Stanford Advisors

Contact

  • Academic
    jjaa@stanford.edu
    University - Scholar Department: Genetics Position: Postdoctoral Scholar

Additional Info

All Publications

  • DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. Nucleic acids research Thumuluri, V., Almagro Armenteros, J. J., Johansen, A. R., Nielsen, H., Winther, O. 2022

    Abstract

    The prediction of protein subcellular localization is of great relevance for proteomics research. Here, we propose an update to the popular tool DeepLoc with multi-localization prediction and improvements in both performance and interpretability. For training and validation, we curate eukaryotic and human multi-location protein datasets with stringent homology partitioning and enriched with sorting signal information compiled from the literature. We achieve state-of-the-art performance in DeepLoc 2.0 by using a pre-trained protein language model. It has the further advantage that it uses sequence input rather than relying on slower protein profiles. We provide two means of better interpretability: an attention output along the sequence and highly accurate prediction of nine different types of protein sorting signals. We find that the attention output correlates well with the position of sorting signals. The webserver is available at services.healthtech.dtu.dk/service.php?DeepLoc-2.0.

    View details for DOI 10.1093/nar/gkac278

    View details for PubMedID 35489069

  • SignalP 6.0 predicts all five types of signal peptides using protein language models. Nature biotechnology Teufel, F., Almagro Armenteros, J. J., Johansen, A. R., Gislason, M. H., Pihl, S. I., Tsirigos, K. D., Winther, O., Brunak, S., von Heijne, G., Nielsen, H. 1800

    Abstract

    Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data.

    View details for DOI 10.1038/s41587-021-01156-3

    View details for PubMedID 34980915

https://orcid.org/0000-0003-0111-1362