Nicolás López Carranza

This paper introduces InstaNovo-FM, a self-supervised foundation model for proteomics that learns from tandem mass spectra to enable transferable applications across datasets and instruments.

InstaNovo-P improves phosphorylated peptide detection and site localization in phosphoproteomics by using a transformer-based model fine-tuned on phosphoproteomics data.

InstaNovo is a transformer model for de novo peptide sequencing that outperforms existing methods, enabling accurate identification of peptides and discovery of novel sequences and organisms.

The paper introduces the Nucleotide Transformer, a foundation model for genomics, showing it can predict molecular phenotypes from DNA sequences with transfer learning across tasks and organisms.

This paper introduces a large language model for plant genomics that provides state-of-the-art predictions for regulatory annotations and variant prioritization, along with a benchmark dataset for deep learning methods.

FrameDiPT is a diffusion model for protein structure inpainting that recovers masked sections using sequence and structural context, achieving comparable accuracy to existing models with limited data.

LightMHC predicts full-atom pMHC structures from sequences using a lightweight model with attention mechanisms, achieving comparable performance to AlphaFold 2 and ESMFold with faster speed.

A COVID-19 Early Warning System combines structural modelling with machine learning to detect and monitor high risk SARS-CoV-2 variants, identifying all 16 WHO designated variants on average more than one and a half months in advance by selecting on average less than 0.3% of the weekly novel variants.

The paper introduces a graph neural network for peptide-MHC structure prediction, achieving accuracy comparable to AlphaFold 2 with significantly fewer parameters.