qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps

por Riley, Blake T., Wankowicz, Stephanie A., de Oliveira, Saulo H. P., van Zundert, Gydo C. P., Hogan, Daniel W., Fraser, James S., Keedy, Daniel A., van den Bedem, Henry
Publicado no Protein Sci (2020)

Everolimus and pazopanib (E/P) benefit genomically selected patients with metastatic urothelial carcinoma

por Bellmunt, Joaquim, Lalani, Aly-Khan A., Jacobus, Sussana, Wankowicz, Stephanie A., Polacek, Laura, Takeda, David Y., Harshman, Lauren C., Wagle, Nikhil, Moreno, Irene, Lundgren, Kevin, Bossé, Dominick, Van Allen, Eliezer M., Choueiri, Toni K., Rosenberg, Jonathan E.
Publicado no Br J Cancer (2018)

Integrative molecular characterization of resistance to neoadjuvant chemoradiation in rectal cancer

por Kamran, Sophia C., Lennerz, Jochen K., Margolis, Claire A., Liu, David, Reardon, Brendan, Wankowicz, Stephanie A., Van Seventer, Emily, Tracy, Adam, Wo, Jennifer Y., Carter, Scott L., Willers, Henning, Corcoran, Ryan B., Hong, Theodore S., Van Allen, Eliezer M.
Publicado no Clin Cancer Res (2019)

Targeted genomic landscape of metastases compared to primary tumours in clear cell metastatic renal cell carcinoma

por de Velasco, Guillermo, Wankowicz, Stephanie A., Madison, Russell, Ali, Siraj M., Norton, Craig, Duquette, Audrey, Ross, Jeffrey S., Bossé, Dominick, Lalani, Aly-Khan A., Miller, Vincent A., Stephens, Philip J., Young, Lauren, Hakimi, A. Ari, Signoretti, Sabina, Pal, Sumanta K., Choueiri, Toni K.
Publicado no Br J Cancer (2018)

Genomic Resistance Patterns to Second-Generation Androgen Blockade in Paired Tumor Biopsies of Metastatic Castration-Resistant Prostate Cancer

por Han, G. Celine, Hwang, Justin, Wankowicz, Stephanie A.M., Zhang, Zhenwei, Liu, David, Cibulskis, Carrie, Gaviola, Glenn C., Ghazikhanian, Varand, McKay, Rana R., Bubley, Glenn J., Carter, Scott L., Balk, Steven P., Hahn, William C., Taplin, Mary-Ellen, Van Allen, Eliezer M.
Publicado no JCO Precis Oncol (2017)

Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer

por Liu, David, Abbosh, Philip, Keliher, Daniel, Reardon, Brendan, Miao, Diana, Mouw, Kent, Weiner-Taylor, Amaro, Wankowicz, Stephanie, Han, Garam, Teo, Min Yuen, Cipolla, Catharine, Kim, Jaegil, Iyer, Gopa, Al-Ahmadie, Hikmat, Dulaimi, Essel, Chen, David Y. T., Alpaugh, R. Katherine, Hoffman-Censits, Jean, Garraway, Levi A., Getz, Gad, Carter, Scott L., Bellmunt, Joaquim, Plimack, Elizabeth R., Rosenberg, Jonathan E., Van Allen, Eliezer M.
Publicado no Nat Commun (2017)

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

por Miao, Diana, Margolis, Claire A., Gao, Wenhua, Voss, Martin H., Li, Wei, Martini, Dylan J., Norton, Craig, Bossé, Dominick, Wankowicz, Stephanie M., Cullen, Dana, Horak, Christine, Wind-Rotolo, Megan, Tracy, Adam, Giannakis, Marios, Hodi, Frank Stephen, Drake, Charles G., Ball, Mark W., Allaf, Mohamad E., Snyder, Alexandra, Hellmann, Matthew D., Ho, Thai, Motzer, Robert J., Signoretti, Sabina, Kaelin, William G., Choueiri, Toni K., Van Allen, Eliezer M.
Publicado no Science (2018)

