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1.

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma.

Hofman, Damon A; Ruiz-Orera, Jorge; Yannuzzi, Ian; Murugesan, Rakesh; Brown, Adam; Clauser, Karl R; Condurat, Alexandra L; van Dinter, Jip T; Engels, Sem A G; Goodale, Amy; van der Lugt, Jasper; Abid, Tanaz; Wang, Li; Zhou, Kevin N; Vogelzang, Jayne; Ligon, Keith L; Phoenix, Timothy N; Roth, Jennifer A; Root, David E; Hubner, Norbert; Golub, Todd R; Bandopadhayay, Pratiti; van Heesch, Sebastiaan; Prensner, John R.

Mol Cell ; 84(2): 261-276.e18, 2024 Jan 18.

Article in English | MEDLINE | ID: mdl-38176414

2.

The Power of Human Cancer Genetics as Revealed by Low-Grade Gliomas.

Jones, David T W; Bandopadhayay, Pratiti; Jabado, Nada.

Annu Rev Genet ; 53: 483-503, 2019 12 03.

Article in English | MEDLINE | ID: mdl-31794268

3.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A; Shapira, Ofer; Tiao, Grace; Hornshøj, Henrik; Hess, Julian M; Juul, Randi Istrup; Lin, Ziao; Feuerbach, Lars; Sabarinathan, Radhakrishnan; Madsen, Tobias; Kim, Jaegil; Mularoni, Loris; Shuai, Shimin; Lanzós, Andrés; Herrmann, Carl; Maruvka, Yosef E; Shen, Ciyue; Amin, Samirkumar B; Bandopadhayay, Pratiti; Bertl, Johanna; Boroevich, Keith A; Busanovich, John; Carlevaro-Fita, Joana; Chakravarty, Dimple; Chan, Calvin Wing Yiu; Craft, David; Dhingra, Priyanka; Diamanti, Klev; Fonseca, Nuno A; Gonzalez-Perez, Abel; Guo, Qianyun; Hamilton, Mark P; Haradhvala, Nicholas J; Hong, Chen; Isaev, Keren; Johnson, Todd A; Juul, Malene; Kahles, Andre; Kahraman, Abdullah; Kim, Youngwook; Komorowski, Jan; Kumar, Kiran; Kumar, Sushant; Lee, Donghoon; Lehmann, Kjong-Van; Li, Yilong; Liu, Eric Minwei.

Nature ; 578(7793): 102-111, 2020 02.

Article in English | MEDLINE | ID: mdl-32025015

4.

Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors.

Giacomini, Giulia; Piquet, Sandra; Chevallier, Odile; Dabin, Juliette; Bai, Siau-Kun; Kim, Byungjin; Siddaway, Robert; Raught, Brian; Coyaud, Etienne; Shan, Chun-Min; Reid, Robert J D; Toda, Takenori; Rothstein, Rodney; Barra, Viviana; Wilhelm, Therese; Hamadat, Sabah; Bertin, Chloé; Crane, Alexander; Dubois, Frank; Forne, Ignasi; Imhof, Axel; Bandopadhayay, Pratiti; Beroukhim, Rameen; Naim, Valeria; Jia, Songtao; Hawkins, Cynthia; Rondinelli, Beatrice; Polo, Sophie E.

Nucleic Acids Res ; 52(5): 2372-2388, 2024 Mar 21.

Article in English | MEDLINE | ID: mdl-38214234

5.

Longitudinal molecular trajectories of diffuse glioma in adults.

Barthel, Floris P; Johnson, Kevin C; Varn, Frederick S; Moskalik, Anzhela D; Tanner, Georgette; Kocakavuk, Emre; Anderson, Kevin J; Abiola, Olajide; Aldape, Kenneth; Alfaro, Kristin D; Alpar, Donat; Amin, Samirkumar B; Ashley, David M; Bandopadhayay, Pratiti; Barnholtz-Sloan, Jill S; Beroukhim, Rameen; Bock, Christoph; Brastianos, Priscilla K; Brat, Daniel J; Brodbelt, Andrew R; Bruns, Alexander F; Bulsara, Ketan R; Chakrabarty, Aruna; Chakravarti, Arnab; Chuang, Jeffrey H; Claus, Elizabeth B; Cochran, Elizabeth J; Connelly, Jennifer; Costello, Joseph F; Finocchiaro, Gaetano; Fletcher, Michael N; French, Pim J; Gan, Hui K; Gilbert, Mark R; Gould, Peter V; Grimmer, Matthew R; Iavarone, Antonio; Ismail, Azzam; Jenkinson, Michael D; Khasraw, Mustafa; Kim, Hoon; Kouwenhoven, Mathilde C M; LaViolette, Peter S; Li, Meihong; Lichter, Peter; Ligon, Keith L; Lowman, Allison K; Malta, Tathiane M; Mazor, Tali; McDonald, Kerrie L.

