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Items: 32

1.

Low expression of the androgen-induced tumor suppressor gene PLZF and lethal prostate cancer.

Stopsack KH, Gerke T, Tyekucheva S, Mazzu YZ, Lee GM, Chakraborty G, Abida W, Mucci LA, Kantoff PW.

Cancer Epidemiol Biomarkers Prev. 2019 Jan 2. pii: cebp.1014.2018. doi: 10.1158/1055-9965.EPI-18-1014. [Epub ahead of print]

PMID:
30602500
2.

Inhibition of de novo lipogenesis targets androgen receptor signaling in castration-resistant prostate cancer.

Zadra G, Ribeiro CF, Chetta P, Ho Y, Cacciatore S, Gao X, Syamala S, Bango C, Photopoulos C, Huang Y, Tyekucheva S, Bastos DC, Tchaicha J, Lawney B, Uo T, D'Anello L, Csibi A, Kalekar R, Larimer B, Ellis L, Butler LM, Morrissey C, McGovern K, Palombella VJ, Kutok JL, Mahmood U, Bosari S, Adams J, Peluso S, Dehm SM, Plymate SR, Loda M.

Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):631-640. doi: 10.1073/pnas.1808834116. Epub 2018 Dec 21.

3.

Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration.

Wang Z, Cao S, Morris JS, Ahn J, Liu R, Tyekucheva S, Gao F, Li B, Lu W, Tang X, Wistuba II, Bowden M, Mucci L, Loda M, Parmigiani G, Holmes CC, Wang W.

iScience. 2018 Nov 30;9:451-460. doi: 10.1016/j.isci.2018.10.028. Epub 2018 Nov 2.

4.

Genetic and Epigenetic Determinants of Aggressiveness in Cribriform Carcinoma of the Prostate.

Elfandy H, Armenia J, Pederzoli F, Pullman E, Pertega-Gomes N, Schultz N, Viswanathan K, Vosoughi A, Blattner M, Stopsack KH, Zadra G, Penney KL, Mosquera JM, Tyekucheva S, Mucci LA, Barbieri C, Loda M.

Mol Cancer Res. 2018 Oct 17. doi: 10.1158/1541-7786.MCR-18-0440. [Epub ahead of print]

PMID:
30333152
5.

MYC Overexpression at the Protein and mRNA Level and Cancer Outcomes among Men Treated with Radical Prostatectomy for Prostate Cancer.

Pettersson A, Gerke T, Penney KL, Lis RT, Stack EC, Pértega-Gomes N, Zadra G, Tyekucheva S, Giovannucci EL, Mucci LA, Loda M.

Cancer Epidemiol Biomarkers Prev. 2018 Feb;27(2):201-207. doi: 10.1158/1055-9965.EPI-17-0637. Epub 2017 Nov 15.

6.

Stromal and epithelial transcriptional map of initiation progression and metastatic potential of human prostate cancer.

Tyekucheva S, Bowden M, Bango C, Giunchi F, Huang Y, Zhou C, Bondi A, Lis R, Van Hemelrijck M, Andrén O, Andersson SO, Watson RW, Pennington S, Finn SP, Martin NE, Stampfer MJ, Parmigiani G, Penney KL, Fiorentino M, Mucci LA, Loda M.

Nat Commun. 2017 Sep 4;8(1):420. doi: 10.1038/s41467-017-00460-4.

7.

Gene expression profiling of prostate tissue identifies chromatin regulation as a potential link between obesity and lethal prostate cancer.

Ebot EM, Gerke T, Labbé DP, Sinnott JA, Zadra G, Rider JR, Tyekucheva S, Wilson KM, Kelly RS, Shui IM, Loda M, Kantoff PW, Finn S, Vander Heiden MG, Brown M, Giovannucci EL, Mucci LA.

Cancer. 2017 Nov 1;123(21):4130-4138. doi: 10.1002/cncr.30831. Epub 2017 Jul 12.

