ArticleNucleic acids research2021
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
- Substrate secretion by different EHEC secretion systems during their interaction with epithelial cells.Virulence · 2026Article
- Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- GeoEPred: A multimodal structure-aware geometric deep learning framework for Gram-negative bacterial secreted effector prediction with sequence semantics.PLoS computational biology · 2026Article
- Article
- DefensePredictor: A machine learning model to discover prokaryotic immune systems.Science (New York, N.Y.) · 2026Article
- MoCETSE: A mixture-of-convolutional experts and transformer-based model for predicting Gram-negative bacterial secreted effectors.PLoS computational biology · 2026Article
- Systematic identification of Salmonella T6SS effectors uncovers diverse new families and lipid-targeting activities.PLoS biology · 2026Article
- PLM-effector: unleashing the potential of protein language models for bacterial secreted protein prediction.Briefings in bioinformatics · 2026Article
- Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.Nature microbiology · 2026Article
- Article
- Machine learning for the prediction of gram-negative bacterial secreted effectors: advances and challenges.Frontiers in chemistry · 2026Review
- A survey of ADP-ribosyltransferase families in the pathogenic Legionella.BMC genomics · 2025Article
- A catalog of proteins released fromMicrobiology spectrum · 2025Article
- The MFα signal sequence in yeast-based protein secretion: challenges and innovations'.Applied microbiology and biotechnology · 2025Review
- Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction.Nature communications · 2025Article
- InTxDB: interaction data between gram-negative bacteria secreted effectors and host proteins.Database : the journal of biological databases and curation · 2025Article
- Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools.Nature microbiology · 2024Article
- T4Seeker: a hybrid model for type IV secretion effectors identification.BMC biology · 2024Article
- Article
- Identification of Parthenogenesis-Inducing Effector Proteins in Wolbachia.Genome biology and evolution · 2024Article
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14 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Gram-negative bacteria utilize secretion systems to export substrates into their surrounding environment or directly into neighboring cells. These substrates are proteins that function to promote bacterial survival: by facilitating nutrient collection, disabling competitor species or, for pathogens, to disable host defenses. Following a rapid development of computational techniques, a growing number of substrates have been discovered and subsequently validated by wet lab experiments. To date, several online databases have been developed to catalogue these substrates but they have limited user options for in-depth analysis, and typically focus on a single type of secreted substrate. We therefore developed a universal platform, BastionHub, that incorporates extensive functional modules to facilitate substrate analysis and integrates the five major Gram-negative secreted substrate types (i.e. from types I-IV and VI secretion systems). To our knowledge, BastionHub is not only the most comprehensive online database available, it is also the first to incorporate substrates secreted by type I or type II secretion systems. By providing the most up-to-date details of secreted substrates and state-of-the-art prediction and visualized relationship analysis tools, BastionHub will be an important platform that can assist biologists in uncovering novel substrates and formulating new hypotheses. BastionHub is freely available at http://bastionhub.erc.monash.edu/.
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