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Cross, M., Kotschi, S., Wu, W., Luciano-Mateo, F., Kwon, Y.Y., Dantas, E., Niazi, T., Chen, S., Rashidfarrokhi, A., Pillai, R., Sanford, J., Kim, J., Hsiang, J., Gamallo-Lana, B., Mar, A.C., Hao, Y., Rajalingam, S., Huang, A., Shan, J., Issa, H.A., Gomez, M., Wang, A.R., Zhao, X., Janowitz, T., White, E., Liu, Y., Wong, K.K., Segal, L.N., Hui, S., Goncalves, M.D., Froemke, R.C., Papagiannakopoulos, T. A dietary switch promotes sensory neuron-dependent cancer-associated cachexia. (2026) Science. 393(6806):90-97. DOI: 10.1126/science.adz4196

Paraskevopoulou, V., Lin, Z., Casado-Pelaez, M., Grases, D., Al-Santli, W., Balandrán, J.C., Zhou, F., Rashidfarrokhi, A., Cross, M., Yeung, S.T., Ntatsoulis, K., Patel, T., Chen, X., Nicolet, D., Escobosa, M., Porta, E., Trowbridge, J.J., Khanna, K.M., Papagiannakopoulos, T., Moreira, A.L., Kanagal-Shamanna, R., Loghavi, S., Tsirigos, A., Eisfeld, A.K., Esteller, M., Aifantis, I. Inflammatory immune modulators of AML lung infiltration and respiratory failure. (2026) Nature Immunology. DOI: 10.1038/s41590-026-02582-8

Chang, W.H., Vaughan, A.J., Stamey, A.G., Mancini, M., Hayashi, M., Yang, R., Robb, R., Andrussier, D., Klomp, J.A., Waters, A.M., Schaefer, A., Wolpin, B.M., Bryant, K.L., Cox, A.D., Simabuco, F.M., Wong, K.K., Aguirre, A.J., Stalnecker, C.A., Papagiannakopoulos, T., Der, C.J. Characterization and therapeutic suppression of KEAP1-NRF2-driven resistance to KRAS inhibitors in pancreatic and lung cancer. (2026) bioRxiv. DOI: 10.64898/2026.04.18.719329

Pillai, R., Rashidfarrokhi, A., Hao, Y., Wu, W.L., Mancini, M.C.S., Karadal-Ferrena, B., Dimitriadoy, S.G., Cross, M., Yeaton, A.H., Huang, S.M., Bhutkar, A., Herrera, A.M., Rajalingam, S., Hayashi, M., Huang, K.L., Bartnicki, E., Zavitsanou, A.M., Ivanova, E., Wohlhieter, C., LeBoeuf, S.E., Chen, T., Loomis, C.A., Kulicke, R., Davis, F.P., Stransky, N., Smolen, G.A., Tsay, J.J., Simabuco, F.M., Rudin, C.M., Moreira, A.L., Khanna, K.M., Pass, H.I., Wong, K.K., Koide, S., Tsirigos, A., Koralov, S.B., Papagiannakopoulos, T. LIF-Induced Tumor Plasticity Establishes an Immunosuppressive Myeloid Niche in LKB1-Mutant Lung Cancer. (2026) Cancer Discovery.:OF1-OF20 DOI: 10.1158/2159-8290.CD-25-0470

Vaughan, A.J., Papagiannakopoulos, T. Drowning in cysteine. (2026) Nat Metab. 8(4):765-767. DOI: 10.1038/s42255-026-01511-1

Patel, A.A.H., Dzanan, J.J., Ali, K.X., Eklund, E.A., Alvarez, S.W., Raj, D., Dankis, M., Altinönder, I., Schwarz, M., Le Gal, K., Bedel, E., El Zowalaty, A.E., Jonasson, E., Albatrok, H., Gul, N., Bossowski, J.P., Pillai, R., Micke, P., Botling, J., Akyürek, L.M., Angeletti, D., Sayin, S.I., Härtlova, A., Papagiannakopoulos, T., Olofsson Bagge, R., Ståhlberg, A., Hallqvist, A., Wiel, C., Sayin, V.I. Ageing promotes metastasis via activation of the integrated stress response. (2026) Nature. 652(8112):1339-1348. DOI: 10.1038/s41586-026-10216-0

Bossowski, J.P., Pillai, R., Kilian, J., Wong Lau, A., Nakamura, M., Rashidfarrokhi, A., Hao, Y., Li, R., Wu, K., Hattori, T., Glasser, E., Koide, A., Wang, L., Moreira, A.L., Hajdu, C., Rajalingam, S., LeBoeuf, S.E., Le, H., Lee, S., Oh, J.W., Joe, C., Kim, H., Ock, C.Y., Lee, S.H., Wang, H., Patel, A.A.H., Sayin, V.I., Tsirigos, A., Wong, K.K., Koralov, S.B., Pende, M., Sánchez-Rivera, F.J., Simeone, D.M., Zervantonakis, I.K., Koide, S., Papagiannakopoulos, T. The integrated stress response promotes immune evasion through lipocalin 2. (2026) Nature. 652(8112):1329-1338. DOI: 10.1038/s41586-026-10143-0

Vaughan, A.J., Palma, M., Ubellacker, J.M., Papagiannakopoulos, T. Ferroptosis surveillance: Insights from in vivo contexts. (2026) Ferroptosis Oxid Stress. 2(3). DOI: 10.70401/fos.2026.0021