8.

Metabolic Profiling in Formalin-Fixed and Paraffin-Embedded Prostate Cancer Tissues.

Cacciatore S, Zadra G, Bango C, Penney KL, Tyekucheva S, Yanes O, Loda M.

Mol Cancer Res. 2017 Apr;15(4):439-447. doi: 10.1158/1541-7786.MCR-16-0262. Epub 2017 Jan 10.

9.

The role of tumor metabolism as a driver of prostate cancer progression and lethal disease: results from a nested case-control study.

Kelly RS, Sinnott JA, Rider JR, Ebot EM, Gerke T, Bowden M, Pettersson A, Loda M, Sesso HD, Kantoff PW, Martin NE, Giovannucci EL, Tyekucheva S, Heiden MV, Mucci LA.

Cancer Metab. 2016 Dec 7;4:22. doi: 10.1186/s40170-016-0161-9. eCollection 2016.

10.

Prognostic Utility of a New mRNA Expression Signature of Gleason Score.

Sinnott JA, Peisch SF, Tyekucheva S, Gerke T, Lis R, Rider JR, Fiorentino M, Stampfer MJ, Mucci LA, Loda M, Penney KL.

Clin Cancer Res. 2017 Jan 1;23(1):81-87. doi: 10.1158/1078-0432.CCR-16-1245. Epub 2016 Sep 23.

11.

Cholesterol Metabolism and Prostate Cancer Lethality.

Stopsack KH, Gerke TA, Sinnott JA, Penney KL, Tyekucheva S, Sesso HD, Andersson SO, Andrén O, Cerhan JR, Giovannucci EL, Mucci LA, Rider JR.

Cancer Res. 2016 Aug 15;76(16):4785-90. doi: 10.1158/0008-5472.CAN-16-0903. Epub 2016 Jun 20.

12.

Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer.

Börnigen D, Tyekucheva S, Wang X, Rider JR, Lee GS, Mucci LA, Sweeney C, Huttenhower C.

PLoS Comput Biol. 2016 Apr 14;12(4):e1004820. doi: 10.1371/journal.pcbi.1004820. eCollection 2016 Apr.

13.

Stress-Related Signaling Pathways in Lethal and Nonlethal Prostate Cancer.

Lu D, Sinnott JA, Valdimarsdóttir U, Fang F, Gerke T, Tyekucheva S, Fiorentino M, Lambe M, Sesso HD, Sweeney CJ, Wilson KM, Giovannucci EL, Loda M, Mucci LA, Fall K.

Clin Cancer Res. 2016 Feb 1;22(3):765-772. doi: 10.1158/1078-0432.CCR-15-0101. Epub 2015 Oct 21.

14.

Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues.

Tyekucheva S, Martin NE, Stack EC, Wei W, Vathipadiekal V, Waldron L, Fiorentino M, Lis RT, Stampfer MJ, Loda M, Parmigiani G, Mucci LA, Birrer M.

J Mol Diagn. 2015 Jul;17(4):374-81. doi: 10.1016/j.jmoldx.2015.02.002. Epub 2015 Apr 30.

15.

Molecular differences in transition zone and peripheral zone prostate tumors.

Sinnott JA, Rider JR, Carlsson J, Gerke T, Tyekucheva S, Penney KL, Sesso HD, Loda M, Fall K, Stampfer MJ, Mucci LA, Pawitan Y, Andersson SO, Andrén O.

Carcinogenesis. 2015 Jun;36(6):632-8. doi: 10.1093/carcin/bgv051. Epub 2015 Apr 13.

16.

Association of prostate cancer risk variants with gene expression in normal and tumor tissue.

Penney KL, Sinnott JA, Tyekucheva S, Gerke T, Shui IM, Kraft P, Sesso HD, Freedman ML, Loda M, Mucci LA, Stampfer MJ.

