04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DBMR Forschung Mu35 > Forschungsgruppe Präzisionsonkologie
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DBMR Forschung Mu35 > Forschungsgruppe Präzisionsonkologie

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2022

Berney, D M; Cree, I; Rao, V; Moch, H; Srigley, J R; Tsuzuki, T; Amin, M B; Comperat, E M; Hartmann, A; Menon, S; Netto, G J; Rubin, M A; Turajlic, S; Raspollini, M R; Tickoo, S K (2022). An Introduction to the WHO 5th Edition 2022 Classification of Testicular tumours. Histopathology, 81(4), pp. 459-466. Wiley 10.1111/his.14675

Lobo, João; Ohashi, Riuko; Amin, Mahul B; Berney, Daniel M; Compérat, Eva M; Cree, Ian A; Gill, Anthony J; Hartmann, Arndt; Menon, Santosh; Netto, George J; Raspollini, Maria R; Rubin, Mark A; Tan, Puay Hoon; Tickoo, Satish K; Tsuzuki, Toyonori; Turajlic, Samra; Zhou, Ming; Srigley, John R; Moch, Holger (2022). The WHO 2022 landscape of papillary and chromophobe renal cell carcinoma. Histopathology, 81(4), pp. 426-438. Wiley 10.1111/his.14700

Kench, James G; Amin, Mahul B; Berney, Daniel M; Compérat, Eva M; Cree, Ian A; Gill, Anthony J; Hartmann, Arndt; Menon, Santosh; Moch, Holger; Netto, George J; Raspollini, Maria R; Rubin, Mark A; Tan, Puay Hoon; Tsuzuki, Toyonori; Turjalic, Samra; van der Kwast, Theo H; Zhou, Ming; Srigley, John R (2022). WHO Classification of Tumours 5th Edition: Evolving Issues in Classification, Diagnosis and Prognostication of Prostate Cancer. Histopathology, 81(4), pp. 447-458. Wiley 10.1111/his.14711

Kashani, Elham; Schnidrig, Désirée; Hashemi Gheinani, Ali; Ninck, Martina Selina; Zens, Philipp; Maragkou, Theoni; Baumgartner, Ulrich; Schucht, Philippe; Rätsch, Gunnar; Rubin, Mark A; Berezowska, Sabina; Ng, Charlotte K Y; Vassella, Erik (2022). Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors. (In Press). Neuro-Oncology Oxford University Press 10.1093/neuonc/noac220

Ferguson, Alison M; Rubin, Mark A (2022). Lineage plasticity in prostate cancer: Looking beyond intrinsic alterations. (In Press). Cancer letters, 548(215901), p. 215901. Elsevier 10.1016/j.canlet.2022.215901

Netto, George J; Amin, Mahul B; Berney, Daniel M; Compérat, Eva M; Gill, Anthony J; Hartmann, Arndt; Menon, Santosh; Raspollini, Maria R; Rubin, Mark A; Srigley, John R; Hoon Tan, Puay; Tickoo, Satish K; Tsuzuki, Toyonori; Turajlic, Samra; Cree, Ian; Moch, Holger (2022). The 2022 World Health Organization Classification of Tumors of the Urinary System and Male Genital Organs-Part B: Prostate and Urinary Tract Tumors. (In Press). European urology Elsevier 10.1016/j.eururo.2022.07.002

Cotter, Kellie; Rubin, Mark A (2022). The evolving landscape of prostate cancer somatic mutations. The Prostate, 82 Suppl 1, S13-S24. Wiley 10.1002/pros.24353

Moch, Holger; Amin, Mahul B; Berney, Daniel M; Compérat, Eva M; Gill, Anthony J; Hartmann, Arndt; Menon, Santosh; Raspollini, Maria R; Rubin, Mark A; Srigley, John R; Hoon Tan, Puay; Tickoo, Satish K; Tsuzuki, Toyonori; Turajlic, Samra; Cree, Ian; Netto, George J (2022). The 2022 World Health Organization Classification of Tumours of the Urinary System and Male Genital Organs-Part A: Renal, Penile, and Testicular Tumours. (In Press). European urology Elsevier 10.1016/j.eururo.2022.06.016

Cyrta, Joanna; Prandi, Davide; Arora, Arshi; Hovelson, Daniel H; Sboner, Andrea; Rodriguez, Antonio; Fedrizzi, Tarcisio; Beltran, Himisha; Robinson, Dan R; Gopalan, Anurandha; True, Lawrence; Nelson, Peter S; Robinson, Brian D; Mosquera, Juan Miguel; Tomlins, Scott A; Shen, Ronglai; Demichelis, Francesca; Rubin, Mark A (2022). Comparative genomics of primary prostate cancer and paired metastases: insights from 12 molecular case studies. The journal of pathology, 257(3), pp. 274-284. Wiley 10.1002/path.5887

Turco, Fabio; Armstrong, Andrew; Attard, Gerhardt; Beer, Tomasz M; Beltran, Himisha; Bjartell, Anders; Bossi, Alberto; Briganti, Alberto; Bristow, Rob G; Bulbul, Muhammad; Caffo, Orazio; Chi, Kim N; Clarke, Caroline S; Clarke, Noel; Davis, Ian D; de Bono, Johann; Duran, Ignacio; Eeles, Ros; Efstathiou, Eleni; Efstathiou, Jason; ... (2022). What Experts Think About Prostate Cancer Management During the COVID-19 Pandemic: Report from the Advanced Prostate Cancer Consensus Conference 2021. European urology, 82(1), pp. 6-11. Elsevier 10.1016/j.eururo.2022.02.010

Turco, Fabio; Armstrong, Andrew; Attard, Gerhardt; Beer, Tomasz M; Beltran, Himisha; Bjartell, Anders; Bossi, Alberto; Briganti, Alberto; Bristow, Rob G; Bulbul, Muhammad; Caffo, Orazio; Chi, Kim N; Clarke, Caroline; Clarke, Noel; Davis, Ian D; de Bono, Johann; Duran, Ignacio; Eeles, Ros; Efstathiou, Eleni; Efstathiou, Jason; ... (2022). Corrigendum to "What Experts Think About Prostate Cancer Management During the COVID-19 Pandemic: Report from the Advanced Prostate Cancer Consensus Conference 2021" [Eur Urol 2022]. European urology, 82(1), e18-e19. Elsevier 10.1016/j.eururo.2022.04.004

Raman, Renuka; Villefranc, Jacques A; Ullmann, Timothy M; Thiesmeyer, Jessica; Anelli, Viviana; Yao, Jun; Hurley, James R; Pauli, Chantal; Bareja, Rohan; Wha Eng, Kenneth; Dorsaint, Princesca; Wilkes, David C; Beg, Shaham; Kudman, Sarah; Shaw, Reid; Churchill, Michael; Ahmed, Adnan; Keefer, Laurel; Misner, Ian; Nichol, Donna; ... (2022). Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer. Journal of experimental medicine, 219(6) Rockefeller University Press 10.1084/jem.20210390

Orlando, Francesco; Romanel, Alessandro; Trujillo, Blanca; Sigouros, Michael; Wetterskog, Daniel; Quaini, Orsetta; Leone, Gianmarco; Xiang, Jenny Z; Wingate, Anna; Tagawa, Scott; Jayaram, Anuradha; Linch, Mark; Jamal-Hanjani, Mariam; Swanton, Charles; Rubin, Mark A; Wyatt, Alexander W; Beltran, Himisha; Attard, Gerhardt; Demichelis, Francesca (2022). Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay. NAR cancer, 4(2), zcac016. Oxford University Press 10.1093/narcan/zcac016

Akhoundova, Dilara; Haberecker, Martina; Fritsch, Ralph; Höller, Sylvia; Kiessling, Michael K; Rechsteiner, Markus; Rüschoff, Jan H; Curioni-Fontecedro, Alessandra (2022). Targeting ALK in Neuroendocrine Tumors of the Lung. Frontiers in oncology, 12, p. 911294. Frontiers Research Foundation 10.3389/fonc.2022.911294

Janowczyk, Andrew; Baumhoer, Daniel; Dirnhofer, Stefan; Grobholz, Rainer; Kipar, Anja; de Leval, Laurence; Merkler, Doron; Michielin, Olivier; Moch, Holger; Perren, Aurel; Rottenberg, Sven; Rubbia-Brandt, Laura; Rubin, Mark A; Sempoux, Christine; Tolnay, Markus; Zlobec, Inti; Koelzer, Viktor Hendrik (2022). Towards a national strategy for digital pathology in Switzerland. (In Press). Virchows Archiv Springer 10.1007/s00428-022-03345-0