Wu, K., Vaughan, A.J., Bossowski, J.P., Hao, Y., Ziogou, A., Kim, S.M., Kim, T.H., Nakamura, M.N., Pillai, R., Mancini, M., Rajalingam, S., Han, M., Nakamura, T., Wang, L., Chung, S., Simeone, D., Shackelford, D., Kang, Y.P., Conrad, M., Papagiannakopoulos, T. Targeting FSP1 triggers ferroptosis in lung cancer. (2026) Nature. 649(8096):487-495. DOI: 10.1038/s41586-025-09710-8

Wu, K., Vaughan, A.J., Bossowski, J.P., Hao, Y., Ziogou, A., Kim, S.M., Kim, T.H., Nakamura, M.N., Pillai, R., Mancini, M., Rajalingam, S., Han, M., Nakamura, T., Wang, L., Chung, S., Simeone, D., Shackelford, D., Kang, Y.P., Conrad, M., Papagiannakopoulos, T. Targeting FSP1 triggers ferroptosis in lung cancer. (2025) bioRxiv. DOI: 10.1101/2025.08.07.668766

Cattle, M.A., Aguado, L.C., Sze, S., Venkittu, S., Wang, Y., Papagiannakopoulos, T., Smith, S., Rice, C.M., Schneider, W.M., Poirier, J.T. An enhanced Eco1 retron editor enables precision genome engineering in human cells without double-strand breaks. (2025) Nucleic Acids Research. 53(14). DOI: 10.1093/nar/gkaf716

Varghese, A., Gusarov, I., Gamallo-Lana, B., Dolgonos, D., Mankan, Y., Shamovsky, I., Phan, M., Jones, R., Gomez-Jenkins, M., White, E., Wang, R., Jones, D.R., Papagiannakopoulos, T., Pacold, M.E., Mar, A.C., Littman, D.R., Nudler, E. Unravelling cysteine-deficiency-associated rapid weight loss. (2025) Nature. 643(8072):776-784. DOI: 10.1038/s41586-025-08996-y

Cattle, M.A., Aguado, L.C., Sze, S., Venkittu, S., Wang, D.Y., Papagiannakopoulos, T., Smith, S., Rice, C.M., Schneider, W.M., Poirier, J.T. An enhanced Eco1 retron editor enables precision genome engineering in human cells without double-strand breaks. (2025) bioRxiv. DOI: 10.1101/2024.08.05.606586

Guzelsoy, G., Elorza, S.D., Ros, M., Schachtner, L.T., Hayashi, M., Hobson-Gutierrez, S., Rundstrom, P., Brunner, J.S., Pillai, R., Walkowicz, W.E., Finley, L.W.S., Deforet, M., Papagiannakopoulos, T., Carmona-Fontaine, C. Cooperative nutrient scavenging is an evolutionary advantage in cancer. (2025) Nature. 640(8058):534-542. DOI: 10.1038/s41586-025-08588-w

Cross, M., Dillin, A., Papagiannakopoulos, T. Bridging brain and body in cancer. (2024) Genes & Development. 38(17-20):814-816. DOI: 10.1101/gad.352300.124

Berndt, C., Alborzinia, H., Amen, V.S., Ayton, S., Barayeu, U., Bartelt, A., Bayir, H., Bebber, C.M., Birsoy, K., Böttcher, J.P., Brabletz, S., Brabletz, T., Brown, A.R., Brüne, B., Bulli, G., Bruneau, A., Chen, Q., DeNicola, G.M., Dick, T.P., Distéfano, A., Dixon, S.J., Engler, J.B., Esser-von Bieren, J., Fedorova, M., Friedmann Angeli, J.P., Friese, M.A., Fuhrmann, D.C., García-Sáez, A.J., Garbowicz, K., Götz, M., Gu, W., Hammerich, L., Hassannia, B., Jiang, X., Jeridi, A., Kang, Y.P., Kagan, V.E., Konrad, D.B., Kotschi, S., Lei, P., Le Tertre, M., Lev, S., Liang, D., Linkermann, A., Lohr, C., Lorenz, S., Luedde, T., Methner, A., Michalke, B., Milton, A.V., Min, J., Mishima, E., Müller, S., Motohashi, H., Muckenthaler, M.U., Murakami, S., Olzmann, J.A., Pagnussat, G., Pan, Z., Papagiannakopoulos, T., Pedrera Puentes, L., Pratt, D.A., Proneth, B., Ramsauer, L., Rodriguez, R., Saito, Y., Schmidt, F., Schmitt, C., Schulze, A., Schwab, A., Schwantes, A., Soula, M., Spitzlberger, B., Stockwell, B.R., Thewes, L., Thorn-Seshold, O., Toyokuni, S., Tonnus, W., Trumpp, A., Vandenabeele, P., Vanden Berghe, T., Venkataramani, V., Vogel, F.C.E., von Karstedt, S., Wang, F., Westermann, F., Wientjens, C., Wilhelm, C., Wölk, M., Wu, K., Yang, X., Yu, F., Zou, Y., Conrad, M. Ferroptosis in health and disease. (2024) Redox Biol. 75:103211. DOI: 10.1016/j.redox.2024.103211