Cancer Epidemiol Biomarkers Prev. 2015 Jan;24(1):255-60. doi: 10.1158/1055-9965.EPI-14-0694-T. Epub 2014 Nov 4.

17.

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.

Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G.

J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju049. doi: 10.1093/jnci/dju049. Review.

18.

A novel direct activator of AMPK inhibits prostate cancer growth by blocking lipogenesis.

Zadra G, Photopoulos C, Tyekucheva S, Heidari P, Weng QP, Fedele G, Liu H, Scaglia N, Priolo C, Sicinska E, Mahmood U, Signoretti S, Birnberg N, Loda M.

EMBO Mol Med. 2014 Apr;6(4):519-38. doi: 10.1002/emmm.201302734. Epub 2014 Feb 4. Erratum in: EMBO Mol Med. 2014 Oct;6(10):1357.

19.

De novo fatty acid synthesis at the mitotic exit is required to complete cellular division.

Scaglia N, Tyekucheva S, Zadra G, Photopoulos C, Loda M.

Cell Cycle. 2014;13(5):859-68. doi: 10.4161/cc.27767. Epub 2014 Jan 13.

20.

A network of epigenetic regulators guides developmental haematopoiesis in vivo.

Huang HT, Kathrein KL, Barton A, Gitlin Z, Huang YH, Ward TP, Hofmann O, Dibiase A, Song A, Tyekucheva S, Hide W, Zhou Y, Zon LI.

Nat Cell Biol. 2013 Dec;15(12):1516-25. doi: 10.1038/ncb2870. Epub 2013 Nov 17.

21.

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome.

Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L.

Database (Oxford). 2013 Apr 2;2013:bat013. doi: 10.1093/database/bat013. Print 2013.

22.

Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.

Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML.

Cell. 2013 Jan 31;152(3):633-41. doi: 10.1016/j.cell.2012.12.034. Review.

23.

Integrating diverse genomic data using gene sets.

Tyekucheva S, Marchionni L, Karchin R, Parmigiani G.

Genome Biol. 2011 Oct 21;12(10):R105. doi: 10.1186/gb-2011-12-10-r105.

24.

Establishing the baseline level of repetitive element expression in the human cortex.

Tyekucheva S, Yolken RH, McCombie WR, Parla J, Kramer M, Wheelan SJ, Sabunciyan S.

BMC Genomics. 2011 Oct 10;12:495. doi: 10.1186/1471-2164-12-495.

25.

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.

Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R.

Cancer Res. 2009 Aug 15;69(16):6660-7. doi: 10.1158/0008-5472.CAN-09-1133. Epub 2009 Aug 4.

26.

Human-macaque comparisons illuminate variation in neutral substitution rates.

Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F.

Genome Biol. 2008 Apr 30;9(4):R76. doi: 10.1186/gb-2008-9-4-r76.

27.

The genome-wide determinants of human and chimpanzee microsatellite evolution.

Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD.

Genome Res. 2008 Jan;18(1):30-8. Epub 2007 Nov 21.

28.

28-way vertebrate alignment and conservation track in the UCSC Genome Browser.

Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ.

Genome Res. 2007 Dec;17(12):1797-808. Epub 2007 Nov 5.

29.

A macaque's-eye view of human insertions and deletions: differences in mechanisms.

Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova KD.

PLoS Comput Biol. 2007 Sep;3(9):1772-82. Epub 2007 Jul 27.

30.

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, Chiaromonte F.

Genome Res. 2006 Dec;16(12):1596-604. Epub 2006 Oct 19.

31.

Genomic environment predicts expression patterns on the human inactive X chromosome.

Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD.

PLoS Genet. 2006 Sep 29;2(9):e151. Epub 2006 Aug 3.

32.

Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison.

Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD.

Mol Biol Evol. 2006 Mar;23(3):565-73. Epub 2005 Nov 9.

PMID:
16280537

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