Rodriguez-Calero, Antonio; Gallon, John; Akhoundova, Dilara; Maletti, Sina; Ferguson, Alison; Cyrta, Joanna; Amstutz, Ursula; Garofoli, Andrea; Paradiso, Viola; Tomlins, Scott A; Hewer, Ekkehard; Genitsch, Vera; Fleischmann, Achim; Vassella, Erik; Rushing, Elisabeth J; Grobholz, Rainer; Fischer, Ingeborg; Jochum, Wolfram; Cathomas, Gieri; Osunkoya, Adeboye O; ... (2022). Alterations in homologous recombination repair genes in prostate cancer brain metastases. Nature Communications, 13(1), p. 2400. Springer Nature 10.1038/s41467-022-30003-5

de Brot, Simone; Lothion-Roy, Jennifer; Grau-Roma, Llorenç; White, Emily; Guscetti, Franco; Rubin, Mark A.; Mongan, Nigel P (2022). Histological and immunohistochemical investigation of canine prostate carcinoma with identification of common intraductal carcinoma component. Veterinary and comparative oncology, 20(1), pp. 38-49. Wiley 10.1111/vco.12704

Pauli, Chantal; De Boni, Lamberto; Pauwels, Jonathan E; Chen, Yanjiang; Planas-Paz, Lara; Shaw, Reid; Emerling, Brooke M; Grandori, Carla; Hopkins, Benjamin D; Rubin, Mark A (2022). A Functional Precision Oncology Approach to Identify Treatment Strategies for Myxofibrosarcoma Patients. Molecular cancer research, 20(2), pp. 244-252. American Association for Cancer Research AACR 10.1158/1541-7786.MCR-21-0255

Ryman-Tubb, Toby; Lothion-Roy, Jennifer H; Metzler, Veronika M; Harris, Anna E; Robinson, Brian D; Rizvanov, Albert A; Jeyapalan, Jennie N; James, Victoria H; England, Gary; Rutland, Catrin S; Persson, Jenny L; Kenner, Lukas; Rubin, Mark A; Mongan, Nigel P; de Brot, Simone (2022). Comparative pathology of dog and human prostate cancer. Veterinary medicine and science, 8(1), pp. 110-120. Wiley 10.1002/vms3.642

Vogl, Ursula M.; Beer, Tomasz M.; Davis, Ian D.; Shore, Neal D.; Sweeney, Christopher J.; Ost, Piet; Attard, Gerhardt; Bossi, Alberto; de Bono, Johann; Drake, Charles G.; Efstathiou, Eleni; Fanti, Stefano; Fizazi, Karim; Halabi, Susan; James, Nicolas; Mottet, Nicolas; Padhani, Anwar R.; Roach, Mack; Rubin, Mark; Sartor, Oliver; ... (2022). Lack of consensus identifies important areas for future clinical research: Advanced Prostate Cancer Consensus Conference (APCCC) 2019 findings. European journal of cancer, 160, pp. 24-60. Elsevier 10.1016/j.ejca.2021.09.036

2021

Bolis, Marco; Bossi, Daniela; Vallerga, Arianna; Ceserani, Valentina; Cavalli, Manuela; Impellizzieri, Daniela; Di Rito, Laura; Zoni, Eugenio; Mosole, Simone; Elia, Angela Rita; Rinaldi, Andrea; Pereira Mestre, Ricardo; D'Antonio, Eugenia; Ferrari, Matteo; Stoffel, Flavio; Jermini, Fernando; Gillessen, Silke; Bubendorf, Lukas; Schraml, Peter; Calcinotto, Arianna; ... (2021). Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression. Nature Communications, 12(1), p. 7033. Springer Nature 10.1038/s41467-021-26840-5

Mukhopadhyay, Chandrani; Yang, Chenyi; Xu, Limei; Liu, Deli; Wang, Yu; Huang, Dennis; Deonarine, Lesa Dayal; Cyrta, Joanna; Davicioni, Elai; Sboner, Andrea; Robinson, Brian D; Chinnaiyan, Arul M; Rubin, Mark A; Barbieri, Christopher E; Zhou, Pengbo (2021). G3BP1 inhibits Cul3SPOP to amplify AR signaling and promote prostate cancer. Nature Communications, 12(1), p. 6662. Springer Nature 10.1038/s41467-021-27024-x

Armstrong, Andrew J; Li, Xiaotong; Tucker, Matthew; Li, Shantao; Mu, Xinmeng Jasmine; Eng, Kenneth Wha; Sboner, Andrea; Rubin, Mark; Gerstein, Mark (2021). Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer. Prostate cancer and prostatic diseases, 24(3), pp. 786-793. Springer Nature 10.1038/s41391-021-00324-5

El Tekle, Geniver; Bernasocchi, Tiziano; Unni, Arun M; Bertoni, Francesco; Rossi, Davide; Rubin, Mark A.; Theurillat, Jean-Philippe (2021). Co-occurrence and mutual exclusivity: what cross-cancer mutation patterns can tell us. Trends in cancer, 7(9), pp. 823-836. Elsevier 10.1016/j.trecan.2021.04.009

Papachristodoulou, Alexandros; Rodríguez-Calero, Antonio; Panja, Sukanya; Margolskee, Elizabeth; Virk, Renu K; Milner, Teresa A; Martina, Luis Pina; Kim, Jaime Y; Di Bernardo, Matteo; Williams, Alanna B; Maliza, Elvis A; Caputo, Joseph M; Haas, Christopher; Wang, Vinson; De Castro, Guarionex Joel; Wenske, Sven; Hibshoosh, Hanina; McKiernan, James M; Shen, Michael M; Rubin, Mark A; ... (2021). NKX3.1 Localization to Mitochondria Suppresses Prostate Cancer Initiation. Cancer discovery, 11(9), pp. 2316-2333. American Association for Cancer Research 10.1158/2159-8290.CD-20-1765

Cotter, Kellie A; Gallon, John; Uebersax, Nadine; Rubin, Philip; Meyer, Kate D; Piscuoglio, Salvatore; Jaffrey, Samie R; Rubin, Mark A (2021). Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-Low Induction of Therapy Resistance. Molecular cancer research, 19(8), pp. 1398-1411. American Association for Cancer Research AACR 10.1158/1541-7786.MCR-21-0014

Servant, Raphaëlle; Garioni, Michele; Vlajnic, Tatjana; Blind, Melanie; Pueschel, Heike; Müller, David C; Zellweger, Tobias; Templeton, Arnoud J; Garofoli, Andrea; Maletti, Sina Laura; Piscuoglio, Salvatore; Rubin, Mark A.; Seifert, Helge; Rentsch, Cyrill A; Bubendorf, Lukas; Le Magnen, Clémentine (2021). Prostate cancer patient-derived organoids: detailed outcome from a prospective cohort of 81 clinical specimens. The journal of pathology, 254(5), pp. 543-555. Wiley 10.1002/path.5698

Ravi, Archna; Palamiuc, Lavinia; Loughran, Ryan M; Triscott, Joanna; Arora, Gurpreet K; Kumar, Avi; Tieu, Vivian; Pauli, Chantal; Reist, Matthias; Lew, Rachel J; Houlihan, Shauna L; Fellmann, Christof; Metallo, Christian; Rubin, Mark A.; Emerling, Brooke M (2021). PI5P4Ks drive metabolic homeostasis through peroxisome-mitochondria interplay. Developmental cell, 56(11), 1661-1676.e10. Elsevier 10.1016/j.devcel.2021.04.019

Guo, Christina; Crespo, Mateus; Gurel, Bora; Dolling, David; Rekowski, Jan; Sharp, Adam; Petremolo, Antonella; Sumanasuriya, Semini; Rodrigues, Daniel N; Ferreira, Ana; Pereira, Rita; Figueiredo, Ines; Mehra, Niven; Lambros, Maryou B K; Neeb, Antje; Gil, Veronica; Seed, George; Terstappen, Leon; Alimonti, Andrea; Drake, Charles G; ... (2021). CD38 in Advanced Prostate Cancers. European urology, 79(6), pp. 736-746. Elsevier 10.1016/j.eururo.2021.01.017

