Publications

Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments
Flowers J, Echols N, Correy G, Jaishankar P, Togo T, Renslo AR, van den Bedem H, Fraser JS, Wankowicz SA
Biorxiv, 2024
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Dynamic allostery drives autocrine and paracrine TGF-β signaling
Jin M, Seed RI, Cai G, Shing T, Wang L, Ito S, Cormier A, Wankowicz SA, Jespersen JM, Baron JL, Carey ND, Campbell MG, Yu Z, Tang PK, Cossio P, Wen W, Lou J, Marks J, Nishimura SL, Cheng Y.
Cell, 2024
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A renewed call for open artificial intelligence in biomedicine
Gitter A, Fraser JS, Gonen T, Patro R, Wayment-Steele HK, Williams A, Haibe-Kains B, Dunbrack RL, Cook C, Kundaje A, Hoffman MM, Carpenter AE, Wankowicz SA, Lindorff-Larsen K
Preprint, 2024
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Comprehensive Encoding of Conformational and Compositional Protein Structural Ensembles through mmCIF Data Structure
Wankowicz SA, Fraser JS
IUCrJ, 2024
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Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM
Wankowicz SA, Ravikumar A, Sharma S, Riley B, Raju A, Flowers J, Hogan DW, van den Bedem H, Keedy DA, Fraser JS
eLife, 2024
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Ten recommendations for hosting a Diversity, Equity, Inclusion, and Justice (DEIJ) journal club
Díaz RE, Wankowicz SA
PLoS Computational Biology, 2024
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AlphaFold3 Transparency and Reproducibility
Wankowicz SA, Beltrao P, Cravatt B, Dunbrack R, Gitter A, Lindorff-Larsen K, Ovchinnikov S, Polizzi N, Shoichet B, Fraser JS
Preprint, 2024
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Making sense of chaos: uncovering the mechanisms of conformational entropy
Wankowicz SA, Fraser JS
Preprint, 2023
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Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data
Du S, Wankowicz SA, Yabukarski F, Doukov T, Herschlag D, Fraser JS
Methods in Enzymology, 2023
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Ligand binding remodels protein side chain conformational heterogeneity
Wankowicz SA, de Oliveira SHP, Hogan DW, van den Bedem H, Fraser JS
eLife, 2022
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A patient-driven clinicogenomic partnership for metastatic prostate cancer
Crowdis J, Balch S, Sterlin L, Thomas BS, Camp SY, Dunphy M, Anastasio E, Shah S, Damon AL, Ramos R, Sosa DM, Small IK, Tomson BN, Nguyen CM, McGillicuddy M, Chastain PS, He MX, Cheung ATM, Wankowicz SA, Tewari AK, Kim D, AlDubayan SH, Dowdye A, Zola B, Nowak J, Manarite J, Henry Gunn I, Olson B, Lander ES, Painter CA, Wagle N, Van Allen EM.
Cell Genomics, 2022
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Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Jr. Herzik MA, Hoh SW, Hou J, Hung L, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W
Nature Methods, 2021
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Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer
Tewari AK, Cheung ATM, Crowdis J, Conway JR, Camp SY, Wankowicz SA, Livitz DG, Park J, Lis RT, Bosma-Moody A, He MX, AlDubayan SH, Zhang Z, McKay RR, Leshchiner I, Brown M, Balk SP, Getz G, Taplin ME, Van Allen EM
Cell Reports, 2021
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qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps
Riley BT, Wankowicz SA, de Oliveira SHP, van Zundert GCP, Hogan DW, Fraser JS, Keedy DA, van den Bedem H
Protein Science, 2021
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Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding
Newberry RW, Arhar T, Costello J, Hartoularos GC, Maxwell AM, Chi Naing ZZ, Pittman M, Reddy NR, Schwarz DM, Wassarman DR, Wu TS, Barrero D, Caggiano C, Catching A, Cavazos TB, Estes L, Faust B, Fink EA, Goldman MA, Gomez YK, Gordon MG, Gunsalus LM, Hoppe N, Jaime-Garza M, Johnson MC, Jones MG, Kung AF, Lopez KE, Lumpe J, Martyn C, McCarthy EE, Miller-Vedam LE, Navarro EJ, Palar A, Pellegrino J, Saylor W, Stephens CA, Strickland J, Torosyan H, Wankowicz SA, Wong Dr, Wong G, Redding S, Chow ED, DeGrado WF, Kampmann M.
