Publications

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Pre-prints / In revision

*denotes equal contribution; †denotes co-corresponding author

  1. Wacholder, A., Deutsch, E.W., Kok, L.W., van Dinter, J.T., Lee, J., Wright, J.C., Leblanc, S., Jayatissa, A.H., Jiang, K., Arefiev, I., Cao, K., Bourassa, F., Trifiro, F.-A., Bassani-Sternberg, M., Baranov, P.V., Bogaert, A., Fierro-Monti, I., Fijalkowska, D., Gevaert, K., Hubner, N., Mudge, J.M., Ruiz-Orera, J, Schulz, J., Vizcaíno, J.A., Prensner, J.R., Brunet, M.A., Martinez, T.F., Slavoff, S.A., Roucou, X., Choudhary, J.S., van Heesch, S. Carvunis, A.-R. Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment. bioRxiv, 2025.02.19.639069; doi: 10.1101/2025.02.19.639069
  2. Kelly, M.E.*, Hoffner, L.A.*, Ramirez, C.B.*, Anica, A.L., Kim, J., Tong, G., Kim, Y., Choi, W., Jang, K., Alam, Y., Jung, S., Le, J., Lopez, M., Bae, H., Chun, Y., Song, W.-S., Tamburini, I., Martinez, T.F.†, Jang, C.†, Lee, G.† Sex-dependent metabolic remodeling of kidneys revealed by arteriovenous metabolomics. bioRxiv, 2024.09.02.610869; doi: 10.1101/2024.09.02.610869 (2024).
  3. Deutsch, E.W.*, Kok, L.W.*, Mudge, J.M.*, Ruiz-Orera, J., Fierro-Monti, I., Sun, Z., Abelin, J.G., Alba, M.M., Aspden, J.L., Bazzini, A.A., Bruford, E., Brunet, M.A., Calviello, L., Carr, S.A., Carvunis, A.-R., Chothani, S., Clauwaert, J., Dean, K., Faridi, P., Frankish, A., Hubner, N., Ingolia, N., Magrane, M., Martin, M.J., Martinez, T.F., Menschaert, G., Ohler, U., Orchard, S., Rackham, O., Roucou, X., Slavoff, S.A., Valen, E., Wacholder, A.C., Weissman, J.S., Wu, W., Xie, Z., Choudhary, J., Bassani-Sternberg, M., Vizcaino, J.A., Ternette, N., Moritz, R.L. †, Prensner, J.†, van Heesch, S.† High-quality peptide evidence for annotating non-canonical open reading frames as human proteins. bioRxiv, 2024.2009.2009.612016; doi: 10.1101/2024.09.09.612016 (2024).

