Selected publications:

Multiplexed in vivo base editing defines functional gene-variant-context interactions | pdf

Computational modeling of human genetic variants in mice | pdf

Prime editing sensors enable multiplexed genome editing | pdf

High throughput evaluation of genetic variants with prime editing sensor libraries | pdf | PEGG Tool | MIT News | HHMI News | Ludwig Link | TheScientist | Technology Networks

A prime editor mouse to model a broad spectrum of somatic mutations in vivo | pdf

Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants | pdf | BE-SCAN

Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1 | pdf

Phase and context shape the function of composite oncogenic mutations | pdf

Rapid modelling of cooperating genetic events in cancer through somatic genome editing | pdf

All publications

☨ PhD student

π Postdoctoral researcher

¥ Research technician

^ Undergraduate student

* Indicates equal contribution

#Indicates a co-corresponding author

Published/In Press/Pre-Prints

  1. Wu, K.☨, Sánchez-Rivera, F.J. (2025). It’s prime time for multiplexed prime editing. Cell Genomics. doi: https://doi.org/10.1016/j.xgen.2025.100852.

  2. Acosta, J.*π, Johnson, G.A.*☨, Gould, S.I.*☨, Dong, K.^, Lendner, Y., Detrés, D.☨, Atwa, O.☨, Bulkens, J.^, Gruber, S., Contreras, M.E.☨, Narendra, V.K., Hemann, M.T.#, Sánchez-Rivera, F.J.# (2025). Multiplexed in vivo base editing defines functional gene-variant-context interactions. bioRxiv. doi: https://doi.org/10.1101/2025.02.23.639770. *Equal contribution. #Co-corresponding authors. In revision at a peer-reviewed journal.

  3. Dong, K.^, Gould, S.I.☨, Li, M., Sánchez-Rivera, F.J. (2025). Computational modeling of human genetic variants in mice. bioRxiv. doi: https://doi.org/10.1101/2025.02.23.639784. In revision at a peer-reviewed journal.

  4. Gould, S.I.☨, Sánchez-Rivera, F.J. (2025). Using Prime Editing Guide Generator (PEGG) for high-throughput generation of prime editing sensor libraries. Methods in Molecular Biology. doi: https://doi.org/10.1016/bs.mie.2025.01.006.

  5. Perr, J., Langen, A., Almahayni, K., Nestola, G., Chai, P., Lebedenko, C.G., Volk, R., Detrés, D.☨, Caldwell, R.M., Spiekermann, M., Hemberger, H., Bisaria, N., Aiba, T., Sánchez-Rivera, F.J., Tzelepis, K., Calo, E., Möckl, L., Zaro, B., Flynn, R.A. (2025). RNA binding proteins and glycoRNAs form domains on the cell surface for cell penetrating peptide entry. Cell. doi: https://doi.org/10.1016/j.cell.2025.01.040.

  6. Schmidt, H.*, Zhang, M.*, Chakarov, D., Bansal, V., Mourelatos, H., Sánchez-Rivera, F.J., Lowe, S.W., Ventura, A.#, Leslie, C.S.#, Pritykin, Y.# (2025). Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2. Genome Biology. 26, 41. doi: https://doi.org/10.1186/s13059-025-03488-8. Previously posted in bioRxiv. doi: https://doi.org/10.1101/2022.05.02.490368. *Equal contribution. #Co-corresponding authors.

  7. Zucker, M.*, Perry, M.A.*, Gould, S.I.☨, Elkrief, A., Safonov, A., Thummalapalli, R., Mehine, M., Chakravarty, D., Brannon, A.R., Ladanyi, M., Razavi, P., Donoghue, M.T.A., Murciano-Goroff, Y.R., Grigoriadis, K., McGranahan, N., Jamal-Hanjani, M., Swanton, C., Chen, Y., Shen, R., Chandarlapaty, S., Solit, D.B., Schultz, N., Berger, M.F., Chang, J., Schoenfeld, A.J., Sánchez-Rivera, F.J., Reznik, E.#, Bandlamudi, C.# (2025). Pan-cancer analysis of biallelic inactivation patterns in tumor suppressor genes identifies KEAP1 zygosity as a predictive biomarker in lung cancer. Cell. doi: https://doi.org/10.1016/j.cell.2024.11.010. *Equal contribution. #Co-corresponding authors.

