Biology subjects

Schaffer, L.

Publications and source records attributed to Schaffer, L..

2 recordsLinked to original sources

bioRxiv2025

Loss of the cytosolic DNA-sensing genes cGAS and STING1 inarmadillos (Cingulata)

The principal sensor of intracellular double-stranded DNA (dsDNA) is cyclic GMP-AMP synthase (CGAS), which generates the second messenger cyclic GMP-AMP that binds stimulator of interferon genes (STING1), leading to the expression of type I interferon genes. CGAS and STING1 also play essential roles in maintaining genome integrity and the initiation and progression of cancer. Here we show that CGAS and STING1 were pseudogenized in the ancestral armadillo branch 45 to 70 million years ago. The complete loss of the CGAS-STING1 pathway in armadillos suggests this lineage has evolved alternate ways to sense intracellular double-stranded DNA, which may be related to their extreme cancer resistance.

evolutionary biology↗

bioRxiv2025

An adversarial scheme for integrating multi-modal data on protein function

In order to begin to decipher the structure of the cell, we need to integrate multiple types of data of different scales on subcellular organization. Such integration requires dealing with multiple data modalities and with missing data. To this end, we developed MIRAGE, a multi-modal generative model for integrating protein sequence, protein-protein interaction and protein localization data. Our approach successfully learns a joint embedding space that captures the complex relationships between these diverse modalities. We evaluate our models performance against existing methods, obtaining superior performance in several key tasks, including protein function prediction and module detection. MIRAGE source code is available at https://github.com/raminass/MIRAGE.

bioinformatics↗