Sugita, Mayumi; Wilkes, David C; Bareja, Rohan; Eng, Kenneth W; Nataraj, Sarah; Jimenez-Flores, Reyna A; Yan, LunBiao; De Leon, Jeanne Pauline; Croyle, Jaclyn A; Kaner, Justin; Merugu, Swathi; Sharma, Sahil; MacDonald, Theresa Y; Noorzad, Zohal; Panchal, Palak; Pancirer, Danielle; Cheng, Shuhua; Xiang, Jenny Z; Olson, Luke; Van Besien, Koen; ... (2021). Targeting the epichaperome as an effective precision medicine approach in a novel PML-SYK fusion acute myeloid leukemia. NPJ precision oncology, 5(1), p. 44. Springer Nature 10.1038/s41698-021-00183-2

Fine, Samson W; Trpkov, Kiril; Amin, Mahul B; Algaba, Ferran; Aron, Manju; Baydar, Dilek E; Beltran, Antonio Lopez; Brimo, Fadi; Cheville, John C; Colecchia, Maurizio; Comperat, Eva; Costello, Tony; da Cunha, Isabela Werneck; Delprado, Warick; DeMarzo, Angelo M; Giannico, Giovanna A; Gordetsky, Jennifer B; Guo, Charles C; Hansel, Donna E; Hirsch, Michelle S; ... (2021). Practice patterns related to prostate cancer grading: results of a 2019 Genitourinary Pathology Society clinician survey. Urologic oncology, 39(5), 295.e1-295.e8. Elsevier 10.1016/j.urolonc.2020.08.027

Hommerding, Oliver; Allory, Yves; Argani, Pedram; Bismar, Tarek A; Bubendorf, Lukas; Canete-Portillo, Sofía; Chaux, Alcides; Chen, Ying-Bei; Cheng, Liang; Cubilla, Antonio L; Egevad, Lars; Gill, Anthony J; Grignon, David J; Hartmann, Arndt; Hes, Ondrej; Idrees, Muhammad T; Kao, Chia-Sui; Knowles, Margaret A; Looijenga, Leendert H J; Lotan, Tamara L; ... (2021). [Molecular pathology of urogenital tumors : Recommendations from the 2019 International Society of Urological Pathology (ISUP) Consensus Conference]. Der Pathologe, 42(3), pp. 310-318. Springer 10.1007/s00292-020-00888-4

Epstein, Jonathan I; Amin, Mahul B; Fine, Samson W; Algaba, Ferran; Aron, Manju; Baydar, Dilek E; Beltran, Antonio Lopez; Brimo, Fadi; Cheville, John C; Colecchia, Maurizio; Comperat, Eva; da Cunha, Isabela Werneck; Delprado, Warick; DeMarzo, Angelo M; Giannico, Giovanna A; Gordetsky, Jennifer B; Guo, Charles C; Hansel, Donna E; Hirsch, Michelle S; Huang, Jiaoti; ... (2021). The 2019 Genitourinary Pathology Society (GUPS) White Paper on Contemporary Grading of Prostate Cancer. Archives of pathology & laboratory medicine, 145(4), pp. 461-493. College of American Pathologists 10.5858/arpa.2020-0015-RA

Krause, Arthur; Roma, Luca; Lorber, Thomas; Dietsche, Tanja; Perrina, Valeria; Müller, David C; Lardinois, Didier; Ruiz, Christian; Savic Prince, Spasenija; Piscuoglio, Salvatore; Ng, Charlotte K. Y.; Bubendorf, Lukas (2021). Genomic evolutionary trajectory of metastatic squamous cell carcinoma of the lung. Translational lung cancer research, 10(4), pp. 1792-1803. AME Publishing 10.21037/tlcr-21-48

Bolis, Marco; Bossi, Daniela; Vallerga, Arianna; Cavalli, Manuela; di Rito, Laura; Zoni, Eugenio; Mosole, Simone; Rinaldi, Andrea; Pereira Mestre, Ricardo; D'Antonio, Eugenia; Ferrari, Matteo; Stoffel, Flavio; Jermini, Fernando; Gillessen Sommer, Silke; Bubendorf, Lukas; Schraml, Peter; Moch, Holger; Spahn, Martin; Thalmann, George; Kruithof-de Julio, Marianna; ... (15 March 2021). Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression. Research Square 10.21203/rs.3.rs-296396/v1

Karkampouna, Sofia; La Manna, Federico; Benjak, Andrej; Kiener, Mirjam; De Menna, Marta; Zoni, Eugenio; Grosjean, Joël; Klima, Irena; Garofoli, Andrea; Bolis, Marco; Vallerga, Arianna; Theurillat, Jean-Philippe; De Filippo, Maria R.; Genitsch, Vera; Keller, David; Booij, Tijmen H; Stirnimann, Christian U; Eng, Kenneth; Sboner, Andrea; Ng, Kiu Yan Charlotte; ... (2021). Patient-derived xenografts and organoids model therapy response in prostate cancer. Nature communications, 12(1), p. 1117. 10.1038/s41467-021-21300-6

Bernasocchi, Tiziano; El Tekle, Geniver; Bolis, Marco; Mutti, Azzurra; Vallerga, Arianna; Brandt, Laura P.; Spriano, Filippo; Svinkina, Tanya; Zoma, Marita; Ceserani, Valentina; Rinaldi, Anna; Janouskova, Hana; Bossi, Daniela; Cavalli, Manuela; Mosole, Simone; Geiger, Roger; Dong, Ze; Yang, Cai-Guang; Albino, Domenico; Rinaldi, Andrea; ... (2021). Dual functions of SPOP and ERG dictate androgen therapy responses in prostate cancer. Nature communications, 12(1), p. 734. Nature Publishing Group 10.1038/s41467-020-20820-x

Formaggio, Nicolò; Rubin, Mark A.; Theurillat, Jean-Philippe (2021). Loss and revival of androgen receptor signaling in advanced prostate cancer. Oncogene, 40(7), pp. 1205-1216. Springer Nature 10.1038/s41388-020-01598-0

2020

Rubin, Mark A.; Bristow, Robert G; Thienger, Phillip D.; Dive, Caroline; Imielinski, Marcin (2020). Impact of Lineage Plasticity to and from a Neuroendocrine Phenotype on Progression and Response in Prostate and Lung Cancers. Molecular cell, 80(4), pp. 562-577. Cell Press 10.1016/j.molcel.2020.10.033

Cyrta, Joanna; Augspach, Anke; De Filippo, Maria Rosaria; Prandi, Davide; Thienger, Phillip; Benelli, Matteo; Cooley, Victoria; Bareja, Rohan; Wilkes, David; Chae, Sung-Suk; Cavaliere, Paola; Dephoure, Noah; Uldry, Anne-Christine; Braga Lagache, Sophie; Roma, Luca; Cohen, Sandra; Jaquet, Muriel; Brandt, Laura P.; Alshalalfa, Mohammed; Puca, Loredana; ... (2020). Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity. Nature Communications, 11(1), p. 5549. Springer Nature 10.1038/s41467-020-19328-1

Bailey, Matthew H; Meyerson, William U; Dursi, Lewis Jonathan; Wang, Liang-Bo; Dong, Guanlan; Liang, Wen-Wei; Weerasinghe, Amila; Li, Shantao; Kelso, Sean; Saksena, Gordon; Ellrott, Kyle; Wendl, Michael C; Wheeler, David A; Getz, Gad; Simpson, Jared T; Gerstein, Mark B; Ding, Li (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11(1), p. 4748. Springer Nature 10.1038/s41467-020-18151-y

Thienger, Phillip; Rubin, Mark A. (2020). SETting Up for Epigenetic Regulation of Advanced Prostate Cancer. Cancer cell, 38(3), pp. 309-311. Cell Press 10.1016/j.ccell.2020.08.009

Lotan, Tamara L; Tomlins, Scott A; Bismar, Tarek A; Van der Kwast, Theodorus H; Grignon, David; Egevad, Lars; Kristiansen, Glen; Pritchard, Colin C; Rubin, Mark A; Bubendorf, Lukas (2020). Report From the International Society of Urological Pathology (ISUP) Consultation Conference on Molecular Pathology of Urogenital Cancers. I. Molecular Biomarkers in Prostate Cancer. The American journal of surgical pathology, 44(7), e15-e29. Wolters Kluwer Health 10.1097/PAS.0000000000001450