  8. Roth, J.F.π, Sánchez-Rivera, F.J. (2024). Precision Mutational Scanning: Your Multipass to the Future of Genetics. Nature Methods. doi: https://doi.org/10.1038/s41592-024-02522-0

  9. Lee, J.H., Sánchez-Rivera, F.J., He, L., Basnet, H., Chen, F., Spina, E., Li, L., Torner, C., Chan, J.E., Yarlagadda, D.V.K., Park, J.S., Sussman, C., Rudin, C.M., Lowe, S.W., Tammela, T., Macias, M.J., Koche, R.P., Massagué, J. (2024). TGF-β and RAS jointly unmask primed enhancers to drive metastasis. Cell. doi: https://doi.org/10.1016/j.cell.2024.08.014.

  10. Abbott, K.L.*, Subudhi, S.*, Ferreira, R.*, Gultekin, Y., Steinbuch, S.C., Bin Munim, M., Honeder, S.E., Kumar, A.S., Ramesh, D., Wu, M., Hansen, J.A., Sivanand, S., Riedmayr, L.M., Duquette, M., Al, A., Henning, N., Shevzov-Zebrun, A., Gourgue, F., Barbeau, A.M., Waite, M., Kunchok, T., Ferraro, G.B., Do, B.T., Spanoudaki, V., Sánchez-Rivera, F.J., Jin, X., Church, G.M.#, Jain, R.K.#, Vander Heiden, M.G.# (2024). Site of breast cancer metastasis is independent of single nutrient levels. bioRxiv. doi: https://doi.org/10.1101/2024.10.24.616714. *Equal contribution. #Co-corresponding authors. In revision at a peer-reviewed journal.

  11. Le Pen, J.*, Paniccia, G.*, Kinast, V.§, Moncada-Velez, M.§, Ashbrook, A.W.§, Bauer, M.§, Hoffmann, H-H.§, Pinharanda, A.§, Ricardo-Lax, I.§, Stenzel, A.F.§, Rosado-Olivieri, E.A.§, Dinnon, K.H., Doyle, W.C., Freije, C.A., Hong, S-H., Lee, D., Lewy, T., Luna, J.M., Peace, A., Schmidt, C., Schneider, W.M., Winkler, R., Yip, E.Z., Larson, C., McGinn, T., Menezes, M-R., Ramos-Espiritu, L., Banerjee, P., Poirier, J.T., Sánchez-Rivera, F.J., Cobat, A., Zhang, Q., Casanova, J-L., Carroll, T.S., Glickman, F.J., Michailidis, E.#, Razooky, B.#, MacDonald, M.R.#, Rice, C.M.# (2024). A Genome-Wide Arrayed CRISPR Screen Reveals PLSCR1 as an Intrinsic Barrier to SARS-CoV-2 Entry. PLoS Biology. doi: https://doi.org/10.1371/journal.pbio.3002767. Previously posted in bioRxiv. doi: https://www.biorxiv.org/content/10.1101/2024.02.16.580725v3. *Equal contribution. §Equal contribution. #Co-corresponding authors.

  12. Johnson, G.A.☨*, Gould, S.I.☨*, Sánchez-Rivera, F.J.# (2024). Deconstructing cancer with precision genome editing technologies. Biochemical Society Transactions. doi: https://doi.org/10.1042/BST20230984. *Equal contribution.

  13. Gould, S.I.☨, Wuest, A.N.¥, Dong, K.^, Johnson, G.A.☨, Hsu, A., Narendra, V.K., Atwa, O.☨, Levine, S.S., Liu, D.R., Sánchez-Rivera, F.J. (2024). High throughput evaluation of genetic variants with prime editing sensor libraries. Nature Biotechnology. doi: https://doi.org/10.1038/s41587-024-02172-9. Previously posted in bioRxiv. doi: https://www.biorxiv.org/content/10.1101/2022.10.26.513842v4.full.

