Software and Methods

Our lab has a special focus on developing open-source software tools, computational methods, databases and cloud-based tools that solve data analysis challenges of wide interest.  

Software – Cloud-based tool

GeneCloudOmics

An easy-to-use web server for high-throughput gene expression analysis a comprehensive range of data analytics tools in one package that no other current standalone software or web-based tool can do currently

Software

openPIP

The Open-source Protein Interaction Platform a customizable web portal designed to host experimental PPI maps.

OpenPIP has been used to build the databases and web portals of two major protein interactome maps, the Human and Yeast Reference Protein Interactome maps (HuRI and YeRI, respectively).


Database

Oryza-PG DB

OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. The database was retired after 10 years and all the data is available on the GitHub repo of the project.

DATABASE

PRM-DB

The peptide recognition modules database  combined data for the large SH3, PDZ, and WW domain families and containing 7,984 unique peptide ligands for 500 PRMs representing 82 structural families.