (ecDNA) is a type of circular and tumor specific genetic element. EcDNA has been reported to display open chromatin structure, facilitate oncogene amplification material unequal segregation, associated with poor cancer patients' prognosis. The ability immune evasion typical feature for progression, however the intrinsic factors that determine remain poorly understood. Here we show presence ecDNA markers evasion, obtaining could be one mechanisms employed by cells escape...
Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools available for signature analysis. However, most them focus on specific type mutation or have limited scope application. A pipeline tool comprehensive analysis is still lacking. Here we present Sigflow pipeline, which provides an one-stop solution de novo extraction, reference fitting, stability analysis, sample...
Copy number alterations (CNAs) are a predominant source of genetic in human cancer and play an important role progression. However comprehensive understanding the mutational processes signatures CNA is still lacking. Here we developed mechanism-agnostic method to categorize based on various fragment properties, which reflect consequences mutagenic can be extracted from different types data, including whole genome sequencing (WGS) single nucleotide polymorphism (SNP) array. The 14 have been...
Summary Copy number alteration (CNA) is a major type of cancer genome that drives progression. CNA signature analysis can reveal underlying etiology and provide biomarkers for treatment, existing analyzes are all performed using bulk tissue samples. However usually affect large proportion genome, the profile sample does not reflect actual profiles individual cells sample, especially in tumors with high heterogeneity, such as hepatocellular carcinoma (HCC). Furthermore, evolutionary...
Abstract DNA methylation analysis has been applied to determine the primary site of cancer; however, robust and accurate prediction cancer types with a minimum number sites is still significant scientific challenge. To build an type tool sites, we internally benchmarked different selection ranking procedures, as well classification models. We used The Cancer Genome Atlas dataset (26 8296 samples) train test models independent (17 2738 for model validation. A deep neural network using...
Abstract Immunoediting includes three temporally distinct stages, termed elimination, equilibrium, and escape, has been proposed to explain the interactions between cancer cells immune system during evolution of cancer. However, status immunoediting in remains unclear, existence neoantigen depletion untreated debated. Here we developed a distribution pattern-based method for quantifying neoantigen-mediated negative selection evolution. The can provide robust reliable quantification signal...
Abstract Homologous recombination deficiency (HRD) renders cancer cells vulnerable to unrepaired double-strand breaks and is an important therapeutic target as exemplified by the clinical efficacy of poly ADP-ribose polymerase (PARP) inhibitors well platinum chemotherapy drugs applied HRD patients. However, it remains a challenge predict status precisely economically. Copy number alteration (CNA), pervasive trait human cancers, can be extracted from variety data sources, including whole...
Introduction: Bronchopulmonary dysplasia (BPD) is a life-threatening lung illness that affects premature infants and has high incidence mortality. Using interpretable machine learning, we aimed to investigate the involvement of endoplasmic reticulum (ER) stress-related genes (ERSGs) in BPD patients. Methods: We evaluated expression profiles immune features bronchopulmonary using GSE32472 dataset. The gene-based molecular clusters associated cell infiltration were studied 62 samples....
Random fluctuations can lead to cooperative effects in complex systems. We here report the experimental observation of noise-induced quantum synchronization a chain superconducting transmon qubits with nearest-neighbor interactions. The application Gaussian white noise single site leads synchronous oscillations entire chain. show that two synchronized end are entangled, nonzero concurrence, and they belong class generalized Bell states known as maximally entangled mixed states, whose...
TCfinder is a tumor cell identification tool, based on pathway activity and deep neural network (DNN). Across different platforms of scRNA-seq datasets, demonstrates robust efficiency. It outperforms existing tools performs under sparse data. freely available as an R package at: https://github.com/XSLiuLab/TCfinder. Traditional RNA sequencing (RNA-seq) bulk tumors only obtains the average information gene expression [1], thus unable to precisely delineate microenvironment infiltrating...
Abstract Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures single base substitution (SBS) have been extensively studied in different types cancer, however, cancer genome copy number (CNA) are still elusive most types, especially prostate (PC), which is particularly driven complex alterations. Here, a user-friendly open source bioinformatics tool “sigminer” has constructed for...
Noncoding DNA sequences occupy more than 98% of the human genome; however, few cancer noncoding drivers have been identified compared with coding drivers, probably because a distinct mutation pattern due to function DNA. Here we performed pan-cancer whole genome analysis screen for functional mutations that influence protein factor binding. Recurrent were in promoter CDC20 gene. These hotspot disrupt binding ELK4 transcription repressor, lead up-regulation transcription. Physiologically...
As the basis for generating multi-particle quantum correlations, inter-particle interaction plays a crucial role in collective phenomena, phase transitions, and information processing. It can profoundly alter band structure of many-body systems give rise to exotic topological phenomena. Conventional pumping, which has been well demonstrated driven linear or noninteracting systems, may break down presence strong interaction. However, interplay between topology could also induce emergent...
Ferroptosis is a recently identified form of cell death that distinct from the conventional modes such as necrosis, apoptosis, and autophagy. Its role in bronchopulmonary dysplasia (BPD) remains inadequately understood. To address this gap, we obtained BPD-related RNA-seq data ferroptosis-related genes (FRGs) GEO database FerrDb, respectively. A total 171 differentially expressed (DE-FRGs) linked to regulation autophagy immune response were identified. Least absolute shrinkage selection...
Superconducting transmon qubits have established as a leading candidate for quantum computation, well flexible platform exploring exotic phases and dynamics. However, physical coupling naturally yields isotropic transverse interactions between qubits, restricting their access to diverse that require spatially dependent interactions. Here, we demonstrate the simultaneous realization of both pairing (XX-YY) hopping (XX+YY) by Floquet engineering. The coherent superposition these enables...
Fock-state lattices (FSLs), composed of photon number states with infinite Hilbert space, have emerged as a promising platform for simulating high-dimensional physics due to their potential extend into arbitrarily high dimensions. Here, we demonstrate the construction multi-dimensional FSLs using superconducting quantum circuits. By controlling artificial gauge fields within internal structures, investigate flux-induced extreme localization dynamics, such Aharonov-Bohm caging, extending from...
Large-scale superconducting quantum computers require massive numbers of high-performance cryogenic low-noise amplifiers (cryo-LNA) for qubit readout. Here we present a C-Band monolithic microwave integrated circuit (MMIC) cryo-LNA this purpose. This is based on 150 nm GaAs pseudomorphic high electron mobility transistor (pHEMT) process and implemented with three-stage cascaded architecture, where the first stage adopts careful impedance match to optimize noise return loss. The integration...
Abstract Immunoediting, which includes three temporally distinct stages, termed elimination, equilibrium, and escape, has been proposed to explain the interactions between cancer cells immune system during evolution of cancer. However status immunoediting in remains unclear, existence neoantigen depletion signal untreated debated. Here we developed a distribution pattern based method for quantifying mediated negative selection evolution. Our provides robust reliable quantification an...
Abstract Copy number alterations (CNAs) are a predominant source of genetic in human cancer and play an important role progression. However comprehensive understanding the mutational processes signatures CNA is still lacking. Here we developed mechanism-agnostic method to categorize based on various fragment properties, which reflect consequences mutagenic can be extracted from different types data, including whole genome sequencing (WGS) SNP array. The 14 have been 2778 pan-cancer analysis...
Supplementary Figure from Quantification of Neoantigen-Mediated Immunoediting in Cancer Evolution
Supplementary Figure from Quantification of Neoantigen-Mediated Immunoediting in Cancer Evolution