  14. Gannon, D., Lagan, E., Silva, A.J., Bibawi, P., Doherty, A., Nimmo, D., McCole, R., Monger, C., Genesi, G., Dibekeme, A.V., Innes, J., Yang, L., Chen, B., van Mierlo, G., Jansen, P., Wynne, K., Sánchez-Rivera, F.J., Soto-Feliciano, Y., Vermeulen, M., Oliverio, G., Chen, C-W., Phillips, R., Bracken, A., Brien, G. (2023). Specific cPRC1 complexes are co-opted to mediate oncogenic gene repression in diffuse midline glioma. bioRxiv. doi: https://doi.org/10.1101/2023.12.02.569451. In revision at a peer-reviewed journal.

  15. Torborg, S.R., Grbovic-Huezo, O., Singhal, A., Holm, M., Wu, K., Han, X., Ho, Y., Haglund, C., Mitchell, M.J., Lowe, S., Dow, L.E., Pitter, K., Sánchez-Rivera, F.J., Levchenko, A., Tammela, T. (2023). Solid tumor growth depends on an intricate equilibrium of malignant cell states. bioRxiv. doi: https://doi.org/10.1101/2023.12.30.573100. Currently in revision at a peer-reviewed journal.

  16. Karagiannis, D., Wu, W., Li, A., Hayashi, M., Chen, X., Yip, M., Mangipudy, V., Xu, X., Sánchez-Rivera, F.J., Soto-Feliciano, Y.M., Ye, J., Papagiannakopoulos, T., Lu, C. (2023). Metabolic Reprogramming by Histone Deacetylase Inhibition Selectively Targets NRF2-activated tumors. Cell Reports. 30;43(1):113629. doi: https://doi.org/10.1016/j.celrep.2023.113629. Previously posted in bioRxiv. doi: https://www.biorxiv.org/content/10.1101/2023.04.24.538118.

  17. Katti, A., Vega-Pérez, A., Foronda, M., Zimmermann, J., Paz Zafra, M., Granowsky, E., Goswami, S., Gardner, E., Diaz, B., Simon, J., Wuest, A.¥, Luan, W., Calvo Fernandez, M.T., Kadina, A., Walker, J., Holden, K., Lowe, S.W., Sánchez-Rivera, F.J., Dow, L.E. (2023). Rapid generation of precision preclinical cancer models using regulatable in vivo base editing. Nature Biotechnology. doi: https://doi.org/10.1038/s41587-023-01900-x. Previously posted in bioRxiv. doi: https://doi.org/10.1101/2022.08.03.502708.

  18. Chen, X., Li, Y., Zhu, F., Xu, X., Estrella, B., Pazos, M.A., McGuire, J.T., Karagiannis, D., Sahu, V., Mustafokulov, M., Scuoppo, C., Sánchez-Rivera, F.J., Soto-Feliciano, Y.M., Pasqualucci, L., Ciccia, A., Amengual, J.E., Lu, C. (2023). Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma. Nature Communications. 14, 4259. doi: https://doi.org/10.1038/s41467-023-39990-5

  19. Ely, Z. A.*, Mathey-Andrews, N.*, Naranjo, S., Gould, S. I.☨, Cabana, C. M., Mercer, K. L., Rideout III W. M., Newby, G. A., Cervantes Jaramillo, G., Holland, K., Randolph, P. B., Freed-Pastor, W. A., Davis, J. R., Westcott, P. M. K., Anzalone, A. V., Pattada, N. B., Sánchez-Rivera, F.J., Liu, D. R., Jacks, T. (2023). A prime editor mouse for modeling a broad spectrum of somatic mutations in vivo. Nature Biotechnology. doi: https://doi.org/10.1038/s41587-023-01783-y. *Equal contribution. 

  20. Hu, J., Sánchez-Rivera, F.J., Johnson, G., Wang, Z., Ho, Y., Ganesh, K., Gan, S., Hampton, J., Zhao, H., Kottapalli, S., de Stanchina, E., Iacobuzio-Donahue, C.A., Pe’er, D., Lowe, S.W., Sun, J., Massagué, J. (2023). STING suppresses the reactivation of dormant metastasis. Nature. 616, 806–813. doi: https://doi.org/10.1038/s41586-023-05880-5.

