Research
Bioinformatics & Open Tools
The Kaplan Lab has a strong commitment to open science and has developed a suite of freely available bioinformatics resources used by cilia and rare disease researchers worldwide. Our tools span gene prediction, variant interpretation, database curation, and cell-type classification — together forming a comprehensive computational infrastructure for the ciliopathy research community.
Our bioinformatics philosophy
We build tools we need ourselves, then release them openly. Every resource listed below emerged from a concrete research problem in the lab — the absence of a comprehensive ciliary gene catalogue, the difficulty of matching patient variants to model organisms, the lack of a cell-type atlas for ciliation status. By making these tools public, we aim to accelerate the broader rare disease community's ability to interpret genomic data.
Tools & databases
A curated, continuously updated database of all experimentally confirmed ciliary genes — an evolution of the original ciliary Gold Standard list. Each entry includes gene description, synonyms, subcellular localisation, OMIM disease links, and key references. Used by researchers worldwide to classify candidate genes from sequencing studies.
A cilia cell atlas classifying 359 human cell types by ciliation status across 13 organ systems. Enables researchers to rapidly determine whether a cell type of interest is ciliated, the cilia subtype present, and which diseases are associated with that cilia type. Built from systematic literature curation.
An integrated method and database for predicting novel ciliary genes by integrating co-expression networks, protein–protein interactions, evolutionary signatures, and proximity to known ciliary loci. Published in Nucleic Acids Research (2024) and shown to recover known ciliary genes with high precision while predicting new candidates.
An interactive bioinformatics platform for exploring gene–disease associations in ciliopathies. Allows users to browse ciliopathy genes, their associated syndromes, model organism data, and expression patterns in a single unified interface. Published in Database (Oxford) (2023).
A search engine for matching human missense variants to equivalent positions in non-human model organisms including C. elegans, zebrafish, and mouse. Helps identify whether a candidate human VUS has a functional counterpart with existing experimental data, dramatically speeding up variant prioritisation. Published in Nucleic Acids Research (2022).
A dynamic, fast JavaScript tool for visualising multiple sequence alignments, variations, and annotations directly in the browser — no server or installation required. Useful for inspecting conservation at patient variant positions across species. Published in Bioinformatics Advances (2021).
GitHub & open code
All tool source code, analysis pipelines, and protocols are available on GitHub under open licences. We maintain two organisations: github.com/thekaplanlab (tools and pipelines) and github.com/rarediseaselab (website and databases).