We develop databases, tools and algorithms to analyze and visualize large-scale biological data.
Cell Type Reference Database
version 2.1 21 February 2021
A knowledgebase of manually collected, curated and annotated cell types in multiple species with associated protein-protein interaction networks. CellKb allows users to search through published cell type signatures from selected single-cell and bulk RNA-seq experiments.
CellKb v3.0 contains 24,132 signatures of 1,977 cell types from 9 species extracted from 475 publications with 610,407 associated protein-protein interactions.
Cell Type Reference Database of mammalian hematopoietic cell types
version 1.0.1 21 February 2021
A knowledgebase of manually collected, curated and annotated cell types related to the immune system in mouse with associated protein-protein interaction networks. CellKb Immune is a subset of CellKb having the same functionality.
CellKb Immune v1.0.1 contains 1,833 signatures of 203 hematopoietic cell types from mouse extracted from 156 publications with 34,154 associated protein-protein interactions. See Preprint
Protein-protein interactions with reliability scores
version 10.0 3 August 2020
An open-source database of experimentally identified protein-protein interactions collected from literature with reliability scores assigned based on the annotations of the interacting proteins. The first version of HitPredict was released in 2005. The HitPredict service and updates are currently provided through Combinatics.
HitPredict v10.0 contains 815,892 protein-protein interactions between 89,685 proteins from 128 species.
Our goal is to develop reliable databases with advanced search features by extensively curating, integrating, annotating and scoring biological data from literature.
Ashwini Patil, PhD.
Ashwini has over 20 years of research and development experience in computational biology. She is an expert in the development of bioinformatics methods for the analysis and visualization of diverse biological data. Previously, Ashwini was a Lecturer at the University of Tokyo, Japan.
CellKb v2.0.3 release
10 January 2021
A new version of CellKb is up now with cell types from 72 new publications across 9 species. Introducing Consensus Signatures - Search and browse consensus marker gene sets for all cell types calculated from more than 24,000 cell type signatures.TRY IT
CellKb Immune v1.0 release
30 October 2020
Today we are annoucing the release of CellKb Immune, a subset of CellKb containing immune cell types from mouse. CellKb Immune is free for academic users.TRY IT