Auguste, Aurélie; Blanc-Durand, Félix; Deloger, Marc; Le Formal, Audrey; Bareja, Rohan; Wilkes, David C; Richon, Catherine; Brunn, Béatrice; Caron, Olivier; Devouassoux-Shisheboran, Mojgan; Gouy, Sébastien; Morice, Philippe; Bentivegna, Enrica; Sboner, Andrea; Elemento, Olivier; Rubin, Mark A; Pautier, Patricia; Genestie, Catherine; Cyrta, Joanna and Leary, Alexandra (2020). Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis. Cells, 9(6) MDPI 10.3390/cells9061496

Pisapia, David J; Ohara, Kentaro; Bareja, Rohan; Wilkes, David C; Hissong, Erika; Croyle, Jaclyn A; Kim, Joon-Hyung; Saab, Jad; MacDonald, Theresa Y; Beg, Shaham; O'Reilly, Catherine; Kudman, Sarah; Rubin, Mark A; Elemento, Olivier; Sboner, Andrea; Greenfield, Jeffrey; Mosquera, Juan Miguel (2020). Fusions involving BCOR and CREBBP are rare events in infiltrating glioma. Acta neuropathologica communications, 8(1), p. 80. BioMed Central 10.1186/s40478-020-00951-4

Rubin, Mark; Largiadèr, Carlo; Staub, Timo (2020). Das Bern Center for Precision Medicine (BCPM). Schweizer Krebsbulletin / Bulletin suisse du cancer(01/20), pp. 48-50. Bern: Istituto oncologico della Svizzera Italiana

Reyna, Matthew A; Haan, David; Paczkowska, Marta; Verbeke, Lieven P C; Vazquez, Miguel; Kahraman, Abdullah; Pulido-Tamayo, Sergio; Barenboim, Jonathan; Wadi, Lina; Dhingra, Priyanka; Shrestha, Raunak; Getz, Gad; Lawrence, Michael S; Pedersen, Jakob Skou; Rubin, Mark Andrew; Wheeler, David A; Brunak, Søren; Izarzugaza, Jose M G; Khurana, Ekta; Marchal, Kathleen; ... (2020). Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications, 11(1), p. 729. Nature Publishing Group 10.1038/s41467-020-14367-0

Shuai, Shimin; Gallinger, Steven; Stein, Lincoln (2020). Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature communications, 11(1), p. 734. Nature Publishing Group 10.1038/s41467-019-13929-1

Jiao, Wei; Atwal, Gurnit; Polak, Paz; Karlic, Rosa; Cuppen, Edwin; Danyi, Alexandra; de Ridder, Jeroen; van Herpen, Carla; Lolkema, Martijn P; Steeghs, Neeltje; Getz, Gad; Morris, Quaid; Stein, Lincoln D (2020). A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communications, 11(1), p. 728. Springer Nature 10.1038/s41467-019-13825-8

Arriaga, Juan M.; Panja, Sukanya; Alshalalfa, Mohammed; Zhao, Junfei; Zou, Min; Giacobbe, Arianna; Madubata, Chioma J.; Kim, Jaime Yeji; Rodriguez, Antonio; Coleman, Ilsa; Virk, Renu K.; Hibshoosh, Hanina; Ertunc, Onur; Ozbek, Büşra; Fountain, Julia; Jeffrey Karnes, R.; Luo, Jun; Antonarakis, Emmanuel S.; Nelson, Peter S.; Feng, Felix Y.; ... (2020). A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance. Nature ancer, 1(11), pp. 1082-1096. Springer Nature 10.1038/s43018-020-00125-0

2019

Beltran, Himisha; Hruszkewycz, Andrew; Scher, Howard I; Hildesheim, Jeffrey; Isaacs, Jennifer; Yu, Evan Y; Kelly, Kathleen; Lin, Daniel; Dicker, Adam; Arnold, Julia; Hecht, Toby; Wicha, Max; Sears, Rosalie; Rowley, David; White, Richard; Gulley, James L; Lee, John; Diaz Meco, Maria; Small, Eric J; Shen, Michael; ... (2019). The Role of Lineage Plasticity in Prostate Cancer Therapy Resistance. Clinical cancer research, 25(23), pp. 6916-6924. American Association for Cancer Research 10.1158/1078-0432.CCR-19-1423

Persi, Erez; Prandi, Davide; Wolf, Yuri I; Pozniak, Yair; Barnabas, Georgina D; Levanon, Keren; Barshack, Iris; Barbieri, Christopher; Gasperini, Paola; Beltran, Himisha; Faltas, Bishoy M; Rubin, Mark A.; Geiger, Tamar; Koonin, Eugene V; Demichelis, Francesca; Horn, David (2019). Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 116(34), pp. 16987-16996. National Academy of Sciences NAS 10.1073/pnas.1908790116

Lou, Shaoke; Cotter, Kellie A.; Li, Tianxiao; Liang, Jin; Mohsen, Hussein; Liu, Jason; Zhang, Jing; Cohen, Sandra; Xu, Jinrui; Yu, Haiyuan; Rubin, Mark A.; Gerstein, Mark (2019). GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. PLoS genetics, 15(8), e1007860. Public Library of Science 10.1371/journal.pgen.1007860

Robinson, Brian D; Vlachostergios, Panagiotis J; Bhinder, Bhavneet; Liu, Weisi; Li, Kailyn; Moss, Tyler J; Bareja, Rohan; Park, Kyung; Tavassoli, Peyman; Cyrta, Joanna; Tagawa, Scott T; Nanus, David M; Beltran, Himisha; Molina, Ana M; Khani, Francesca; Miguel Mosquera, Juan; Xylinas, Evanguelos; Shariat, Shahrokh F; Scherr, Douglas S; Rubin, Mark A.; ... (2019). Upper tract urothelial carcinoma has a luminal-papillary T-cell depleted contexture and activated FGFR3 signaling. Nature Communications, 10(1), p. 2977. Springer Nature 10.1038/s41467-019-10873-y

Shen, Michael M; Rubin, Mark Andrew (2019). Prostate Cancer Research at the Crossroads. Cold Spring Harbor perspectives in medicine, 9(7) Cold Spring Harbor Laboratory Press 10.1101/cshperspect.a036277

Abida, Wassim; Cyrta, Joanna; Heller, Glenn; Prandi, Davide; Armenia, Joshua; Coleman, Ilsa; Cieslik, Marcin; Benelli, Matteo; Robinson, Dan; Van Allen, Eliezer M; Sboner, Andrea; Fedrizzi, Tarcisio; Mosquera, Juan Miguel; Robinson, Brian D; De Sarkar, Navonil; Kunju, Lakshmi P; Tomlins, Scott; Wu, Yi Mi; Nava Rodrigues, Daniel; Loda, Massimo; ... (2019). Genomic correlates of clinical outcome in advanced prostate cancer. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 116(23), pp. 11428-11436. National Academy of Sciences NAS 10.1073/pnas.1902651116

Augello, Michael A; Liu, Deli; Deonarine, Lesa D; Robinson, Brian D; Huang, Dennis; Stelloo, Suzan; Blattner, Mirjam; Doane, Ashley S; Wong, Elissa W P; Chen, Yu; Rubin, Mark A.; Beltran, Himisha; Elemento, Olivier; Bergman, Andries M; Zwart, Wilbert; Sboner, Andrea; Dephoure, Noah; Barbieri, Christopher E (2019). CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer cell, 35(4), 603-617.e8. Cell Press 10.1016/j.ccell.2019.03.001

Lee, Rachel S; Zhang, Luxi; Berger, Adeline; Lawrence, Mitchell G; Song, Jiangning; Niranjan, Birunthi; Davies, Rebecca G; Lister, Natalie L; Sandhu, Shahneen K; Rubin, Mark A.; Risbridger, Gail P; Taylor, Renea A; Rickman, David S; Horvath, Lisa G; Daly, Roger J (2019). Characterization of the ERG-regulated Kinome in Prostate Cancer Identifies TNIK as a Potential Therapeutic Target. Neoplasia, 21(4), pp. 389-400. Elsevier 10.1016/j.neo.2019.02.005

Rubin, Mark A.; Demichelis, Francesca (2019). The Genomics of Prostate Cancer: A Historic Perspective. Cold Spring Harbor perspectives in medicine, 9(3) Cold Spring Harbor Laboratory Press 10.1101/cshperspect.a034942

Skvortsova, Ksenia; Masle-Farquhar, Etienne; Luu, Phuc-Loi; Song, Jenny Z; Qu, Wenjia; Zotenko, Elena; Gould, Cathryn M; Du, Qian; Peters, Timothy J; Colino-Sanguino, Yolanda; Pidsley, Ruth; Nair, Shalima S; Khoury, Amanda; Smith, Grady C; Miosge, Lisa A; Reed, Joanne H; Kench, James G; Rubin, Mark A.; Horvath, Lisa; Bogdanovic, Ozren; ... (2019). DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns. Cancer cell, 35(2), 297-314.e8. Cell Press 10.1016/j.ccell.2019.01.004

