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Items: 22

1.

MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature.

Gendoo DMA, Zon M, Sandhu V, Manem VSK, Ratanasirigulchai N, Chen GM, Waldron L, Haibe-Kains B.

Sci Rep. 2019 Jun 19;9(1):8770. doi: 10.1038/s41598-019-45165-4.

2.

A subgroup of microRNAs defines PTEN-deficient, triple-negative breast cancer patients with poorest prognosis and alterations in RB1, MYC, and Wnt signaling.

Wang DY, Gendoo DMA, Ben-David Y, Woodgett JR, Zacksenhaus E.

Breast Cancer Res. 2019 Jan 31;21(1):18. doi: 10.1186/s13058-019-1098-z.

3.

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer.

Gendoo DMA, Denroche RE, Zhang A, Radulovich N, Jang GH, Lemire M, Fischer S, Chadwick D, Lungu IM, Ibrahimov E, Cao PJ, Stein LD, Wilson JM, Bartlett JMS, Tsao MS, Dhani N, Hedley D, Gallinger S, Haibe-Kains B.

PLoS Comput Biol. 2019 Jan 10;15(1):e1006596. doi: 10.1371/journal.pcbi.1006596. eCollection 2019 Jan.

4.

Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma.

Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L.

Clin Cancer Res. 2018 Oct 15;24(20):5037-5047. doi: 10.1158/1078-0432.CCR-18-0784. Epub 2018 Jul 3.

PMID:
30084834
5.

Administration of Hypoxia-Activated Prodrug Evofosfamide after Conventional Adjuvant Therapy Enhances Therapeutic Outcome and Targets Cancer-Initiating Cells in Preclinical Models of Colorectal Cancer.

Haynes J, McKee TD, Haller A, Wang Y, Leung C, Gendoo DMA, Lima-Fernandes E, Kreso A, Wolman R, Szentgyorgyi E, Vines DC, Haibe-Kains B, Wouters BG, Metser U, Jaffray DA, Smith M, O'Brien CA.

Clin Cancer Res. 2018 May 1;24(9):2116-2127. doi: 10.1158/1078-0432.CCR-17-1715. Epub 2018 Feb 23.

6.

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.

El-Hachem N, Gendoo DMA, Ghoraie LS, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader GD, Goldenberg A, Haibe-Kains B.

Cancer Res. 2017 Jun 1;77(11):3057-3069. doi: 10.1158/0008-5472.CAN-17-0096. Epub 2017 Mar 17.

7.

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors.

Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, Gendoo DMA, Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, McGlade CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, Bader GD, Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N, Huang A.

Cancer Cell. 2016 Dec 12;30(6):891-908. doi: 10.1016/j.ccell.2016.11.003.

8.

The molecular basis of breast cancer pathological phenotypes.

Heng YJ, Lester SC, Tse GM, Factor RE, Allison KH, Collins LC, Chen YY, Jensen KC, Johnson NB, Jeong JC, Punjabi R, Shin SJ, Singh K, Krings G, Eberhard DA, Tan PH, Korski K, Waldman FM, Gutman DA, Sanders M, Reis-Filho JS, Flanagan SR, Gendoo DM, Chen GM, Haibe-Kains B, Ciriello G, Hoadley KA, Perou CM, Beck AH.

J Pathol. 2017 Feb;241(3):375-391. doi: 10.1002/path.4847. Epub 2016 Dec 29.

9.

MM2S: personalized diagnosis of medulloblastoma patients and model systems.

Gendoo DM, Haibe-Kains B.

Source Code Biol Med. 2016 Apr 11;11:6. doi: 10.1186/s13029-016-0053-y. eCollection 2016.

10.

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DM, Grossmann P, Beck AH, Aerts HJ, Lupien M, Goldenberg A, Haibe-Kains B.

Bioinformatics. 2016 Apr 15;32(8):1244-6. doi: 10.1093/bioinformatics/btv723. Epub 2015 Dec 9.

PMID:
26656004
11.

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.

Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B.

Bioinformatics. 2016 Apr 1;32(7):1097-9. doi: 10.1093/bioinformatics/btv693. Epub 2015 Nov 24.

12.

Public data and open source tools for multi-assay genomic investigation of disease.

Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L.

Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Review.

13.

CD73 is associated with poor prognosis in high-grade serous ovarian cancer.

Turcotte M, Spring K, Pommey S, Chouinard G, Cousineau I, George J, Chen GM, Gendoo DM, Haibe-Kains B, Karn T, Rahimi K, Le Page C, Provencher D, Mes-Masson AM, Stagg J.

Cancer Res. 2015 Nov 1;75(21):4494-503. doi: 10.1158/0008-5472.CAN-14-3569. Epub 2015 Sep 11.

14.

Erratum: The First Small-Molecule Inhibitors of Members of the Ribonuclease E Family.

Kime L, Vincent HA, Gendoo DM, Jourdan SS, Fishwick CW, Callaghan AJ, McDowall KJ.

Sci Rep. 2015 Jul 13;5:9781. doi: 10.1038/srep09781. No abstract available.

15.

Personalized diagnosis of medulloblastoma subtypes across patients and model systems.

Gendoo DM, Smirnov P, Lupien M, Haibe-Kains B.

Genomics. 2015 Aug;106(2):96-106. doi: 10.1016/j.ygeno.2015.05.002. Epub 2015 May 12.

16.

Medulloblastoma subgroups remain stable across primary and metastatic compartments.

Wang X, Dubuc AM, Ramaswamy V, Mack S, Gendoo DM, Remke M, Wu X, Garzia L, Luu B, Cavalli F, Peacock J, López B, Skowron P, Zagzag D, Lyden D, Hoffman C, Cho YJ, Eberhart C, MacDonald T, Li XN, Van Meter T, Northcott PA, Haibe-Kains B, Hawkins C, Rutka JT, Bouffet E, Pfister SM, Korshunov A, Taylor MD.

Acta Neuropathol. 2015 Mar;129(3):449-57. doi: 10.1007/s00401-015-1389-0. Epub 2015 Jan 21.

17.

The first small-molecule inhibitors of members of the ribonuclease E family.

Kime L, Vincent HA, Gendoo DM, Jourdan SS, Fishwick CW, Callaghan AJ, McDowall KJ.

Sci Rep. 2015 Jan 26;5:8028. doi: 10.1038/srep08028. Erratum in: Sci Rep. 2015;5:9781.

18.

The landscape of the prion protein's structural response to mutation revealed by principal component analysis of multiple NMR ensembles.

Gendoo DM, Harrison PM.

PLoS Comput Biol. 2012;8(8):e1002646. doi: 10.1371/journal.pcbi.1002646. Epub 2012 Aug 9.

19.

PrionHome: a database of prions and other sequences relevant to prion phenomena.

Harbi D, Parthiban M, Gendoo DM, Ehsani S, Kumar M, Schmitt-Ulms G, Sowdhamini R, Harrison PM.

PLoS One. 2012;7(2):e31785. doi: 10.1371/journal.pone.0031785. Epub 2012 Feb 20.

20.

Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids.

Gendoo DM, Harrison PM.

PLoS One. 2011;6(11):e27342. doi: 10.1371/journal.pone.0027342. Epub 2011 Nov 11.

21.

Discordant and chameleon sequences: their distribution and implications for amyloidogenicity.

Gendoo DM, Harrison PM.

Protein Sci. 2011 Mar;20(3):567-79. doi: 10.1002/pro.590.

22.

Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

Gendoo DM, El-Hefnawi MM, Werner M, Siam R.

Virol J. 2008 Aug 5;5:91. doi: 10.1186/1743-422X-5-91.

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