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Items: 1 to 20 of 96

1.

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.

Ding J, Condon A, Shah SP.

Nat Commun. 2018 May 21;9(1):2002. doi: 10.1038/s41467-018-04368-5.

2.

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.

Zhang AW, McPherson A, Milne K, Kroeger DR, Hamilton PT, Miranda A, Funnell T, Little N, de Souza CPE, Laan S, LeDoux S, Cochrane DR, Lim JLP, Yang W, Roth A, Smith MA, Ho J, Tse K, Zeng T, Shlafman I, Mayo MR, Moore R, Failmezger H, Heindl A, Wang YK, Bashashati A, Grewal DS, Brown SD, Lai D, Wan ANC, Nielsen CB, Huebner C, Tessier-Cloutier B, Anglesio MS, Bouchard-Côté A, Yuan Y, Wasserman WW, Gilks CB, Karnezis AN, Aparicio S, McAlpine JN, Huntsman DG, Holt RA, Nelson BH, Shah SP.

Cell. 2018 Jun 14;173(7):1755-1769.e22. doi: 10.1016/j.cell.2018.03.073. Epub 2018 May 10.

PMID:
29754820
3.

TERT promoter mutation in adult granulosa cell tumor of the ovary.

Pilsworth JA, Cochrane DR, Xia Z, Aubert G, Färkkilä AEM, Horlings HM, Yanagida S, Yang W, Lim JLP, Wang YK, Bashashati A, Keul J, Wong A, Norris K, Brucker SY, Taran FA, Krämer B, Staebler A, Oliva E, Shah SP, Kommoss S, Kommoss F, Gilks CB, Baird DM, Huntsman DG.

Mod Pathol. 2018 Feb 15. doi: 10.1038/s41379-018-0007-9. [Epub ahead of print]

PMID:
29449679
4.

LINE-1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers.

Xia Z, Cochrane DR, Anglesio MS, Wang YK, Nazeran T, Tessier-Cloutier B, McConechy MK, Senz J, Lum A, Bashashati A, Shah SP, Huntsman DG.

Gynecol Oncol. 2017 Dec;147(3):642-647. doi: 10.1016/j.ygyno.2017.09.032. Epub 2017 Oct 9.

PMID:
29032825
5.

The driver landscape of sporadic chordoma.

Tarpey PS, Behjati S, Young MD, Martincorena I, Alexandrov LB, Farndon SJ, Guzzo C, Hardy C, Latimer C, Butler AP, Teague JW, Shlien A, Futreal PA, Shah S, Bashashati A, Jamshidi F, Nielsen TO, Huntsman D, Baumhoer D, Brandner S, Wunder J, Dickson B, Cogswell P, Sommer J, Phillips JJ, Amary MF, Tirabosco R, Pillay N, Yip S, Stratton MR, Flanagan AM, Campbell PJ.

Nat Commun. 2017 Oct 12;8(1):890. doi: 10.1038/s41467-017-01026-0.

6.

Correction to: ReMixT: clone-specific genomic structure estimation in cancer.

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP.

Genome Biol. 2017 Oct 6;18(1):188. doi: 10.1186/s13059-017-1327-7. No abstract available.

7.

Prognostic Model to Predict Post-Autologous Stem-Cell Transplantation Outcomes in Classical Hodgkin Lymphoma.

Chan FC, Mottok A, Gerrie AS, Power M, Nijland M, Diepstra A, van den Berg A, Kamper P, d'Amore F, d'Amore AL, Hamilton-Dutoit S, Savage KJ, Shah SP, Connors JM, Gascoyne RD, Scott DW, Steidl C.

J Clin Oncol. 2017 Nov 10;35(32):3722-3733. doi: 10.1200/JCO.2017.72.7925. Epub 2017 Sep 12.

PMID:
28898161
8.

ReMixT: clone-specific genomic structure estimation in cancer.

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP.

Genome Biol. 2017 Jul 27;18(1):140. doi: 10.1186/s13059-017-1267-2. Erratum in: Genome Biol. 2017 Oct 6;18(1):188.

9.

Genetic and epigenetic inactivation of SESTRIN1 controls mTORC1 and response to EZH2 inhibition in follicular lymphoma.

Oricchio E, Katanayeva N, Donaldson MC, Sungalee S, Pasion JP, Béguelin W, Battistello E, Sanghvi VR, Jiang M, Jiang Y, Teater M, Parmigiani A, Budanov AV, Chan FC, Shah SP, Kridel R, Melnick AM, Ciriello G, Wendel HG.

Sci Transl Med. 2017 Jun 28;9(396). pii: eaak9969. doi: 10.1126/scitranslmed.aak9969.

10.