  21. Soto-Feliciano, Y.M.*, Sánchez-Rivera, F.J.*, Perner, F.*, Barrows, D., Kastenhuber, E.R., Ho, Y., Carroll, T., Xiong, J., Soshnev, A., Gates, L., Beytagh, M.C., Cheon, D., Gu, S., Liu, X.S., Krivtsov, A.V., Meneses, M., de Stanchina, E., Armstrong, S.A.#, Lowe, S.W.#, Allis, C.D.# (2023). A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition. Cancer Discovery. https://doi.org/10.1158/2159-8290.CD-22-0416. *Equal contribution. #Co-corresponding authors. Previously posted in bioRxiv. doi: https://doi.org/10.1101/2021.10.22.465184.

  22. Benabdallah, N., Dalal, V., Scott, R.W., Marcous, F., Sotiriou, A., Kommoss, F., Pejkovska, A., Gaspar, L., Wagner, L., Sánchez-Rivera, F.J., Ta, M., Thornton, S., Nielsen, T., Underhill, T., Banito, A. (2023). Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability. Nature Structural & Molecular Biology. In press. Previously posted in bioRxiv. doi: https://doi.org/10.1101/2022.07.18.499263.

  23. Leibold, J.*#, Amor, C.*, Tsanov, K.M.*, Ho, Y., Sánchez-Rivera, F.J., Feucht, J., Baslan, T., Chen, H., Tian, S., Simon, J., Wuest, A., Wilkinson, J.E., Lowe, S.W.# (2023). Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease. Nature Cancer. In press. *Equal contribution. #Co-corresponding authors. Previously posted in bioRxiv. doi: https://doi.org/10.1101/2022.06.15.494941.

  24. Sánchez-Rivera, F.J.*, Díaz, B.J.*, Kastenhuber, E.R.*, Schmidt, H., Katti, A., Kennedy, M., Tem, V., Ho, Y., Leibold, J., Paffenholz, S.V., Barriga, F.M., Chu, K., Goswami, S., Wuest, A.N., Simon, J.M., Tsanov, K.M., Chakravarty, D., Zhang, H., Leslie, C.S., Lowe, S.W., Dow, L.E. (2022). Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Nature Biotechnology. 40, 862–873. doi: https://doi.org/10.1038/s41587-021-01172-3. *Equal contribution.

  25. Li, X.*, Huang, C.*, Sánchez-Rivera, F.J., Kennedy, M., Tschaharganeh, D.F., Morris IV, J.P., Montinaro, A., O’Rourke, K.P., Banito, A., Wilkinson, J.E., Chen, C., Ho, Y., Dow, L.E., Tian, S., Luan, W., de Stanchina, E., Zhang, T., Gray, N.S., Walczak, H., Lowe, S.W. (2022). A preclinical platform for assessing anti-tumor effects and systemic toxicities of cancer drug targets. Proceedings of the National Academy of Sciences. doi: https://doi.org/10.1073/pnas.2110557119. *Equal contribution.

  26. Gearty, S.V., Dündar, F., Zumbo, P., Espinosa-Carrasco, G., Shakiba, M., Sánchez-Rivera, F.J., Socci, N.D., Trivedi, P., Lowe, S.W., Lauer, P., Mohibullah, N., Viale, A., DiLorenzo, T.P., Betel, D., Schietinger, A. (2021). A stem-like CD8 T cell population initiates and sustains beta cell destruction in type 1 diabetes. Nature. 602, 156-161. doi: https://doi.org/10.1038/s41586-021-04248-x.

  27. Shakiba, M., Zumbo, P., Espinosa-Carrasco, G., Menocal, L., Dündar, F., Carson, S.E., Bruno, E.M., Sánchez-Rivera, F.J., Lowe, S.W., Camara, S., Koche, R.P., Reuter, V.P., Socci, N.D., Whitlock, B., Tamzalit, F., Huse, M., Hellmann, M.D., Wells, D.K., Defranoux, N.A., Betel, D., Philip, M., Schietinger, A. (2021). TCR affinity dictates T cell functional states in tumors. Journal of Experimental Medicine. doi: https://doi.org/10.1084/jem.20201966.