Varghese, A., Gusarov, I., Gamallo-Lana, B., Dolgonos, D., Mankan, Y., Shamovsky, I., Phan, M., Jones, R., Gomez-Jenkins, M., White, E., Wang, R., Jones, D., Papagiannakopoulos, T., Pacold, M.E., Mar, A.C., Littman, D.R., Nudler, E. Unraveling cysteine deficiency-associated rapid weight loss. (2024) bioRxiv. DOI: 10.1101/2024.07.30.605703

França, G.S., Baron, M., King, B.R., Bossowski, J.P., Bjornberg, A., Pour, M., Rao, A., Patel, A.S., Misirlioglu, S., Barkley, D., Tang, K.H., Dolgalev, I., Liberman, D.A., Avital, G., Kuperwaser, F., Chiodin, M., Levine, D.A., Papagiannakopoulos, T., Marusyk, A., Lionnet, T., Yanai, I. Cellular adaptation to cancer therapy along a resistance continuum. (2024) Nature. 631(8022):876-883. DOI: 10.1038/s41586-024-07690-9

Pillai, R., LeBoeuf, S.E., Hao, Y., New, C., Blum, J.L.E., Rashidfarrokhi, A., Huang, S.M., Bahamon, C., Wu, W.L., Karadal-Ferrena, B., Herrera, A., Ivanova, E., Cross, M., Bossowski, J.P., Ding, H., Hayashi, M., Rajalingam, S., Karakousi, T., Sayin, V.I., Khanna, K.M., Wong, K.K., Wild, R., Tsirigos, A., Poirier, J.T., Rudin, C.M., Davidson, S.M., Koralov, S.B., Papagiannakopoulos, T. Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer. (2024) Science Advances. 10(13):eadm9859. DOI: 10.1126/sciadv.adm9859

Wu, K., El Zowalaty, A.E., Sayin, V.I., Papagiannakopoulos, T. The pleiotropic functions of reactive oxygen species in cancer. (2024) Nat Cancer. 5(3):384-399. DOI: 10.1038/s43018-024-00738-9

Ge, M., Papagiannakopoulos, T., Bar-Peled, L. Reductive stress in cancer: coming out of the shadows. (2024) Trends in Cancer. 10(2):103-112. DOI: 10.1016/j.trecan.2023.10.002

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. Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors. (2024) Cell Reports. 43(1):113629. DOI: 10.1016/j.celrep.2023.113629

Dolgalev, I., Zhou, H., Murrell, N., Le, H., Sakellaropoulos, T., Coudray, N., Zhu, K., Vasudevaraja, V., Yeaton, A., Goparaju, C., Li, Y., Sulaiman, I., Tsay, J.J., Meyn, P., Mohamed, H., Sydney, I., Shiomi, T., Ramaswami, S., Narula, N., Kulicke, R., Davis, F.P., Stransky, N., Smolen, G.A., Cheng, W.Y., Cai, J., Punekar, S., Velcheti, V., Sterman, D.H., Poirier, J.T., Neel, B., Wong, K.K., Chiriboga, L., Heguy, A., Papagiannakopoulos, T., Nadorp, B., Snuderl, M., Segal, L.N., Moreira, A.L., Pass, H.I., Tsirigos, A. Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma. (2023) Nature Communications. 14(1):6764. DOI: 10.1038/s41467-023-42327-x

Zavitsanou, A.M., Pillai, R., Hao, Y., Wu, W.L., Bartnicki, E., Karakousi, T., Rajalingam, S., Herrera, A., Karatza, A., Rashidfarrokhi, A., Solis, S., Ciampricotti, M., Yeaton, A.H., Ivanova, E., Wohlhieter, C.A., Buus, T.B., Hayashi, M., Karadal-Ferrena, B., Pass, H.I., Poirier, J.T., Rudin, C.M., Wong, K.K., Moreira, A.L., Khanna, K.M., Tsirigos, A., Papagiannakopoulos, T., Koralov, S.B. KEAP1 mutation in lung adenocarcinoma promotes immune evasion and immunotherapy resistance. (2023) Cell Reports. 42(11):113295. DOI: 10.1016/j.celrep.2023.113295

Schraink, T., Blumenberg, L., Hussey, G., George, S., Miller, B., Mathew, N., González-Robles, T.J., Sviderskiy, V., Papagiannakopoulos, T., Possemato, R., Fenyö, D., Ruggles, K.V. PhosphoDisco: A Toolkit for Co-regulated Phosphorylation Module Discovery in Phosphoproteomic Data. (2023) Molecular & Cellular Proteomics. 22(8):100596. DOI: 10.1016/j.mcpro.2023.100596

Rashidfarrokhi, A., Pillai, R., Hao, Y., Wu, W.L., Karadal-Ferrena, B., Dimitriadoy, S.G., Cross, M., Yeaton, A.H., Huang, S.M., Bhutkar, A.J., Herrera, A., Rajalingam, S., Hayashi, M., Huang, K.L., Bartnicki, E., Zavitsanou, A.M., Wohlhieter, C.A., Leboeuf, S.E., Chen, T., Loomis, C., Mezzano, V., Kulicke, R., Davis, F.P., Stransky, N., Smolen, G.A., Rudin, C.M., Moreira, A.L., Khanna, K.M., Pass, H.I., Wong, K.K., Koide, S., Tsirigos, A., Koralov, S.B., Papagiannakopoulos, T. Tumor-intrinsic LKB1-LIF signaling axis establishes a myeloid niche to promote immune evasion and tumor growth. (2023) bioRxiv. DOI: 10.1101/2023.07.15.549147