ACS Chemical Biology, 2020
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A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
Gordon DE*, Jang GM*, Bouhaddou M*, Xu J*, Obernier K*, White KM*, O’Meara MJ*, Rezelj VV*, Guo JZ, Swaney DL, Tummino TA, Huttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O’Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard D, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d’Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ
Nature, 2020
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Ensemble refinement produces consistent R-free values but smaller ensemble sizes than previously reported
Wankowicz SA, Fraser JS
Computational Crystallography Newsletter, 2020
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The long tail of oncogenic drivers in prostate cancer
Armenia J#, Wankowicz SAM#, Liu D#, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski, CM, Penson, AV, Tolonen, C, Huang FW, Robinson, D, Wu YM, Lonigro, R, Garraway LA, Demichelis, F, Kantoff PW, Taplin, M., Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers C., Chinnaiyan A, PCF/SU2C International Prostate Cancer Dream Team, Schultz, N., Van Allen, E.M. #Co-First Authors
Nature Genetics, 2019
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Integrative molecular characterization of resistance to neoadjuvant chemoradiation in rectal cancer
Kamran SC, Lennerz JK, Margolis CA, Liu D, Reardon B, Wankowicz SA, Van Seventer EE, Tracy A, Wo JY, Carter SL, Willers H, Corcoran RB, Hong TS, Van Allen EM.
Clinical Cancer Research, 2019
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CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer
Hwang JH, Seo J, Beshiri ML, Wankowicz SA, Liu D, Cheung A, Li J, Qiu X, Hong AL, Botta G, Golumb L, Richter C, So J, Sandoval GJ, Giacomelli AO, Ly SH, Han C, Dai C, Pakula H, Sheahan A, Piccioni F, Gjoerup O, Loda M, Sowalsky AG, Ellis L, Long H, Root DE, Kelly K, Van Allen EM, Freedman ML, Choudhury AC, Hahn WC.
Cell Reports, 2019
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Genomic correlates of response to anti-PD-1/PD-L1 therapy in metastatic clear cell renal cell carcinoma
Miao D, Margolis C, Gao W, Voss MH, Li W, Martini D, Norton C, Bossé D, Wankowicz SA, Cullen D, Horak C, Wind-Rotolo M, Tracy A, Giannakis M, Hodi FS, Drake CG, Ball MW, Allaf ME, Snyder Charen A, Hellmann M, Ho T, Motzer RJ, Signoretti S, Kaelin Jr WG, Choueiri TK, Van Allen EM.
Science, 2018
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Targeted genomic landscape of metastases compared to primary tumours in clear cell metastatic renal cell carcinoma
de Velasco G#, Wankowicz SA#, Madison R, Ali SM, Norton C, Duquette A, Ross JS, Bossé D, Lalani AKA, Miller VA, Stephens PJ, Young L, Hakimi AA, Signoretti SS, Pal SK, Choueiri TK.
British Journal of Cancer, 2018
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Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors
Miao D, Margolis CA, Vokes NI, Liu D, Taylor-Weiner A, Wankowicz SA, Adeegbe D, Keliher D, Schilling B, Tracy A, Manos M, Chau N, Hanna G, Polak P, Rodig SJ, Signoretti S, Sholl L, Engelman J, Getz G, Janne PA, Haddad RI, Choueiri TK, Barbie DA, Haq R, Awad MM, Schadendorf D, Hodi FS, Bellmunt J, Wong KK, Hammerman P, Van Allen, EM.
Nature Genetics, 2018
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Structural alterations driving castration-resistant prostate cancer revealed by linked-read genome sequencing
Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan, CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zheng Z, Gydush GJ, Rotem D, Love CJ, Getz G, Gabriel S, Zhang C, Dehm SM, Nelson PS, Van Allen EM, Choudhury A, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M.
Cell, 2018
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Patient-driven efforts to liberate clinical cancer genomic data
Wankowicz SA, Maile B, Deutsch K, Hayden A, Brown E, Marsilje T, Caldwell B, Simoncelli T, Van Allen E.
Preprint, 2018
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The clinical activity of PD-1/PD-L1 inhibitors in metastatic non–clear cell renal cell carcinoma
McKay RR, Bossé D, Xie W, Wankowicz SA, Flaifel A, Brandao R, Lalani AKA, Martini DJ, Wei XX, Braun DA, Van Allen EM.
Cancer Immunology Research, 2018
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Everolimus and pazopanib (E/P) benefit genomically selected patients with metastatic urothelial carcinoma
Bellmunt J, Lalani AKA, Jacobus S, Wankowicz SA, Polacek L, Takeda DY, Harshman LC, Wagle N, Moreno I, Lundgren K, Bossé D, Van Allen E, Choueiri T, Rosenberg J.
