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Paper

Moresco, Philip, Kastan, Jonathan P, Yang, Jung-In, Prabakar, Rishvanth, Kelley, Z Larkin, Minicozzi, Francesca, Adams, Dexter W, Cifani, Paolo, Tuveson, David A, Fearon, Douglas T (July 2025) Signal peptide-independent secretion of keratin-19 by pancreatic cancer cells. Proceedings of the National Academy of Sciences of the United States of America, 122 (27). e2426218122. ISSN 1091-6490 (Public Dataset)

Garg, Ankur, On, Kin Fan, Xiao, Yang, Elkayam, Elad, Cifani, Paolo, David, Yael, Joshua-Tor, Leemor (January 2025) The molecular basis of Human FN3K mediated phosphorylation of glycated substrates. Nature Communications, 16 (1). p. 941. ISSN 2041-1723 (Public Dataset)

Moresco, Philip, Kastan, Jonathan P, Yang, Jung-In, Prabakar, Rishvanth, Minicozzi, Francesca, Adams, Dexter W, Cifani, Paolo, Tuveson, David A, Fearon, Douglas T (January 2025) Signal peptide-independent secretion of keratin-19 by pancreatic cancer cells. bioRxiv. ISSN 2692-8205 (Submitted)

Swamynathan, Manojit M, Kuang, Shan, Watrud, Kaitlin E, Doherty, Mary R, Gineste, Charlotte, Mathew, Grinu, Gong, Grace Q, Cox, Hilary, Cheng, Eileen, Reiss, David, Kendall, Jude, Ghosh, Diya, Reczek, Colleen R, Zhao, Xiang, Herzka, Tali, Špokaitė, Saulė, Dessus, Antoine N, Kim, Seung Tea, Klingbeil, Olaf, Liu, Juan, Nowak, Dawid G, Alsudani, Habeeb, Wee, Tse-Luen, Park, Youngkyu, Minicozzi, Francesca, Rivera, Keith, Almeida, Ana S, Chang, Kenneth, Chakrabarty, Ram P, Wilkinson, John E, Gimotty, Phyllis A, Diermeier, Sarah D, Egeblad, Mikala, Vakoc, Christopher R, Locasale, Jason W, Chandel, Navdeep S, Janowitz, Tobias, Hicks, James B, Wigler, Michael, Pappin, Darryl J, Williams, Roger L, Cifani, Paolo, Tuveson, David A, Laporte, Jocelyn, Trotman, Lloyd C (October 2024) Dietary pro-oxidant therapy by a vitamin K precursor targets PI 3-kinase VPS34 function. Science, 386 (6720). eadk9167. ISSN 0036-8075

Yang, Xiaochun, Bhowmick, Krishanu, Rao, Shuyun, Xiang, Xiyan, Ohshiro, Kazufumi, Amdur, Richard L, Hassan, Md Imtaiyaz, Mohammad, Taj, Crandall, Keith, Cifani, Paolo, Shetty, Kirti, Lyons, Scott K, Merrill, Joseph R, Vegesna, Anil K, John, Sahara, Latham, Patricia S, Crawford, James M, Mishra, Bibhuti, Dasarathy, Srinivasan, Wang, Xin Wei, Yu, Herbert, Wang, Zhanwei, Huang, Hai, Krainer, Adrian R, Mishra, Lopa (August 2024) Aldehydes alter TGF-β signaling and induce obesity and cancer. Cell Reports, 43 (9). p. 114676. ISSN 2211-1247 (Public Dataset)

Garg, Ankur, On, Kin Fan, Xiao, Yang, Elkayam, Elad, Cifani, Paolo, David, Yael, Joshua-Tor, Leemor (August 2024) The molecular basis of Human FN3K mediated phosphorylation of glycated substrate. bioRxiv. (Public Dataset) (Submitted)

Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Yoshimoto, Toyoki, Alpsoy, Aktan, Panepinto, Maria C, Minicozzi, Francesca, Merrill, Joseph R, Cafiero, Amanda M, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Wee, Tse-Luen, Spector, David L, Lyons, Scott K, Tuveson, David A, Cifani, Paolo, Vakoc, Christopher R (July 2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. Cancer Discovery. ISSN 2159-8274 (Public Dataset)

Segovia, Danilo, Adams, Dexter W, Hoffman, Nickolas, Safaric Tepes, Polona, Wee, Tse-Luen, Cifani, Paolo, Joshua-Tor, Leemor, Krainer, Adrian R (May 2024) SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23. Proceedings of the National Academy of Sciences of the United States of America, 121 (21). e2322974121. ISSN 0027-8424 (Public Dataset)