Pillai, R., LeBoeuf, S.E., Hao, Y., New, C., Blum, J.L.E., Rashidfarrokhi, A., Huang, S.M., Bahamon, C., Wu, W.L., Karadal-Ferrena, B., Herrera, A., Ivanova, E., Cross, M., Bossowski, J.P., Ding, H., Hayashi, M., Rajalingam, S., Karakousi, T., Sayin, V.I., Khanna, K.M., Wong, K.K., Wild, R., Tsirigos, A., Poirier, J.T., Rudin, C.M., Davidson, S.M., Koralov, S.B., Papagiannakopoulos, T. Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer. (2023) bioRxiv. DOI: 10.1101/2023.06.27.546750

Zhong, H., Lu, W., Tang, Y., Wiel, C., Wei, Y., Cao, J., Riedlinger, G., Papagiannakopoulos, T., Guo, J.Y., Bergo, M.O., Kang, Y., Ganesan, S., Sabaawy, H.E., Pine, S.R. SOX9 drives KRAS-induced lung adenocarcinoma progression and suppresses anti-tumor immunity. (2023) Oncogene. 42(27):2183-2194. DOI: 10.1038/s41388-023-02715-5

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. Metabolic Reprogramming by Histone Deacetylase Inhibition Selectively Targets NRF2-activated tumors. (2023) bioRxiv. DOI: 10.1101/2023.04.24.538118

Deng, J., Peng, D.H., Fenyo, D., Yuan, H., Lopez, A., Levin, D.S., Meynardie, M., Quinteros, M., Ranieri, M., Sahu, S., Lau, S.C.M., Shum, E., Velcheti, V., Punekar, S.R., Rekhtman, N., Dowling, C.M., Weerasekara, V., Xue, Y., Ji, H., Siu, Y., Jones, D., Hata, A.N., Shimamura, T., Poirier, J.T., Rudin, C.M., Hattori, T., Koide, S., Papagiannakopoulos, T., Neel, B.G., Bardeesy, N., Wong, K.K. In vivo metabolomics identifies CD38 as an emergent vulnerability in LKB1 -mutant lung cancer. (2023) bioRxiv. DOI: 10.1101/2023.04.18.537350

Weiss-Sadan, T., Ge, M., Hayashi, M., Gohar, M., Yao, C.H., de Groot, A., Harry, S., Carlin, A., Fischer, H., Shi, L., Wei, T.Y., Adelmann, C.H., Wolf, K., Vornbäumen, T., Dürr, B.R., Takahashi, M., Richter, M., Zhang, J., Yang, T.Y., Vijay, V., Fisher, D.E., Hata, A.N., Haigis, M.C., Mostoslavsky, R., Bardeesy, N., Papagiannakopoulos, T., Bar-Peled, L. NRF2 activation induces NADH-reductive stress, providing a metabolic vulnerability in lung cancer. (2023) Cell Metabolism. 35(4):722. DOI: 10.1016/j.cmet.2023.03.011

Weiss-Sadan, T., Ge, M., Hayashi, M., Gohar, M., Yao, C.H., de Groot, A., Harry, S., Carlin, A., Fischer, H., Shi, L., Wei, T.Y., Adelmann, C.H., Wolf, K., Vornbäumen, T., Dürr, B.R., Takahashi, M., Richter, M., Zhang, J., Yang, T.Y., Vijay, V., Fisher, D.E., Hata, A.N., Haigis, M.C., Mostoslavsky, R., Bardeesy, N., Papagiannakopoulos, T., Bar-Peled, L. NRF2 activation induces NADH-reductive stress, providing a metabolic vulnerability in lung cancer. (2023) Cell Metabolism. 35(3):487-503.e7. DOI: 10.1016/j.cmet.2023.01.012

Guidry, K., Vasudevaraja, V., Labbe, K., Mohamed, H., Serrano, J., Guidry, B.W., DeLorenzo, M., Zhang, H., Deng, J., Sahu, S., Almonte, C., Moreira, A.L., Tsirigos, A., Papagiannakopoulos, T., Pass, H., Snuderl, M., Wong, K.K. DNA Methylation Profiling Identifies Subgroups of Lung Adenocarcinoma with Distinct Immune Cell Composition, DNA Methylation Age, and Clinical Outcome. (2022) Clinical Cancer Research. 28(17):3824-3835. DOI: 10.1158/1078-0432.CCR-22-0391

Pillai, R., Hayashi, M., Zavitsanou, A.M., Papagiannakopoulos, T. NRF2: KEAPing Tumors Protected. (2022) Cancer Discovery. 12(3):625-643. DOI: 10.1158/2159-8290.CD-21-0922

Marzio, A., Kurz, E., Sahni, J.M., Di Feo, G., Puccini, J., Jiang, S., Hirsch, C.A., Arbini, A.A., Wu, W.L., Pass, H.I., Bar-Sagi, D., Papagiannakopoulos, T., Pagano, M. EMSY inhibits homologous recombination repair and the interferon response, promoting lung cancer immune evasion. (2022) Cell. 185(1):169-183.e19. DOI: 10.1016/j.cell.2021.12.005