The Clinical Activity of PD-1/PD-L1 Inhibitors in Metastatic Non-Clear Cell Renal Cell Carcinoma

por McKay, Rana R., Bossé, Dominick, Xie, Wanling, Wankowicz, Stephanie A.M., Flaifel, Abdallah, Brandao, Raphael, Lalani, Aly-Khan A., Martini, Dylan J., Wei, Xiao X., Braun, David A., Van Allen, Eliezer, Castellano, Daniel, De Velasco, Guillermo, Wells, J. Connor, Heng, Daniel Y., Fay, Andre P., Schutz, Fabio A., Hsu, JoAnn, Pal, Sumanta K., Lee, Jae Lyun, Hsieh, James J., Harshman, Lauren C., Signoretti, Sabina, Motzer, Robert J., Feldman, Darren, Choueiri, Toni K.
Publicado no Cancer Immunol Res (2018)

Structural alterations driving castration-resistant prostate cancer revealed by linked-read genome sequencing

por Viswanathan, Srinivas R., Ha, Gavin, Hoff, Andreas M., Wala, Jeremiah A., Carrot-Zhang, Jian, Whelan, Christopher W., Haradhvala, Nicholas J., Freeman, Samuel S., Reed, Sarah C., Rhoades, Justin, Polak, Paz, Cipicchio, Michelle, Wankowicz, Stephanie A., Wong, Alicia, Kamath, Tushar, Zhang, Zhenwei, Gydush, Gregory J., Rotem, Denisse, Love, J. Christopher, Getz, Gad, Gabriel, Stacey, Zhang, Cheng-Zhong, Dehm, Scott M., Nelson, Peter S., Van Allen, Eliezer M., Choudhury, Atish D., Adalsteinsson, Viktor A., Beroukhim, Rameen, Taplin, Mary-Ellen, Meyerson, Matthew
Publicado no Cell (2018)

CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer

por Hwang, Justin H., Seo, Ji-Heui, Beshiri, Michael L., Wankowicz, Stephanie, Liu, David, Cheung, Alexander, Li, Ji, Qiu, Xintao, Hong, Andrew L., Botta, Ginevra, Golumb, Lior, Richter, Camden, So, Jonathan, Sandoval, Gabriel J., Giacomelli, Andrew O., Ly, Seav Huong, Han, Celine, Dai, Chao, Pakula, Hubert, Sheahan, Anjali, Piccioni, Federica, Gjoerup, Ole, Loda, Massimo, Sowalsky, Adam G., Ellis, Leigh, Long, Henry, Root, David E., Kelly, Kathleen, Van Allen, Eliezer M., Freedman, Matthew L., Choudhury, Atish D., Hahn, William C.
Publicado no Cell Rep (2019)

Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors

por Miao, Diana, Margolis, Claire A., Vokes, Natalie I., Liu, David, Taylor-Weiner, Amaro, Wankowicz, Stephanie M., Adeegbe, Dennis, Keliher, Daniel, Schilling, Bastian, Tracy, Adam, Manos, Michael, Chau, Nicole G., Hanna, Glenn J., Polak, Paz, Rodig, Scott J., Signoretti, Sabina, Sholl, Lynette M., Engelman, Jeffrey A., Getz, Gad, Jänne, Pasi A., Haddad, Robert I., Choueiri, Toni K., Barbie, David A., Haq, Rizwan, Awad, Mark M., Schadendorf, Dirk, Hodi, F. Stephen, Bellmunt, Joaquim, Wong, Kwok-Kin, Hammerman, Peter, Van Allen, Eliezer M.
Publicado no Nat Genet (2018)