Klingbeil, Olaf, Skopelitis, Damianos, Tonelli, Claudia, Alpsoy, Aktan, Minicozzi, Francesca, Aggarwal, Disha, Russo, Suzanne, Ha, Taehoon, Demerdash, Osama E, Spector, David L, Tuveson, David A, Cifani, Paolo, Vakoc, Christopher R (February 2024) MARK2/MARK3 kinases are catalytic co-dependencies of YAP/TAZ in human cancer. bioRxiv. (Submitted)

Segovia, Danilo, Adams, Dexter W, Hoffman, Nickolas, Tepes, Polona Safaric, Wee, Tse-Luen, Cifani, Paolo, Joshua-Tor, Leemor, Krainer, Adrian R (2024) SRSF1 interactome determined by proximity labeling reveals direct interaction with spliceosomal RNA helicase DDX23 (correction). Proceedings of the National Academy of Sciences of the United States of America, 121 (30). ISSN 0027-8424

Perlee, Sarah, Kikuchi, Sota, Nakadai, Tomoyoshi, Masuda, Takeshi, Ohtsuki, Sumio, Matsumoto, Makoto, Rahmutulla, Bahityar, Fukuyo, Masaki, Cifani, Paolo, Kentsis, Alex, Roeder, Robert G, Kaneda, Atsushi, Hoshii, Takayuki (October 2023) SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3. EMBO Reports, 24 (10). e57108. ISSN 1469-221X

Yao, Min, Preall, Jonathan, Yeh, Johannes, Pappin, Darryl J, Cifani, Paolo, Zhao, Yixin, Shen, Sophia, Moresco, Philip, He, Brian, Patel, Hardik, Habowski, Amber N, King, Daniel A, Raphael, Kara L, Rishi, Arvind, Sejpal, Divyesh V, Weiss, Matthew, Tuveson, David, Fearon, Douglas T (September 2023) Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens. JCI Insight. e172449. ISSN 2379-3708 (Public Dataset)

Herrejon Chavez, Florisela, Luo, Hanzhi, Cifani, Paolo, Pine, Alli, Chu, Karen L, Joshi, Suhasini, Barin, Ersilia, Schurer, Alexandra, Chan, Mandy, Chang, Kathryn, Han, Grace YQ, Pierson, Aspen J, Xiao, Michael, Yang, Xuejing, Kuehm, Lindsey M, Hong, Yuning, Nguyen, Diu TT, Chiosis, Gabriela, Kentsis, Alex, Leslie, Christina, Vu, Ly P, Kharas, Michael G (April 2023) RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nature Communications, 14 (1). p. 2290. ISSN 2041-1723 (Public Dataset)

Zhang, Lifang, Braynen, Janeen, Fahey, Audrey, Chopra, Kriti, Cifani, Paolo, Tadesse, Dimiru, Regulski, Michael, Hu, Fangle, van Dam, Hubertus JJ, Xie, Meng, Ware, Doreen, Blaby-Haas, Crysten E (2023) Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. Frontiers in Plant Science, 14. p. 1237722. ISSN 1664-462X

Cifani, Paolo, Kentsis, Alex (October 2022) Quantitative Cell Proteomic Atlas: Pathway-Scale Targeted Mass Spectrometry for High-Resolution Functional Profiling of Cell Signaling. Journal of Proteome Research, 21 (10). pp. 2535-2544. ISSN 1535-3893

Paul, Shilpi, Cifani, Paolo, Pappin, Darryl, Spratt, Thomas (May 2022) Unique DNA Polymerase kappa Interactome Suggests Novel Cellular Functions. The FASEB Journal, 36 Sup (S1). ISSN 0892-6638

Paul, Shilpi, Rebok, Abbey, Cifani, Paolo, Paul, Anirban, Pappin, Darryl, Huang, Tony, Spratt, Thomas (2022) Translesion DNA synthesis polymerase κ is essential to a carcinogen-induced nucleolar stress response. bioRxiv. (Submitted)

Cifani, Paolo, Li, Zhi, Luo, Danmeng, Grivainis, Mark, Intlekofer, Andrew M, Fenyö, David, Kentsis, Alex (April 2021) Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. Journal of Proteome Research, 20 (4). pp. 1835-1848. ISSN 1535-3893

Antao, Noelle V, Marcet-Ortega, Marina, Cifani, Paolo, Kentsis, Alex, Foley, Emily A (September 2019) A Cancer-Associated Missense Mutation in PP2A-Aα Increases Centrosome Clustering during Mitosis. iScience, 19. pp. 74-82. ISSN 2589-0042

Ortiz, Michael V, Ahmed, Saima, Burns, Melissa, Henssen, Anton G, Hollmann, Travis J, MacArthur, Ian, Gunasekera, Shehana, Gaewsky, Lyvia, Bradwin, Gary, Ryan, Jeremy, Letai, Anthony, He, Ying, Naranjo, Arlene, Chi, Yueh-Yun, LaQuaglia, Michael, Heaton, Todd, Cifani, Paolo, Dome, Jeffrey S, Gadd, Samantha, Perlman, Elizabeth, Mullen, Elizabeth, Steen, Hanno, Kentsis, Alex (August 2019) Prohibitin is a prognostic marker and therapeutic target to block chemotherapy resistance in Wilms’ tumor. JCI Insight, 4 (15). ISSN 2379-3708

