The landscape of drug sensitivity and resistance in sarcoma

Authors: Al Shihabi, Ahmad ^{1, 2, 17}, Tebon, Peyton J. ^{1, 3, 17}, Nguyen, Huyen Thi Lam ^{1, 17}, Chantharasamee, Jomjit ^{4, 16}, Sartini, Sara ¹, Davarifar, Ardalan ^{1, 4, 5}, Jensen, Alexandra Y. ¹, Diaz-Infante, Miranda ¹, Cox, Hannah ¹, Gonzalez, Alfredo Enrique ⁵, Norris, Summer ¹, Sperry, Jantzen ⁶, Nakashima, Jonathan ⁶, Tavanaie, Nasrin ¹, Winata, Helena ⁵, Fitz-Gibbon, Sorel T. ⁵, Yamaguchi, Takafumi N. ⁵, Jeong, Jae H. ⁵, Dry, Sarah ², Singh, Arun S. ⁴, Chmielowski, Bartosz ⁴, Crompton, Joseph G. ^{7, 8}, Kalbasi, Anusha K. ⁹, Eilber, Fritz C. ⁸, Hornicek, Francis ¹⁰, Bernthal, Nicholas M. ¹, Nelson, Scott D. ², Boutros, Paul C. ^{5, 7, 11, 12, 13}, Federman, Noah C. ^{1, 7, 14}, Yanagawa, Jane ¹⁵, Soragni, Alice ^{1, 7, 12, 18, ∗}

Source: In Cell Stem Cell 3 October 2024 31(10):1524-1542

The genomic and evolutionary landscapes of anaplastic thyroid carcinoma

Authors: Zeng, Peter Y.F. ^{1, 2, 3, 4, 47}, Prokopec, Stephenie D. ^{5, 45, 46, 47}, Lai, Stephen Y. ^{6, 47}, Pinto, Nicole ¹, Chan-Seng-Yue, Michelle A. ⁵, Clifton-Bligh, Roderick ⁷, Williams, Michelle D. ⁸, Howlett, Christopher J. ⁹, Plantinga, Paul ⁹, Cecchini, Matthew J. ¹⁰, Lam, Alfred K. ¹⁰, Siddiqui, Iram ¹¹, Wang, Jianxin ⁵, Sun, Ren X. ⁵, Watson, John D. ^{5, 45, 46}, Korah, Reju ¹², Carling, Tobias ¹², Agrawal, Nishant ¹³, Cipriani, Nicole ¹⁴, Ball, Douglas ¹⁵, Nelkin, Barry ¹⁶, Rooper, Lisa M. ¹⁷, Bishop, Justin A. ¹⁸, Garnis, Cathie ¹⁹, Berean, Ken ¹⁹, Nicolson, Norman G. ¹², Weinberger, Paul ^{20, 21}, Henderson, Ying C. ⁶, Lalansingh, Christopher M. ⁵, Tian, Mao ^{45, 46}, Yamaguchi, Takafumi N. ^{5, 45, 46}, Livingstone, Julie ^{5, 45, 46}, Salcedo, Adriana ^{5, 22, 42}, Patel, Krupal ^{1, 5}, Vizeacoumar, Frederick ²³, Datti, Alessandro ^{24, 25}, Xi, Liu ²⁶, Nikiforov, Yuri E. ²⁷, Smallridge, Robert ²⁸, Copland, John A. ²⁹, Marlow, Laura A. ²⁹, Hyrcza, Martin D. ³⁰, Delbridge, Leigh ^{31, 32}, Sidhu, Stan ^{31, 32}, Sywak, Mark ^{31, 32}, Robinson, Bruce ^{32, 33}, Fung, Kevin ^{1, 4}, Ghasemi, Farhad ¹, Kwan, Keith ⁹, MacNeil, S. Danielle ^{1, 4}, Mendez, Adrian ^{1, 4}, Palma, David A. ^{2, 3, 4}, Khan, Mohammed I. ¹, Shaikh, Mushfiq ¹, Ruicci, Kara M. ¹, Wehrli, Bret ⁹, Winquist, Eric ^{2, 3, 4}, Yoo, John ^{1, 4}, Mymryk, Joe S. ^{1, 2, 4, 34}, Rocco, James W. ³⁵, Wheeler, David ²⁶, Scherer, Steve ²⁶, Giordano, Thomas J. ³⁶, Barrett, John W. ¹, Faquin, William C. ³⁷, Gill, Anthony J. ^{32, 38, 39}, Clayman, Gary ^{40, 47}, Boutros, Paul C. ^{22, 41, 42, 43, 44, 45, 46, 47, ∗}, Nichols, Anthony C. ^{1, 2, 3, 4, 47, 48, ∗∗}

Source: In Cell Reports 26 March 2024 43(3)

Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective

Authors: Mathur, Radhika, Wang, Qixuan, Schupp, Patrick G., Nikolic, Ana, Hilz, Stephanie, Hong, Chibo, Grishanina, Nadia R., Kwok, Darwin, Stevers, Nicholas O., Jin, Qiushi, Youngblood, Mark W., Stasiak, Lena Ann, Hou, Ye, Wang, Juan, Yamaguchi, Takafumi N., Lafontaine, Marisa, Shai, Anny, Smirnov, Ivan V., Solomon, David A., Chang, Susan M., Hervey-Jumper, Shawn L., Berger, Mitchel S., Lupo, Janine M., Okada, Hideho, Phillips, Joanna J., Boutros, Paul C., Gallo, Marco, Oldham, Michael C., Yue, Feng, Costello, Joseph F.

Source: In Cell 18 January 2024 187(2):446-463

Upgrading of Grade Group 1 Prostate Cancer at Prostatectomy: Germline Risk Factors in a Prospective Cohort.

Authors: Liss, Michael A., Zeltser, Nicole, Yingye Zheng, Lopez, Camden, Menghan Liu, Patel, Yash, Yamaguchi, Takafumi N., Eng, Stefan E., Mao Tian, Semmes, Oliver J., Lin, Daniel W., Brooks, James D., Wei, John T., Klein, Eric A., Tewari, Ashutosh K., Mosquera, Juan Miguel, Khani, Francesca, Robinson, Brian D., Aasad, Muhammad, Troyer, Dean A.

Source: Cancer Epidemiology, Biomarkers & Prevention; Nov2024, Vol. 33 Issue 11, p1500-1511, 12p

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression

Authors: Espiritu, Shadrielle Melijah G., Liu, Lydia Y., Rubanova, Yulia, Bhandari, Vinayak, Holgersen, Erle M., Szyca, Lesia M., Fox, Natalie S., Chua, Melvin L.K., Yamaguchi, Takafumi N., Heisler, Lawrence E., Livingstone, Julie, Wintersinger, Jeff, Yousif, Fouad, Lalonde, Emilie, Rouette, Alexandre, Salcedo, Adriana, Houlahan, Kathleen E., Li, Constance H., Huang, Vincent, Fraser, Michael, van der Kwast, Theodorus, Morris, Quaid D., Bristow, Robert G., Boutros, Paul C.

Source: In Cell 3 May 2018 173(4):1003-1013

Exploring genetic suppression interactions on a global scale

Authors: van Leeuwen, Jolanda, Pons, Carles, Mellor, Joseph C., Yamaguchi, Takafumi N., Friesen, Helena, Koschwanez, John, Ušaj, Mojca Mattiazzi, Pechlaner, Maria, Takar, Mehmet, Ušaj, Matej, VanderSluis, Benjamin, Andrusiak, Kerry, Bansal, Pritpal, Baryshnikova, Anastasia, Boone, Claire E., Cao, Jessica, Cote, Atina, Gebbia, Marinella, Horecka, Gene, Horecka, Ira, Kuzmin, Elena, Legro, Nicole, Liang, Wendy, van Lieshout, Natascha, McNee, Margaret, San Luis, Bryan-Joseph, Shaeri, Fatemeh, Shuteriqi, Ermira, Sun, Song, Yang, Lu, Youn, Ji-Young, Yuen, Michael, Costanzo, Michael, Gingras, Anne-Claude, Aloy, Patrick, Oostenbrink, Chris, Murray, Andrew, Graham, Todd R., Myers, Chad L., Andrews, Brenda J., Roth, Frederick P., Boone, Charles

Source: Science, 2016 Nov 01. 354(6312), 599-599.

Access URL: https://www.jstor.org/stable/44710937

NFTest: automated testing of Nextflow pipelines.

Authors: Patel, Yash^1,2, Zhu, Chenghao^1,2,3, Yamaguchi, Takafumi N^1,2,3, Bugh, Yuan Zhe¹, Tian, Mao^1,2,3, Holmes, Aaron^1,2, Fitz-Gibbon, Sorel T^1,2,3, Boutros, Paul C^1,2,3,4,5, pboutros@mednet.ucla.edu

Source: Bioinformatics; Feb2024, Vol. 40 Issue 2, p1-5, 5p

PipeVal: light-weight extensible tool for file validation.

