Pan-cancer analysis of biallelic inactivation in tumor suppressor genes identifies KEAP1 zygosity as a predictive biomarker in lung cancer

Authors: Zucker, Mark ^{1, 15}, Perry, Maria A. ^{2, 3, 15}, Gould, Samuel I. ^{4, 5}, Elkrief, Arielle ^{3, 6, 7}, Safonov, Anton ⁶, Thummalapalli, Rohit ⁶, Mehine, Miika ³, Chakravarty, Debyani ^{2, 3}, Brannon, A. Rose ³, Ladanyi, Marc ³, Razavi, Pedram ⁶, Donoghue, Mark T.A. ², Murciano-Goroff, Yonina R. ⁶, Grigoriadis, Kristiana ^{8, 9, 10}, McGranahan, Nicholas ^{9, 10}, Jamal-Hanjani, Mariam ^{9, 11, 12}, Swanton, Charles ^{8, 9, 12}, Chen, Yuan ¹³, Shen, Ronglai ¹³, Chandarlapaty, Sarat ^{6, 7}, Solit, David B. ^{2, 6}, Schultz, Nikolaus ^{1, 2, 7, 14}, Berger, Michael F. ^{1, 2, 3, 7, 14}, Chang, Jason ³, Schoenfeld, Adam J. ⁶, Sánchez-Rivera, Francisco J. ^{4, 5}, Reznik, Ed ^{1, 2, ∗}, Bandlamudi, Chaitanya ^{2, 3, 16, ∗∗}

Source: In Cell 6 February 2025 188(3):851-867

A Phase 2 Trial of Talazoparib and Avelumab in Genomically Defined Metastatic Kidney Cancer

Authors: Kotecha, Ritesh R., Doshi, Sahil D., Knezevic, Andrea, Chaim, Joshua, Chen, Yingbei, Jacobi, Rachel, Zucker, Mark, Reznik, Ed, McHugh, Deaglan, Shah, Neil J., Feld, Emily, Aggen, David H., Rafelson, William, Xiao, Han, Carlo, Maria I., Feldman, Darren R., Lee, Chung-Han, Motzer, Robert J., Voss, Martin H.

Source: In European Urology Oncology August 2024 7(4):804-811

Gene expression of prostate-specific membrane antigen (FOLH1) in clear cell renal cell carcinoma predicts angiogenesis and response to tyrosine kinase inhibitors

Authors: Khaleel, Sari ^{a, b, #}, Perera, Marlon ^{c, d, #}, Papa, Nathan ^e, Kuo, Fengshen ^f, Golkaram, Mahdi ^g, Rappold, Phillip ^h, Kotecha, Ritesh R. ⁱ, Coleman, Jonathan ^j, Russo, Paul ^j, Motzer, Robert ⁱ, Reznik, Ed ^f, Hakimi, A. Ari ^{j, ⁎}

Source: In Urologic Oncology: Seminars and Original Investigations March 2025 43(3):192-192

Immunometabolic coevolution defines unique microenvironmental niches in ccRCC

Authors: Tang, Cerise, Xie, Amy X., Liu, Eric Minwei, Kuo, Fengshen, Kim, Minsoo, DiNatale, Renzo G., Golkaram, Mahdi, Chen, Ying-Bei, Gupta, Sounak, Motzer, Robert J., Russo, Paul, Coleman, Jonathan, Carlo, Maria I., Voss, Martin H., Kotecha, Ritesh R., Lee, Chung-Han, Tansey, Wesley, Schultz, Nikolaus, Hakimi, A. Ari, Reznik, Ed

Source: In Cell Metabolism 8 August 2023 35(8):1424-1440

Learning cellular objectives from fluxes by inverse optimization

Authors: Zhao, Qi, Stettner, Arion, Reznik, Ed, Segre, Daniel, Paschalidis, Ioannis Ch.

Source: 2015 54th IEEE Conference on Decision and Control (CDC) Decision and Control (CDC), 2015 IEEE 54th Annual Conference on. :1271-1276 Dec, 2015

Relation: 2015 54th IEEE Conference on Decision and Control (CDC)

Mitochondrial DNA is a major source of driver mutations in cancer

Authors: Kim, Minsoo, Mahmood, Mahnoor, Reznik, Ed, Gammage, Payam A.