Beltran, Himisha; Oromendia, Clara; Danila, Daniel C; Montgomery, Bruce; Hoimes, Christopher; Szmulewitz, Russell Z; Vaishampayan, Ulka; Armstrong, Andrew J; Stein, Mark; Pinski, Jacek; Mosquera, Juan M; Sailer, Verena; Bareja, Rohan; Romanel, Alessandro; Gumpeni, Naveen; Sboner, Andrea; Dardenne, Etienne; Puca, Loredana; Prandi, Davide; Rubin, Mark A.; ... (2019). A Phase II Trial of the Aurora Kinase A Inhibitor Alisertib for Patients with Castration-resistant and Neuroendocrine Prostate Cancer: Efficacy and Biomarkers. Clinical cancer research, 25(1), pp. 43-51. American Association for Cancer Research 10.1158/1078-0432.CCR-18-1912

Fernandez, Evan M; Eng, Kenneth; Beg, Shaham; Beltran, Himisha; Faltas, Bishoy M; Mosquera, Juan Miguel; Nanus, David M; Pisapia, David J; Rao, Rema A; Robinson, Brian D; Rubin, Mark A.; Elemento, Olivier; Sboner, Andrea; Shah, Manish A; Song, Wei (2019). Cancer-Specific Thresholds Adjust for Whole Exome Sequencing-based Tumor Mutational Burden Distribution. JCO precision oncology, 3 American Society of Clinical Oncology 10.1200/PO.18.00400

Karkampouna, Sofia; Grosjean, Joël; Klima, Irena; Genitsch, Vera; Sboner, A.; K. Y. Ng, C.; De Filippo, M.R.; Piscuoglio, S.; Spahn, M.; Rubin, Mark Andrew; Thalmann, G.N.; Kruithof-de Julio, Marianna (2019). Establishment of an androgen-sensitive patient derived xenograft model of prostate cancer. European Urology Supplements, 18(1), e1154. Elsevier 10.1016/S1569-9056(19)30831-0

2018

Boysen, Gunther; Rodrigues, Daniel N; Rescigno, Pasquale; Seed, George; Dolling, David; Riisnaes, Ruth; Crespo, Mateus; Zafeiriou, Zafeiris; Sumanasuriya, Semini; Bianchini, Diletta; Hunt, Joanne; Moloney, Deirdre; Perez-Lopez, Raquel; Tunariu, Nina; Miranda, Susana; Figueiredo, Inês; Ferreira, Ana; Christova, Rossitza; Gil, Veronica; Aziz, Sara; ... (2018). SPOP-Mutated/CHD1-Deleted Lethal Prostate Cancer and Abiraterone Sensitivity. Clinical cancer research, 24(22), pp. 5585-5593. American Association for Cancer Research 10.1158/1078-0432.CCR-18-0937

Kahles, André; Lehmann, Kjong-Van; Toussaint, Nora C; Hüser, Matthias; Stark, Stefan G; Sachsenberg, Timo; Stegle, Oliver; Kohlbacher, Oliver; Sander, Chris; Rätsch, Gunnar (2018). Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer cell, 34(2), 211-224.e6. Cell Press 10.1016/j.ccell.2018.07.001

Bailey, Matthew H; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C; Kim, Jaegil; Reardon, Brendan; Kwok-Shing Ng, Patrick; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; ... (2018). Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell, 174(4), pp. 1034-1035. Cell Press 10.1016/j.cell.2018.07.034

Cotter, Kellie Anne; Rubin, Mark Andrew (2018). Sequence of events in prostate cancer. Nature, 560(7720), pp. 557-559. Macmillan Journals Ltd. 10.1038/d41586-018-06029-5

Hopkins, Benjamin D; Pauli, Chantal; Du, Xing; Wang, Diana G; Li, Xiang; Wu, David; Amadiume, Solomon C; Goncalves, Marcus D; Hodakoski, Cindy; Lundquist, Mark R; Bareja, Rohan; Ma, Yan; Harris, Emily M; Sboner, Andrea; Beltran, Himisha; Rubin, Mark Andrew; Mukherjee, Siddhartha; Cantley, Lewis C (2018). Suppression of insulin feedback enhances the efficacy of PI3K inhibitors. Nature, 560(7719), pp. 499-503. Macmillan Journals Ltd. 10.1038/s41586-018-0343-4

Ricketts, Christopher J; De Cubas, Aguirre A; Fan, Huihui; Smith, Christof C; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A; Akbani, Rehan; Beroukhim, Rameen; Bottaro, Donald P; Choueiri, Toni K; Gibbs, Richard A; Godwin, Andrew K; Haake, Scott; Hakimi, A Ari; Henske, Elizabeth P; Hsieh, James J; Ho, Thai H; Kanchi, Rupa S; ... (2018). The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell reports, 23(12), p. 3698. Cell Press 10.1016/j.celrep.2018.06.032

Triscott, Joanna; Rubin, Mark A. (2018). Prostate Power Play: Does Accelerate -Deficient Cancer Progression? Cancer discovery, 8(6), pp. 682-685. American Association for Cancer Research 10.1158/2159-8290.CD-18-0369

Mateo, Joaquin; Cheng, Heather H; Beltran, Himisha; Dolling, David; Xu, Wen; Pritchard, Colin C; Mossop, Helen; Rescigno, Pasquale; Perez-Lopez, Raquel; Sailer, Verena; Kolinsky, Michael; Balasopoulou, Ada; Bertan, Claudia; Nanus, David M; Tagawa, Scott T; Thorne, Heather; Montgomery, Bruce; Carreira, Suzanne; Sandhu, Shahneen; Rubin, Mark Andrew; ... (2018). Clinical Outcome of Prostate Cancer Patients with Germline DNA Repair Mutations: Retrospective Analysis from an International Study. European urology, 73(5), pp. 687-693. Elsevier 10.1016/j.eururo.2018.01.010

Thorsson, Vésteinn; Gibbs, David L; Brown, Scott D; Wolf, Denise; Bortone, Dante S; Ou Yang, Tai-Hsien; Porta-Pardo, Eduard; Gao, Galen F; Plaisier, Christopher L; Eddy, James A; Ziv, Elad; Culhane, Aedin C; Paull, Evan O; Sivakumar, I K Ashok; Gentles, Andrew J; Malhotra, Raunaq; Farshidfar, Farshad; Colaprico, Antonio; Parker, Joel S; Mose, Lisle E; ... (2018). The Immune Landscape of Cancer. Immunity, 48(4), 812-830.e14. Cell Press 10.1016/j.immuni.2018.03.023

Liu, Yang; Sethi, Nilay S; Hinoue, Toshinori; Schneider, Barbara G; Cherniack, Andrew D; Sanchez-Vega, Francisco; Seoane, Jose A; Farshidfar, Farshad; Bowlby, Reanne; Islam, Mirazul; Kim, Jaegil; Chatila, Walid; Akbani, Rehan; Kanchi, Rupa S; Rabkin, Charles S; Willis, Joseph E; Wang, Kenneth K; McCall, Shannon J; Mishra, Lopa; Ojesina, Akinyemi I; ... (2018). Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer cell, 33(4), 721-735.e8. Cell Press 10.1016/j.ccell.2018.03.010

Wang, Zehua; Yang, Bo; Zhang, Min; Guo, Weiwei; Wu, Zhiyuan; Wang, Yue; Jia, Lin; Li, Song; Xie, Wen; Yang, Da (2018). lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer cell, 33(4), 706-720.e9. Cell Press 10.1016/j.ccell.2018.03.006

Berger, Ashton C; Korkut, Anil; Kanchi, Rupa S; Hegde, Apurva M; Lenoir, Walter; Liu, Wenbin; Liu, Yuexin; Fan, Huihui; Shen, Hui; Ravikumar, Visweswaran; Rao, Arvind; Schultz, Andre; Li, Xubin; Sumazin, Pavel; Williams, Cecilia; Mestdagh, Pieter; Gunaratne, Preethi H; Yau, Christina; Bowlby, Reanne; Robertson, A Gordon; ... (2018). A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer cell, 33(4), 690-705.e9. Cell Press 10.1016/j.ccell.2018.03.014