  28. Ricardo-Lax, I.*, Luna, J.M.*, Thao, T.T.N., Le Pen, J., Yu, Y., Hoffmann, H.H., Schneider, W.M., Fernandez-Martinez, J., Schmidt, F., Weisblum, Y., Trüeb, B.S., Veiga, I.B., Schmied, K., Ebert, N., Michailidis, E., Razooky, B.S., Peace, A., Sánchez-Rivera, F.J., Lowe, S.W., Rout, M.P., Hatziioannou, T., Bieniasz, P.D., Poirier, J.T., MacDonald, M.R., Thiel, V.#, Rice, C.M.# (2021). Replication and single-cycle delivery of SARS-CoV-2 replicons. Science. 374, 1099-1106. *Equal contribution. #Co-corresponding authors.

  29. Concepcion, C.P., Ma, S.*, LaFave, L.M.*, Bhutkar, A.*, Liu, M., DeAngelo, L.P., Kim, J.Y., Del Priore, I., Schoenfeld, A.J., Miller, M., Kartha, V.K., Westcott, P.M.K., Sánchez-Rivera, F.J., Meli, K., Gupta, M., Bronson R.T., Riely, G.J., Rekhtman, N., Rudin, C.M., Kim, C.F., Regev, A., Buenrostro, J.D., Jacks, T. (2021). Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung. Cancer Discovery. doi: https://doi.org/10.1158/2159-8290.CD-21-0248. *Equal contribution.

  30. Ciampricotti, M., Karakousi, T.*, Richards, A.L.*, Quintanal-Villalonga, A., Karatza, A., Caeser, R., Costa, E.A., Allaj, V., Manoj, P., Spainhower, K.B., Kombak, F.E., Sánchez-Rivera, F.J., Jaspers, J., Zavitsanou, A., Maddalo, D., Ventura, A., Rideout III, W.M., Akama-Garren, E.H., Jacks, T., Donoghue, M., Sen, T., Oliver, T.G., Poirier, J.T., Papagiannakopoulos, T.#, Rudin, C.M.# (2021). Rlf-Mycl1 gene fusion drives tumorigenesis and metastasis in a novel mouse model of small cell lung cancer. Cancer Discovery. doi: https://doi.org/10.1158/2159-8290.CD-21-0441. *Equal contribution. #Co-corresponding authors.

  31. Sánchez-Rivera, F.J.*, Ryan, J.*, Soto-Feliciano, Y.M., Beytagh, M.C., Xuan, L., Feldser, D.M., Hemann, M.T., Letai, A.#, Jacks, T.# (2021). Mitochondrial apoptotic priming is a key determinant of cell fate upon p53 restoration. Proceedings of the National Academy of Sciences. 118 (23) e2019740118. https://doi.org/10.1073/pnas.2019740118. *Equal contribution. #Co-corresponding authors.

  32. Schneider, W.M.*, Luna, J.M.*, Hoffmann, H.H.*, Sánchez-Rivera, F.J.*, Leal, A.A., Ashbrook, A.W., Le Pen, J., Ricardo-Lax, I., Michailidis, E., Peace, A., Stenzel, A.F., Lowe, S.W., MacDonald, M.R., Rice, C.M.#, Poirier, J.T.# (2021). Genome-scale identification of SARS-CoV-2 and pan-coronavirus host factor networks. Cell. 184, 120–132. *Equal contribution. #Co-corresponding authors. Cover article.

  33. Hoffmann, H.H.*, Sánchez-Rivera, F.J.*, Schneider, W.M.*, Luna, J.M.*, Soto-Feliciano, Y.M., Ashbrook, A.W., Le Pen, J., Leal, A.A., Ricardo-Lax, I., Michailidis, E., Hao, Y., Stenzel, A.F., Peace, A., Zuber, J., Allis, C.D., Lowe, S.W., MacDonald, M.R., Poirier, J.T.#, Rice, C.M.# (2021). Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors. Cell Host & Microbe. 29, 1–14. *Equal contribution. #Co-corresponding authors.

