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Page 1
The transcriptional landscape of Shh medulloblastoma.
Skowron P, Farooq H, Cavalli FMG, Morrissy AS, Ly M, Hendrikse LD, Wang EY, Djambazian H, Zhu H, Mungall KL, Trinh QM, Zheng T, Dai S, Stucklin ASG, Vladoiu MC, Fong V, Holgado BL, Nor C, Wu X, Abd-Rabbo D, Bérubé P, Wang YC, Luu B, Suarez RA, Rastan A, Gillmor AH, Lee JJY, Zhang XY, Daniels C, Dirks P, Malkin D, Bouffet E, Tabori U, Loukides J, Doz FP, Bourdeaut F, Delattre OO, Masliah-Planchon J, Ayrault O, Kim SK, Meyronet D, Grajkowska WA, Carlotti CG, de Torres C, Mora J, Eberhart CG, Van Meir EG, Kumabe T, French PJ, Kros JM, Jabado N, Lach B, Pollack IF, Hamilton RL, Rao AAN, Giannini C, Olson JM, Bognár L, Klekner A, Zitterbart K, Phillips JJ, Thompson RC, Cooper MK, Rubin JB, Liau LM, Garami M, Hauser P, Li KKW, Ng HK, Poon WS, Yancey Gillespie G, Chan JA, Jung S, McLendon RE, Thompson EM, Zagzag D, Vibhakar R, Ra YS, Garre ML, Schüller U, Shofuda T, Faria CC, López-Aguilar E, Zadeh G, Hui CC, Ramaswamy V, Bailey SD, Jones SJ, Mungall AJ, Moore RA, Calarco JA, Stein LD, Bader GD, Reimand J, Ragoussis J, Weiss WA, Marra MA, Suzuki H, Taylor MD. Skowron P, et al. Among authors: stein ld. Nat Commun. 2021 Mar 19;12(1):1749. doi: 10.1038/s41467-021-21883-0. Nat Commun. 2021. PMID: 33741928 Free PMC article.
Pathway and network analysis of cancer genomes.
Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD; Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium. Creixell P, et al. Among authors: stein ld. Nat Methods. 2015 Jul;12(7):615-621. doi: 10.1038/nmeth.3440. Nat Methods. 2015. PMID: 26125594 Free PMC article.
Childhood cerebellar tumours mirror conserved fetal transcriptional programs.
Vladoiu MC, El-Hamamy I, Donovan LK, Farooq H, Holgado BL, Sundaravadanam Y, Ramaswamy V, Hendrikse LD, Kumar S, Mack SC, Lee JJY, Fong V, Juraschka K, Przelicki D, Michealraj A, Skowron P, Luu B, Suzuki H, Morrissy AS, Cavalli FMG, Garzia L, Daniels C, Wu X, Qazi MA, Singh SK, Chan JA, Marra MA, Malkin D, Dirks P, Heisler L, Pugh T, Ng K, Notta F, Thompson EM, Kleinman CL, Joyner AL, Jabado N, Stein L, Taylor MD. Vladoiu MC, et al. Among authors: stein l. Nature. 2019 Aug;572(7767):67-73. doi: 10.1038/s41586-019-1158-7. Epub 2019 May 1. Nature. 2019. PMID: 31043743 Free PMC article.
The U1 spliceosomal RNA is recurrently mutated in multiple cancers.
Shuai S, Suzuki H, Diaz-Navarro A, Nadeu F, Kumar SA, Gutierrez-Fernandez A, Delgado J, Pinyol M, López-Otín C, Puente XS, Taylor MD, Campo E, Stein LD. Shuai S, et al. Among authors: stein ld. Nature. 2019 Oct;574(7780):712-716. doi: 10.1038/s41586-019-1651-z. Epub 2019 Oct 9. Nature. 2019. PMID: 31597163
Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma.
Suzuki H, Kumar SA, Shuai S, Diaz-Navarro A, Gutierrez-Fernandez A, De Antonellis P, Cavalli FMG, Juraschka K, Farooq H, Shibahara I, Vladoiu MC, Zhang J, Abeysundara N, Przelicki D, Skowron P, Gauer N, Luu B, Daniels C, Wu X, Forget A, Momin A, Wang J, Dong W, Kim SK, Grajkowska WA, Jouvet A, Fèvre-Montange M, Garrè ML, Nageswara Rao AA, Giannini C, Kros JM, French PJ, Jabado N, Ng HK, Poon WS, Eberhart CG, Pollack IF, Olson JM, Weiss WA, Kumabe T, López-Aguilar E, Lach B, Massimino M, Van Meir EG, Rubin JB, Vibhakar R, Chambless LB, Kijima N, Klekner A, Bognár L, Chan JA, Faria CC, Ragoussis J, Pfister SM, Goldenberg A, Wechsler-Reya RJ, Bailey SD, Garzia L, Morrissy AS, Marra MA, Huang X, Malkin D, Ayrault O, Ramaswamy V, Puente XS, Calarco JA, Stein L, Taylor MD. Suzuki H, et al. Nature. 2019 Oct;574(7780):707-711. doi: 10.1038/s41586-019-1650-0. Epub 2019 Oct 9. Nature. 2019. PMID: 31664194 Free PMC article.
scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy.
Ocasio JK, Babcock B, Malawsky D, Weir SJ, Loo L, Simon JM, Zylka MJ, Hwang D, Dismuke T, Sokolsky M, Rosen EP, Vibhakar R, Zhang J, Saulnier O, Vladoiu M, El-Hamamy I, Stein LD, Taylor MD, Smith KS, Northcott PA, Colaneri A, Wilhelmsen K, Gershon TR. Ocasio JK, et al. Among authors: stein ld. Nat Commun. 2019 Dec 20;10(1):5829. doi: 10.1038/s41467-019-13657-6. Nat Commun. 2019. PMID: 31863004 Free PMC article.
Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution.
Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, Wilson JM, Jang GH, Zhang A, Dodd A, Liang SB, Borgida A, Chadwick D, Kalimuthu S, Lungu I, Bartlett JMS, Krzyzanowski PM, Sandhu V, Tiriac H, Froeling FEM, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Jones SJM, Marra MA, Laskin J, Chetty R, Stein LD, Zogopoulos G, Haibe-Kains B, Campbell PJ, Tuveson DA, Knox JJ, Fischer SE, Gallinger S, Notta F. Chan-Seng-Yue M, et al. Among authors: stein ld. Nat Genet. 2020 Feb;52(2):231-240. doi: 10.1038/s41588-019-0566-9. Epub 2020 Jan 13. Nat Genet. 2020. PMID: 31932696
Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.
Zhu H, Uusküla-Reimand L, Isaev K, Wadi L, Alizada A, Shuai S, Huang V, Aduluso-Nwaobasi D, Paczkowska M, Abd-Rabbo D, Ocsenas O, Liang M, Thompson JD, Li Y, Ruan L, Krassowski M, Dzneladze I, Simpson JT, Lupien M, Stein LD, Boutros PC, Wilson MD, Reimand J. Zhu H, et al. Among authors: stein ld. Mol Cell. 2020 Mar 19;77(6):1307-1321.e10. doi: 10.1016/j.molcel.2019.12.027. Epub 2020 Jan 17. Mol Cell. 2020. PMID: 31954095 Free article.
237 results