Kronos: a workflow assembler for genome analytics and informatics.

Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP.

Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.

11.

Observing Clonal Dynamics across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer.

McPherson AW, Chan FC, Shah SP.

Cold Spring Harb Perspect Med. 2018 Feb 1;8(2). pii: a029603. doi: 10.1101/cshperspect.a029603. Review.

PMID:
28630229
12.

E-scape: interactive visualization of single-cell phylogenetics and cancer evolution.

Smith MA, Nielsen CB, Chan FC, McPherson A, Roth A, Farahani H, Machev D, Steif A, Shah SP.

Nat Methods. 2017 May 30;14(6):549-550. doi: 10.1038/nmeth.4303. No abstract available.

PMID:
28557980
13.

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.

Wang YK, Bashashati A, Anglesio MS, Cochrane DR, Grewal DS, Ha G, McPherson A, Horlings HM, Senz J, Prentice LM, Karnezis AN, Lai D, Aniba MR, Zhang AW, Shumansky K, Siu C, Wan A, McConechy MK, Li-Chang H, Tone A, Provencher D, de Ladurantaye M, Fleury H, Okamoto A, Yanagida S, Yanaihara N, Saito M, Mungall AJ, Moore R, Marra MA, Gilks CB, Mes-Masson AM, McAlpine JN, Aparicio S, Huntsman DG, Shah SP.

Nat Genet. 2017 Jun;49(6):856-865. doi: 10.1038/ng.3849. Epub 2017 Apr 24.

PMID:
28436987
14.

Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin-specific clinical impact.

Ennishi D, Mottok A, Ben-Neriah S, Shulha HP, Farinha P, Chan FC, Meissner B, Boyle M, Hother C, Kridel R, Lai D, Saberi S, Bashashati A, Shah SP, Morin RD, Marra MA, Savage KJ, Sehn LH, Steidl C, Connors JM, Gascoyne RD, Scott DW.

Blood. 2017 May 18;129(20):2760-2770. doi: 10.1182/blood-2016-11-747022. Epub 2017 Mar 28.

15.

CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion.

Tien JF, Mazloomian A, Cheng SG, Hughes CS, Chow CCT, Canapi LT, Oloumi A, Trigo-Gonzalez G, Bashashati A, Xu J, Chang VC, Shah SP, Aparicio S, Morin GB.

Nucleic Acids Res. 2017 Jun 20;45(11):6698-6716. doi: 10.1093/nar/gkx187.

16.

Enhancing knowledge discovery from cancer genomics data with Galaxy.

Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD.

Gigascience. 2017 May 1;6(5):1-13. doi: 10.1093/gigascience/gix015.

17.

ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.

Salehi S, Steif A, Roth A, Aparicio S, Bouchard-Côté A, Shah SP.

Genome Biol. 2017 Mar 1;18(1):44. doi: 10.1186/s13059-017-1169-3.

18.

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

Funnell T, Tasaki S, Oloumi A, Araki S, Kong E, Yap D, Nakayama Y, Hughes CS, Cheng SG, Tozaki H, Iwatani M, Sasaki S, Ohashi T, Miyazaki T, Morishita N, Morishita D, Ogasawara-Shimizu M, Ohori M, Nakao S, Karashima M, Sano M, Murai A, Nomura T, Uchiyama N, Kawamoto T, Hara R, Nakanishi O, Shumansky K, Rosner J, Wan A, McKinney S, Morin GB, Nakanishi A, Shah S, Toyoshiba H, Aparicio S.

Nat Commun. 2017 Feb 23;8(1):7. doi: 10.1038/s41467-016-0008-7.

19.

CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours.

Xu H, Di Antonio M, McKinney S, Mathew V, Ho B, O'Neil NJ, Santos ND, Silvester J, Wei V, Garcia J, Kabeer F, Lai D, Soriano P, Banáth J, Chiu DS, Yap D, Le DD, Ye FB, Zhang A, Thu K, Soong J, Lin SC, Tsai AH, Osako T, Algara T, Saunders DN, Wong J, Xian J, Bally MB, Brenton JD, Brown GW, Shah SP, Cescon D, Mak TW, Caldas C, Stirling PC, Hieter P, Balasubramanian S, Aparicio S.

Nat Commun. 2017 Feb 17;8:14432. doi: 10.1038/ncomms14432.

20.

Scalable whole-genome single-cell library preparation without preamplification.

Zahn H, Steif A, Laks E, Eirew P, VanInsberghe M, Shah SP, Aparicio S, Hansen CL.

Nat Methods. 2017 Feb;14(2):167-173. doi: 10.1038/nmeth.4140. Epub 2017 Jan 9.

PMID:
28068316

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