Taylor, Alison M; Shih, Juliann; Ha, Gavin; Gao, Galen F; Zhang, Xiaoyang; Berger, Ashton C; Schumacher, Steven E; Wang, Chen; Hu, Hai; Liu, Jianfang; Lazar, Alexander J; Cherniack, Andrew D; Beroukhim, Rameen; Meyerson, Matthew (2018). Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer cell, 33(4), 676-689.e3. Cell Press 10.1016/j.ccell.2018.03.007

Liu, Jianfang; Lichtenberg, Tara; Hoadley, Katherine A; Poisson, Laila M; Lazar, Alexander J; Cherniack, Andrew D; Kovatich, Albert J; Benz, Christopher C; Levine, Douglas A; Lee, Adrian V; Omberg, Larsson; Wolf, Denise M; Shriver, Craig D; Thorsson, Vesteinn (2018). An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell, 173(2), 400-416.e11. Cell Press 10.1016/j.cell.2018.02.052

Chen, Han; Li, Chunyan; Peng, Xinxin; Zhou, Zhicheng; Weinstein, John N; Liang, Han (2018). A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell, 173(2), 386-399.e12. Cell Press 10.1016/j.cell.2018.03.027

Bailey, Matthew H; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C; Kim, Jaegil; Reardon, Brendan; Ng, Patrick Kwok-Shing; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; ... (2018). Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell, 173(2), 371-385.e18. Cell Press 10.1016/j.cell.2018.02.060

Huang, Kuan-Lin; Mashl, R Jay; Wu, Yige; Ritter, Deborah I; Wang, Jiayin; Oh, Clara; Paczkowska, Marta; Reynolds, Sheila; Wyczalkowski, Matthew A; Oak, Ninad; Scott, Adam D; Krassowski, Michal; Cherniack, Andrew D; Houlahan, Kathleen E; Jayasinghe, Reyka; Wang, Liang-Bo; Zhou, Daniel Cui; Liu, Di; Cao, Song; Kim, Young Won; ... (2018). Pathogenic Germline Variants in 10,389 Adult Cancers. Cell, 173(2), 355-370.e14. Cell Press 10.1016/j.cell.2018.03.039

Malta, Tathiane M; Sokolov, Artem; Gentles, Andrew J; Burzykowski, Tomasz; Poisson, Laila; Weinstein, John N; Kamińska, Bożena; Huelsken, Joerg; Omberg, Larsson; Gevaert, Olivier; Colaprico, Antonio; Czerwińska, Patrycja; Mazurek, Sylwia; Mishra, Lopa; Heyn, Holger; Krasnitz, Alex; Godwin, Andrew K; Lazar, Alexander J; Stuart, Joshua M; Hoadley, Katherine A; ... (2018). Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell, 173(2), 338-354.e15. Cell Press 10.1016/j.cell.2018.03.034

Sanchez-Vega, Francisco; Mina, Marco; Armenia, Joshua; Chatila, Walid K; Luna, Augustin; La, Konnor C; Dimitriadoy, Sofia; Liu, David L; Kantheti, Havish S; Saghafinia, Sadegh; Chakravarty, Debyani; Daian, Foysal; Gao, Qingsong; Bailey, Matthew H; Liang, Wen-Wei; Foltz, Steven M; Shmulevich, Ilya; Ding, Li; Heins, Zachary; Ochoa, Angelica; ... (2018). Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell, 173(2), 321-337.e10. Cell Press 10.1016/j.cell.2018.03.035

Ding, Li; Bailey, Matthew H; Porta-Pardo, Eduard; Thorsson, Vesteinn; Colaprico, Antonio; Bertrand, Denis; Gibbs, David L; Weerasinghe, Amila; Huang, Kuan-Lin; Tokheim, Collin; Cortés-Ciriano, Isidro; Jayasinghe, Reyka; Chen, Feng; Yu, Lihua; Sun, Sam; Olsen, Catharina; Kim, Jaegil; Taylor, Alison M; Cherniack, Andrew D; Akbani, Rehan; ... (2018). Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell, 173(2), 305-320.e10. Cell Press 10.1016/j.cell.2018.03.033

Hoadley, Katherine A; Yau, Christina; Hinoue, Toshinori; Wolf, Denise M; Lazar, Alexander J; Drill, Esther; Shen, Ronglai; Taylor, Alison M; Cherniack, Andrew D; Thorsson, Vésteinn; Akbani, Rehan; Bowlby, Reanne; Wong, Christopher K; Wiznerowicz, Maciej; Sanchez-Vega, Francisco; Robertson, A Gordon; Schneider, Barbara G; Lawrence, Michael S; Noushmehr, Houtan; Malta, Tathiane M; ... (2018). Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell, 173(2), 291-304.e6. Cell Press 10.1016/j.cell.2018.03.022

Ricketts, Christopher J; De Cubas, Aguirre A; Fan, Huihui; Smith, Christof C; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A; Akbani, Rehan; Beroukhim, Rameen; Bottaro, Donald P; Choueiri, Toni K; Gibbs, Richard A; Godwin, Andrew K; Haake, Scott; Hakimi, A Ari; Henske, Elizabeth P; Hsieh, James J; Ho, Thai H; Kanchi, Rupa S; ... (2018). The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell reports, 23(1), 313-326.e5. Cell Press 10.1016/j.celrep.2018.03.075

Chiu, Hua-Sheng; Somvanshi, Sonal; Patel, Ektaben; Chen, Ting-Wen; Singh, Vivek P; Zorman, Barry; Patil, Sagar L; Pan, Yinghong; Chatterjee, Sujash S; Sood, Anil K; Gunaratne, Preethi H; Sumazin, Pavel (2018). Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell reports, 23(1), 297-312.e12. Cell Press 10.1016/j.celrep.2018.03.064

Seiler, Michael; Peng, Shouyong; Agrawal, Anant A; Palacino, James; Teng, Teng; Zhu, Ping; Smith, Peter G; Buonamici, Silvia; Yu, Lihua (2018). Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell reports, 23(1), 282-296.e4. Cell Press 10.1016/j.celrep.2018.01.088

Jayasinghe, Reyka G; Cao, Song; Gao, Qingsong; Wendl, Michael C; Vo, Nam Sy; Reynolds, Sheila M; Zhao, Yanyan; Climente-González, Héctor; Chai, Shengjie; Wang, Fang; Varghese, Rajees; Huang, Mo; Liang, Wen-Wei; Wyczalkowski, Matthew A; Sengupta, Sohini; Li, Zhi; Payne, Samuel H; Fenyö, David; Miner, Jeffrey H; Walter, Matthew J; ... (2018). Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell reports, 23(1), 270-281.e3. Cell Press 10.1016/j.celrep.2018.03.052

Peng, Xinxin; Chen, Zhongyuan; Farshidfar, Farshad; Xu, Xiaoyan; Lorenzi, Philip L; Wang, Yumeng; Cheng, Feixiong; Tan, Lin; Mojumdar, Kamalika; Du, Di; Ge, Zhongqi; Li, Jun; Thomas, George V; Birsoy, Kivanc; Liu, Lingxiang; Zhang, Huiwen; Zhao, Zhongming; Marchand, Calena; Weinstein, John N; Bathe, Oliver F; ... (2018). Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell reports, 23(1), 255-269.e4. Cell Press 10.1016/j.celrep.2018.03.077

Knijnenburg, Theo A; Wang, Linghua; Zimmermann, Michael T; Chambwe, Nyasha; Gao, Galen F; Cherniack, Andrew D; Fan, Huihui; Shen, Hui; Way, Gregory P; Greene, Casey S; Liu, Yuexin; Akbani, Rehan; Feng, Bin; Donehower, Lawrence A; Miller, Chase; Shen, Yang; Karimi, Mostafa; Chen, Haoran; Kim, Pora; Jia, Peilin; ... (2018). Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell reports, 23(1), 239-254.e6. Cell Press 10.1016/j.celrep.2018.03.076

Gao, Qingsong; Liang, Wen-Wei; Foltz, Steven M; Mutharasu, Gnanavel; Jayasinghe, Reyka G; Cao, Song; Liao, Wen-Wei; Reynolds, Sheila M; Wyczalkowski, Matthew A; Yao, Lijun; Yu, Lihua; Sun, Sam Q; Chen, Ken; Lazar, Alexander J; Fields, Ryan C; Wendl, Michael C; Van Tine, Brian A; Vij, Ravi; Chen, Feng; Nykter, Matti; ... (2018). Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell reports, 23(1), 227-238.e3. Cell Press 10.1016/j.celrep.2018.03.050