The long tail of oncogenic drivers in prostate cancer

por Armenia, Joshua, Wankowicz, Stephanie A.M., Liu, David, Gao, Jianjiong, Kundra, Ritika, Reznik, Ed, Chatila, Walid K., Chakravarty, Debyani, Han, G. Celine, Coleman, Ilsa, Montgomery, Bruce, Pritchard, Colin, Morrissey, Colm, Barbieri, Christopher E., Beltran, Himisha, Sboner, Andrea, Zafeiriou, Zafeiris, Miranda, Susana, Bielski, Craig M., Penson, Alexander V., Tolonen, Charlotte, Huang, Franklin W., Robinson, Dan, Wu, Yi Mi, Lonigro, Robert, Garraway, Levi A., Demichelis, Francesca, Kantoff, Philip W., Taplin, Mary-Ellen, Abida, Wassim, Taylor, Barry S., Scher, Howard I., Nelson, Peter S., de Bono, Johann S., Rubin, Mark A., Sawyers, Charles L., Chinnaiyan, Arul M., Schultz, Nikolaus, Van Allen, Eliezer M.
Publicado no Nat Genet (2018)

Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding

por Newberry, Robert W., Arhar, Taylor, Costello, Jean, Hartoularos, George C., Maxwell, Alison M., Naing, Zun Zar Chi, Pittman, Maureen, Reddy, Nishith R., Schwarz, Daniel M. C., Wassarman, Douglas R., Wu, Taia S., Barrero, Daniel, Caggiano, Christa, Catching, Adam, Cavazos, Taylor B., Estes, Laurel S., Faust, Bryan, Fink, Elissa A., Goldman, Miriam A., Gomez, Yessica K., Grace Gordon, M., Gunsalus, Laura M., Hoppe, Nick, Jaime-Garza, Maru, Johnson, Matthew C., Jones, Matthew G., Kung, Andrew F., Lopez, Kyle E., Lumpe, Jared, Martyn, Calla, McCarthy, Elizabeth E., Miller-Vedam, Lakshmi E., Navarro, Erik J., Palar, Aji, Pellegrino, Jenna, Saylor, Wren, Stephens, Christina A., Strickland, Jack, Torosyan, Hayarpi, Wankowicz, Stephanie A., Wong, Daniel R., Wong, Garrett, Redding, Sy, Chow, Eric D., DeGrado, William F., Kampmann, Martin
Publicado no ACS Chem Biol (2020)

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

por Lawson, Catherine L., Kryshtafovych, Andriy, Adams, Paul D., Afonine, Pavel V., Baker, Matthew L., Barad, Benjamin A., Bond, Paul, Burnley, Tom, Cao, Renzhi, Cheng, Jianlin, Chojnowski, Grzegorz, Cowtan, Kevin, Dill, Ken A., DiMaio, Frank, Farrell, Daniel P., Fraser, James S., Herzik, Mark A., Hoh, Soon Wen, Hou, Jie, Hung, Li-Wei, Igaev, Maxim, Joseph, Agnel P., Kihara, Daisuke, Kumar, Dilip, Mittal, Sumit, Monastyrskyy, Bohdan, Olek, Mateusz, Palmer, Colin M., Patwardhan, Ardan, Perez, Alberto, Pfab, Jonas, Pintilie, Grigore D., Richardson, Jane S., Rosenthal, Peter B., Sarkar, Daipayan, Schäfer, Luisa U., Schmid, Michael F., Schröder, Gunnar F., Shekhar, Mrinal, Si, Dong, Singharoy, Abishek, Terashi, Genki, Terwilliger, Thomas C., Vaiana, Andrea, Wang, Liguo, Wang, Zhe, Wankowicz, Stephanie A., Williams, Christopher J., Winn, Martyn, Wu, Tianqi, Yu, Xiaodi, Zhang, Kaiming, Berman, Helen M., Chiu, Wah
Publicado no Nat Methods (2021)