Nature ; 576(7785): 112-120, 2019 12.

Article in English | MEDLINE | ID: mdl-31748746

6.

Genetic and transcriptional evolution alters cancer cell line drug response.

Ben-David, Uri; Siranosian, Benjamin; Ha, Gavin; Tang, Helen; Oren, Yaara; Hinohara, Kunihiko; Strathdee, Craig A; Dempster, Joshua; Lyons, Nicholas J; Burns, Robert; Nag, Anwesha; Kugener, Guillaume; Cimini, Beth; Tsvetkov, Peter; Maruvka, Yosef E; O'Rourke, Ryan; Garrity, Anthony; Tubelli, Andrew A; Bandopadhayay, Pratiti; Tsherniak, Aviad; Vazquez, Francisca; Wong, Bang; Birger, Chet; Ghandi, Mahmoud; Thorner, Aaron R; Bittker, Joshua A; Meyerson, Matthew; Getz, Gad; Beroukhim, Rameen; Golub, Todd R.

Nature ; 560(7718): 325-330, 2018 08.

Article in English | MEDLINE | ID: mdl-30089904

7.

Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A; Shapira, Ofer; Tiao, Grace; Hornshøj, Henrik; Hess, Julian M; Juul, Randi Istrup; Lin, Ziao; Feuerbach, Lars; Sabarinathan, Radhakrishnan; Madsen, Tobias; Kim, Jaegil; Mularoni, Loris; Shuai, Shimin; Lanzós, Andrés; Herrmann, Carl; Maruvka, Yosef E; Shen, Ciyue; Amin, Samirkumar B; Bandopadhayay, Pratiti; Bertl, Johanna; Boroevich, Keith A; Busanovich, John; Carlevaro-Fita, Joana; Chakravarty, Dimple; Chan, Calvin Wing Yiu; Craft, David; Dhingra, Priyanka; Diamanti, Klev; Fonseca, Nuno A; Gonzalez-Perez, Abel; Guo, Qianyun; Hamilton, Mark P; Haradhvala, Nicholas J; Hong, Chen; Isaev, Keren; Johnson, Todd A; Juul, Malene; Kahles, Andre; Kahraman, Abdullah; Kim, Youngwook; Komorowski, Jan; Kumar, Kiran; Kumar, Sushant; Lee, Donghoon; Lehmann, Kjong-Van; Li, Yilong; Liu, Eric Minwei.

Nature ; 614(7948): E40, 2023 Feb.

Article in English | MEDLINE | ID: mdl-36697832

8.

Molecular genetics of paediatric brain tumours and opportunities for precision medicine - a focus on infant tumours.

Rosenberg, Tom; Bandopadhayay, Pratiti.

Curr Opin Neurol ; 35(6): 772-778, 2022 12 01.

Article in English | MEDLINE | ID: mdl-36226704

9.

Towards Immunotherapy for Pediatric Brain Tumors.

Wang, Stacie Shiqi; Bandopadhayay, Pratiti; Jenkins, Misty Rayna.

Trends Immunol ; 40(8): 748-761, 2019 08.

Article in English | MEDLINE | ID: mdl-31229353

10.

SvABA: genome-wide detection of structural variants and indels by local assembly.

Wala, Jeremiah A; Bandopadhayay, Pratiti; Greenwald, Noah F; O'Rourke, Ryan; Sharpe, Ted; Stewart, Chip; Schumacher, Steve; Li, Yilong; Weischenfeldt, Joachim; Yao, Xiaotong; Nusbaum, Chad; Campbell, Peter; Getz, Gad; Meyerson, Matthew; Zhang, Cheng-Zhong; Imielinski, Marcin; Beroukhim, Rameen.

Genome Res ; 28(4): 581-591, 2018 04.

Article in English | MEDLINE | ID: mdl-29535149

11.

Advances in the classification and treatment of pediatric brain tumors.

Fangusaro, Jason; Bandopadhayay, Pratiti.

Curr Opin Pediatr ; 33(1): 26-32, 2021 02 01.