Ge, Zhongqi; Leighton, Jake S; Wang, Yumeng; Peng, Xinxin; Chen, Zhongyuan; Chen, Hu; Sun, Yutong; Yao, Fan; Li, Jun; Zhang, Huiwen; Liu, Jianfang; Shriver, Craig D; Hu, Hai; Piwnica-Worms, Helen; Ma, Li; Liang, Han (2018). Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell reports, 23(1), 213-226.e3. Cell Press 10.1016/j.celrep.2018.03.047

Campbell, Joshua D; Yau, Christina; Bowlby, Reanne; Liu, Yuexin; Brennan, Kevin; Fan, Huihui; Taylor, Alison M; Wang, Chen; Walter, Vonn; Akbani, Rehan; Byers, Lauren Averett; Creighton, Chad J; Coarfa, Cristian; Shih, Juliann; Cherniack, Andrew D; Gevaert, Olivier; Prunello, Marcos; Shen, Hui; Anur, Pavana; Chen, Jianhong; ... (2018). Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell reports, 23(1), 194-212.e6. Cell Press 10.1016/j.celrep.2018.03.063

Saltz, Joel; Gupta, Rajarsi; Hou, Le; Kurc, Tahsin; Singh, Pankaj; Nguyen, Vu; Samaras, Dimitris; Shroyer, Kenneth R; Zhao, Tianhao; Batiste, Rebecca; Van Arnam, John (2018). Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell reports, 23(1), 181-193.e7. Cell Press 10.1016/j.celrep.2018.03.086

Way, Gregory P; Sanchez-Vega, Francisco; La, Konnor; Armenia, Joshua; Chatila, Walid K; Luna, Augustin; Sander, Chris; Cherniack, Andrew D; Mina, Marco; Ciriello, Giovanni; Schultz, Nikolaus (2018). Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell reports, 23(1), 172-180.e3. Cell Press 10.1016/j.celrep.2018.03.046

Schaub, Franz X; Dhankani, Varsha; Berger, Ashton C; Trivedi, Mihir; Richardson, Anne B; Shaw, Reid; Zhao, Wei; Zhang, Xiaoyang; Ventura, Andrea; Liu, Yuexin; Ayer, Donald E; Hurlin, Peter J; Cherniack, Andrew D; Eisenman, Robert N; Bernard, Brady; Grandori, Carla (2018). Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell systems, 6(3), 282-300.e2. Elsevier 10.1016/j.cels.2018.03.003

Ellrott, Kyle; Bailey, Matthew H; Saksena, Gordon; Covington, Kyle R; Kandoth, Cyriac; Stewart, Chip; Hess, Julian; Ma, Singer; Chiotti, Kami E; McLellan, Michael; Sofia, Heidi J; Hutter, Carolyn; Getz, Gad; Wheeler, David; Ding, Li (2018). Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell systems, 6(3), 271-281.e7. Elsevier 10.1016/j.cels.2018.03.002

Sailer, Verena; Schiffman, Marc H; Kossai, Myriam; Cyrta, Joanna; Beg, Shaham; Sullivan, Brian; Pua, Bradley B; Lee, Kyungmouk Steve; Talenfeld, Adam D; Nanus, David M; Tagawa, Scott T; Robinson, Brian D; Rao, Rema A; Pauli, Chantal; Bareja, Rohan; Beltran, Luis S; Sigaras, Alexandros; Eng, Kenneth Wa; Elemento, Olivier; Sboner, Andrea; ... (2018). Bone biopsy protocol for advanced prostate cancer in the era of precision medicine. Cancer, 124(5), pp. 1008-1015. John Wiley & Sons 10.1002/cncr.31173

Shoag, Jonathan; Liu, Deli; Blattner, Mirjam; Sboner, Andrea; Park, Kyung; Deonarine, Lesa; Robinson, Brian D; Mosquera, Juan Miguel; Chen, Yu; Rubin, Mark Andrew; Barbieri, Christopher E (2018). SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG. Journal of clinical investigation, 128(1), pp. 381-386. American Society for Clinical Investigation 10.1172/JCI96551

McNair, Christopher; Xu, Kexin; Mandigo, Amy C; Benelli, Matteo; Leiby, Benjamin; Rodrigues, Daniel; Lindberg, Johan; Gronberg, Henrik; Crespo, Mateus; De Laere, Bram; Dirix, Luc; Visakorpi, Tapio; Li, Fugen; Feng, Felix Y; de Bono, Johann; Demichelis, Francesca; Rubin, Mark Andrew; Brown, Myles; Knudsen, Karen E (2018). Differential impact of RB status on E2F1 reprogramming in human cancer. Journal of clinical investigation, 128(1), pp. 341-358. American Society for Clinical Investigation 10.1172/JCI93566

D'Alfonso, Timothy M; Subramaniyam, Shivakumar; Ginter, Paula S; Mosquera, Juan Miguel; Croyle, Jaclyn; Liu, Yi-Fang; Rubin, Mark Andrew; Shin, Sandra J (2018). Characterization of CD34-deficient myofibroblastomas of the breast. The breast journal, 24(1), pp. 55-61. Wiley 10.1111/tbj.12835

Rubin, Mark Andrew; Demichelis, Francesca (2018). The Genomics of Prostate Cancer: emerging understanding with technologic advances. Modern pathology, 31(S1), S1-11. Nature Publishing Group 10.1038/modpathol.2017.166

2017

Shukla, Shipra; Cyrta, Joanna; Murphy, Devan A; Walczak, Edward G; Ran, Leili; Agrawal, Praveen; Xie, Yuanyuan; Chen, Yuedan; Wang, Shangqian; Zhan, Yu; Li, Dan; Wong, Elissa W P; Sboner, Andrea; Beltran, Himisha; Mosquera, Juan Miguel; Sher, Jessica; Cao, Zhen; Wongvipat, John; Koche, Richard P; Gopalan, Anuradha; ... (2017). Aberrant Activation of a Gastrointestinal Transcriptional Circuit in Prostate Cancer Mediates Castration Resistance. Cancer cell, 32(6), 792-806.e7. Cell Press 10.1016/j.ccell.2017.10.008

Lee, D; Fontugne, J; Gumpeni, N; Park, K; MacDonald, T Y; Robinson, B D; Sboner, A; Rubin, Mark Andrew; Mosquera, J M; Barbieri, C E (2017). Molecular alterations in prostate cancer and association with MRI features. Prostate cancer and prostatic diseases, 20(4), pp. 430-435. Nature 10.1038/pcan.2017.33

Pauli, C; Moch, H; Rubin, Mark Andrew (2017). [Establishment of a living biobank : Improved guidance of precision cancer care with in vitro and in vivo cancer models]. Der Pathologe, 38(Suppl 2), pp. 160-168. Springer 10.1007/s00292-017-0346-1

Wilkes, David C; Sailer, Verena; Xue, Hui; Cheng, Hongwei; Collins, Colin C; Gleave, Martin; Wang, Yuzhuo; Demichelis, Francesca; Beltran, Himisha; Rubin, Mark Andrew; Rickman, David S (2017). A germline FANCA alteration that is associated with increased sensitivity to DNA damaging agents. Cold Spring Harbor molecular case studies, 3(5) Cold Spring Harbor Laboratory Press 10.1101/mcs.a001487

Dai, Xiangpeng; Gan, Wenjian; Li, Xiaoning; Wang, Shangqian; Zhang, Wei; Huang, Ling; Liu, Shengwu; Zhong, Qing; Guo, Jianping; Zhang, Jinfang; Chen, Ting; Shimizu, Kouhei; Beca, Francisco; Blattner, Mirjam; Vasudevan, Divya; Buckley, Dennis L; Qi, Jun; Buser, Lorenz; Liu, Pengda; Inuzuka, Hiroyuki; ... (2017). Prostate cancer-associated SPOP mutations confer resistance to BET inhibitors through stabilization of BRD4. Nature medicine, 23(9), pp. 1063-1071. Nature Publishing Group 10.1038/nm.4378

Minciacchi, V R; Zijlstra, A; Rubin, Mark Andrew; Di Vizio, D (2017). Extracellular vesicles for liquid biopsy in prostate cancer: where are we and where are we headed? Prostate cancer and prostatic diseases, 20(3), pp. 251-258. Nature 10.1038/pcan.2017.7

