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Thomas Farid Martinez

Title(s)Assistant Professor, Pharmaceutical Sciences
SchoolSchool of Pharmacy and Pharmaceutical Sciences
Address101 Theory, Suite 100
Irvine CA 92697-3958
Phone(949) 824-0943
ORCID ORCID Icon0000-0002-4011-8164 Additional info
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    Collapse Biography 
    Collapse education and training
    Massachusetts Institute of Technology, Cambridge, MABS06/2009Biological Engineering
    California Institute of Technology, Pasadena, CAPh.D.07/2015Biochemistry & Molecular Biophysics
    Salk Institute of Biological Studies, La Jolla, CA08/2021Peptide Biology

    Collapse Research 
    Collapse research activities and funding
    The Roles of a Novel Microprotein in Wound Healing and Cancer
    NIH K01CA249038Sep 1, 2021 - Aug 31, 2026
    Role: Principal Investigator
    An Integrative Approach for the Annotation of Functional smORFs
    NIH F32GM123685Apr 1, 2017 - Mar 31, 2019
    Role: Principal Investigator
    Interrogation of Androgen Receptor:Forkhead Interaction Using Py-Im Polyamides
    NIH F31CA159896Sep 1, 2011 - Aug 31, 2016
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Comparative Analysis of Primary and Liver Fibroblasts Reveals MET as a Potent Target in Pancreatic Cancer Metastasis. bioRxiv. 2025 Sep 11. Singh R, Yousefian N, Allen WM, Anaraki C, Beutel AK, Calderon S, Loveless IM, McDonald OG, Morton JP, Imagawa D, Jutric Z, Martinez TF, Steele NG, Halbrook CJ. PMID: 40964260; PMCID: PMC12440037.
      View in: PubMed   Mentions:
    2. Translon: a single term for translated regions. Nat Methods. 2025 Sep 01. Swirski MI, Tierney JAS, Albà MM, Andreev DE, Aspden JL, Atkins JF, Bassani-Sternberg M, Berry MJ, Biffo S, Boris-Lawrie K, Borodovsky M, Brierley I, Brook M, Brunet MA, Bujnicki JM, Caliskan N, Calviello L, Carvunis AR, Cate JHD, Cenik C, Chang KY, Chen Y, Chothani S, Choudhary JS, Clark PL, Clauwaert J, Cooley L, Dassi E, Dean K, Diaz JJ, Dieterich C, Dikstein R, Dinman JD, Dmitriev SE, Dontsova OA, Dunham CM, Eswarappa SM, Farabaugh PJ, Faridi P, Fierro-Monti I, Firth AE, Gatfield D, Gebauer F, Gelfand MS, Gray NK, Green R, Hill CH, Hou YM, Hübner N, Ignatova Z, Ivanov P, Iwasaki S, Johnson R, Jomaa A, Jovanovic M, Jungreis I, Kellis M, Kieft JS, Kochetov AV, Koonin EV, Korostelev AA, Kufel J, Kulakovskiy IV, Kurian L, Lafontaine DLJ, Larsson O, Loughran G, Lukeš J, Mariotti M, Martens-Uzunova ES, Martinez TF, Matsumoto A, McManus J, Medenbach J, Melnikov SV, Menschaert G, Merchante C, Mikl M, Miller WA, Mühlemann O, Namy O, Nedialkova DD, Nosek J, Orchard S, Ozretic P, Pertea M, Pervouchine DD, Romão L, Ron D, Roucou X, Rubtsova MP, Ruiz-Orera J, Saghatelian A, Salzberg SL, Seale LA, Seoighe C, Sergiev PV, Shah P, Shirokikh N, Slavoff SA, Sonenberg N, Stasevich TJ, Szczesny RJ, Tamm T, Tchórzewski M, Topisirovic I, Tremblay ML, Tuller T, Ulitsky I, Valášek LS, Van Damme P, Viero G, Vizcaino JA, Vogel C, Wallace EWJ, Weissman JS, Westhof E, Whiffin N, Wilson DN, Xie Z, Yewdell JW, Yordanova MM, Yu CH, Yurchenko V, Zagrovic B, TRANSLACORE, Valen E, Baranov PV. PMID: 40890551.