Peer-reviewed

*denotes equal contribution; †denotes co-corresponding author

  1. Schlesinger, D., Dirks, C., Navarro, C., Lafranchi, L., Spinner, A. Raja, G.L., Tong, G., Eirich, J., Martinez, T.F., Elsässer, S.J. A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness. iScience (2025).
  2. Tong G., Martinez T.F. Ribosome Profiling Reveals Hidden World of Small Proteins. Trends Genet (2025). [Spotlight]
  3. Tong G., Hah N., Martinez T.F. Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq. Brief Bioinform 25(4), bbae268 (2024).
  4. Kelly M.E., Martinez T.F., Jang C. The landscape of fetus metabolism in maternal hyperglycemia. Trends Endocrinol Metab. doi: 10.1016/j.tem.2024.01.012 (2024). [Spotlight]
  5. Cao, K., Heydary Y.H., Tong, G., Martinez, T.F. Integrated workflow for discovery of microprotein-coding small open reading frames. STAR Protoc 4(4), 102649 (2023).
  6. Morgado-Palacin, L.*, Brown, J.A.*, Martinez, T.F., Garcia-Pedrero, J.M., Forouhar, F., Quinn, S.A., Reglero, C., Vaughan, J., Heydary, Y.H., Donaldson, C., Rodriguez-Perales, S., Allonca, E., Granda-Diaz, R., Fernandez, A.F., Fraga, M.F., Kim, A.L., Santos-Juanes, J., Owens, D.M., Rodrigo, J.P., Saghatelian, A. & Ferrando, A.A. The TINCR ubiquitin-like microprotein is a tumor suppressor in squamous cell carcinoma. Nat Commun 14, 1328 (2023).
  7. Martinez, T.F., Lyons-Abbott, S., Bookout, A.L., De Souza, E.V., Donaldson, C., Vaughan,
    J.M., Lau, C., Abramov, A., Baquero, A.F., Baquero, K., Friedrich, D., Huard, J., Davis, R., Kim, B., Koch, T., Mercer, A.J., Misquith, A., Murray, S.A., Perry, S., Pino, L.K., Sanford, C., Simon, A., Zhang, Y., Zipp, G., Bizarro, C.V., Shokhirev, M.N., Whittle, A.J., Searle, B.C., MacCoss, M.J., Saghatelian, A.† & Barnes, C.A.† Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant Small ORFs and Functional Microproteins. Cell Metab 35(1), 166-183 (2023). Press Coverage
  8. Mudge, J.M.†, Ruiz-Orera, J.†, Prensner, J.R.†, Brunet, M.A., Gonzalez, J.M., Magrane, M., Martinez, T.F., Schulz, J.F., Yang, Y.T., Albà, M.M., Baranov, P.V., Bazzini, A., Bruford, E., Martin, M.J., Carvunis, A.-R., Chen, J., Couso, J.P., Flicek, P., Frankish, A., Gerstein, M., Hubner, N., Ingolia, N.T., Menschaert, G., Ohler, U., Roucou, X., Saghatelian, A., Weissman, J. & van Heesch, S.† Standardized Annotation of translated open reading frames. Nat Biotechnol 40, 994-999 (2022). Press Coverage
  9. Koh, M., Ahmad, I., Ko, Y., Zhang, Y., Martinez, T.F., Diedrich, J.K., Chu, Q., Moresco, J.J., Erb, M.A., Saghatelian, A.†, Schultz, P.G.†, Bollong, M.J.† A Short ORF-encoded Transcriptional Regulator. PNAS 118(4), e2021943118 (2021).
  10. Martinez, T.F., Vaughan, J., Saghatelian, A. Insights into GLP-1 Receptor Activation with a Nonpeptide Agonist. Biochemistry 59(16), 1549-1559 (2020). [Viewpoint]
  11. Chen C., Li Y., Jia T., He L., Hare A.A., Silberstein A., Gallagher J., Martinez, T.F., Stiles J.W., Olenyuk B., Dervan P.B., Stiles B.L. Repression of the transcriptional activity of ERRα with sequence-specific DNA-binding polyamides. Med Chem Res. 29, 607-616 (2020).
  12. Martinez, T.F.†, Chu, Q.C., Donaldson C., Tan, D., Shokhirev, M., Saghatelian, A.† Accurate
    Volume 16 Issue 4
    annotation of protein-coding small open reading frames in multiple human cell lines. Nat Chem Biol 16, 458-468 (2019). Press Coverage F1000Prime Recommended Article
  13. Chu, Q., Martinez, T.F., Novak, S.W., Donaldson, C., Tan, D., Vaughan, J.M., Chang, T., Diedrich, J.K., Andrade, L., Kim, A., Zhang, T., Manor, U.†, Saghatelian, A.† Regulation of the ER stress response by a Mitochondrial Microprotein. Nat Commun 10, 4883 (2019).
  14. Choi, S.H., Martinez, T.F., Kim, S., Donaldson, C., Shokhirev, M.N., Saghatelian, A. & Jones, K.A. CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability. Genes Dev 33, 418-435 (2019).
  15. Rathore, A., Martinez, T.F., Chu, Q. & Saghatelian, A. Small, but mighty? Searching for human microproteins and their potential for understanding health and disease. Expert Rev Proteomics 15, 963-965 (2018). [Review]
  16. Rathore, A., Chu, Q., Tan, D., Martinez, T.F., Donaldson, C.J., Diedrich, J.K., Yates, J.R., 3rd & Saghatelian, A. MIEF1 Microprotein Regulates Mitochondrial Translation. Biochemistry 57, 5564-5575 (2018).
  17. Hargrove, A.E., Martinez, T.F., Hare, A.A., Kurmis, A.A., Phillips, J.W., Sud, S., Pienta, K.J. & Dervan, P.B. Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide. PLoS One 10, e0143161 (2015).
  18. Martinez, T.F.*, Phillips, J.W.*, Karanja, K.K., Polaczek, P., Wang, C.M., Li, B.C., Campbell, J.L.† & Dervan, P.B.† Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response. Nucleic Acids Res 42, 11546-59 (2014).
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