  34. Jiang, T., Sánchez-Rivera, F.J., Soto-Feliciano, Y.M., Yang, Q., Song, C., Bhutkar, A., Haynes, C.M., Hemann, M.T., Xue, W. (2020). Targeting de novo purine synthesis pathway via ADSL depletion impairs liver cancer growth by perturbing mitochondrial function. Hepatology. 74: 233-247.

  35. Gupta, M., Concepcion, C.P., Fahey, C.G., Fillmore-Brainson, C., Sánchez-Rivera, F.J., Pessina, P., Bhutkar, A., Kim, J.Y., Simoneau, A., Beytagh, M.C., Keshishian, H., Stanclift, C., Schenone, M., Mani, D.R., Li, C., Oh, A., Li, F., Hu, H., Karatza, A., Wong, K.K., Shaw, A.T., Hata, A.N., Carr, S.A., Zou, L., Jacks, T., Kim, C.F. (2020). BRG1 loss predisposes lung cancers to replicative stress and ATR dependency. Cancer Research. (80) (18), 3841-3854.

  36. Romero, R.*, Sánchez-Rivera, F.J.*, Westcott, P.M.K., Mercer, K.L., Bhutkar, A., Muir, A., González-Robles, T.J., Lamboy-Rodríguez, S.A., Liao, L.Z., Ng, S.R., Li, L., Colón, C.I., Naranjo, S., Beytagh, M.C., Lewis, C.A., Hsu, P.P., Bronson, R.T., Vander Heiden, M.G., Jacks, T. (2020). Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1. Nature Cancer. 1, 589–602. *Equal contribution.

  37. Gorelick, A.N., Sánchez-Rivera, F.J., Cai, Y., Bielski, C.M., Biederstedt, E., Jonsson, P., Richards, A.L., Vasan, N., Penson, A.V., Friedman, N.D., Ho, Y., Baslan, T., Bandlamudi, C., Scaltriti, M., Schultz, N., Lowe, S.W., Reznik, E.#, Taylor, B.S.# (2020). Phase and context shape the function of composite oncogenic mutations. Nature. 582, 100–103. #Co-corresponding authors.

  38. Oni, T.E.*, Biffi, G.*, Baker, L.A., Hao, Y., Tonelli, C., Somerville, T.D.D., Deschênes, A., Belleau, P., Hwang, C., Sánchez-Rivera, F.J., Cox, H., Brosnan, E., Doshi, A., Lumia, R.P., Khaledi, K., Park, Y., Trotman, L.C., Lowe, S.W., Krasnitz, A., Vakoc, C.R., Tuveson, D.A. (2020). SOAT1 abrogates cholesterol feedback inhibition to promote mevalonate pathway dependency in pancreatic cancer. Journal of Experimental Medicine. 217 (9): e20192389. doi: https://doi.org/10.1084/jem.20192389. *Equal contribution.

  39. Leibold, J.*, Ruscetti, M.*, Cao, Z.*, Ho, Y., Baslan, T., Zou, M., Abida, W., Feucht, J., Han, T., Barriga, F.M., Tsanov, K.M., Zamechek, L., Kulick, A., Amor, C., Tian, S., Salgado, N.R., Sánchez-Rivera, F.J., Watson, P.A., de Stanchina, E., Wilkinson, J.E., Dow, L.E., Abate-Shen, C., Sawyers, C.L.#, Lowe, S.W.# (2020). Somatic tissue engineering in mouse models reveals an actionable role for WNT pathway alterations in prostate cancer metastasis. Cancer Discovery. (10) (7), 1038-1057. *Equal contribution. #Co-corresponding authors.

  40. Yuan, S., Natesan, R., Sánchez-Rivera, F.J., Li, J., Bhanu, N.V., Yamazoe, T., Lin, J.H., Merrell, A.J., Thomas, S.K., Miller, E.M., Shi, J., Garcia, B.A., Lowe, S.W., Asangani, I.A., Stanger, B.Z. (2020). Global regulation of the histone mark H3K36me2 underlies epithelial plasticity and metastatic progression. Cancer Discovery. (10) (6), 854-871.