Source: In Trends in Cancer December 2022 8(12):1046-1059

Genomic and Metabolic Hallmarks of SDH- and FH-deficient Renal Cell Carcinomas

Authors: Yoo, Angela, Tang, Cerise, Zucker, Mark, Fitzgerald, Kelly, DiNatale, Renzo G., Rappold, Phillip M., Weiss, Kate, Freeman, Benjamin, Lee, Chung-Han, Schultz, Nikolaus, Motzer, Robert, Russo, Paul, Coleman, Jonathan, Reuter, Victor E., Chen, Ying-Bei, Carlo, Maria I., Gill, Anthony J., Kotecha, Ritesh R., Ari Hakimi, A., Reznik, Ed

Source: In European Urology Focus September 2022 8(5):1278-1288

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

Authors: Nguyen, Bastien, Fong, Christopher, Luthra, Anisha, Smith, Shaleigh A., DiNatale, Renzo G., Nandakumar, Subhiksha, Walch, Henry, Chatila, Walid K., Madupuri, Ramyasree, Kundra, Ritika, Bielski, Craig M., Mastrogiacomo, Brooke, Donoghue, Mark T.A., Boire, Adrienne, Chandarlapaty, Sarat, Ganesh, Karuna, Harding, James J., Iacobuzio-Donahue, Christine A., Razavi, Pedram, Reznik, Ed, Rudin, Charles M., Zamarin, Dmitriy, Abida, Wassim, Abou-Alfa, Ghassan K., Aghajanian, Carol, Cercek, Andrea, Chi, Ping, Feldman, Darren, Ho, Alan L., Iyer, Gopakumar, Janjigian, Yelena Y., Morris, Michael, Motzer, Robert J., O’Reilly, Eileen M., Postow, Michael A., Raj, Nitya P., Riely, Gregory J., Robson, Mark E., Rosenberg, Jonathan E., Safonov, Anton, Shoushtari, Alexander N., Tap, William, Teo, Min Yuen, Varghese, Anna M., Voss, Martin, Yaeger, Rona, Zauderer, Marjorie G., Abu-Rustum, Nadeem, Garcia-Aguilar, Julio, Bochner, Bernard, Hakimi, Abraham, Jarnagin, William R., Jones, David R., Molena, Daniela, Morris, Luc, Rios-Doria, Eric, Russo, Paul, Singer, Samuel, Strong, Vivian E., Chakravarty, Debyani, Ellenson, Lora H., Gopalan, Anuradha, Reis-Filho, Jorge S., Weigelt, Britta, Ladanyi, Marc, Gonen, Mithat, Shah, Sohrab P., Massague, Joan, Gao, Jianjiong, Zehir, Ahmet, Berger, Michael F., Solit, David B., Bakhoum, Samuel F., Sanchez-Vega, Francisco, Schultz, Nikolaus

Source: In Cell 3 February 2022 185(3):563-575

Mitochondria-based Renal Cell Carcinoma Subtyping: Learning from Deep vs. Flat Feature Representations

Authors: Schüffler, Peter J., Sarungbam, Judy, Muhammad, Hassan, Reznik, Ed, Tickoo, Satish K., Fuchs, Thomas J.

Subject Terms: Computer Science - Learning

Access URL: http://arxiv.org/abs/1608.00842

The Clinicopathologic and Molecular Landscape of Clear Cell Papillary Renal Cell Carcinoma: Implications in Diagnosis and Management

Authors: Weng, Stanley, DiNatale, Renzo G., Silagy, Andrew, Mano, Roy, Attalla, Kyrollis, Kashani, Mahyar, Weiss, Kate, Benfante, Nicole E., Winer, Andrew G., Coleman, Jonathan A., Reuter, Victor E., Russo, Paul, Reznik, Ed, Tickoo, Satish K. ^⁎, Hakimi, A. Ari ^⁎

Source: In European Urology April 2021 79(4):468-477

Single-Cell Technologies for Studying the Evolution and Function of Mitochondrial DNA Heteroplasmy in Cancer.

Authors: Boscenco, Sonia, Cumming, Erin M., Kim, Minsoo, Lareau, Caleb, Reznik, Ed

Source: Annual Review of Cancer Biology; 2025, Vol. 9 Issue 1, p161-180, 15p

Metabolomics informs common patterns of molecular dysfunction across histologies of renal cell carcinoma

Authors: DiNatale, Renzo G., Sanchez, Alejandro, Hakimi, A. Ari, Reznik, Ed

Source: In Urologic Oncology: Seminars and Original Investigations October 2020 38(10):755-762

