A bioinformatical method is only as useful as its accessibility. Therefore, to make our methods, data and algorithms accessible to the scientific community, we produce user-friendly tools and databases. Below, you can find them, in chronological order:
1. GeneCAT (Gene Co-expression Analysis Toolbox). Published in 2008 in Nucleic Acid Research. GeneCAT was the first tool that allowed a comparative co-expression analysis in plants. Retired in 2017 after 10 years of service.
2. PlaNet (Plant Networks, www.gene2function.de). Published in 2011 in Plant Cell, PlaNet allows you to browse and compare co-expression networks of multiple species.
3. FamNet (extension of PlaNet). Published in 2016 in Plant Physiology, FamNet allows you to identify conserved (across species) and duplicated (within species) gene modules.
4. PhyloNet (extension of PlaNet). Published in 2017 in the Plant Journal. The tool combines phylostratigraphic and phylogenetic information with comparative co-expression network analyses to elucidate when gene modules were created and duplicated.
5. BrachyNet (extension of PlaNet). Published in 2017 in New Phytologist. BrachyNet introduces an expression atlas for Brachypodium distachyon, an important model for grasses. We have also introduced an eFP browser for Brachypodium.
6. LSTrAP (Large-Scale Transcriptome Analysis Pipeline). Published in 2017 in BMC Bioinformatics, the tool allows you to produce co-expression networks from RNA sequencing data using a computer cluster.
7. PhytoNet (extension of PlaNet). Published in 2018 in Nucleic Acid Research, this tool introduced comparative co-expression analyses for 10 species of phyto-plankton.
8. CoNekT (Co-expression Network Toolkit, www.conekt.plant.tools). Published in 2018 in Nucleic Acid Research, CoNekT is an open-source platform for comparative co-expression analyses and includes diverse members of the Archaeplastida kingdom. The tool allows you to set up your own PlaNet-like database.
9. EnsembleNet (www.gene2function.de/ensemblenet.html). Published in 2018 in New Phytologist. EnsembleNet provides a powerful ensemble gene function predictions for Arabidopsis thaliana.
10. Malaria.tools (https://malaria.sbs.ntu.edu.sg/). Published in 2019 in Nucleic Acid Research. The database provides comparative genomic and transcriptomic analyses to malaria researchers.
11. LSTrAP-Lite (https://github.com/mutwil/LSTrAP-Lite). Published in 2019 in Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. This collection of scripts is conceptually based on Large-Scale Transcriptome Analysis Pipeline, but is designed to run on a credit card-sized ARM computer.
12. Diurnal.plant.tools (https://diurnal.sbs.ntu.edu.sg/). Published in 2019 in Plant Cell and Physiology, the database provides tools to study the diurnal gene expression in 17 members of Archaeplastida.
13. Fungi.guru (www.fungi.guru). Published in 2020 in Computational and Structural Biotechnology Journal by BS1009 (Introduction to Computational Thinking) students, the database gives access to gene expression and genomic tools for the fungi kingdom.
14. LSTrAP-Kingdom (https://github.com/wirriamm/plants-pipeline). Published in 2021 in Bioinformatics by William Goh, an intern in our group during 2020-2021. The pipeline allows the download, quality control and annotation of gene expression atlases for kingdoms of life.
15. Removal of auto-activators from yeast-two-hybrid assays. Published in 2021 in Scientific Reports by Devendra. We developed an experimental method to remove auto-activators by using a pGAL2-driven URA3, that can be used as a conditional negative selection marker.
16. Bacteria.guru (www.bacteria.guru). We provide a curated gene expression and co-expression database for 17 bacterial pathogens. Published in JMB.
17. Protist.guru (www.protist.guru). Here, we constructed an online database for 17 protists. Published in JMB.
18. FINder database (https://sweekwang.github.io/golabel/) allows you to study which gene features (e.g., protein length, gene family age, maximum expression) are associated. Published in FIPS.
19. LSTrAP-denovo (https://github.com/pengkenlim/LSTrAP-denovo/) is an automated transcriptome assembly pipeline, that makes it easy to obtain gene expression matrices for species without a genome. Published in Physiologia Plantarum.
20. Plant Expression Omnibus (https://expression.plant.tools/) is a new gene expression database that is focused on providing comparative expression tools for hundreds of species. Published in the Plant Journal.
21. PlantConnectome (http://plant.connectome.tools/) contains knowledge graphs representing relationships between genes, metabolites, organs, treatments and other entities. In revision.
22. TEA-GCN: Two-Tier Ensemble Aggregation Gene Co-expression Network (https://github.com/pengkenlim/TEA-GCN) is a new method that achieves state-of-the-art performance in generating co-expression and gene regulatory networks. In review.
