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2. DNA demethylation triggers cell free DNA release in colorectal cancer cells

Author

Pessei, Valeria, Macagno, Marco, Mariella, Elisa, Congiusta, Noemi, Battaglieri, Vittorio, Battuello, Paolo, Viviani, Marco, Gionfriddo, Giulia, Lamba, Simona, Lorenzato, Annalisa, Oddo, Daniele, Idrees, Fariha, Cavaliere, Alessandro, Bartolini, Alice, Guarrera, Simonetta, Linnebacher, Michael, Monteonofrio, Laura, Cardone, Luca, Milella, Michele, Bertotti, Andrea, Soddu, Silvia, Grassi, Elena, Crisafulli, Giovanni, Bardelli, Alberto, Barault, Ludovic, and Di Nicolantonio, Federica

Published
2024
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3. XENTURION is a population-level multidimensional resource of xenografts and tumoroids from metastatic colorectal cancer patients

Author

Leto, Simonetta M., Grassi, Elena, Avolio, Marco, Vurchio, Valentina, Cottino, Francesca, Ferri, Martina, Zanella, Eugenia R., Borgato, Sofia, Corti, Giorgio, di Blasio, Laura, Somale, Desiana, Vara-Messler, Marianela, Galimi, Francesco, Sassi, Francesco, Lupo, Barbara, Catalano, Irene, Pinnelli, Marika, Viviani, Marco, Sperti, Luca, Mellano, Alfredo, Ferrero, Alessandro, Zingaretti, Caterina C., Puliafito, Alberto, Primo, Luca, Bertotti, Andrea, and Trusolino, Livio

Published
2024
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4. Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer

Author

Malla, Sudhir B., Byrne, Ryan M., Lafarge, Maxime W., Corry, Shania M., Fisher, Natalie C., Tsantoulis, Petros K., Mills, Megan L., Ridgway, Rachel A., Lannagan, Tamsin R. M., Najumudeen, Arafath K., Gilroy, Kathryn L., Amirkhah, Raheleh, Maguire, Sarah L., Mulholland, Eoghan J., Belnoue-Davis, Hayley L., Grassi, Elena, Viviani, Marco, Rogan, Emily, Redmond, Keara L., Sakhnevych, Svetlana, McCooey, Aoife J., Bull, Courtney, Hoey, Emily, Sinevici, Nicoleta, Hall, Holly, Ahmaderaghi, Baharak, Domingo, Enric, Blake, Andrew, Richman, Susan D., Isella, Claudio, Miller, Crispin, Bertotti, Andrea, Trusolino, Livio, Loughrey, Maurice B., Kerr, Emma M., Tejpar, Sabine, Maughan, Timothy S., Lawler, Mark, Campbell, Andrew D., Leedham, Simon J., Koelzer, Viktor H., Sansom, Owen J., and Dunne, Philip D.

Published
2024
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7. Author Correction: Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer

Author

Malla, Sudhir B., Byrne, Ryan M., Lafarge, Maxime W., Corry, Shania M., Fisher, Natalie C., Tsantoulis, Petros K., Mills, Megan L., Ridgway, Rachel A., Lannagan, Tamsin R. M., Najumudeen, Arafath K., Gilroy, Kathryn L., Amirkhah, Raheleh, Maguire, Sarah L., Mulholland, Eoghan J., Belnoue-Davis, Hayley L., Grassi, Elena, Viviani, Marco, Rogan, Emily, Redmond, Keara L., Sakhnevych, Svetlana, McCooey, Aoife J., Bull, Courtney, Hoey, Emily, Sinevici, Nicoleta, Hall, Holly, Ahmaderaghi, Baharak, Domingo, Enric, Blake, Andrew, Richman, Susan D., Isella, Claudio, Miller, Crispin, Bertotti, Andrea, Trusolino, Livio, Loughrey, Maurice B., Kerr, Emma M., Tejpar, Sabine, Maughan, Timothy S., Lawler, Mark, Campbell, Andrew D., Leedham, Simon J., Koelzer, Viktor H., Sansom, Owen J., and Dunne, Philip D.

