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Up-regulation of IGF2BP2 by multiple mechanisms in pancreatic cancer promotes cancer proliferation by activating the PI3K/Akt signaling pathway
A survey of best practices for RNA-seq data analysis
转录组和代谢组的综合分析揭示 CO2 处理黄瓜的应激反应
肝细胞癌相关成纤维细胞介导癌症进展和影响预后的基因特征的鉴定
环状RNA:潜在的新型miRNA活性调控分子
巨噬细胞M1/M2极化分型的研究进展
基于胆固醇代谢基因探索肝细胞肝癌中不同的肿瘤微环境特征及其预后
佛波酯诱导THP-1分化为M0型巨噬细胞的条件优化
Whole-transcriptome analysis reveals a potential hsa_circ_0001955/hsa_circ_0000977-mediated miRNA-mRNA regulatory sub-network in colorectal cancer
WGCNA: An R package for weighted correlation network analysis
Up-regulation of IGF2BP2 by multiple mechanisms in pancreatic cancer promotes cancer proliferation by activating the PI3K/Akt signaling pathway
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Transcriptome integration analysis and specific diagnosis model construction for Hodgkin's lymphoma, diffuse large B-cell lymphoma, and mantle cell lymphoma
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
TopHat: discovering splice junctions with RNA-Seq
Tools for Sequence-Based miRNA Target Prediction: What to Choose?
TIMER: A web server for comprehensive analysis of tumor-infiltrating immune cells
The Sequence Alignment/Map format and SAMtools
The Current State of Nanoparticle-Induced Macrophage Polarization and Reprogramming Research
The Bioinformatics-Based Analysis Identifies 7 Immune-Related Genes as Prognostic Biomarkers for Colon Cancer
The biochemical basis of microRNA targeting efficacy
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
STAR: ultrafast universal RNA-seq aligner
Single-cell transcriptomics identifies divergent developmental lineage trajectories during human pituitary development
Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection
Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancer
Single-cell RNA sequencing to explore immune cell heterogeneity
Single-Cell RNA Sequencing Resolves Spatiotemporal Development of Pre-thymic Lymphoid Progenitors and Thymus Organogenesis in Human Embryos
Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma
RNAhybrid: microRNA target prediction easy, fast and flexible
RNA-Seq differential expression analysis: An extended review and a software tool
RNA sequencing: the teenage years
rmda: Risk Model Decision Analysis
Quantitative single-cell RNA-seq with unique molecular identifiers
Profiling cell type abundance and expression in bulk tissues with CIBERSORTx
pROC: An open-source package for R and S+ to analyze and compare ROC curves
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling
Prediction of cancer-associated piRNA-mRNA and piRNA-lncRNA interactions by integrated analysis of expression and sequence data
Predicting effective microRNA target sites in mammalian mRNAs
Pleiotrophin promotes vascular abnormalization in gliomas and correlates with poor survival in patients with astrocytomas
piRBase: integrating piRNA annotation in all aspects
piRBase: a comprehensive database of piRNA sequences
Novel pathways of HIV latency reactivation revealed by integrated analysis of transcriptome and target profile of bryostatin
Novel Gene Signature Reveals Prognostic Model in Acute Myeloid Leukemia
Next-generation transcriptome assembly
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
miRWalk: An online resource for prediction of microRNA binding sites
miRDB: an online database for prediction of functional microRNA targets
MicroRNA-7 as a Potential Biomarker for Prognosis in Pancreatic Cancer
MicroRNA targets in Drosophila.
Methods for ChIP-seq analysis: A practical workflow and advanced applications
Maftools: Efficient and comprehensive analysis of somatic variants in cancer
Macrophage plasticity and polarization: in vivo veritas
limma powers differential expression analyses for RNA-sequencing and microarray studies
KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases
Integration of Bioinformatic Predictions and Experimental Data to Identify circRNA-miRNA Associations
Integrated bioinformatics analysis reveals marker genes and potential therapeutic targets for pulmonary arterial hypertension
In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse
Implications of macrophage polarization in autoimmunity
Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression
Identifying Potential Diagnostic Genes for Diabetic Nephropathy Based on Hypoxia and Immune Status
Identification of the circRNA-miRNA-mRNA regulatory network and its prognostic effect in colorectal cancer
Identification of Potential ceRNA Network and Patterns of Immune Cell Infiltration in Systemic Sclerosis-Associated Interstitial Lung Disease
Identification of hub ubiquitin ligase genes affecting Alzheimer’s disease by analyzing transcriptome data from multiple brain regions
Identification of Differentially Expressed Circular RNAs as miRNA Sponges in Lung Adenocarcinoma
Identification of circRNA-miRNA-mRNA regulatory network in gastric cancer by analysis of microarray data
Identification of a competing endogenous RNA network associated with prognosis of pancreatic adenocarcinoma
Identification and Validation of a Novel DNA Damage and DNA Repair Related Genes Based Signature for Colon Cancer Prognosis
Identification and external validation of a prognostic signature associated with DNA repair genes in gastric cancer
Human MicroRNA Targets
Hsa_circ_0004831 serves as a blood-based prognostic biomarker for colorectal cancer and its potentially circRNA-miRNA-mRNA regulatory network construction
GSVA: Gene set variation analysis for microarray and RNA-Seq data
GSVA: gene set variation analysis
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Glycation of macrophages induces expression of pro-inflammatory cytokines and reduces phagocytic efficiency
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Fast and effective prediction of microRNA/target duplexes
Fast and accurate short read alignment with Burrows-Wheeler transform
Exploration of the immune-related signature and immune infiltration analysis for breast ductal and lobular carcinoma
Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data
Dimensionality reduction by UMAP to visualize physical and genetic interactions
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
DIANA-miRPath v3.0: deciphering microRNA function with experimental support
Cytotherapy with M1-polarized macrophages ameliorates liver fibrosis by modulating immune microenvironment in mice
Current best practices in single‐cell RNA‐seq analysis: a tutorial
Coupling mRNA processing with transcription in time and space
Construction of the circRNA-miRNA-mRNA Regulatory Network of an Abdominal Aortic Aneurysm to Explore Its Potential Pathogenesis
Construction of circRNA-Based ceRNA Network to Reveal the Role of circRNAs in the Progression and Prognosis of Hepatocellular Carcinoma
Computational methods for transcriptome annotation and quantification using RNA-seq
Comprehensive analyses of tumor immunity: Implications for cancer immunotherapy
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data
circRNA-miRNA-mRNA调控网络在非小细胞肺癌诊断、预后及治疗抵抗中的研究进展
Circbank: a comprehensive database for circRNA with standard nomenclature
Cancer Statistics, 2021
Beyond bulk: a review of single cell transcriptomics methodologies and applications
Automated methods for cell type annotation on scRNA-seq data
A survey of best practices for RNA-seq data analysis
A benchmark of batch-effect correction methods for single-cell RNA sequencing data