https://alirezaomidi.github.io Ph.D. candidate in Bioinformatics at UBC, focusing on protein design and AI applications in drug discovery. en-us https://alirezaomidi.github.io/blog/de-novo-design-of-protein-switches-with-diffusion-based-ensemble-sampling https://alirezaomidi.github.io/blog/de-novo-design-of-protein-switches-with-diffusion-based-ensemble-sampling Diff-Switch samples switch-like backbone ensembles from pretrained protein diffusion models to design de novo protein switches Tue, 21 Jul 2026 00:00:00 GMT https://alirezaomidi.github.io/blog/insulin-receptor-trafficking-and-interactions-in-muscle-cells https://alirezaomidi.github.io/blog/insulin-receptor-trafficking-and-interactions-in-muscle-cells Mapping how the insulin receptor internalizes in muscle cells, and the CAV1- and clathrin-dependent pathways it uses Wed, 28 Jan 2026 00:00:00 GMT https://alirezaomidi.github.io/blog/predicting-protein-interfaces-in-the-age-of-alphafold-why-dynamics-and-disorder-remain-a-challenge https://alirezaomidi.github.io/blog/predicting-protein-interfaces-in-the-age-of-alphafold-why-dynamics-and-disorder-remain-a-challenge A perspective on why protein dynamics matter for interface prediction and how two Cell Systems studies advance the field Wed, 21 Jan 2026 00:00:00 GMT https://alirezaomidi.github.io/blog/challenging-alphafold-in-predicting-proteins-with-large-scale-allosteric-transitions https://alirezaomidi.github.io/blog/challenging-alphafold-in-predicting-proteins-with-large-scale-allosteric-transitions Our research on benchmarking AlphaFold2, AlphaFold3, and recent variants on autoinhibited proteins Wed, 26 Nov 2025 00:00:00 GMT https://alirezaomidi.github.io/blog/integration-and-querying-of-multimodal-single-cell-data-with-poe-vae https://alirezaomidi.github.io/blog/integration-and-querying-of-multimodal-single-cell-data-with-poe-vae Our research on integrating multimodal single-cell data using product-of-experts VAE Fri, 25 Apr 2025 00:00:00 GMT https://alirezaomidi.github.io/blog/alphafold-multimer-accurately-captures-interactions-and-dynamics-of-intrinsically-disordered-protein-regions https://alirezaomidi.github.io/blog/alphafold-multimer-accurately-captures-interactions-and-dynamics-of-intrinsically-disordered-protein-regions Our research on AlphaFold-Multimer's capabilities in predicting IDR interactions Thu, 24 Oct 2024 00:00:00 GMT https://alirezaomidi.github.io/blog/multimodal-weakly-supervised-learning-to-identify-disease-specific-changes-in-single-cell-atlases https://alirezaomidi.github.io/blog/multimodal-weakly-supervised-learning-to-identify-disease-specific-changes-in-single-cell-atlases Our research on identifying disease-specific changes in single-cell data using multimodal learning Mon, 29 Jul 2024 00:00:00 GMT https://alirezaomidi.github.io/blog/learning-cancer-progression-network-from-mutation-allele-frequencies https://alirezaomidi.github.io/blog/learning-cancer-progression-network-from-mutation-allele-frequencies Our research on modeling cancer progression using mutation allele frequencies Fri, 17 Jul 2020 00:00:00 GMT