  41. Morris IV, J.P.*, Yashinskie, J.J.*, Koche, R., Chandwani, R., Tian, S., Chen, C., Baslan, T., Marinkovic, Z.S., Sánchez-Rivera, F.J., Leach, S.D., Carmona-Fontaine, C., Thompson, C.B., Finley, L.W.S.#, Lowe, S.W.# (2019). α-Ketoglutarate links p53 to cell fate during tumour suppression. Nature. 573, 595-599. *Equal contribution. #Co-corresponding authors.

  42. Loizou, E., Banito, A., Livshits, G., Ho, Y., Koche, R., Sánchez-Rivera, F.J., Mayle, A., Chen, C., Kinalis, S., Bagger, F.O., Kastenhuber, E., Durham, B.H., Lowe, S.W. (2019). A gain-of-function p53 mutant oncogene promotes cell fate plasticity and myeloid leukemia through the pluripotency factor Foxh1. Cancer Discovery. 9 (7), 926-979.

  43. Ruscetti, M.*, Leibold, J.*, Bott, M.J.*, Fennell, M., Kulick, A., Salgado, N.R., Chen, C., Ho, Y., Sánchez-Rivera, F.J., Feucht, J., Baslan, T., Tian, S., Chen, H., Romesser, P.B., Poirier, J.T., Rudin, C.M., de Stanchina, E., Manchado, E., Sherr, C.J., Lowe, S.W. (2018). NK cell-mediated cytotoxicity contributes to the efficacy of a cytostatic drug combination in lung cancer. Science. 362, 1416-1422. *Equal contribution.

  44. Zafra, M.P.*, Schatoff, E.M.*, Katti, A., Foronda, M., Breinig, M., Schweitzer, A.Y., Simon, A., Han, T., Goswami, S., Montgomery, E., Thibado, J., Kastenhuber, E.R., Sánchez-Rivera, F.J., Shi, J., Vakoc, C.R., Lowe, S.W., Tschaharganeh, D.F., Dow, L. (2018). Optimized base editors enable efficient editing in cells, organoids and mice. Nature Biotechnology. 36, 888–893. *Equal contribution.

  45. González-Vallinas, M., Rodríguez-Paredes, M., Albrecht, M., Sticht, C., Stichel, D., Gutekunst, J., Pitea, A., Sass, S., Sánchez-Rivera, F.J., Lorenzo-Bermejo, J., Schmitt, J., De La Torre, C., Warth, A., Theis, F.J., Müller, N.S., Gretz, N., Muley, T., Meister, M., Tschaharganeh, D.F., Schirmacher, P., Matthäus, F., Breuhahn, K. (2018). Epigenetically Regulated Chromosome 14q32 miRNA Cluster Induces Metastasis and Predicts Poor Prognosis in Lung Adenocarcinoma Patients. Molecular Cancer Research. 16, 390-402.

  46. Romero, R.*, Sayin, V.I.*, Davidson, S.M., Bauer, M., Singh, S.X., LeBoeuf, S.E., Karakousi, T.R., Ellis, D.C., Bhutkar, A., Sánchez-Rivera, F.J., Subbaraj, L., Martinez, B., Bronson, R.T., Prigge, J.R., Schmidt, E.E., Thomas, C.J., Davies, A., Dolgalev, I., Heguy, A., Allaj, V., Poirier, J.T., Moreira, A.L., Rudin, C.M., Pass, H.I., Vander Heiden, M.G., Jacks, T#., Papagiannakopoulos, T.# (2017). Loss of Keap1 promotes KRAS-driven lung cancer and results in genotype specific metabolic vulnerabilities. Nature Medicine. 23, 1362-1368. *Equal contribution. #Co-corresponding authors.

  47. Gocheva, V., Naba, A., Bhutkar, A., Guardia, T., Miller, K.M., Li, C.M., Dayton, T.L., Sánchez-Rivera, F.J., Kim-Kiselak, C., Jailkhani, N., Winslow, M.M., Del Rosario, A., Hynes, R.O., Jacks, T. (2017). Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival. Proceedings of the National Academy of Sciences. 114, E5625–E5634.