      View in: PubMed   Mentions:    Fields:    
    3. An expanded reference catalog of translated open reading frames for biomedical research. bioRxiv. 2025 Jul 07. Chothani S, Ruiz-Orera J, Tierney JAS, Clauwaert J, Deutsch EW, Alba MM, Aspden JL, Baranov PV, Bazzini AA, Bruford EA, Brunet MA, Cardon T, Carvunis AR, Casola C, Choudhary JS, Dean K, Faridi P, Fierro-Monti I, Fournier I, Frankish A, Gerstein M, Hubner N, Jiang Y, Kellis M, Kok LW, Martinez TF, Menschaert G, Ni P, Orchard S, Roucou X, Rozowsky J, Salzet M, Siragusa M, Slavoff S, Swirski MI, Valen E, Vizcaino JA, Wacholder A, Wu W, Xie Z, Yang YT, Moritz RL, Mudge J, van Heesch S, Prensner JR, Rackham OJ. PMID: 40672165; PMCID: PMC12265627.
      View in: PubMed   Mentions:
    4. Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment. bioRxiv. 2025 Feb 26. Wacholder A, Deutsch EW, Kok LW, van Dinter JT, Lee J, Wright JC, Leblanc S, Jayatissa AH, Jiang K, Arefiev I, Cao K, Bourassa F, Trifiro FA, Bassani-Sternberg M, Baranov PV, Bogaert A, Chothani S, Fierro-Monti I, Fijalkowska D, Gevaert K, Hubner N, Mudge JM, Ruiz-Orera J, Schulz J, Vizcaino JA, Prensner JR, Brunet MA, Martinez TF, Slavoff SA, Roucou X, Choudhary JS, van Heesch S, Moritz RL, Carvunis AR. PMID: 40027765; PMCID: PMC11870587.
      View in: PubMed   Mentions:
    5. A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness. iScience. 2025 Mar 21; 28(3):111884. Schlesinger D, Dirks C, Navarro C, Lafranchi L, Spinner A, Raja GL, Mun-Sum Tong G, Eirich J, Martinez TF, Elsässer SJ. PMID: 40124493; PMCID: PMC11929002.
      View in: PubMed   Mentions:
    6. Ribosome profiling reveals hidden world of small proteins. Trends Genet. 2025 Feb; 41(2):101-103. Tong G, Martinez TF. PMID: 39814675.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    7. High-quality peptide evidence for annotating non-canonical open reading frames as human proteins. bioRxiv. 2024 Sep 09. Deutsch EW, Kok LW, Mudge JM, Ruiz-Orera J, Fierro-Monti I, Sun Z, Abelin JG, Alba MM, Aspden JL, Bazzini AA, Bruford EA, Brunet MA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Hubner N, Ingolia NT, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Rackham O, Roucou X, Slavoff SA, Valen E, Wacholder A, Weissman JS, Wu W, Xie Z, Choudhary J, Bassani-Sternberg M, Vizcaíno JA, Ternette N, Moritz RL, Prensner JR, van Heesch S. PMID: 39314370; PMCID: PMC11419116.
      View in: PubMed   Mentions:
    8. Sex-dependent metabolic remodeling of kidneys revealed by arteriovenous metabolomics. bioRxiv. 2024 Sep 02. Kelly ME, Hoffner LA, Ramirez CB, Anica AL, Kim J, Tong G, Kim Y, Choi W, Jang K, Alam YH, Jung S, Le J, Tamburini I, Lopez ML, Bae H, Chun Y, Song WS, Martinez TF, Jang C, Lee G. PMID: 39282331; PMCID: PMC11398387.
      View in: PubMed   Mentions:
    9. Fiber-Reinforced Equibiaxial Dielectric Elastomer Actuator for Out-of-Plane Displacement. Materials (Basel). 2024 Jul 25; 17(15). Holzer S, Konstantinidi S, Koenigsdorff M, Martinez T, Civet Y, Gerlach G, Perriard Y. PMID: 39124336; PMCID: PMC11313582.
      View in: PubMed   Mentions: 2  
    10. Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq. Brief Bioinform. 2024 May 23; 25(4). Tong G, Hah N, Martinez TF. PMID: 38842510; PMCID: PMC11155197.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    11. Dielectric elastomer actuator-based valveless pump as Fontan failure assist device: introduction and preliminary study. Interdiscip Cardiovasc Thorac Surg. 2024 Mar 29; 38(4). Benouhiba A, Walter A, Jahren SE, Martinez T, Clavica F, Heinisch PP, Obrist D, Civet Y, Perriard Y. PMID: 38514398; PMCID: PMC11001492.
