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Items: 36

1.

Regulation of PRMT5-MDM4 axis is critical in the response to CDK4/6 inhibitors in melanoma.

AbuHammad S, Cullinane C, Martin C, Bacolas Z, Ward T, Chen H, Slater A, Ardley K, Kirby L, Chan KT, Brajanovski N, Smith LK, Rao AD, Lelliott EJ, Kleinschmidt M, Vergara IA, Papenfuss AT, Lau P, Ghosh P, Haupt S, Haupt Y, Sanij E, Poortinga G, Pearson RB, Falk H, Curtis DJ, Stupple P, Devlin M, Street I, Davies MA, McArthur GA, Sheppard KE.

Proc Natl Acad Sci U S A. 2019 Sep 3;116(36):17990-18000. doi: 10.1073/pnas.1901323116. Epub 2019 Aug 22.

2.

Correction to: Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.

Semenec L, Vergara IA, Laloo AE, Mathews ER, Bond PL, Franks AE.

Microb Ecol. 2019 Mar 30. doi: 10.1007/s00248-019-01370-2. [Epub ahead of print]

PMID:
30929044
3.

Somatic Hypermutation of the YAP Oncogene in a Human Cutaneous Melanoma.

Zhang X, Tang JZ, Vergara IA, Zhang Y, Szeto P, Yang L, Mintoff C, Colebatch A, McIntosh L, Mitchell KA, Shaw E, Rizos H, Long GV, Hayward N, McArthur GA, Papenfuss AT, Harvey KF, Shackleton M.

Mol Cancer Res. 2019 Jul;17(7):1435-1449. doi: 10.1158/1541-7786.MCR-18-0407. Epub 2019 Mar 4.

PMID:
30833299
4.

Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.

Semenec L, Vergara IA, Laloo AE, Mathews ER, Bond PL, Franks AE.

Microb Ecol. 2019 Oct;78(3):618-630. doi: 10.1007/s00248-019-01316-8. Epub 2019 Feb 13. Erratum in: Microb Ecol. 2019 Mar 30;:.

PMID:
30759269
5.

Deciphering the electric code of Geobacter sulfurreducens in cocultures with Pseudomonas aeruginosa via SWATH-MS proteomics.

Semenec L, Laloo AE, Schulz BL, Vergara IA, Bond PL, Franks AE.

Bioelectrochemistry. 2018 Feb;119:150-160. doi: 10.1016/j.bioelechem.2017.09.013. Epub 2017 Oct 3.

PMID:
28992596
6.

Multi-institutional Analysis Shows that Low PCAT-14 Expression Associates with Poor Outcomes in Prostate Cancer.

White NM, Zhao SG, Zhang J, Rozycki EB, Dang HX, McFadden SD, Eteleeb AM, Alshalalfa M, Vergara IA, Erho N, Arbeit JM, Karnes RJ, Den RB, Davicioni E, Maher CA.

Eur Urol. 2017 Feb;71(2):257-266. doi: 10.1016/j.eururo.2016.07.012. Epub 2016 Jul 22.

7.

A community-based model of rapid autopsy in end-stage cancer patients.

Alsop K, Thorne H, Sandhu S, Hamilton A, Mintoff C, Christie E, Spruyt O, Williams S, McNally O, Mileshkin L, Ananda S, Hallo J, Loi S, Scott C, Savas P, Devereux L, O'Brien P, Gunawardena S, Hampson C, Strachan K, Jaravaza RD, Francis V, Young G, Ranson D, Samaranayake R, Stevens D, Boyle S, Fedele C, Topp M, Ho G, Teo ZL, Taylor RA, Papargiris MM, Lawrence MG, Wang H, Risbridger GP, Haynes NM, Medon M, Johnstone RW, Vidacs E, Arnau GM, Vergara IA, Papenfuss AT, McArthur G, Waring P, Carvosso S, Angel C, Gyorki D, Solomon B, Mitchell G, Shanley S, Francis PA, Dawson SJ, Haffenden A, Tidball E, Volchek M, Pyman J, Madadin M, Leditschke J, Cordner S; Melbourne Melanoma Project; Australian Ovarian Cancer Study Group (AOCS); Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Shackleton M, Bowtell DD.

Nat Biotechnol. 2016 Oct;34(10):1010-1014. doi: 10.1038/nbt.3674. Epub 2016 Sep 12. No abstract available.

PMID:
27617737
8.

UV-Associated Mutations Underlie the Etiology of MCV-Negative Merkel Cell Carcinomas.

Wong SQ, Waldeck K, Vergara IA, Schröder J, Madore J, Wilmott JS, Colebatch AJ, De Paoli-Iseppi R, Li J, Lupat R, Semple T, Arnau GM, Fellowes A, Leonard JH, Hruby G, Mann GJ, Thompson JF, Cullinane C, Johnston M, Shackleton M, Sandhu S, Bowtell DD, Johnstone RW, Fox SB, McArthur GA, Papenfuss AT, Scolyer RA, Gill AJ, Hicks RJ, Tothill RW.

Cancer Res. 2015 Dec 15;75(24):5228-34. doi: 10.1158/0008-5472.CAN-15-1877. Epub 2015 Dec 1.