Authors: Patel, Yash^1,2, Beshlikyan, Arpi^1,2, Jordan, Madison^1,2,3, Kim, Gina^1,2, Holmes, Aaron^1,2, Yamaguchi, Takafumi N^1,2,3, Boutros, Paul C^1,2,3,4,5, pboutros@mednet.ucla.edu

Source: Bioinformatics; Feb2024, Vol. 40 Issue 2, p1-4, 4p

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer

Authors: Zhou, Stanley, Hawley, James R., Soares, Fraser, Grillo, Giacomo, Teng, Mona, Madani Tonekaboni, Seyed Ali, Hua, Junjie Tony, Kron, Ken J., Mazrooei, Parisa, Ahmed, Musaddeque, Arlidge, Christopher, Yun, Hwa Young, Livingstone, Julie, Huang, Vincent, Yamaguchi, Takafumi N., Espiritu, Shadrielle M. G., Zhu, Yanyun, Severson, Tesa M., Murison, Alex, Cameron, Sarina, Zwart, Wilbert, van der Kwast, Theodorus, Pugh, Trevor J., Fraser, Michael, Boutros, Paul C., Bristow, Robert G., He, Housheng Hansen, Lupien, Mathieu

Source: Nature communications. 11(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131051826.0x000001&indx=1&recIds=ETOCvdc_100131051826.0x000001

Cistrome Partitioning Reveals Convergence of Somatic Mutations and Risk Variants on Master Transcription Regulators in Primary Prostate Tumors

Authors: Mazrooei, Parisa, Kron, Ken J., Zhu, Yanyun, Zhou, Stanley, Grillo, Giacomo, Mehdi, Tahmid, Ahmed, Musaddeque, Severson, Tesa M., Guilhamon, Paul, Armstrong, Nicholas Sinnott, Huang, Vincent, Yamaguchi, Takafumi N., Fraser, Michael, van der Kwast, Theodorus, Boutros, Paul C., He, Housheng Hansen, Bergman, Andries M., Bristow, Robert G., Zwart, Wilbert, Lupien, Mathieu

Source: Cancer cell. 36(6):674-689.e6

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100093950896.0x000001&indx=1&recIds=ETOCvdc_100093950896.0x000001

The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact

Authors: van Dessel, Lisanne F., van Riet, Job, Smits, Minke, Zhu, Yanyun, Hamberg, Paul, van der Heijden, Michiel S., Bergman, Andries M., van Oort, Inge M., de Wit, Ronald, Voest, Emile E., Steeghs, Neeltje, Yamaguchi, Takafumi N., Livingstone, Julie, Boutros, Paul C., Martens, John W. M., Sleijfer, Stefan, Cuppen, Edwin, Zwart, Wilbert, van de Werken, Harmen J. G., Mehra, Niven, Lolkema, Martijn P.

Source: Nature communications. 10(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131100553.0x000001&indx=1&recIds=ETOCvdc_100131100553.0x000001

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories

Authors: Gerhauser, Clarissa, Favero, Francesco, Risch, Thomas, Simon, Ronald, Feuerbach, Lars, Assenov, Yassen, Heckmann, Doreen, Sidiropoulos, Nikos, Waszak, Sebastian M., Hübschmann, Daniel, Urbanucci, Alfonso, Girma, Etsehiwot G., Kuryshev, Vladimir, Klimczak, Leszek J., Saini, Natalie, Stütz, Adrian M., Weichenhan, Dieter, Böttcher, Lisa-Marie, Toth, Reka, Hendriksen, Josephine D., Koop, Christina, Lutsik, Pavlo, Matzk, Sören, Warnatz, Hans-Jörg, Amstislavskiy, Vyacheslav, Feuerstein, Clarissa, Raeder, Benjamin, Bogatyrova, Olga, Schmitz, Eva-Maria, Hube-Magg, Claudia, Kluth, Martina, Huland, Hartwig, Graefen, Markus, Lawerenz, Chris, Henry, Gervaise H., Yamaguchi, Takafumi N., Malewska, Alicia, Meiners, Jan, Schilling, Daniela, Reisinger, Eva, Eils, Roland, Schlesner, Matthias, Strand, Douglas W., Bristow, Robert G., Boutros, Paul C., von Kalle, Christof, Gordenin, Dmitry, Sültmann, Holger, Brors, Benedikt, Sauter, Guido, Plass, Christoph, Yaspo, Marie-Laure, Korbel, Jan O., Schlomm, Thorsten, Weischenfeldt, Joachim

Source: Cancer cell. 34(6):996-1011.e8

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100142431587.0x000001&indx=1&recIds=ETOCvdc_100142431587.0x000001

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Authors: Lee, Anna Y., Ewing, Adam D., Ellrott, Kyle, Hu, Yin, Houlahan, Kathleen E., Bare, J. Christopher, Espiritu, Shadrielle Melijah G., Huang, Vincent, Dang, Kristen, Chong, Zechen, Caloian, Cristian, Yamaguchi, Takafumi N., Kellen, Michael R., Chen, Ken, Norman, Thea C., Friend, Stephen H., Guinney, Justin, Stolovitzky, Gustavo, Haussler, David, Margolin, Adam A., Stuart, Joshua M., Boutros, Paul C.