Huang, Franklin W; Mosquera, Juan Miguel; Garofalo, Andrea; Oh, Coyin; Baco, Maria; Amin-Mansour, Ali; Rabasha, Bokang; Bahl, Samira; Mullane, Stephanie A; Robinson, Brian D; Aldubayan, Saud; Khani, Francesca; Karir, Beerinder; Kim, Eejung; Chimene-Weiss, Jeremy; Hofree, Matan; Romanel, Alessandro; Osborne, Joseph R; Kim, Jong Wook; Azabdaftari, Gissou; ... (2017). Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer discovery, 7(9), pp. 973-983. American Association for Cancer Research 10.1158/2159-8290.CD-16-0960

Wang, Hui; Barbieri, Christopher E; He, Jintang; Gao, Yuqian; Shi, Tujin; Wu, Chaochao; Schepmoes, Athena A; Fillmore, Thomas L; Chae, Sung-Suk; Huang, Dennis; Mosquera, Juan Miguel; Qian, Wei-Jun; Smith, Richard D; Srivastava, Sudhir; Kagan, Jacob; Camp, David G; Rodland, Karin D; Rubin, Mark Andrew; Liu, Tao (2017). Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics. Journal of translational medicine, 15(1), p. 175. BioMed Central 10.1186/s12967-017-1276-7

Sanda, Martin G; Feng, Ziding; Howard, David H; Tomlins, Scott A; Sokoll, Lori J; Chan, Daniel W; Regan, Meredith M; Groskopf, Jack; Chipman, Jonathan; Patil, Dattatraya H; Salami, Simpa S; Scherr, Douglas S; Kagan, Jacob; Srivastava, Sudhir; Thompson, Ian M; Siddiqui, Javed; Fan, Jing; Joon, Aron Y; Bantis, Leonidas E; Rubin, Mark Andrew; ... (2017). Association Between Combined TMPRSS2:ERG and PCA3 RNA Urinary Testing and Detection of Aggressive Prostate Cancer. JAMA oncology, 3(8), pp. 1085-1093. American Medical Association 10.1001/jamaoncol.2017.0177

Dhingra, Priyanka; Martinez-Fundichely, Alexander; Berger, Adeline; Huang, Franklin W; Forbes, Andre Neil; Liu, Eric Minwei; Liu, Deli; Sboner, Andrea; Tamayo, Pablo; Rickman, David S; Rubin, Mark Andrew; Khurana, Ekta (2017). Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome biology, 18(1), p. 141. BioMed Central Ltd. 10.1186/s13059-017-1266-3

Zou, Min; Toivanen, Roxanne; Mitrofanova, Antonina; Floch, Nicolas; Hayati, Sheida; Sun, Yanping; Le Magnen, Clémentine; Chester, Daniel; Mostaghel, Elahe A; Califano, Andrea; Rubin, Mark Andrew; Shen, Michael M; Abate-Shen, Cory (2017). Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer. Cancer discovery, 7(7), pp. 736-749. American Association for Cancer Research 10.1158/2159-8290.CD-16-1174

Romanel, Alessandro; Garritano, Sonia; Stringa, Blerta; Blattner, Mirjam; Dalfovo, Davide; Chakravarty, Dimple; Soong, David; Cotter, Kellie Anne; Petris, Gianluca; Dhingra, Priyanka; Gasperini, Paola; Cereseto, Anna; Elemento, Olivier; Sboner, Andrea; Khurana, Ekta; Inga, Alberto; Rubin, Mark Andrew; Demichelis, Francesca (2017). Inherited determinants of early recurrent somatic mutations in prostate cancer. Nature communications, 8(1), p. 48. Nature Publishing Group 10.1038/s41467-017-00046-0

Huang, Linda; Fernandes, Helen; Zia, Hamid; Tavassoli, Peyman; Rennert, Hanna; Pisapia, David; Imielinski, Marcin; Sboner, Andrea; Rubin, Mark Andrew; Kluk, Michael; Elemento, Olivier (2017). The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations. Journal of the American Medical Informatics Association, 24(3), pp. 513-519. Oxford University Press 10.1093/jamia/ocw148

Imielinski, Marcin; Rubin, Mark Andrew (2017). Prostate cancer: Clinical hallmarks in whole cancer genomes. Nature reviews - clinical oncology, 14(5), pp. 265-266. Nature Publishing Group 10.1038/nrclinonc.2017.45

Pauli, Chantal; Hopkins, Benjamin D; Prandi, Davide; Shaw, Reid; Fedrizzi, Tarcisio; Sboner, Andrea; Sailer, Verena; Augello, Michael; Puca, Loredana; Rosati, Rachele; McNary, Terra J; Churakova, Yelena; Cheung, Cynthia; Triscott, Joanna Catherine Caprio; Pisapia, David; Rao, Rema; Mosquera, Juan Miguel; Robinson, Brian; Faltas, Bishoy M; Emerling, Brooke E; ... (2017). Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine. Cancer discovery, 7(5), pp. 462-477. American Association for Cancer Research 10.1158/2159-8290.CD-16-1154

Sailer, Verena; Pauli, Chantal; Merzier, Elyze C; Mosquera, Juan Miguel; Beltran, Himisha; Rubin, Mark Andrew; Rao, Rema A (2017). On-site Cytology for Development of Patient-Derived Three-dimensional Organoid Cultures - A Pilot Study. Anticancer research, 37(4), pp. 1569-1573. International Inst. of Anticancer Research 10.21873/anticanres.11486

Blattner, Mirjam; Liu, Deli; Robinson, Brian D; Huang, Dennis; Poliakov, Anton; Gao, Dong; Nataraj, Srilakshmi; Deonarine, Lesa D; Augello, Michael A; Sailer, Verena; Ponnala, Lalit; Ittmann, Michael; Chinnaiyan, Arul M; Sboner, Andrea; Chen, Yu; Rubin, Mark Andrew; Barbieri, Christopher E (2017). SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling. Cancer cell, 31(3), pp. 436-451. Cell Press 10.1016/j.ccell.2017.02.004

Mateo, Joaquin; Boysen, Gunther; Barbieri, Christopher E; Bryant, Helen E; Castro, Elena; Nelson, Pete S; Olmos, David; Pritchard, Colin C; Rubin, Mark Andrew; de Bono, Johann S (2017). DNA Repair in Prostate Cancer: Biology and Clinical Implications. European urology, 71(3), pp. 417-425. Elsevier 10.1016/j.eururo.2016.08.037

Barbieri, Christopher E; Chinnaiyan, Arul M; Lerner, Seth P; Swanton, Charles; Rubin, Mark Andrew (2017). The Emergence of Precision Urologic Oncology: A Collaborative Review on Biomarker-driven Therapeutics. European urology, 71(2), pp. 237-246. Elsevier 10.1016/j.eururo.2016.08.024

Villers, Arnauld; Rubin, Mark Andrew (2017). Re: Prognostic Significance of Percentage and Architectural Types of Contemporary Gleason Pattern 4 Prostate Cancer in Radical Prostatectomy. European urology, 71(2), p. 301. Elsevier 10.1016/j.eururo.2016.09.017

Mu, Ping; Zhang, Zeda; Benelli, Matteo; Karthaus, Wouter R; Hoover, Elizabeth; Chen, Chi-Chao; Wongvipat, John; Ku, Sheng-Yu; Gao, Dong; Cao, Zhen; Shah, Neel; Adams, Elizabeth J; Abida, Wassim; Watson, Philip A; Prandi, Davide; Huang, Chun-Hao; de Stanchina, Elisa; Lowe, Scott W; Ellis, Leigh; Beltran, Himisha; ... (2017). SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science, 355(6320), pp. 84-88. American Association for the Advancement of Science 10.1126/science.aah4307

Bishop, Jennifer L; Thaper, Daksh; Vahid, Sepideh; Davies, Alastair; Ketola, Kirsi; Kuruma, Hidetoshi; Jama, Randy; Nip, Ka Mun; Angeles, Arkhjamil; Johnson, Fraser; Wyatt, Alexander W; Fazli, Ladan; Gleave, Martin E; Lin, Dong; Rubin, Mark Andrew; Collins, Colin C; Wang, Yuzhuo; Beltran, Himisha; Zoubeidi, Amina (2017). The Master Neural Transcription Factor BRN2 Is an Androgen Receptor-Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer. Cancer discovery, 7(1), pp. 54-71. American Association for Cancer Research 10.1158/2159-8290.CD-15-1263

This list was generated on Wed Oct 5 04:19:47 2022 CEST.
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