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

por Gordon, David E., Jang, Gwendolyn M., Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, O’Meara, Matthew J., Guo, Jeffrey Z., Swaney, Danielle L., Tummino, Tia A., Huettenhain, Ruth, Kaake, Robyn M., Richards, Alicia L., Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J., Braberg, Hannes, Fabius, Jacqueline M., Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J., Cakir, Merve, McGregor, Michael J., Li, Qiongyu, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Kirby, Ilsa T., Melnyk, James E., Chorba, John S., Lou, Kevin, Dai, Shizhong A., Shen, Wenqi, Shi, Ying, Zhang, Ziyang, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Mathy, Christopher J.P., Perica, Tina, Pilla, Kala B., Ganesan, Sai J., Saltzberg, Daniel J., Ramachandran, Rakesh, Liu, Xi, Rosenthal, Sara B., Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Wankowicz, Stephanie A., Bohn, Markus, Sharp, Phillip P., Trenker, Raphael, Young, Janet M., Cavero, Devin A., Hiatt, Joseph, Roth, Theodore L., Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Roesch, Ferdinand, Vallet, Thomas, Meyer, Björn, White, Kris M., Miorin, Lisa, Rosenberg, Oren S., Verba, Kliment A, Agard, David, Ott, Melanie, Emerman, Michael, Ruggero, Davide, García-Sastre, Adolfo, Jura, Natalia, von Zastrow, Mark, Taunton, Jack, Ashworth, Alan, Schwartz, Olivier, Vignuzzi, Marco, d’Enfert, Christophe, Mukherjee, Shaeri, Jacobson, Matt, Malik, Harmit S., Fujimori, Danica G., Ideker, Trey, Craik, Charles S., Floor, Stephen, Fraser, James S., Gross, John, Sali, Andrej, Kortemme, Tanja, Beltrao, Pedro, Shokat, Kevan, Shoichet, Brian K., Krogan, Nevan J.
Publicado no bioRxiv (2020)

A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing

por Gordon, David E., Jang, Gwendolyn M., Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, White, Kris M., O’Meara, Matthew J., Rezelj, Veronica V., Guo, Jeffrey Z., Swaney, Danielle L., Tummino, Tia A., Huettenhain, Ruth, Kaake, Robyn M., Richards, Alicia L., Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J., Braberg, Hannes, Fabius, Jacqueline M., Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J., Cakir, Merve, McGregor, Michael J., Li, Qiongyu, Meyer, Bjoern, Roesch, Ferdinand, Vallet, Thomas, Kain, Alice Mac, Miorin, Lisa, Moreno, Elena, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Shi, Ying, Zhang, Ziyang, Shen, Wenqi, Kirby, Ilsa T., Melnyk, James E., Chorba, John S., Lou, Kevin, Dai, Shizhong A., Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Lyu, Jiankun, Mathy, Christopher J.P., Perica, Tina, Pilla, Kala B., Ganesan, Sai J., Saltzberg, Daniel J., Rakesh, Ramachandran, Liu, Xi, Rosenthal, Sara B., Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Huang, Xi-Ping, Liu, YongFeng, Wankowicz, Stephanie A., Bohn, Markus, Safari, Maliheh, Ugur, Fatima S., Koh, Cassandra, Savar, Nastaran Sadat, Tran, Quang Dinh, Shengjuler, Djoshkun, Fletcher, Sabrina J, O’Neal, Michael C., Cai, Yiming, C.J.Chang, Jason, Broadhurst, David J., Klippsten, Saker, Sharp, Phillip P., Wenzell, Nicole A., Kuzuoglu, Duygu, Wang, Hao-Yuan, Trenker, Raphael, Young, Janet M., Cavero, Devin A., Hiatt, Joseph, Roth, Theodore L., Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Stroud, Robert M., Frankel, Alan D., Rosenberg, Oren S., Verba, Kliment A, Agard, David A., Ott, Melanie, Emerman, Michael, Jura, Natalia, von Zastrow, Mark, Verdin, Eric, Ashworth, Alan, Schwartz, Olivier, d’Enfert, Christophe, Mukherjee, Shaeri, Jacobson, Matt, Malik, Harmit S., Fujimori, Danica G., Ideker, Trey, Craik, Charles S., Floor, Stephen N., Fraser, James S., Gross, John D., Sali, Andrej, Roth, Bryan L., Ruggero, Davide, Taunton, Jack, Kortemme, Tanja, Beltrao, Pedro, Vignuzzi, Marco, García-Sastre, Adolfo, Shokat, Kevan M., Shoichet, Brian K., Krogan, Nevan J.
Publicado no Nature (2020)