Source: Genome biology. 19(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100129318048.0x000001&indx=1&recIds=ETOCvdc_100129318048.0x000001

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Authors: Sendorek, Dorota H., Caloian, Cristian, Ellrott, Kyle, Bare, J. Christopher, Yamaguchi, Takafumi N., Ewing, Adam D., Houlahan, Kathleen E., Norman, Thea C., Margolin, Adam A., Stuart, Joshua M., Boutros, Paul C.

Source: BMC bioinformatics. 19(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100129444071.0x000001&indx=1&recIds=ETOCvdc_100129444071.0x000001

Valection: design optimization for validation and verification studies

Authors: Cooper, Christopher I, Yao, Delia, Sendorek, Dorota H, Yamaguchi, Takafumi N, P'ng, Christine, Houlahan, Kathleen E, Caloian, Cristian, Fraser, Michael, Ellrott, Kyle, Margolin, Adam A, Bristow, Robert G, Stuart, Joshua M, Boutros, Paul C

Source: BMC bioinformatics. 19(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100128789206.0x000001&indx=1&recIds=ETOCvdc_100128789206.0x000001

Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations

Authors: Böttcher, René, Kweldam, Charlotte F., Livingstone, Julie, Lalonde, Emilie, Yamaguchi, Takafumi N., Huang, Vincent, Yousif, Fouad, Fraser, Michael, Bristow, Robert G., van der Kwast, Theodorus, Boutros, Paul C., Jenster, Guido, van Leenders, Geert J. L. H.

Source: BMC cancer. 18(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100127179187.0x000001&indx=1&recIds=ETOCvdc_100127179187.0x000001

Oncolytic DNX-2401 virotherapy plus pembrolizumab in recurrent glioblastoma: a phase 1/2 trial

Authors: Nassiri, Farshad, Patil, Vikas, Yefet, Leeor S., Singh, Olivia, Liu, Jeff, Dang, Rachel M. A., Yamaguchi, Takafumi N., Daras, Mariza, Cloughesy, Timothy F., Colman, Howard, Kumthekar, Priya U., Chen, Clark C., Aiken, Robert, Groves, Morris D., Ong, Shirley S., Ramakrishna, Rohan, Vogelbaum, Michael A., Khagi, Simon, Kaley, Thomas, Melear, Jason M., Peereboom, David M., Rodriguez, Analiz, Yankelevich, Maxim, Nair, Suresh G., Puduvalli, Vinay K., Aldape, Kenneth, Gao, Andrew, López-Janeiro, Álvaro, de Andrea, Carlos E., Alonso, Marta M., Boutros, Paul, Robbins, Joan, Mason, Warren P., Sonabend, Adam M., Stupp, Roger, Fueyo, Juan, Gomez-Manzano, Candelaria, Lang, Frederick F., Zadeh, Gelareh

Source: Nature Medicine; 20230101, Issue: Preprints p1-9, 9p

The telomere length landscape of prostate cancer.

Authors: Livingstone, Julie, Shiah, Yu-Jia, Yamaguchi, Takafumi N., Heisler, Lawrence E., Huang, Vincent, Lesurf, Robert, Gebo, Tsumugi, Carlin, Benjamin, Eng, Stefan, Drysdale, Erik, Green, Jeffrey, van der Kwast, Theodorus, Bristow, Robert G., Fraser, Michael, Boutros, Paul C.

Source: Nature Communications; 11/25/2021, Vol. 12 Issue 1, p1-13, 13p

Subject Terms: TELOMERES, PROSTATE cancer, TREATMENT effectiveness, TRANSCRIPTOMES, CELL communication, CELL proliferation

Precision Radiotherapy: Reduction in Radiation for Oropharyngeal Cancer in the 30 ROC Trial.

Authors: Riaz, Nadeem, Sherman, Eric, Pei, Xin, Schöder, Heiko, Grkovski, Milan, Paudyal, Ramesh, Katabi, Nora, Selenica, Pier, Yamaguchi, Takafumi N, Ma, Daniel, Lee, Simon K, Shah, Rachna, Kumar, Rahul, Kuo, Fengshen, Ratnakumar, Abhirami, Aleynick, Nathan, Brown, David, Zhang, Zhigang, Hatzoglou, Vaios, Liu, Lydia Y

Source: JNCI: Journal of the National Cancer Institute; Jun2021, Vol. 113 Issue 6, p742-751, 10p

Subject Terms: OROPHARYNGEAL cancer, CELL-free DNA, POSITRON emission tomography, OVERALL survival, MAGNETIC resonance imaging, RESEARCH, RESEARCH methodology, EVALUATION research, COMPARATIVE studies, RADIATION doses, RESEARCH funding, EMISSION-computed tomography, LONGITUDINAL method

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