      View in: PubMed   Mentions: 1     Fields:    
    12. Novel para-aortic cardiac assistance using a pre-stretched dielectric elastomer actuator. Interdiscip Cardiovasc Thorac Surg. 2024 Mar 05; 38(3). Jahren SE, Martinez T, Walter A, Clavica F, Heinisch PP, Buffle E, Luedi MM, Hörer J, Obrist D, Carrel T, Civet Y, Perriard Y. PMID: 38419585; PMCID: PMC10955250.
      View in: PubMed   Mentions: 1     Fields:    
    13. The landscape of fetus metabolism in maternal hyperglycemia. Trends Endocrinol Metab. 2024 Apr; 35(4):282-284. Kelly ME, Martinez TF, Jang C. PMID: 38341338; PMCID: PMC11070186.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    14. Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq. bioRxiv. 2023 Dec 30. Tong G, Hah N, Martinez TF. PMID: 38234848; PMCID: PMC10793472.
      View in: PubMed   Mentions:
    15. Integrated workflow for discovery of microprotein-coding small open reading frames. STAR Protoc. 2023 12 15; 4(4):102649. Cao K, Hajy Heydary Y, Tong G, Martinez TF. PMID: 37874679; PMCID: PMC10618807.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    16. Dielectric Elastomer Actuator-Based Valveless Impedance-Driven Pumping for Meso- and Macroscale Applications. Soft Robot. 2024 Apr; 11(2):198-206. Benouhiba A, Walter A, Jahren SE, Martinez T, Clavica F, Obrist D, Civet Y, Perriard Y. PMID: 37729065.
      View in: PubMed   Mentions: 1     Fields:    
    17. Hemodynamic effects of a dielectric elastomer augmented aorta on aortic wave intensity: An in-vivo study. J Biomech. 2023 10; 159:111777. Jahren SE, Martinez T, Walter A, Ferrari L, Clavica F, Obrist D, Civet Y, Perriard Y. PMID: 37666100.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    18. Development of a lung-liver in vitro coculture model for inhalation-like toxicity assessment. Toxicol In Vitro. 2023 Oct; 92:105641. Madiedo-Podvrsan S, Sebillet L, Martinez T, Bacari S, Zhu F, Cattelin M, Leclerc E, Merlier F, Jellali R, Lacroix G, Vayssade M. PMID: 37437822.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    19. The TINCR ubiquitin-like microprotein is a tumor suppressor in squamous cell carcinoma. Nat Commun. 2023 03 10; 14(1):1328. Morgado-Palacin L, Brown JA, Martinez TF, Garcia-Pedrero JM, Forouhar F, Quinn SA, Reglero C, Vaughan J, Heydary YH, Donaldson C, Rodriguez-Perales S, Allonca E, Granda-Diaz R, Fernandez AF, Fraga MF, Kim AL, Santos-Juanes J, Owens DM, Rodrigo JP, Saghatelian A, Ferrando AA. PMID: 36899004; PMCID: PMC10006087.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimalsCells
    20. Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins. Cell Metab. 2023 01 03; 35(1):166-183.e11. Martinez TF, Lyons-Abbott S, Bookout AL, De Souza EV, Donaldson C, Vaughan JM, Lau C, Abramov A, Baquero AF, Baquero K, Friedrich D, Huard J, Davis R, Kim B, Koch T, Mercer AJ, Misquith A, Murray SA, Perry S, Pino LK, Sanford C, Simon A, Zhang Y, Zipp G, Bizarro CV, Shokhirev MN, Whittle AJ, Searle BC, MacCoss MJ, Saghatelian A, Barnes CA. PMID: 36599300; PMCID: PMC9889109.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    21. A novel soft cardiac assist device based on a dielectric elastomer augmented aorta: An in vivo study. Bioeng Transl Med. 2023 Mar; 8(2):e10396. Martinez T, Jahren SE, Walter A, Chavanne J, Clavica F, Ferrari L, Heinisch PP, Casoni D, Haeberlin A, Luedi MM, Obrist D, Carrel T, Civet Y, Perriard Y. PMID: 36925677; PMCID: PMC10013878.
      View in: PubMed   Mentions: 5  
    22. Standardized annotation of translated open reading frames. Nat Biotechnol. 2022 07; 40(7):994-999. Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. PMID: 35831657; PMCID: PMC9757701.
      View in: PubMed   Mentions: 120     Fields:    Translation:Cells
    23. Evaluation of dielectric elastomers to develop materials suitable for actuation. Soft Matter. 2021 Dec 15; 17(48):10786-10805. Banet P, Zeggai N, Chavanne J, Nguyen GTM, Chikh L, Plesse C, Almanza M, Martinez T, Civet Y, Perriard Y, Fichet O. PMID: 34859250.