Published
2024
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9. Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

Author

Woo, Xing Yi, Giordano, Jessica, Srivastava, Anuj, Zhao, Zi-Ming, Lloyd, Michael W, de Bruijn, Roebi, Suh, Yun-Suhk, Patidar, Rajesh, Chen, Li, Scherer, Sandra, Bailey, Matthew H, Yang, Chieh-Hsiang, Cortes-Sanchez, Emilio, Xi, Yuanxin, Wang, Jing, Wickramasinghe, Jayamanna, Kossenkov, Andrew V, Rebecca, Vito W, Sun, Hua, Mashl, R Jay, Davies, Sherri R, Jeon, Ryan, Frech, Christian, Randjelovic, Jelena, Rosains, Jacqueline, Galimi, Francesco, Bertotti, Andrea, Lafferty, Adam, O’Farrell, Alice C, Modave, Elodie, Lambrechts, Diether, ter Brugge, Petra, Serra, Violeta, Marangoni, Elisabetta, El Botty, Rania, Kim, Hyunsoo, Kim, Jong-Il, Yang, Han-Kwang, Lee, Charles, Dean, Dennis A, Davis-Dusenbery, Brandi, Evrard, Yvonne A, Doroshow, James H, Welm, Alana L, Welm, Bryan E, Lewis, Michael T, Fang, Bingliang, Roth, Jack A, Meric-Bernstam, Funda, Herlyn, Meenhard, Davies, Michael A, Ding, Li, Li, Shunqiang, Govindan, Ramaswamy, Isella, Claudio, Moscow, Jeffrey A, Trusolino, Livio, Byrne, Annette T, Jonkers, Jos, Bult, Carol J, Medico, Enzo, and Chuang, Jeffrey H

Subjects
Cancer Genomics, Clinical Research, Genetics, Human Genome, Women's Health, Biotechnology, Cancer, Digestive Diseases, Good Health and Well Being, Animals, DNA Copy Number Variations, Databases, Genetic, Gene Expression Regulation, Neoplastic, Humans, Mice, Neoplasm Metastasis, Polymorphism, Single Nucleotide, Exome Sequencing, Xenograft Model Antitumor Assays, PDXNET Consortium, EurOPDX Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, affecting the accuracy of PDX modeling of human cancer. Here, we exhaustively analyze copy number alterations (CNAs) in 1,451 PDX and matched patient tumor (PT) samples from 509 PDX models. CNA inferences based on DNA sequencing and microarray data displayed substantially higher resolution and dynamic range than gene expression-based inferences, and they also showed strong CNA conservation from PTs through late-passage PDXs. CNA recurrence analysis of 130 colorectal and breast PT/PDX-early/PDX-late trios confirmed high-resolution CNA retention. We observed no significant enrichment of cancer-related genes in PDX-specific CNAs across models. Moreover, CNA differences between patient and PDX tumors were comparable to variations in multiregion samples within patients. Our study demonstrates the lack of systematic copy number evolution driven by the PDX mouse host.

Published
2021

12. Effective drug combinations in breast, colon and pancreatic cancer cells

Author

Jaaks, Patricia, Coker, Elizabeth A., Vis, Daniel J., Edwards, Olivia, Carpenter, Emma F., Leto, Simonetta M., Dwane, Lisa, Sassi, Francesco, Lightfoot, Howard, Barthorpe, Syd, van der Meer, Dieudonne, Yang, Wanjuan, Beck, Alexandra, Mironenko, Tatiana, Hall, Caitlin, Hall, James, Mali, Iman, Richardson, Laura, Tolley, Charlotte, Morris, James, Thomas, Frances, Lleshi, Ermira, Aben, Nanne, Benes, Cyril H., Bertotti, Andrea, Trusolino, Livio, Wessels, Lodewyk, and Garnett, Mathew J.

Published
2022
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13. Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin

Author

Tedesco, Martina, Giannese, Francesca, Lazarević, Dejan, Giansanti, Valentina, Rosano, Dalia, Monzani, Silvia, Catalano, Irene, Grassi, Elena, Zanella, Eugenia R., Botrugno, Oronza A., Morelli, Leonardo, Panina Bordignon, Paola, Caravagna, Giulio, Bertotti, Andrea, Martino, Gianvito, Aldrighetti, Luca, Pasqualato, Sebastiano, Trusolino, Livio, Cittaro, Davide, and Tonon, Giovanni

Published
2022
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14. The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization

Author

Dudová, Zdenka, Conte, Nathalie, Mason, Jeremy, Stuchlík, Dalibor, Peša, Radim, Halmagyi, Csaba, Perova, Zinaida, Mosaku, Abayomi, Thorne, Ross, Follette, Alex, Pivarč, Ľuboslav, Šašinka, Radim, Usman, Muhammad, Neuhauser, Steven, Begley, Dale A., Krupke, Debra M., Frassà, Massimiliano, Fiori, Alessandro, Corsi, Riccardo, Vezzadini, Luca, Isella, Claudio, Bertotti, Andrea, Bult, Carol, Parkinson, Helen, Medico, Enzo, Meehan, Terrence, and Křenek, Aleš

Published
2022
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16. PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models

Author

Meehan, Terrence F, Conte, Nathalie, Goldstein, Theodore, Inghirami, Giorgio, Murakami, Mark A, Brabetz, Sebastian, Gu, Zhiping, Wiser, Jeffrey A, Dunn, Patrick, Begley, Dale A, Krupke, Debra M, Bertotti, Andrea, Bruna, Alejandra, Brush, Matthew H, Byrne, Annette T, Caldas, Carlos, Christie, Amanda L, Clark, Dominic A, Dowst, Heidi, Dry, Jonathan R, Doroshow, James H, Duchamp, Olivier, Evrard, Yvonne A, Ferretti, Stephane, Frese, Kristopher K, Goodwin, Neal C, Greenawalt, Danielle, Haendel, Melissa A, Hermans, Els, Houghton, Peter J, Jonkers, Jos, Kemper, Kristel, Khor, Tin O, Lewis, Michael T, Lloyd, KC Kent, Mason, Jeremy, Medico, Enzo, Neuhauser, Steven B, Olson, James M, Peeper, Daniel S, Rueda, Oscar M, Seong, Je Kyung, Trusolino, Livio, Vinolo, Emilie, Wechsler-Reya, Robert J, Weinstock, David M, Welm, Alana, Weroha, S John, Amant, Frédéric, Pfister, Stefan M, Kool, Marcel, Parkinson, Helen, Butte, Atul J, and Bult, Carol J

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, 2.6 Resources and infrastructure (aetiology), Good Health and Well Being, Animals, Databases as Topic, Disease Models, Animal, Humans, Mice, Neoplasms, Patients, Xenograft Model Antitumor Assays, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Patient-derived tumor xenograft (PDX) mouse models have emerged as an important oncology research platform to study tumor evolution, mechanisms of drug response and resistance, and tailoring chemotherapeutic approaches for individual patients. The lack of robust standards for reporting on PDX models has hampered the ability of researchers to find relevant PDX models and associated data. Here we present the PDX models minimal information standard (PDX-MI) for reporting on the generation, quality assurance, and use of PDX models. PDX-MI defines the minimal information for describing the clinical attributes of a patient's tumor, the processes of implantation and passaging of tumors in a host mouse strain, quality assurance methods, and the use of PDX models in cancer research. Adherence to PDX-MI standards will facilitate accurate search results for oncology models and their associated data across distributed repository databases and promote reproducibility in research studies using these models. Cancer Res; 77(21); e62-66. ©2017 AACR.

Published
2017

20. Supplementary Figure 1 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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21. Supplementary Table 1 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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22. Supplementary Table 8 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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23. Supplementary Table 5 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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24. Supplementary Figure 5 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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25. Supplementary Table 2 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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26. Supplementary Table 9 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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27. Supplementary Table 7 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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28. Supplementary Figure 6 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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29. Supplementary Table 3 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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30. Supplementary Methods 1 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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31. Supplementary Figure 3 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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32. Supplementary Table 6 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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33. Supplementary Figure 2 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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34. Supplementary Table 4 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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35. Supplementary Figure 4 from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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36. Data from RAS/RAF Comutation and ERBB2 Copy Number Modulates HER2 Heterogeneity and Responsiveness to HER2-directed Therapy in Colorectal Cancer