Thandapani, P., Kloetgen, A., Witkowski, M.T., Glytsou, C., Lee, A.K., Wang, E., Wang, J., LeBoeuf, S.E., Avrampou, K., Papagiannakopoulos, T., Tsirigos, A., Aifantis, I. Valine tRNA levels and availability regulate complex I assembly in leukaemia. (2022) Nature. 601(7893):428-433. DOI: 10.1038/s41586-021-04244-1

Ciampricotti, M., Karakousi, T., Richards, A.L., Quintanal-Villalonga, Ã.€., Karatza, A., Caeser, R., Costa, E.A., Allaj, V., Manoj, P., Spainhower, K.B., Kombak, F.E., Sanchez-Rivera, F.J., Jaspers, J.E., Zavitsanou, A.M., Maddalo, D., Ventura, A., Rideout, W.M., Akama-Garren, E.H., Jacks, T., Donoghue, M.T.A., Sen, T., Oliver, T.G., Poirier, J.T., Papagiannakopoulos, T., Rudin, C.M. Rlf-Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung Cancer. (2021) Cancer Discovery. 11(12):3214-3229. DOI: 10.1158/2159-8290.CD-21-0441

Ding, H., Chen, Z., Wu, K., Huang, S.M., Wu, W.L., LeBoeuf, S.E., Pillai, R.G., Rabinowitz, J.D., Papagiannakopoulos, T. Activation of the NRF2 antioxidant program sensitizes tumors to G6PD inhibition. (2021) Science Advances. 7(47):eabk1023. DOI: 10.1126/sciadv.abk1023

Kerk, S.A., Papagiannakopoulos, T., Shah, Y.M., Lyssiotis, C.A. Metabolic networks in mutant KRAS-driven tumours: tissue specificities and the microenvironment. (2021) Nature Reviews Cancer. 21(8):510-525. DOI: 10.1038/s41568-021-00375-9

Zavitsanou, A.M., Papagiannakopoulos, T. Hunger brings down the tumor fort. (2021) Trends in Cell Biology. 31(8):616-617. DOI: 10.1016/j.tcb.2021.05.005

Deng, J., Thennavan, A., Dolgalev, I., Chen, T., Li, J., Marzio, A., Poirier, J.T., Peng, D.H., Bulatovic, M., Mukhopadhyay, S., Silver, H., Papadopoulos, E., Pyon, V., Thakurdin, C., Han, H., Li, F., Li, S., Ding, H., Hu, H., Pan, Y., Weerasekara, V., Jiang, B., Wang, E.S., Ahearn, I., Philips, M., Papagiannakopoulos, T., Tsirigos, A., Rothenberg, E., Gainor, J., Freeman, G.J., Rudin, C.M., Gray, N.S., Hammerman, P.S., Pagano, M., Heymach, J.V., Perou, C.M., Bardeesy, N., Wong, K.K. ULK1 inhibition overcomes compromised antigen presentation and restores antitumor immunity in LKB1 mutant lung cancer. (2021) Nat Cancer. 2(5):503-514. DOI: 10.1038/s43018-021-00208-6

Buus, T.B., Herrera, A., Ivanova, E., Mimitou, E., Cheng, A., Herati, R.S., Papagiannakopoulos, T., Smibert, P., Odum, N., Koralov, S.B. Improving oligo-conjugated antibody signal in multimodal single-cell analysis. (2021) Elife. 10. DOI: 10.7554/eLife.61973

Purohit, V., Wang, L., Yang, H., Li, J., Ney, G.M., Gumkowski, E.R., Vaidya, A.J., Wang, A., Bhardwaj, A., Zhao, E., Dolgalev, I., Zamperone, A., Abel, E.V., Magliano, M.P.D., Crawford, H.C., Diolaiti, D., Papagiannakopoulos, T.Y., Lyssiotis, C.A., Simeone, D.M. ATDC binds to KEAP1 to drive NRF2-mediated tumorigenesis and chemoresistance in pancreatic cancer. (2021) Genes & Development. 35(3-4):218-233. DOI: 10.1101/gad.344184.120

Tsay, J.J., Wu, B.G., Sulaiman, I., Gershner, K., Schluger, R., Li, Y., Yie, T.A., Meyn, P., Olsen, E., Perez, L., Franca, B., Carpenito, J., Iizumi, T., El-Ashmawy, M., Badri, M., Morton, J.T., Shen, N., He, L., Michaud, G., Rafeq, S., Bessich, J.L., Smith, R.L., Sauthoff, H., Felner, K., Pillai, R., Zavitsanou, A.M., Koralov, S.B., Mezzano, V., Loomis, C.A., Moreira, A.L., Moore, W., Tsirigos, A., Heguy, A., Rom, W.N., Sterman, D.H., Pass, H.I., Clemente, J.C., Li, H., Bonneau, R., Wong, K.K., Papagiannakopoulos, T., Segal, L.N. Lower Airway Dysbiosis Affects Lung Cancer Progression. (2021) Cancer Discovery. 11(2):293-307. DOI: 10.1158/2159-8290.CD-20-0263

Wu, W.L., Papagiannakopoulos, T. The Center Cannot Hold: NRF2 Battles Ferroptosis in the 3rd Dimension. (2020) Molecular Cell. 80(5):760-761. DOI: 10.1016/j.molcel.2020.11.022