Sher, Falak, Hossain, Mir, Seruggia, Davide, Schoonenberg, Vivien AC, Yao, Qiuming, Cifani, Paolo, Dassama, Laura MK, Cole, Mitchel A, Ren, Chunyan, Vinjamur, Divya S, Macias-Trevino, Claudio, Luk, Kevin, McGuckin, Connor, Schupp, Patrick G, Canver, Matthew C, Kurita, Ryo, Nakamura, Yukio, Fujiwara, Yuko, Wolfe, Scot A, Pinello, Luca, Maeda, Takahiro, Kentsis, Alex, Orkin, Stuart H, Bauer, Daniel E (July 2019) Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Nature Genetics, 51 (7). pp. 1149-1159. ISSN 1061-4036

Ser, Zheng, Cifani, Paolo, Kentsis, Alex (June 2019) Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. Journal of Proteome Research, 18 (6). pp. 2545-2558. ISSN 1535-3893

Griswold, Andrew R, Cifani, Paolo, Rao, Sahana D, Axelrod, Abram J, Miele, Matthew M, Hendrickson, Ronald C, Kentsis, Alex, Bachovchin, Daniel A (June 2019) A Chemical Strategy for Protease Substrate Profiling. Cell chemical biology, 26 (6). 901-907.e6. ISSN 2451-9456

Pronier, Elodie, Cifani, Paolo, Merlinsky, Tiffany R, Berman, Katharine Barr, Somasundara, Amritha Varshini Hanasoge, Rampal, Raajit K, LaCava, John, Wei, Karen E, Pastore, Friederike, Maag, Jesper LV, Park, Jane, Koche, Richard, Kentsis, Alex, Levine, Ross L (November 2018) Targeting the CALR interactome in myeloproliferative neoplasms. JCI Insight, 3 (22). ISSN 2379-3708

Brown, Fiona C, Still, Eric, Koche, Richard P, Yim, Christina Y, Takao, Sumiko, Cifani, Paolo, Reed, Casie, Gunasekera, Shehana, Ficarro, Scott B, Romanienko, Peter, Mark, Willie, McCarthy, Craig, de Stanchina, Elisa, Gonen, Mithat, Seshan, Venkatraman, Bhola, Patrick, O'Donnell, Conor, Spitzer, Barbara, Stutzke, Crystal, Lavallée, Vincent-Philippe, Hébert, Josée, Krivtsov, Andrei V, Melnick, Ari, Paietta, Elisabeth M, Tallman, Martin S, Letai, Anthony, Sauvageau, Guy, Pouliot, Gayle, Levine, Ross, Marto, Jarrod A, Armstrong, Scott A, Kentsis, Alex (April 2018) MEF2C Phosphorylation Is Required for Chemotherapy Resistance in Acute Myeloid Leukemia. Cancer Discovery, 8 (4). pp. 478-497. ISSN 2159-8274

Hoshii, Takayuki, Cifani, Paolo, Feng, Zhaohui, Huang, Chun-Hao, Koche, Richard, Chen, Chun-Wei, Delaney, Christopher D, Lowe, Scott W, Kentsis, Alex, Armstrong, Scott A (February 2018) A Non-catalytic Function of SETD1A Regulates Cyclin K and the DNA Damage Response. Cell, 172 (5). 1007-1021.e17. ISSN 0092-8674

Cifani, Paolo, Shakiba, Mojdeh, Chhangawala, Sagar, Kentsis, Alex (December 2017) ProteoModlR for functional proteomic analysis. BMC Bioinformatics, 18 (1). ISSN 1471-2105

Cifani, Paolo, Kentsis, Alex (November 2017) High Sensitivity Quantitative Proteomics Using Automated Multidimensional Nano-flow Chromatography and Accumulated Ion Monitoring on Quadrupole-Orbitrap-Linear Ion Trap Mass Spectrometer. Molecular and Cellular Proteomics, 16 (11). pp. 2006-2016. ISSN 1535-9476

Brown, Fiona C, Cifani, Paolo, Drill, Esther, He, Jie, Still, Eric, Zhong, Shan, Balasubramanian, Sohail, Pavlick, Dean, Yilmazel, Bahar, Knapp, Kristina M, Alonzo, Todd A, Meshinchi, Soheil, Stone, Richard M, Kornblau, Steven M, Marcucci, Guido, Gamis, Alan S, Byrd, John C, Gonen, Mithat, Levine, Ross L, Kentsis, Alex (January 2017) Genomics of primary chemoresistance and remission induction failure in paediatric and adult acute myeloid leukaemia. British Journal of Haematology, 176 (1). pp. 86-91. ISSN 0007-1048