Article in English | MEDLINE | ID: mdl-33278109

12.

Outcomes after first relapse of childhood intracranial ependymoma.

Tsai, Jessica W; Manoharan, Neevika; Alexandrescu, Sanda; Zimmerman, Mary Ann; Scully, Jacqueline; Chordas, Christine; Clymer, Jessica; Wright, Karen D; Filbin, Mariella; Ullrich, Nicole J; Marcus, Karen J; Haas-Kogan, Daphne; Chi, Susan N; Bandopadhayay, Pratiti; Yeo, Kee Kiat.

Pediatr Blood Cancer ; 68(8): e28930, 2021 08.

Article in English | MEDLINE | ID: mdl-33565268

13.

CloneSifter: enrichment of rare clones from heterogeneous cell populations.

Feldman, David; Tsai, FuNien; Garrity, Anthony J; O'Rourke, Ryan; Brenan, Lisa; Ho, Patricia; Gonzalez, Elizabeth; Konermann, Silvana; Johannessen, Cory M; Beroukhim, Rameen; Bandopadhayay, Pratiti; Blainey, Paul C.

BMC Biol ; 18(1): 177, 2020 11 24.

Article in English | MEDLINE | ID: mdl-33234154

14.

Trametinib for the treatment of recurrent/progressive pediatric low-grade glioma.

Manoharan, Neevika; Choi, Jungwhan; Chordas, Christine; Zimmerman, Mary Ann; Scully, Jacqueline; Clymer, Jessica; Filbin, Mariella; Ullrich, Nicole J; Bandopadhayay, Pratiti; Chi, Susan N; Yeo, Kee Kiat.

J Neurooncol ; 149(2): 253-262, 2020 Sep.

Article in English | MEDLINE | ID: mdl-32780261

15.

Increasing value of autopsies in patients with brain tumors in the molecular era.

Ahrendsen, Jared T; Filbin, Mariella G; Chi, Susan N; Manley, Peter E; Wright, Karen D; Bandopadhayay, Pratiti; Clymer, Jessica R; Yeo, Kee Kiat; Kieran, Mark W; Jones, Robert; Lidov, Hart G; Ligon, Keith L; Alexandrescu, Sanda.

J Neurooncol ; 145(2): 349-355, 2019 Nov.

Article in English | MEDLINE | ID: mdl-31571114

16.

Management of pediatric low-grade glioma.

de Blank, Peter; Bandopadhayay, Pratiti; Haas-Kogan, Daphne; Fouladi, Maryam; Fangusaro, Jason.

Curr Opin Pediatr ; 31(1): 21-27, 2019 02.

Article in English | MEDLINE | ID: mdl-30531227

17.

Landscapes of childhood tumours.

Bandopadhayay, Pratiti; Meyerson, Matthew.

Nature ; 555(7696): 316-317, 2018 03 15.

Article in English | MEDLINE | ID: mdl-29542703

18.

Immunophenotyping of pediatric brain tumors: correlating immune infiltrate with histology, mutational load, and survival and assessing clonal T cell response.

Plant, Ashley S; Koyama, Shohei; Sinai, Claire; Solomon, Isaac H; Griffin, Gabriel K; Ligon, Keith L; Bandopadhayay, Pratiti; Betensky, Rebecca; Emerson, Ryan; Dranoff, Glenn; Kieran, Mark W; Ritz, Jerome.

J Neurooncol ; 137(2): 269-278, 2018 Apr.

Article in English | MEDLINE | ID: mdl-29322427

19.

Open data: Spot data glitches before publication.

Greenwald, Noah F; Bandopadhayay, Pratiti; Beroukhim, Rameen.

Nature ; 550(7676): 333, 2017 10 18.

Article in English | MEDLINE | ID: mdl-29052624

20.

An in-tumor genetic screen reveals that the BET bromodomain protein, BRD4, is a potential therapeutic target in ovarian carcinoma.

Baratta, Maria Giuseppina; Schinzel, Anna C; Zwang, Yaara; Bandopadhayay, Pratiti; Bowman-Colin, Christian; Kutt, Jennifer; Curtis, Jennifer; Piao, Huiying; Wong, Laura C; Kung, Andrew L; Beroukhim, Rameen; Bradner, James E; Drapkin, Ronny; Hahn, William C; Liu, Joyce F; Livingston, David M.

Proc Natl Acad Sci U S A ; 112(1): 232-7, 2015 Jan 06.

Article in English | MEDLINE | ID: mdl-25535366

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