1. GeneCAT (Gene Co-expression Analysis Toolbox). Published in 2008 in Nucleic Acid Research. GeneCAT was the first tool that allowed a comparative co-expression analysis in plants. Retired in 2017 after 10 years of service.
2. PlaNet (Plant Networks, www.gene2function.de). Published in 2011 in Plant Cell, PlaNet allows you to browse and compare co-expression networks of multiple species.
3. FamNet (extension of PlaNet). Published in 2016 in Plant Physiology, FamNet allows you to identify conserved (across species) and duplicated (within species) gene modules.
4. PhyloNet (extension of PlaNet). Published in 2017 in the Plant Journal. The tool combines phylostratigraphic and phylogenetic information with comparative co-expression network analyses to elucidate when gene modules were created and duplicated.
5. BrachyNet (extension of PlaNet). Published in 2017 in New Phytologist. BrachyNet introduces an expression atlas for Brachypodium distachyon, an important model for grasses. We have also introduced an eFP browser for Brachypodium.
6. LSTrAP (Large-Scale Transcriptome Analysis Pipeline). Published in 2017 in BMC Bioinformatics, the tool allows you to produce co-expression networks from RNA sequencing data using a computer cluster.
7. PhytoNet (extension of PlaNet). Published in 2018 in Nucleic Acid Research, this tool introduced comparative co-expression analyses for 10 species of phyto-plankton.
8. CoNekT (Co-expression Network Toolkit, www.conekt.plant.tools). Published in 2018 in Nucleic Acid Research, CoNekT is an open-source platform for comparative co-expression analyses and includes diverse members of the Archaeplastida kingdom. The tool allows you to set up your own PlaNet-like database.
9. EnsembleNet (www.gene2function.de/ensemblenet.html). Published in 2018 in New Phytologist. EnsembleNet provides a powerful ensemble gene function predictions for Arabidopsis thaliana.
10. Malaria.tools (https://malaria.sbs.ntu.edu.sg/). Published in 2019 in Nucleic Acid Research. The database provides comparative genomic and transcriptomic analyses to malaria researchers.
11. LSTrAP-Lite (https://github.com/mutwil/LSTrAP-Lite). Published in 2019 in Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. This collection of scripts is conceptually based on Large-Scale Transcriptome Analysis Pipeline, but is designed to run on a credit card-sized ARM computer.
12. Diurnal.plant.tools (https://diurnal.sbs.ntu.edu.sg/). Published in 2019 in Plant Cell and Physiology, the database provides tools to study the diurnal gene expression in 17 members of Archaeplastida.
13. Fungi.guru (www.fungi.guru). Published in 2020 in Computational and Structural Biotechnology Journal by BS1009 (Introduction to Computational Thinking) students, the database gives access to gene expression and genomic tools for the fungi kingdom.
14. LSTrAP-Kingdom (https://github.com/wirriamm/plants-pipeline). Published in 2021 in Bioinformatics by William Goh, an intern in our group during 2020-2021. The pipeline allows the download, quality control and annotation of gene expression atlases for kingdoms of life.
15. Removal of auto-activators from yeast-two-hybrid assays. Published in 2021 in Scientific Reports by Devendra. We developed an experimental method to remove auto-activators by using a pGAL2-driven URA3, that can be used as a conditional negative selection marker.
16. Bacteria.guru (www.bacteria.guru). We provide a curated gene expression and co-expression database for 17 bacterial pathogens. Published in JMB.
17. Protist.guru (www.protist.guru). Here, we constructed an online database for 17 protists. Published in JMB.
18. FINder database (https://sweekwang.github.io/golabel/) allows you to study which gene features (e.g., protein length, gene family age, maximum expression) are associated. Published in FIPS.
19. LSTrAP-denovo (https://github.com/pengkenlim/LSTrAP-denovo/) is an automated transcriptome assembly pipeline, that makes it easy to obtain gene expression matrices for species without a genome. Published in Physiologia Plantarum.
20. Plant Expression Omnibus (https://expression.plant.tools/) is a new gene expression database that is focused on providing comparative expression tools for hundreds of species. Published in the Plant Journal.
21. PlantConnectome (http://plant.connectome.tools/) contains knowledge graphs representing relationships between genes, metabolites, organs, treatments and other entities. In revision.
22. TEA-GCN: Two-Tier Ensemble Aggregation Gene Co-expression Network (https://github.com/pengkenlim/TEA-GCN) is a new method that achieves state-of-the-art performance in generating co-expression and gene regulatory networks. In review.