Research

Origins of Neurotransmission

Neurons are built from parts that are older than neurons. We trace the enzymes, vesicular transporters and receptors of chemical neurotransmission across animals, fungi and their unicellular relatives, to find when each part appeared and what it did before there were synapses.

Monoamine synthesis and vesicular transporters’ orthologs are present in fungi, where they sit in the endolysosomal system and modulate secondary metabolism. In sponges and cnidarians, acetylcholine and the monoamines are made by broad-specificity enzymes and expressed in neuronal and non-neuronal cells alike. Specialization into the dedicated transmitter systems of bilaterians came later, through gene duplication.

• Monoamines
• Acetylcholine
• Opisthokonta
• Phylogenetics
• Metabolomics

Cell Type Evolution

We compare single-cell transcriptomic atlases across animals to trace the evolutionary history of cell types. Gene families with well-resolved phylogenies act as markers: where their members are expressed, and with what, tells us how cell identities were assembled and later split.

In cnidarians, for example, muscle-type nicotinic receptor subunits are co-expressed with Rapsyn-related genes in muscle cells, placing cholinergic neuromuscular signaling in the cnidarian–bilaterian ancestor.

• Cell atlases
• scRNA-seq
• Neuronal origins
• Comparative transcriptomics

Olfactory System Evolution

Olfactory receptors are the largest gene family devoted to a single function in animals, and each odorant is read by a combination of them. We ask how this combinatorial code was first assembled and how gene duplication reshaped it.

Combining phylogenetics, receptor–odorant interactions predicted with paired protein and chemical language models, and ancestral sequence reconstruction, we place the origin of the code at the first duplication of the family, in the gnathostome ancestor, where the two copies diverged into distinct chemical subspaces.

• Olfactory receptors
• GPCRs
• Ancestral reconstruction
• Protein language models

Glutamate Signaling Evolution

Glutamate is the main excitatory neurotransmitter of vertebrate nervous systems, acting through both ionotropic and metabotropic receptors. We trace the evolutionary history of these receptor families across the tree of life.

By combining protein domain phylogenetics with single-cell expression data, we investigate how glutamate receptor families diversified and how their expression is partitioned among cell types and species.

• iGluRs
• mGluRs
• Domain evolution
• Cross-species expression

Comparative Genomics Tools

We build tools that make comparative genomics usable without code. KEDROS builds gene trees for any protein family across UniProt reference proteomes, splits them into subfamilies at gene duplications, and profiles each subfamily across organism sets chosen by the user — from lineage-specific genes down to the residues that separate them.

• Phylogenetic profiling
• Gene trees
• Web server