TCellSI is a novel method to evaluate T cell states via transcriptome data, using specific marker gene sets and a compiled reference spectrum. TCellSI calculates T cell state scores for eight states: quiescence, regulating, proliferation, helper, cytotoxicity, progenitor exhaustion, terminal exhaustion, and senescence, offering valuable insights into the immune environment.

Through integrative analysis of immune multiomics data and single-cell RNA-seq data, this study identifies lymphotoxin β receptor (LTBR) as a potential immune checkpoint of tumor-associated macrophages (TAMs). LTBR+ TAMs are associated with lung adenocarcinoma stages, immunotherapy failure, and poor prognosis. Mechanistically, LTΒR maintains TAM immunosuppressive activity and M2 phenotype by noncanonical nuclear factor kappa B and Wnt/β-catenin signaling pathways. Disruption of LTΒR in TAMs enhances the therapeutic effect of cancer immunotherapy.

Microbes play a significant role in human tumor development and profoundly impact treatment efficacy, particularly in immunotherapy. The respiratory tract extensively interacts with the external environment and possesses a mucosal immune system. This prompts consideration of the relationship between respiratory microbiota and lung cancer. Advancements in culture-independent techniques have revealed unique communities within the lower respiratory tract. Here, we provide an overview of the respiratory microbiota composition, dysbiosis characteristics in lung cancer patients, and microbiota profiles within lung cancer. We delve into how the lung microbiota contributes to lung cancer onset and progression through direct functions, sustained immune activation, and immunosuppressive mechanisms. Furthermore, we emphasize the clinical utility of respiratory microbiota in prognosis and treatment optimization for lung cancer.

Hi-C can obtain three-dimensional chromatin structure information and is widely used for genome assembly. We constructed the GutHi-C technology. As shown in the graphical abstract, it is a highly efficient and quick-to-operate method and can be widely used for human, livestock, and poultry gut microorganisms. It provides a reference for the Hi-C methodology of the microbial metagenome. DPBS, Dulbecco's phosphate-buffered saline; Hi-C, high-through chromatin conformation capture; LB, Luria-Bertani; NGS, next-generation sequencing; PCR, polymerase chain reaction; QC, quality control.

The Tumor Immunotherapy Gene Expression R package (tigeR) toolkit provides four distinct yet closely interconnected modules, including the Biomarker Evaluation module, Tumor Microenvironment Deconvolution module, Prediction Model Construction module, and Response Prediction module, to explore biomarkers and construct predictive models via built-in or custom immunotherapy gene expression data. With a comprehensive suite of functionalities, tigeR not only streamlines the analysis process but also catalyzes discoveries in the realm of tumor immunotherapy.

Overview of personalized dietary therapies. This flow chart exhibits the future prospect for integrating human microbiome and bio-medical research to revolutionize the precise personalized dietary therapies. With the development of artificial intelligence (AI), incorporating database may achieve personalized dietary therapies with high precision.

The OmicShare tools platform is a user-friendly online resource for data analysis and visualization, encompassing 161 bioinformatic tools. Users can easily track the progress of projects in real-time through an overview interface. The platform has a powerful interactive graphics engine that allows for the custom-tailored modification of charts generated from analyses. The visually appealing charts produced by OmicShare improve data interpretability and meet the requirements for publication. It has been acknowledged in over 4000 publications and is available in https://www.omicshare.com/tools/.

Fastp is a widely adopted tool for FASTQ data preprocessing and quality control. It is ultrafast and versatile and can perform adapter removal, global or quality trimming, read filtering, unique molecular identifier processing, base correction, and many other actions within a single pass of data scanning. Fastp has been reconstructed and upgraded with some new features. Compared to fastp 0.20.0, the new fastp 0.23.2 is even 80% faster.

Representative visualization results of ImageGP. ImageGP supports 16 types of images and four types of online analysis with up to 26 parameters for customization. ImageGP also contains specialized plots like volcano plot, functional enrichment plot for most omics-data analysis, and other 4 specialized functions for microbiome analysis. Since 2017, ImageGP has been running for nearly 5 years and serving 336,951 visits from all over the world. Together, ImageGP (http://www.ehbio.com/ImageGP/) is an effective and efficient tool for experimental researchers to comprehensively visualize and interpret data generated from wet-lab and dry-lab.

The ggtree object is designed to store phylogenetic tree and associated data, and the object itself is a graphic object that can be rendered as an image file. This work will increase the reproducibility and reusability of phylogenetic data, as well as facilitate integrative and comparative studies.

A new release of PhyloSuite, capable of conducting tree-based analyses. Detailed guidelines for each step of phylogenetic and tree-based analyses, following the “What? Why? and How?” structure. This protocol will help beginners learn how to conduct multilocus phylogenetic analyses and help experienced scientists improve their efficiency.