ncRNA Database
A Database for Functional Circular RNAs
PceRBase: Plant Competing Endogenous RNA DataBase
PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks
Manually Curated Database of Experimentally Validated Stress-Responsive Non-coding RNAs in Plants
The Leaf Circular RNA Resources
Arabidopsis thaliana ncRNA coding potential database
A comprehensive compilation of 233 databases/webservers/tools catering to 46 types of ncRNAs.
A plant ncRNA database with potential ncPEP information and cell type-specific interaction
Plant Database
Comprehensive regulatory database on Oryza Sativa based on genome annotation.
A Comprehensive Resource Database for Caragana korshinskii genomics.
An integrated omics database for soybean germplasm and molecular breeding
iP3Dome: an interactive Plant 3D genome portal
A comprehensive physiological traits database covers multiple significant crops
Plant Stress Gene Database (PSGDb) is a comprehensive database resource of providing important annotation information about stress genes existed in plant.
Disease Database
To tide over COVID-19, the web portal OverCOVID is provided to share bioinformatics resources and information that may contribute to research advances.
Neurodegenerative Disease Atlas (NDAtlas) is a database for the collective information of the proteins involved in NDs, the related PPIs, and interactive visualizations.
LBD (Lymphoma Biomarker Database) is a manually curated database of literature-supported biomarkers for lymphoma.
Human aging and longevity database
Single Cell Atlas
Cell Landscape is a database of single cell RNA sequencing atlas from multiple species. Click “Browse” on the top of the homepage to get an overview of this website.
This is a single cell browser for exploration of gene and transposable element (TE) activities during the endothelial-to-hematopoietic transition (EHT) in human and mouse.
This database exhaustively collects hematopoiesis-related single-cell sequencing data to provide an easily accessible resource for in-depth understanding of the complexity of the origin and development of hematopoietic system
MCA is a public database that uses single-cell RNA sequencing to determine the cell type composition of mouse major organs and build mouse cell Atlas.
HCL is a public databases used single-cell RNA sequencing to determine the cell type composition of major human organs and construct a basic scheme for the human cell landscape.
Using HH-seq to construct a single-cell transcriptome database covering major cancers with high morbidity and mortality in China.
ACA is a publlic database used single-cell RNA sequencing to determine the cell type composition of Axolotl and construct a basic scheme for the Axolotl cell Atlas.
Cell Landscapes for Zebrafish, Drosophila, and Earthworm.
Using CH-ATAC-seq to profile chromatin accessibility landscapes in vertebrates and invertebrates.
Landscape of cell-type-specific genetic variation of gene regulation.
We used single-cell RNA sequencing to determine the cell type composition of Drosophila and construct a basic scheme for the Drosophila cell landscape (DCL).
Web-based resources for Zebrafish Cell Landscape. We used single-cell RNA sequencing to determine the cell type composition of major zebrafish organs and construct a basic scheme for the Zebrafish Cell Landscape (ZCL).
A developmental single-cell Basic Local Alignment Search Tool.The dscBLAST is particularly better at developmental data, and it also performs very well on adult data.
A Earthworm cell landscape (ECL) websit.We used single-cell RNA sequencing to determine the cell type composition of Earthworm and construct a basic scheme for the Earthworm cell landscape (ECL).
Tools
An integrated tool to detect circRNAs and interactions with miRNAs in plants
CircPro: an integrated tool for the identification of circRNAs with protein-coding potential
Tool for large-scale identifiction of the new microRNA genes by screening the cleavage signals resided within the genome.
sRNA analysis tool
A web-based toolkit for automatic computation and evaluation of cytometry data.
Based on the clonal evolution theory, we construct a deliberately simplified model to simulate tumor progressionBased on the clonal evolution theory, we construct a deliberately simplified model to simulate tumor progression.
Antigenic variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization
PBSK Browser for systems biology is a web service for reading some standard file formats of biological pathway, including PSI-MI, BioPAX, SBML and KGML.
A gene composer software that optimizes coding sequences and calculates corresponding RiPS to illustrate their translation rates
MTide: an integrated tool for the identification of miRNA-target interaction in plants
An R package for position effect comparison on short oligonucleotide microarrays
A deep learning frame for predicting subcellular localization information of lncRNA and miRNA
A ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks
A bioinformatic tool which quantifies the sequence repetitiveness based on weighted k-mer coverage
A unified T4SE prediction pipeline based on deep learning model
An R package for constructing gene regulatory networks from microarray data using Bayesian network
An updated version for cloning primer design with significantly expanded utilities
DaTo: The atlas of biological database and Tools
RNAret: RNA Language Model based on Retentive Network.
Other Database
A Predicted Trichoderma reesei Interactome Network
BioPepDB is a searchable database of food-derived bioactive peptides and their related articles, including more than four thousand bioactive peptide entries.
A database of anticancer peptides, searchable by peptide name, uniprot ID, cancer type, origin and sequence.
An Integrative Database for Cell Signal Transduction Classification Alignment
Education
An online programming platform designed for bioinformatics programming enthusiasts and learners.
Collections of various biology databases and tools
A practical SCI IF Search Engine
教育部生物科学“101计划”生物信息学核心课程及虚拟教研室建设平台
PlncRNADB: Repository of lncRNAs in Plant