Thomas Farid Martinez

The paper compares primary and liver PDAC lesions using single-cell transcriptomics to identify MET as a target in pancreatic cancer metastasis.

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.

The paper identifies NISM, a microprotein encoded by HDAC5, which regulates nucleolar formation and rRNA synthesis by modulating DHX9 activity and phase separation.

This study identifies mevalonate biosynthesis as a therapeutic target and biomarker for gemcitabine-resistant pancreatic cancer.

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.

The paper assesses MS-based identifications of unannotated human microproteins, finding large variation in reported proteins and PSM quality across studies.

The paper performs a CRISPR/Cas9 screen of sORFs to identify microproteins involved in cancer cell growth, finding several candidates with functional roles and localization data.

This study identifies sex-dependent metabolic differences in kidneys using arteriovenous metabolomics and transcriptomics, revealing distinct metabolic responses to a ketogenic diet.

The paper compares Ribo-seq analysis tools for detecting translated small open reading frames, finding low agreement and tool-specific biases.

The paper identifies and characterizes small ORFs and microproteins in adipose cells, showing their metabolic relevance and potential roles in obesity and inflammation.

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

The paper improves smORF annotation by integrating de novo transcriptome assembly and Ribo-Seq, identifying thousands of novel translated smORFs in human cell lines and highlighting their functional potential.