Wu, L., Hollinshead, K.E.R., Hao, Y., Au, C., Kroehling, L., Ng, C., Lin, W.Y., Li, D., Silva, H.M., Shin, J., Lafaille, J.J., Possemato, R., Pacold, M.E., Papagiannakopoulos, T., Kimmelman, A.C., Satija, R., Littman, D.R. Niche-Selective Inhibition of Pathogenic Th17 Cells by Targeting Metabolic Redundancy. (2020) Cell. 182(3):641-654.e20. DOI: 10.1016/j.cell.2020.06.014

Okazaki, K., Papagiannakopoulos, T., Motohashi, H. Metabolic features of cancer cells in NRF2 addiction status. (2020) Biophys Rev. 12(2):435-441. DOI: 10.1007/s12551-020-00659-8

LeBoeuf, S.E., Wu, W.L., Karakousi, T.R., Karadal, B., Jackson, S.R., Davidson, S.M., Wong, K.K., Koralov, S.B., Sayin, V.I., Papagiannakopoulos, T. Activation of Oxidative Stress Response in Cancer Generates a Druggable Dependency on Exogenous Non-essential Amino Acids. (2020) Cell Metabolism. 31(2):339-350.e4. DOI: 10.1016/j.cmet.2019.11.012

Li, F., Huang, Q., Luster, T.A., Hu, H., Zhang, H., Ng, W.L., Khodadadi-Jamayran, A., Wang, W., Chen, T., Deng, J., Ranieri, M., Fang, Z., Pyon, V., Dowling, C.M., Bagdatlioglu, E., Almonte, C., Labbe, K., Silver, H., Rabin, A.R., Jani, K., Tsirigos, A., Papagiannakopoulos, T., Hammerman, P.S., Velcheti, V., Freeman, G.J., Qi, J., Miller, G., Wong, K.K. In Vivo Epigenetic CRISPR Screen Identifies Asf1a as an Immunotherapeutic Target in Kras-Mutant Lung Adenocarcinoma. (2020) Cancer Discovery. 10(2):270-287. DOI: 10.1158/2159-8290.CD-19-0780

Sayin, V.I., LeBoeuf, S.E., Papagiannakopoulos, T. Targeting Metabolic Bottlenecks in Lung Cancer. (2019) Trends in Cancer. 5(8):457-459. DOI: 10.1016/j.trecan.2019.06.001

Lignitto, L., LeBoeuf, S.E., Homer, H., Jiang, S., Askenazi, M., Karakousi, T.R., Pass, H.I., Bhutkar, A.J., Tsirigos, A., Ueberheide, B., Sayin, V.I., Papagiannakopoulos, T., Pagano, M. Nrf2 Activation Promotes Lung Cancer Metastasis by Inhibiting the Degradation of Bach1. (2019) Cell. 178(2):316-329.e18. DOI: 10.1016/j.cell.2019.06.003

McLoughlin, M.R., Orlicky, D.J., Prigge, J.R., Krishna, P., Talago, E.A., Cavigli, I.R., Eriksson, S., Miller, C.G., Kundert, J.A., Sayin, V.I., Sabol, R.A., Heinemann, J., Brandenberger, L.O., Iverson, S.V., Bothner, B., Papagiannakopoulos, T., Shearn, C.T., Arnér, E.S.J., Schmidt, E.E. TrxR1, Gsr, and oxidative stress determine hepatocellular carcinoma malignancy. (2019) Proceedings of the National Academy of Sciences of the United States of America. 116(23):11408-11417. DOI: 10.1073/pnas.1903244116

Hamza, B., Ng, S.R., Prakadan, S.M., Delgado, F.F., Chin, C.R., King, E.M., Yang, L.F., Davidson, S.M., DeGouveia, K.L., Cermak, N., Navia, A.W., Winter, P.S., Drake, R.S., Tammela, T., Li, C.M., Papagiannakopoulos, T., Gupta, A.J., Shaw Bagnall, J., Knudsen, S.M., Vander Heiden, M.G., Wasserman, S.C., Jacks, T., Shalek, A.K., Manalis, S.R. Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer. (2019) Proceedings of the National Academy of Sciences of the United States of America. 116(6):2232-2236. DOI: 10.1073/pnas.1814102116

Garcia-Bermudez, J., Baudrier, L., La, K., Zhu, X.G., Fidelin, J., Sviderskiy, V.O., Papagiannakopoulos, T., Molina, H., Snuderl, M., Lewis, C.A., Possemato, R.L., Birsoy, K. Publisher Correction: Aspartate is a limiting metabolite for cancer cell proliferation under hypoxia and in tumours. (2018) Nature Cell Biology. 20(10):1228. DOI: 10.1038/s41556-018-0184-2

Snuderl, M., Kannan, K., Pfaff, E., Wang, S., Stafford, J.M., Serrano, J., Heguy, A., Ray, K., Faustin, A., Aminova, O., Dolgalev, I., Stapleton, S.L., Zagzag, D., Chiriboga, L., Gardner, S.L., Wisoff, J.H., Golfinos, J.G., Capper, D., Hovestadt, V., Rosenblum, M.K., Placantonakis, D.G., LeBoeuf, S.E., Papagiannakopoulos, T.Y., Chavez, L., Ahsan, S., Eberhart, C.G., Pfister, S.M., Jones, D.T.W., Karajannis, M.A. Recurrent homozygous deletion of DROSHA and microduplication of PDE4DIP in pineoblastoma. (2018) Nature Communications. 9(1):2868. DOI: 10.1038/s41467-018-05029-3

