Jim Clauwaert

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

An expanded reference catalog of translated open reading frames for biomedical research

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

Deep learning to decode sites of RNA translation in normal and cancerous tissues

This paper introduces RiboTIE, a transformer model for mapping RNA translation, showing high precision and sensitivity in normal and cancerous tissues.

RIBO-former: leveraging ribosome profiling information to improve the detection of translated open reading frames.

RIBO-former improves translated open reading frame detection using ribosome profiling data and transformer models, outperforming existing methods and identifying non-canonical ORFs and polycistronic mRNAs.

TIS transformer: Remapping the human proteome using deep learning

The paper introduces TIS Transformer, a deep learning model that improves the mapping of translation initiation sites in the human proteome by analyzing transcript sequences.

CpG Transformer for imputation of single-cell methylomes

The paper introduces CpG Transformer, a model for imputing single-cell methylomes, achieving state-of-the-art performance on scBS-seq and scRRBS-seq datasets.

Novel transformer networks for improved sequence labeling in genomics

The paper introduces transformer networks for sequence labeling in genomics, achieving state-of-the-art performance on tasks like transcription start site annotation in E. coli.

Explainable Transformer Models for Functional Genomics in Prokaryotes

This paper introduces transformer-based models for prokaryotic genome annotation and shows that attention heads specialize in identifying DNA binding sites.

DeepRibo: precise gene annotation of prokaryotes using deep learning and ribosome profiling data

DeepRibo uses deep learning and ribosome profiling data to accurately annotate gene expression in prokaryotes, outperforming traditional methods.