ArticleBioinformatics (Oxford, England)2023
TSignal: a transformer model for signal peptide prediction.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.
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Who cites it
10 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models.Database : the journal of biological databases and curation · 2025Pooled it
- ViralMap: predicting features in viral proteins from primary sequence.Journal of virology · 2026Article
- Contemporary data-driven innovations in peptide-based therapeutic design.Briefings in bioinformatics · 2026Review
- Graph-Contrastive Convolutional Neural Network for Extracting and Classifying Peptide-Based Periodontal Immunomodulatory and Anti-Inflammatory Signatures.International dental journal · 2026Article
- A Co-attention Mechanism of Jointly Capturing Sequence and Structure Features for Signal Peptide Prediction.Computational and structural biotechnology journal · 2026Article
- Engineering mammalian protein secretion: Toward the convergence of high-throughput biology and computational methods.Cell systems · 2025Review
- Fine-tuning protein language models boosts predictions across diverse tasks.Nature communications · 2024Article
- Improving Signal and Transit Peptide Predictions Using AlphaFold2-predicted Protein Structures.Journal of molecular biology · 2024Article
- SignalP: The Evolution of a Web Server.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Functional Characterization of Eight Zinc Finger Motif-Containing Proteins inPathogens (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationSignal peptides (SPs) are short amino acid segments present at the N-terminus of newly synthesized proteins that facilitate protein translocation into the lumen of the endoplasmic reticulum, after which they are cleaved off. Specific regions of SPs influence the efficiency of protein translocation, and small changes in their primary structure can abolish protein secretion altogether. The lack of conserved motifs across SPs, sensitivity to mutations, and variability in the length of the peptides make SP prediction a challenging task that has been extensively pursued over the years.
resultsWe introduce TSignal, a deep transformer-based neural network architecture that utilizes BERT language models and dot-product attention techniques. TSignal predicts the presence of SPs and the cleavage site between the SP and the translocated mature protein. We use common benchmark datasets and show competitive accuracy in terms of SP presence prediction and state-of-the-art accuracy in terms of cleavage site prediction for most of the SP types and organism groups. We further illustrate that our fully data-driven trained model identifies useful biological information on heterogeneous test sequences. AVAILABILITY AND IMPLEMENTATION: TSignal is available at: https://github.com/Dumitrescu-Alexandru/TSignal.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.