Author

Singh, Harshabad, primary, Sahgal, Pranshu, primary, Kapner, Kevin, primary, Corsello, Steven M., primary, Gupta, Hersh, primary, Gujrathi, Rahul, primary, Li, Yvonne Y., primary, Cherniack, Andrew D., primary, El Alam, Raquelle, primary, Kerfoot, Joseph, primary, Andrews, Elizabeth, primary, Lee, Annette, primary, Nambiar, Chetan, primary, Hannigan, Alison M., primary, Remland, Joshua, primary, Brais, Lauren, primary, Leahy, Meghan E., primary, Rubinson, Douglas A., primary, Schlechter, Benjamin L., primary, Meyerson, Matthew, primary, Kuang, Yanan, primary, Paweletz, Cloud P., primary, Lee, Jessica K., primary, Quintanilha, Julia C.F., primary, Aguirre, Andrew J., primary, Perez, Kimberly J., primary, Huffman, Brandon M., primary, Rossi, Humberto, primary, Abrams, Thomas A., primary, Kabraji, Sheheryar, primary, Trusolino, Livio, primary, Bertotti, Andrea, primary, Sicinska, Ewa T., primary, Parikh, Aparna R., primary, Wolpin, Brian M., primary, Schrock, Alexa B., primary, Giannakis, Marios, primary, Ng, Kimmie, primary, Meyerhardt, Jeffrey A., primary, Hornick, Jason L., primary, Sethi, Nilay S., primary, and Cleary, James M., primary

Published
2024
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37. Heterogeneity and evolution of DNA mutation rates in microsatellite stable colorectal cancer

Author

Grassi, Elena, primary, Vurchio, Valentina, additional, Cresswell, George David, additional, Catalano, Irene, additional, Lupo, Barbara, additional, Sassi, Francesco, additional, Galimi, Francesco, additional, Borgato, Sofia, additional, Ferri, Martina, additional, Viviani, Marco, additional, Pompei, Simone, additional, Urgese, Gianvito, additional, Chen, Bingjie, additional, Zanella, Eugenia Rosalinda, additional, Cottino, Francesca, additional, Bardelli, Alberto, additional, Cosentino Lagormarsino, Marco, additional, Sottoriva, Andrea, additional, Trusolino, Livio, additional, and Bertotti, Andrea, additional

Published
2024
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38. Quantifying single-cell ERK dynamics in colorectal cancer organoids reveals EGFR as an amplifier of oncogenic MAPK pathway signalling

Author

Ponsioen, Bas, Post, Jasmin B., Buissant des Amorie, Julian R., Laskaris, Dimitrios, van Ineveld, Ravian L., Kersten, Simone, Bertotti, Andrea, Sassi, Francesco, Sipieter, François, Cappe, Benjamin, Mertens, Sander, Verlaan-Klink, Ingrid, Boj, Sylvia F., Vries, Rob G. J., Rehmann, Holger, Vandenabeele, Peter, Riquet, Franck B., Trusolino, Livio, Bos, Johannes L., and Snippert, Hugo J. G.

Published
2021
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39. Adaptive mutability of colorectal cancers in response to targeted therapies

Author

Russo, Mariangela, Crisafulli, Giovanni, Sogari, Alberto, Reilly, Nicole M., Arena, Sabrina, Lamba, Simona, Bartolini, Alice, Amodio, Vito, Magrì, Alessandro, Novara, Luca, Sarotto, Ivana, Nagel, Zachary D., Piett, Cortt G., Amatu, Alessio, Sartore-Bianchi, Andrea, Siena, Salvatore, Bertotti, Andrea, Trusolino, Livio, Corigliano, Mattia, Gherardi, Marco, Lagomarsino, Marco Cosentino, Di Nicolantonio, Federica, and Bardelli, Alberto

Published
2019

44. Pathway level subtyping identifies a slow-cycling and transcriptionally lethargic biological phenotype associated with poor clinical outcomes in colon cancer independent of genetics

Author

Malla, Sudhir B, primary, Byrne, Ryan M, additional, Lafarge, Maxime, additional, Corry, Shania M, additional, Fisher, Natalie C, additional, Tsantoulis, Petros, additional, Campbell, Andrew, additional, Lannagan, Tamsin, additional, Najumudeen, Arafath K, additional, Gilroy, Kathryn, additional, Amirkhah, Raheleh, additional, Maguire, Sarah, additional, Mulholland, Eoghan, additional, Belnoue-Davis, Hayley L, additional, Grassi, Elena, additional, Viviani, Marco, additional, Rogan, Emily, additional, Redmond, Keara, additional, Sakhnevych, Svetlana, additional, McCooey, Aoife, additional, Bull, Courtney, additional, Hoey, Emily, additional, Sinevici, Nicoleta, additional, Hall, Holly, additional, Ahmaderaghi, Baharak, additional, Domingo, Enric, additional, Blake, Andrew, additional, Richman, Susan, additional, Isella, Claudio, additional, Miller, Crispin, additional, Bertotti, Andrea, additional, Trusolino, Livio, additional, Loughrey, Maurice, additional, Kerr, Emma, additional, Tejpar, Sabine, additional, Maughan, Tim, additional, Lawler, Mark, additional, Leedham, Simon J, additional, Koelzer, Viktor H, additional, Sansom, Owen J, additional, and Dunne, Philip D, additional