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Authors: Hadi, Kevin, Yao, Xiaotong, Behr, Julie M., Deshpande, Aditya, Xanthopoulakis, Charalampos, Tian, Huasong, Kudman, Sarah, Rosiene, Joel, Darmofal, Madison, DeRose, Joseph, Mortensen, Rick, Adney, Emily M., Shaiber, Alon, Gajic, Zoran, Sigouros, Michael, Eng, Kenneth, Wala, Jeremiah A., Wrzeszczyński, Kazimierz O., Arora, Kanika, Shah, Minita, Emde, Anne-Katrin, Felice, Vanessa, Frank, Mayu O., Darnell, Robert B., Ghandi, Mahmoud, Huang, Franklin, Dewhurst, Sally, Maciejowski, John, de Lange, Titia, Setton, Jeremy, Riaz, Nadeem, Reis-Filho, Jorge S., Powell, Simon, Knowles, David A., Reznik, Ed, Mishra, Bud, Beroukhim, Rameen, Zody, Michael C., Robine, Nicolas, Oman, Kenji M., Sanchez, Carissa A., Kuhner, Mary K., Smith, Lucian P., Galipeau, Patricia C., Paulson, Thomas G., Reid, Brian J., Li, Xiaohong, Wilkes, David, Sboner, Andrea, Mosquera, Juan Miguel, Elemento, Olivier, Imielinski, Marcin

Source: In Cell 1 October 2020 183(1):197-210

Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors

Authors: Vasan, Neil, Razavi, Pedram, Johnson, Jared L., Shao, Hong, Shah, Hardik, Antoine, Alesia, Ladewig, Erik, Gorelick, Alexander, Lin, Ting-Yu, Toska, Eneda, Xu, Guotai, Kazmi, Abiha, Chang, Matthew T., Taylor, Barry S., Dickler, Maura N., Jhaveri, Komal, Chandarlapaty, Sarat, Rabadan, Raul, Reznik, Ed, Smith, Melissa L., Sebra, Robert, Schimmoller, Frauke, Wilson, Timothy R., Friedman, Lori S., Cantley, Lewis C., Scaltriti, Maurizio, Baselga, José

Source: Science, 2019 Nov 01. 366(6466), 714-723.

Access URL: https://www.jstor.org/stable/26843823

The Association Between Small Primary Tumor Size and Prognosis in Metastatic Renal Cell Carcinoma: Insights from Two Independent Cohorts of Patients Who Underwent Cytoreductive Nephrectomy

Authors: DiNatale, Renzo G., Xie, Wanling, Becerra, Maria F., Silagy, Andrew W., Attalla, Kyrollis, Sanchez, Alejandro, Mano, Roy, Marcon, Julian, Blum, Kyle A., Benfante, Nicole E., Voss, Martin H., Motzer, Robert J., Coleman, Jonathan, Choueiri, Toni K., Reznik, Ed, Russo, Paul, Heng, Daniel Y.C., Hakimi, A. Ari ^*

Source: In European Urology Oncology February 2020 3(1):47-56

Hyperpolarized MRI of Human Prostate Cancer Reveals Increased Lactate with Tumor Grade Driven by Monocarboxylate Transporter 1

Authors: Granlund, Kristin L., Tee, Sui-Seng, Vargas, Hebert A., Lyashchenko, Serge K., Reznik, Ed, Fine, Samson, Laudone, Vincent, Eastham, James A., Touijer, Karim A., Reuter, Victor E., Gonen, Mithat, Sosa, Ramon E., Nicholson, Duane, Guo, YanWei W., Chen, Albert P., Tropp, James, Robb, Fraser, Hricak, Hedvig, Keshari, Kayvan R.

Source: In Cell Metabolism 7 January 2020 31(1):105-114

The Dynamics of Hybrid Metabolic-Genetic Oscillators

Authors: Reznik, Ed, Kaper, Tasso J., Segre, Daniel

Source: Chaos. 2013 Mar;23(1):013132

Subject Terms: Quantitative Biology - Molecular Networks, Nonlinear Sciences - Adaptation and Self-Organizing Systems, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1305.2954

The Stubborn Roots of Metabolic Cycles

Authors: Reznik, Ed, Watson, Alex, Chaudhary, Osman

Source: Journal of the Royal Society Interface, June 2013, Vol. 10, No. 83

Subject Terms: Quantitative Biology - Molecular Networks, Nonlinear Sciences - Adaptation and Self-Organizing Systems, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1304.6463

Characterization and Impact of TERT Promoter Region Mutations on Clinical Outcome in Renal Cell Carcinoma

Authors: Casuscelli, Jozefina, Becerra, Maria F., Manley, Brandon J., Zabor, Emily C., Reznik, Ed, Redzematovic, Almedina, Arcila, Maria E., Tennenbaum, Daniel M., Ghanaat, Mazyar, Kashan, Mahyar, Stief, Christian G., Carlo, Maria, Voss, Martin H., Feldman, Darren R., Motzer, Robert J., Chen, Yingbei, Reuter, Victor E., Coleman, Jonathan A., Russo, Paul, Hsieh, James J., Hakimi, Abraham Ari

Source: In European Urology Focus July 2019 5(4):642-649

The Quasi-Steady State Assumption in an Enzymatically Open System

Authors: Reznik, Ed, Segre, Daniel, Sherwood, William Erik

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1103.1200