Garcia-Bermudez, J., Baudrier, L., La, K., Zhu, X.G., Fidelin, J., Sviderskiy, V.O., Papagiannakopoulos, T., Molina, H., Snuderl, M., Lewis, C.A., Possemato, R.L., Birsoy, K. Aspartate is a limiting metabolite for cancer cell proliferation under hypoxia and in tumours. (2018) Nature Cell Biology. 20(7):775-781. DOI: 10.1038/s41556-018-0118-z

Petersen, D.R., Saba, L.M., Sayin, V.I., Papagiannakopoulos, T., Schmidt, E.E., Merrill, G.F., Orlicky, D.J., Shearn, C.T. Elevated Nrf-2 responses are insufficient to mitigate protein carbonylation in hepatospecific PTEN deletion mice. (2018) PLOS One. 13(5):e0198139. DOI: 10.1371/journal.pone.0198139

Minton, D.R., Nam, M., McLaughlin, D.J., Shin, J., Bayraktar, E.C., Alvarez, S.W., Sviderskiy, V.O., Papagiannakopoulos, T., Sabatini, D.M., Birsoy, K., Possemato, R. Serine Catabolism by SHMT2 Is Required for Proper Mitochondrial Translation Initiation and Maintenance of Formylmethionyl-tRNAs. (2018) Molecular Cell. 69(4):610-621.e5. DOI: 10.1016/j.molcel.2018.01.024

Alvarez, S.W., Sviderskiy, V.O., Terzi, E.M., Papagiannakopoulos, T., Moreira, A.L., Adams, S., Sabatini, D.M., Birsoy, K., Possemato, R. NFS1 undergoes positive selection in lung tumours and protects cells from ferroptosis. (2017) Nature. 551(7682):639-643. DOI: 10.1038/nature24637

Romero, R., Sayin, V.I., Davidson, S.M., Bauer, M.R., 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., Goparaju, C., 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. Keap1 loss promotes Kras-driven lung cancer and results in dependence on glutaminolysis. (2017) Nature Medicine. 23(11):1362-1368. DOI: 10.1038/nm.4407

Sayin, V.I., LeBoeuf, S.E., Singh, S.X., Davidson, S.M., Biancur, D., Guzelhan, B.S., Alvarez, S.W., Wu, W.L., Karakousi, T.R., Zavitsanou, A.M., Ubriaco, J., Muir, A., Karagiannis, D., Morris, P.J., Thomas, C.J., Possemato, R., Vander Heiden, M.G., Papagiannakopoulos, T. Activation of the NRF2 antioxidant program generates an imbalance in central carbon metabolism in cancer. (2017) Elife. 6. DOI: 10.7554/eLife.28083

Sayin, V.I., Papagiannakopoulos, T. Application of CRISPR-mediated genome engineering in cancer research. (2017) Cancer Letters. 387:10-17. DOI: 10.1016/j.canlet.2016.03.029

Ashouri, A., Sayin, V.I., Van den Eynden, J., Singh, S.X., Papagiannakopoulos, T., Larsson, E. Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. (2016) Nature Communications. 7:13197. DOI: 10.1038/ncomms13197

Mayers, J.R., Torrence, M.E., Danai, L.V., Papagiannakopoulos, T., Davidson, S.M., Bauer, M.R., Lau, A.N., Ji, B.W., Dixit, P.D., Hosios, A.M., Muir, A., Chin, C.R., Freinkman, E., Jacks, T., Wolpin, B.M., Vitkup, D., Vander Heiden, M.G. Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. (2016) Science. 353(6304):1161-5. DOI: 10.1126/science.aaf5171

Papagiannakopoulos, T.*, Bauer, M.R., Davidson, S.M., Heimann, M., Subbaraj, L., Bhutkar, A., Bartlebaugh, J., Vander Heiden, M.G., Jacks, T. Circadian Rhythm Disruption Promotes Lung Tumorigenesis. (2016) Cell Metabolism. 24(2):324-31. DOI: 10.1016/j.cmet.2016.07.001

Masri, S., Papagiannakopoulos, T., Kinouchi, K., Liu, Y., Cervantes, M., Baldi, P., Jacks, T., Sassone-Corsi, P. Lung Adenocarcinoma Distally Rewires Hepatic Circadian Homeostasis. (2016) Cell. 165(4):896-909. DOI: 10.1016/j.cell.2016.04.039

Davidson, S.M., Papagiannakopoulos, T., Olenchock, B.A., Heyman, J.E., Keibler, M.A., Luengo, A., Bauer, M.R., Jha, A.K., O’Brien, J.P., Pierce, K.A., Gui, D.Y., Sullivan, L.B., Wasylenko, T.M., Subbaraj, L., Chin, C.R., Stephanopolous, G., Mott, B.T., Jacks, T., Clish, C.B., Vander Heiden, M.G. Environment Impacts the Metabolic Dependencies of Ras-Driven Non-Small Cell Lung Cancer. (2016) Cell Metabolism. 23(3):517-28. DOI: 10.1016/j.cmet.2016.01.007