British Journal of Cancer, 2018
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Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer
Rodrigues DN, Rescigno P, Liu D, Yuan W, Carreira S, Lambros MB, Seed G, Mateo J, Riisnaes R, Mullane S, Margolis C, Miao D, Miranda S, Dolling D, Clarke M, Bertan C, Crespo M, Boysen G, Ferreria A, Sharp A, Figueiredo I, Keliher D, Aldubayan S, Burke K, Sumanasyriya S, Fontes M, Bianchini D, Zafeiriou Z, Mendes L, Mouw K, Schweizer M, Pritchard C, Salipante S, Taplin ME, Beltran H, Rubin M, Cieslik M, Robinson D, Heath E, Schultz N, Armenia J, Abida W, Scher H, Lord C, D’Andrea A, Sawyers C, Chinnaiyan A, Alimonti A, Nelson P, Drake C, Van Allen E, de Bono, JS.
The Journal of clinical investigation, 2018
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Racial disparity in quality of care and overall survival among black vs. white patients with muscle-invasive bladder cancer treated with radical cystectomy: A national cancer database analysis
Gild P#, Wankowicz SA#, Sood A, von Landenberg N, Friedlander DF, Alanee S, Bellmunt, J. #Co-First Authors
Urological Oncology, 2018
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Nomogram to assess the survival benefit of new salvage agents for metastatic urothelial carcinoma in the era of immunotherapy
Sonpavde G, Pond GR, Rosenberg JE, Choueiri TK, Bellmunt J, Regazzi AM, Mullane SA, Necchi A, Raggi D, Lee JL, Lee S.
Clinical Cancer Research, 2018
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Differential expression of PD-L1 in high grade T1 vs muscle invasive bladder carcinoma and its prognostic implications
Wankowicz SA, Werner L, Orsola A, Novak J, Bowden M, Choueiri TK, de Torres I, Morote J, Freeman GJ, Signoretti S, Bellmunt J.
The Journal of Urology, 2017
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Neoadjuvant chemotherapy prior to radical cystectomy for muscle‐invasive bladder cancer with variant histology
Wankowicz SA#, Vetterlein MW#, Seisen T, Lander R, Löppenberg B, Chun FK, Menon M, Sun M, Barletta JA, Choueiri TK, Bellmunt J, Trinh QD, Preston, MA. #Co-First Authors
Cancer, 2017
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Exome sequencing of African-American prostate cancer reveals loss-of-function ERF mutations
Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M, Amin-Mansour A, Rabasha B, Bahl S, Mullane SA, Robinson BD, Aldubayan S, Khani F, Karir B, Kim E, Chimene-Weiss J, Hofree M, Romanel A, Osborne JR, Kim JW, Azabdaftari G, Woloszynska-Read A, Sfanos K, De Marzo AM, Demichelis F Gabriel S, Van Allen EM, Mesirov J, Tamayo P, Rubin MA, Powell IJ, Garraway LA.
Cancer Discovery, 2017
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Mutational patterns in chemotherapy resistant muscle-invasive bladder cancer
Liu D, Abbosh P, Keliher D, Reardon B, Miao D, Mouw K, Taylor-Weiner A, Mullane SA, Han C, Teo MY, Cipolla C, Kim J, Iyer G, Al-Ahmadie H, Dulaimi E, Chen DYT, Alpaugh R, Hoffman-Censits J, Garraway L, Getz G, Carter S, Bellmunt J, Plimack E, Rosenberg J, Van Allen EM.
Nature Communications, 2017
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Genomic resistance patterns to second-generation androgen blockade in paired tumor biopsies of metastatic castration-resistant prostate cancer
Han GC, Hwang J, Wankowicz SA, Zhang Z, Liu D, Cibulskis C, Gaviola GC, Ghazikhanian V, McKay RR, Bubley GJ, Carter SL, Balk SP, Hahn WH, Taplin EM, Van Allen EM.
Journal of Clinical Oncology Precision Medicine, 2017
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Upper Tract Urothelial Carcinomas: Prognostic Factors and Outcomes in Patients With Non–Lymph Node Distant Metastasis
Sevillano E, Werner L, Bossé D, Lalani AA, Wankowicz SA, de Velasco G, Farina M, Lundgren K, Choueiri TK, González Del Alba A, Bellmunt J.
Clinical Genitourinary Cancer, 2017
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Cancer immunotherapy: new applications in urologic oncology
Mullane SA, Bellmunt J.
Current Opinions in Urology, 2016
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Precision medicine for advanced prostate cancer
Mullane SA, Van Allen EM.
Current Opinion in Urology, 2016
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Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles
Cejas P, Li L, O’Neill NK, Duarte M, Rao P, Bowden M, Zhou CW, Mendiola M, Burgos E, Feliu J, Moreno-Rubio J, Guadalajara H, Moreno V, García-Olmo D, Bellmunt J, Mullane SA, Hirsch M, Sweeney CJ, Richardson A, Liu XS, Brown M, Shivdasani RA, Long HW.
Nature Medicine, 2016
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Expression levels of DNA damage repair proteins are associated with overall survival in platinum-treated advanced urothelial carcinoma
Mullane SA, Werner L, Guancial EA, Lis RT, Stack EC, Loda, M, Kantoff PW, Choueiri TK, Rosenberg J, Bellmunt, J.