Published
2024
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45. Radiologic and Genomic Evolution of Individual Metastases during HER2 Blockade in Colorectal Cancer

Author

Siravegna, Giulia, Lazzari, Luca, Crisafulli, Giovanni, Sartore-Bianchi, Andrea, Mussolin, Benedetta, Cassingena, Andrea, Martino, Cosimo, Lanman, Richard B., Nagy, Rebecca J., Fairclough, Stephen, Rospo, Giuseppe, Corti, Giorgio, Bartolini, Alice, Arcella, Pamela, Montone, Monica, Lodi, Francesca, Lorenzato, Annalisa, Vanzati, Alice, Valtorta, Emanuele, Cappello, Giovanni, Bertotti, Andrea, Lonardi, Sara, Zagonel, Vittorina, Leone, Francesco, Russo, Mariangela, Balsamo, Antonella, Truini, Mauro, Di Nicolantonio, Federica, Amatu, Alessio, Bonazzina, Erica, Ghezzi, Silvia, Regge, Daniele, Vanzulli, Angelo, Trusolino, Livio, Siena, Salvatore, Marsoni, Silvia, and Bardelli, Alberto

Published
2018
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46. Rituximab Treatment Prevents Lymphoma Onset in Gastric Cancer Patient-Derived Xenografts

Author

Corso, Simona, Cargnelutti, Marilisa, Durando, Stefania, Menegon, Silvia, Apicella, Maria, Migliore, Cristina, Capeloa, Tania, Ughetto, Stefano, Isella, Claudio, Medico, Enzo, Bertotti, Andrea, Sassi, Francesco, Sarotto, Ivana, Casorzo, Laura, Pisacane, Alberto, Mangioni, Monica, Sottile, Antonino, Degiuli, Maurizio, Fumagalli, Uberto, Sgroi, Giovanni, Molfino, Sarah, De Manzoni, Giovanni, Rosati, Riccardo, De Simone, Michele, Marrelli, Daniele, Saragoni, Luca, Rausei, Stefano, Pallabazzer, Giovanni, Roviello, Franco, Cassoni, Paola, Sapino, Anna, Bass, Adam, and Giordano, Silvia

Published
2018
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47. Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

Author

Behan, Fiona M., Iorio, Francesco, Picco, Gabriele, Gonçalves, Emanuel, Beaver, Charlotte M., Migliardi, Giorgia, Santos, Rita, Rao, Yanhua, Sassi, Francesco, Pinnelli, Marika, Ansari, Rizwan, Harper, Sarah, Jackson, David Adam, McRae, Rebecca, Pooley, Rachel, Wilkinson, Piers, van der Meer, Dieudonne, Dow, David, Buser-Doepner, Carolyn, Bertotti, Andrea, Trusolino, Livio, Stronach, Euan A., Saez-Rodriguez, Julio, Yusa, Kosuke, and Garnett, Mathew J.

Published
2019
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48. Phosphoproteomics of patient-derived xenographs identifies targets and markers associated with sensitivity and resistance to EGFR blockade in colorectal cancer

Author

Beekhof, Robin, primary, Bertotti, Andrea, additional, Böttger, Franziska, additional, Vurchio, Valentina, additional, Cottino, Francesca, additional, Zanella, Eugenia R., additional, Migliardi, Giorgia, additional, Viviani, Marco, additional, Grassi, Elena, additional, Lupo, Barbara, additional, Henneman, Alex A., additional, Knol, Jaco C., additional, Pham, Thang V., additional, de Goeij-de Haas, Richard, additional, Piersma, Sander R., additional, Labots, Mariette, additional, Verheul, Henk M.W., additional, Trusolino, Livio, additional, and Jimenez, Connie R., additional

Published
2023
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