Akama-Garren, E.H., Joshi, N.S., Tammela, T., Chang, G.P., Wagner, B.L., Lee, D.Y., Rideout, W.M., Papagiannakopoulos, T., Xue, W., Jacks, T. A Modular Assembly Platform for Rapid Generation of DNA Constructs. (2016) Scientific Reports. 6:16836. DOI: 10.1038/srep16836

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. Rapid modelling of cooperating genetic events in cancer through somatic genome editing. (2014) Nature. 516(7531):428-31. DOI: 10.1038/nature13906

Mayers, J.R., Wu, C., Clish, C.B., Kraft, P., Torrence, M.E., Fiske, B.P., Yuan, C., Bao, Y., Townsend, M.K., Tworoger, S.S., Davidson, S.M., Papagiannakopoulos, T., Yang, A., Dayton, T.L., Ogino, S., Stampfer, M.J., Giovannucci, E.L., Qian, Z.R., Rubinson, D.A., Ma, J., Sesso, H.D., Gaziano, J.M., Cochrane, B.B., Liu, S., Wactawski-Wende, J., Manson, J.E., Pollak, M.N., Kimmelman, A.C., Souza, A., Pierce, K., Wang, T.J., Gerszten, R.E., Fuchs, C.S., Vander Heiden, M.G., Wolpin, B.M. Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development. (2014) Nature Medicine. 20(10):1193-1198. DOI: 10.1038/nm.3686

Xue, W., Chen, S., Yin, H., Tammela, T., Papagiannakopoulos, T., Joshi, N.S., Cai, W., Yang, G., Bronson, R., Crowley, D.G., Zhang, F., Anderson, D.G., Sharp, P.A., Jacks, T. CRISPR-mediated direct mutation of cancer genes in the mouse liver. (2014) Nature. 514(7522):380-4. DOI: 10.1038/nature13589

McFadden, D.G., Papagiannakopoulos, T., Taylor-Weiner, A., Stewart, C., Carter, S.L., Cibulskis, K., Bhutkar, A., McKenna, A., Dooley, A., Vernon, A., Sougnez, C., Malstrom, S., Heimann, M., Park, J., Chen, F., Farago, A.F., Dayton, T., Shefler, E., Gabriel, S., Getz, G., Jacks, T. Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing. (2014) Cell. 156(6):1298-1311. DOI: 10.1016/j.cell.2014.02.031

Papagiannakopoulos, T.*, Friedmann-Morvinski, D., Neveu, P., Dugas, J.C., Gill, R.M., Huillard, E., Liu, C., Zong, H., Rowitch, D.H., Barres, B.A., Verma, I.M., Kosik, K.S. Pro-neural miR-128 is a glioma tumor suppressor that targets mitogenic kinases. (2012) Oncogene. 31(15):1884-95. DOI: 10.1038/onc.2011.380

Papagiannakopoulos, T.*, Kosik, K.S. MicroRNA-124: micromanager of neurogenesis. (2009) Cell Stem Cell. 4(5):375-6. DOI: 10.1016/j.stem.2009.04.007

Xu, N., Papagiannakopoulos, T., Pan, G., Thomson, J.A., Kosik, K.S. MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. (2009) Cell. 137(4):647-58. DOI: 10.1016/j.cell.2009.02.038

Carrettiero, D.C., Hernandez, I., Neveu, P., Papagiannakopoulos, T., Kosik, K.S. The cochaperone BAG2 sweeps paired helical filament- insoluble tau from the microtubule. (2009) Journal of Neuroscience. 29(7):2151-61. DOI: 10.1523/JNEUROSCI.4660-08.2009

Papagiannakopoulos, T.*, Shapiro, A., Kosik, K.S. MicroRNA-21 targets a network of key tumor-suppressive pathways in glioblastoma cells. (2008) Cancer Research. 68(19):8164-72. DOI: 10.1158/0008-5472.CAN-08-1305

Papagiannakopoulos, T.*, Kosik, K.S. MicroRNAs: regulators of oncogenesis and stemness. (2008) BMC Med. 6:15. DOI: 10.1186/1741-7015-6-15

Partridge, J.J., Madsen, M.A., Ardi, V.C., Papagiannakopoulos, T., Kupriyanova, T.A., Quigley, J.P., Deryugina, E.I. Functional analysis of matrix metalloproteinases and tissue inhibitors of metalloproteinases differentially expressed by variants of human HT-1080 fibrosarcoma exhibiting high and low levels of intravasation and metastasis. (2007) Journal of Biological Chemistry. 282(49):35964-77. DOI: 10.1074/jbc.M705993200

Liu, T., Papagiannakopoulos, T., Puskar, K., Qi, S., Santiago, F., Clay, W., Lao, K., Lee, Y., Nelson, S.F., Kornblum, H.I., Doyle, F., Petzold, L., Shraiman, B., Kosik, K.S. Detection of a microRNA signal in an in vivo expression set of mRNAs. (2007) PLOS One. 2(8):e804. DOI: 10.1371/journal.pone.0000804

Deryugina, E.I., Zijlstra, A., Partridge, J.J., Kupriyanova, T.A., Madsen, M.A., Papagiannakopoulos, T., Quigley, J.P. Unexpected effect of matrix metalloproteinase down-regulation on vascular intravasation and metastasis of human fibrosarcoma cells selected in vivo for high rates of dissemination. (2005) Cancer Research. 65(23):10959-69. DOI: 10.1158/0008-5472.CAN-05-2228