Cifani, Paolo, Kentsis, Alex (January 2017) Towards comprehensive and quantitative proteomics for diagnosis and therapy of human disease. Proteomics, 17 (1-2). p. 1600079. ISSN 1615-9853

Waldemarson, Sofia, Kurbasic, Emila, Krogh, Morten, Cifani, Paolo, Berggård, Tord, Borg, Åke, James, Peter (December 2016) Proteomic analysis of breast tumors confirms the mRNA intrinsic molecular subtypes using different classifiers: a large-scale analysis of fresh frozen tissue samples. Breast Cancer Research, 18 (1). ISSN 1465-542X

Dhabaria, Avantika, Cifani, Paolo, Reed, Casie, Steen, Hanno, Kentsis, Alex (August 2015) A High-Efficiency Cellular Extraction System for Biological Proteomics. Journal of Proteome Research, 14 (8). pp. 3403-3408. ISSN 1535-3893

Cifani, Paolo, Kirik, Ufuk, Waldemarson, Sofia, James, Peter (July 2015) Molecular Portrait of Breast-Cancer-Derived Cell Lines Reveals Poor Similarity with Tumors. Journal of Proteome Research, 14 (7). pp. 2819-2827. ISSN 1535-3893

Franchin, Cinzia, Cesaro, Luca, Salvi, Mauro, Millioni, Renato, Iori, Elisabetta, Cifani, Paolo, James, Peter, Arrigoni, Giorgio, Pinna, Lorenzo (June 2015) Quantitative analysis of a phosphoproteome readily altered by the protein kinase CK2 inhibitor quinalizarin in HEK-293T cells. BBA: Proteins and Proteomics, 1854 (6). pp. 609-623. ISSN 1570-9639

Antberg, Linn, Cifani, Paolo, Sandin, Marianne, Levander, Fredrik, James, Peter (May 2012) Critical Comparison of Multidimensional Separation Methods for Increasing Protein Expression Coverage. Journal of Proteome Research, 11 (5). pp. 2644-2652. ISSN 1535-3893

Kirik, Ufuk, Cifani, Paolo, Albrekt, Ann-Sofie, Lindstedt, Malin, Heyden, Anders, Levander, Fredrik (May 2012) Multimodel Pathway Enrichment Methods for Functional Evaluation of Expression Regulation. Journal of Proteome Research, 11 (5). pp. 2955-2967. ISSN 1535-3893

Stella, Roberto, Cifani, Paolo, Peggion, Caterina, Hansson, Karin, Lazzari, Cristian, Bendz, Maria, Levander, Fredrik, Sorgato, Maria Catia, Bertoli, Alessandro, James, Peter (February 2012) Relative Quantification of Membrane Proteins in Wild-Type and Prion Protein (PrP)-Knockout Cerebellar Granule Neurons. Journal of Proteome Research, 11 (2). pp. 523-536. ISSN 1535-3893

Cifani, Paolo, Bendz, Maria, Wårell, Kristofer, Hansson, Karin, Levander, Fredrik, Sandin, Marianne, Krogh, Morten, Ovenberger, Marie, Fredlund, Erik, Vaapil, Marica, Pietras, Alexander, Påhlman, Sven, James, Peter (April 2011) Hunting for Protein Markers of Hypoxia by Combining Plasma Membrane Enrichment with a New Approach to Membrane Protein Analysis. Journal of Proteome Research, 10 (4). pp. 1645-1656. ISSN 1535-3893

Conference or Workshop Item

Lan, Wenjun, Sun, Shoujun, Nigri, Jeremy, Homer, Josh, Park, Young, Deschenes, Astrid, Cifani, Paolo, Cross, Justin, Gaeth, Victoria, Kim, Sunny, Ting, Shawn, Rubino, Rachel, Moses, John, Tuveson, David (January 2024) SOAT1 as a targetable KRAS dependency in PDAC. In: AACR Special Conference in Cancer Research: Pancreatic Cancer, 2023 Sep 27-30, Boston, Massachusetts.

Paul, S, Heinbaugh, A, Paul, A, Cifani, P, Pappin, D, Spratt, T (2023) Novel role of Translesion DNA synthesis polymerase kappa in the nucleolus and in nucleolar stress response recovery. In: Annual Meeting of the American-Society-for-Cell-Biology/ European-Molecular-Biology-Organisation, DEC 03-07, 2022, Washington, DC.

Book

Cifani, Paolo (2022) Automated Multidimensional Nanoscale Chromatography for Ultrasensitive Targeted Mass Spectrometry. Methods in Molecular Biology, 1 . Humana Press, New York, New York.