Clinical Genitourinary Cancer, 2016
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Re: John P. Sfakianos, Eugene K. Cha, Gopa Iyer, et al. Genomic Characterization of Upper Tract Urothelial Carcinoma
Mullane SA, Bellmunt J.
European Urology, 2016
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Association of tumour microRNA profiling with outcomes in patients with advanced urothelial carcinoma receiving first-line platinum-based chemotherapy
Bellmunt J, Zhou CW, Mullane SA, Werner L, Taplin ME, Fay AP, Choueiri TK, Orsola A, Takeda DY, Hahn WC, Kim J, Sonpavde G, Bowden M.
British Journal of Cancer, 2016
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Letter to the Editor, Re: van der Heijden AG, Mengual L, Lozano JJ, Ingelmo-Torres M, Ribal MJ, Fernández PL, Oosterwijk E, Schalken JA, Alcaraz A, Witjes JA. A five-gene expressionsignature to predict progression in T1G3 bladder cancer.
Orsola A, Mullane SA, Bellmunt J.
European Journal of Cancer, 2016
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Outcomes in patients with advanced urothelial carcinoma after discontinuation of programmed death (PD)-1 or PD ligand 1 inhibitor therapy
Sonpavde G, Pond GR, Mullane S, Ramirez AA, Vogelzang NJ, Necchi A, Powles T, Bellmunt J.
BJU International, 2016
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DNA damage response and repair gene alterations are associated with improved survival in patients with platinum-treated advanced urothelial carcinoma
Teo MY, Bambury RM, Zabor EC, Jordan E, Al-Ahmadie H, Boyd ME, Bouvier N, Mullane SA, Cha EK, Roper N, Ostrovnaya I, Hyman DM, Bochner BH, Arcila ME, Solit DB, Berger MF, Bajorin DF, Bellmunt J, Iyer G, Rosenberg JE.
Clinical Cancer Research, 2016
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Impact of Prior Platinum-Based Therapy on Patients Receiving Salvage Systemic Treatment for Advanced Urothelial Carcinoma
Sonpavde G, Pond GR, Di Lorenzo G, Buonerba C, Rozzi A, Lanzetta G, Necchi A, Giannatempo P, Raggi D6, Matsumoto K, Choueiri TK, Mullane SA, Niegisch G, Albers P, Lee JL, Kitamura H, Kume H, Bellmunt J.
Clinical Genitourinary Cancer, 2016
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Single-agent taxane versus taxane-containing combination chemotherapy as salvage therapy for advanced urothelial carcinoma
Sonpavde G, Pond GR, Choueiri TK, Mullane SA, Niegisch G, Albers, P, Necchi A5, Di Lorenzo G, Buonerba C, RozziA, Matsumoto K, Lee JL, Kitamura H, Kume H, Bellmunt J.
European Urology, 2016
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Association of PD-L1 expression on tumor-infiltrating mononuclear cells and overall survival in patients with urothelial carcinoma
Bellmunt J, Mullane SA, Werner L, Fay AP, Callea M, Leow J, Choueiri TK, Hodi FS, Freeman GJ, Signoretti S.
Annals of Oncology, 2015
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Somatic Copy Number Abnormalities and Mutations in PI3K/AKT/mTOR Pathway Have Prognostic Significance for Overall Survival in Platinum Treated Locally Advanced or Metastatic Urothelial Tumors.
Bellmunt J, Werner L, Leow JJ, Mullane SA, Fay AP, Riester M, Van Hummelen P, Taplin ME, Choueiri TK, Van Allen E, Rosenberg, J.
PloS One, 2015
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Reexamining treatment of high-grade T1 bladder cancer according to depth of lamina propria invasion: a prospective trial of 200 patients
Orsola A, L. Werner, de Torres I, Martin-Doyle W, Raventos CX, Lozano F, Mullane SA, Leow JJ, Barletta JA, Bellmunt J, Morote J.
British Journal of Cancer, 2015
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Temporal trends in receipt of adequate lymphadenectomy in bladder cancer 1988 to 2010
Cole AP, Dalela D, Hanske J, Mullane SA, Choueiri TK, Meyer CP, Nguyen Pl, Menon M, Kibel AS, Preston MA, Bellmunt J, Trinh Q.
Urologic Oncology, 2015
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HER2 as a target in invasive urothelial carcinoma
Bellmunt J, Werner L, Bamias A, Fay AP, Park RS, Riester M, Selvarajah S, Barletta J, Berman D, de Muga S, Salido M, Gallardo E, Rojo F, Guancial E, Bambury R, Mullane SA, Choueiri TK, Loda M, Stack E, Rosenberg, J.
Cancer Medicine, 2015
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