  48. Soto-Feliciano, Y.M.*, Bartlebaugh, J.M.E.*, Liu, Y.*, Sánchez-Rivera, F.J., Bhutkar, A., Weintraub, A.S., Buenrostro, J.D., Cheng, C.S., Regev, A., Jacks, T., Young, R.A., Hemann, M.T. (2017). PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. Genes & Development. 31, 973-989. *Equal contribution. Cover article.

  49. Tammela, T., Sánchez-Rivera F.J., Cetinbas, N.M., Wu, K., Joshi, N.S., Helenius, K., Park, Y., Azimi, R., Kerper, N.R., Wesselhoeft, R.A., Gu, X., Schmidt, L., Cornwall-Brady, M., Yilmaz, Ö.H., Xue, W., Katajisto, P., Bhutkar, A., and Jacks, T. (2017). A Wnt-producing niche drives proliferative potential and progression in lung adenocarcinoma. Nature. 545, 355-359.

  50. Roper, J.*, Tammela, T.*, Cetinbas, N.M., Akkad, A., Roghanian, A., Rickelt, S., Almeqdadi, M., Wu, K., Oberli, M.A., Sánchez-Rivera F.J., Park, Y., Liang, X., Eng, G., Taylor, M.S., Azimi, R., Kedrin, D., Neupane, R., Beyaz, S., Sicinska, E.T., Suarez, Y., Yoo, J., Chen, L., Zukerberg, L., Katajisto, P., Deshpande, V., Bass, A.J., Tsichlis, P.N., Lees, J., Langer, R., Hynes, R.O., Chen, J., Bhutkar, A.J., Jacks, T., Yilmaz, Ö.H. (2017). In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis. Nature Biotechnology. 35, 569-576. *Equal contribution. 

  51. Mazur, P.K.*#, Herner, A.*, Mello, S.S., Wirth, M., Hausmann, S., Kuschma, T., Sánchez-Rivera, F.J., Lofgren, S., Hahn, S.A., Vangala, D., Trajkovic-Arsic, M., Gupta, A., Heid, I., Noël, P.B., Braren, R., Erkan, M., Kleeff, J., Sipos, B., Sayles, L.C., Heikenwälder, M., Heßmann, E., Ellenrieder, V., Esposito, I., Jacks, T., Bradner, J.E., Khatri, P., Sweet-Cordero, E.A., Attardi, L.D., Schmid, R.M., Schneider, G., Sage, J.#, Siveke, J.T.# (2015). Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma. Nature Medicine. 21, 1163-1171. *Equal contribution. #Co-corresponding authors.

  52. Sánchez-Rivera, F.J., Jacks, T. (2015). Applications of the CRISPR-Cas9 system in cancer biology. Nature Reviews Cancer. 15, 387-395.

  53. Sánchez-Rivera, F.J.*, Papagiannakopoulos, T.*, Romero, R., Tammela, T., Bauer, M.R., Bhutkar, A., Joshi, N.S., Subbaraj, L., Bronson, R.T., Xue, W., Jacks, T. (2014). Rapid modelling of cooperating genetic events in cancer through somatic genome editing. Nature. 516, 428–431. *Equal contribution.

  54. Feldser, D.M., Kostova, K.K., Winslow, M.M., Taylor, S.E., Cashman, C., Whittaker, C.A.,Sánchez-Rivera, F.J.,Resnick, R., Bronson, R.T., Hemann, M.T., Jacks, T. (2010). Stage-specific sensitivity to p53 restoration during lung cancer progression. Nature. 468, 572-575.

Book Chapters

  1. Sánchez-Rivera, F.J.#, Dow, L.E.# (2024). How CRISPR is Revolutionizing the Generation of New Models for Cancer Research. In Cold Spring Harbor Perspectives in Medicine: Advances in modeling cancer in mice. doi: https://doi.org/10.1101/cshperspect.a041384. #Co-corresponding authors.