      View in: PubMed   Mentions: 10     Fields:    
    24. A short ORF-encoded transcriptional regulator. Proc Natl Acad Sci U S A. 2021 01 26; 118(4). Koh M, Ahmad I, Ko Y, Zhang Y, Martinez TF, Diedrich JK, Chu Q, Moresco JJ, Erb MA, Saghatelian A, Schultz PG, Bollong MJ. PMID: 33468658; PMCID: PMC7848545.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    25. Insights into GLP-1 Receptor Activation with a Nonpeptide Agonist. Biochemistry. 2020 04 28; 59(16):1549-1550. Martinez TF, Vaughan J, Saghatelian A. PMID: 32297516.
      View in: PubMed   Mentions:    Fields:    
    26. Repression of the transcriptional activity of ERRα with sequence-specific DNA-binding polyamides. Med Chem Res. 2020 Apr; 29(4):607-616. Chen CY, Li Y, Jia T, He L, Hare AA, Silberstein A, Gallagher J, Martinez TF, Stiles JW, Olenyuk B, Dervan PB, Stiles BL. PMID: 34552311; PMCID: PMC8455084.
      View in: PubMed   Mentions: 3  
    27. Accurate annotation of human protein-coding small open reading frames. Nat Chem Biol. 2020 04; 16(4):458-468. Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. PMID: 31819274; PMCID: PMC7085969.
      View in: PubMed   Mentions: 109     Fields:    Translation:HumansCells
    28. Regulation of the ER stress response by a mitochondrial microprotein. Nat Commun. 2019 10 25; 10(1):4883. Chu Q, Martinez TF, Novak SW, Donaldson CJ, Tan D, Vaughan JM, Chang T, Diedrich JK, Andrade L, Kim A, Zhang T, Manor U, Saghatelian A. PMID: 31653868; PMCID: PMC6814811.
      View in: PubMed   Mentions: 98     Fields:    Translation:HumansAnimalsCells
    29. BioBits Health: Classroom Activities Exploring Engineering, Biology, and Human Health with Fluorescent Readouts. ACS Synth Biol. 2019 05 17; 8(5):1001-1009. Stark JC, Huang A, Hsu KJ, Dubner RS, Forbrook J, Marshalla S, Rodriguez F, Washington M, Rybnicky GA, Nguyen PQ, Hasselbacher B, Jabri R, Kamran R, Koralewski V, Wightkin W, Martinez T, Jewett MC. PMID: 30925042.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    30. CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability. Genes Dev. 2019 04 01; 33(7-8):418-435. Choi SH, Martinez TF, Kim S, Donaldson C, Shokhirev MN, Saghatelian A, Jones KA. PMID: 30819820; PMCID: PMC6446539.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    31. Small, but mighty? Searching for human microproteins and their potential for understanding health and disease. Expert Rev Proteomics. 2018 12; 15(12):963-965. Rathore A, Martinez TF, Chu Q, Saghatelian A. PMID: 30415582; PMCID: PMC6497149.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    32. MIEF1 Microprotein Regulates Mitochondrial Translation. Biochemistry. 2018 09 25; 57(38):5564-5575. Rathore A, Chu Q, Tan D, Martinez TF, Donaldson CJ, Diedrich JK, Yates JR, Saghatelian A. PMID: 30215512; PMCID: PMC6443411.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansCells
    33. Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide. PLoS One. 2015; 10(11):e0143161. Hargrove AE, Martinez TF, Hare AA, Kurmis AA, Phillips JW, Sud S, Pienta KJ, Dervan PB. PMID: 26571387; PMCID: PMC4646452.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    34. Probing the Functions of Carbohydrate Binding Modules in the CBEL Protein from the Oomycete Phytophthora parasitica. PLoS One. 2015; 10(9):e0137481. Martinez T, Texier H, Nahoum V, Lafitte C, Cioci G, Heux L, Dumas B, O'Donohue M, Gaulin E, Dumon C. PMID: 26390127; PMCID: PMC4577117.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    35. Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response. Nucleic Acids Res. 2014 Oct; 42(18):11546-59. Martínez TF, Phillips JW, Karanja KK, Polaczek P, Wang CM, Li BC, Campbell JL, Dervan PB. PMID: 25249630; PMCID: PMC4191428.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
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