9.

Germline Variants in Asporin Vary by Race, Modulate the Tumor Microenvironment, and Are Differentially Associated with Metastatic Prostate Cancer.

Hurley PJ, Sundi D, Shinder B, Simons BW, Hughes RM, Miller RM, Benzon B, Faraj SF, Netto GJ, Vergara IA, Erho N, Davicioni E, Karnes RJ, Yan G, Ewing C, Isaacs SD, Berman DM, Rider JR, Jordahl KM, Mucci LA, Huang J, An SS, Park BH, Isaacs WB, Marchionni L, Ross AE, Schaeffer EM.

Clin Cancer Res. 2016 Jan 15;22(2):448-58. doi: 10.1158/1078-0432.CCR-15-0256. Epub 2015 Oct 7.

10.

Androgen-Regulated SPARCL1 in the Tumor Microenvironment Inhibits Metastatic Progression.

Hurley PJ, Hughes RM, Simons BW, Huang J, Miller RM, Shinder B, Haffner MC, Esopi D, Kimura Y, Jabbari J, Ross AE, Erho N, Vergara IA, Faraj SF, Davicioni E, Netto GJ, Yegnasubramanian S, An SS, Schaeffer EM.

Cancer Res. 2015 Oct 15;75(20):4322-34. doi: 10.1158/0008-5472.CAN-15-0024. Epub 2015 Aug 20.

11.

Clinical and genomic analysis of metastatic prostate cancer progression with a background of postoperative biochemical recurrence.

Alshalalfa M, Crisan A, Vergara IA, Ghadessi M, Buerki C, Erho N, Yousefi K, Sierocinski T, Haddad Z, Black PC, Karnes RJ, Jenkins RB, Davicioni E.

BJU Int. 2015 Oct;116(4):556-67. doi: 10.1111/bju.13013. Epub 2015 Mar 12.

12.

The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer.

Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S, Mosquera JM, Pauwels J, Park K, Kossai M, MacDonald TY, Fontugne J, Erho N, Vergara IA, Ghadessi M, Davicioni E, Jenkins RB, Palanisamy N, Chen Z, Nakagawa S, Hirose T, Bander NH, Beltran H, Fox AH, Elemento O, Rubin MA.

Nat Commun. 2014 Nov 21;5:5383. doi: 10.1038/ncomms6383.

13.

Discovery and validation of novel expression signature for postcystectomy recurrence in high-risk bladder cancer.

Mitra AP, Lam LL, Ghadessi M, Erho N, Vergara IA, Alshalalfa M, Buerki C, Haddad Z, Sierocinski T, Triche TJ, Skinner EC, Davicioni E, Daneshmand S, Black PC.

J Natl Cancer Inst. 2014 Oct 24;106(11). pii: dju290. doi: 10.1093/jnci/dju290. Print 2014 Nov.

14.

The IncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer.

Prensner JR, Sahu A, Iyer MK, Malik R, Chandler B, Asangani IA, Poliakov A, Vergara IA, Alshalalfa M, Jenkins RB, Davicioni E, Feng FY, Chinnaiyan AM.

Oncotarget. 2014 Mar 30;5(6):1434-8.

15.

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans.

Vergara IA, Tarailo-Graovac M, Frech C, Wang J, Qin Z, Zhang T, She R, Chu JS, Wang K, Chen N.

BMC Genomics. 2014 Apr 2;15:255. doi: 10.1186/1471-2164-15-255.

16.

Metabolomic profiling identifies biochemical pathways associated with castration-resistant prostate cancer.

Kaushik AK, Vareed SK, Basu S, Putluri V, Putluri N, Panzitt K, Brennan CA, Chinnaiyan AM, Vergara IA, Erho N, Weigel NL, Mitsiades N, Shojaie A, Palapattu G, Michailidis G, Sreekumar A.

J Proteome Res. 2014 Feb 7;13(2):1088-100. doi: 10.1021/pr401106h. Epub 2013 Dec 31.

17.

A genomic classifier predicting metastatic disease progression in men with biochemical recurrence after prostatectomy.

Ross AE, Feng FY, Ghadessi M, Erho N, Crisan A, Buerki C, Sundi D, Mitra AP, Vergara IA, Thompson DJ, Triche TJ, Davicioni E, Bergstralh EJ, Jenkins RB, Karnes RJ, Schaeffer EM.

Prostate Cancer Prostatic Dis. 2014 Mar;17(1):64-9. doi: 10.1038/pcan.2013.49. Epub 2013 Oct 22.

18.

The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex.

Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, Vergara IA, Davicioni E, Erho N, Ghadessi M, Jenkins RB, Triche TJ, Malik R, Bedenis R, McGregor N, Ma T, Chen W, Han S, Jing X, Cao X, Wang X, Chandler B, Yan W, Siddiqui J, Kunju LP, Dhanasekaran SM, Pienta KJ, Feng FY, Chinnaiyan AM.

Nat Genet. 2013 Nov;45(11):1392-8. doi: 10.1038/ng.2771. Epub 2013 Sep 29.

19.

Whole-transcriptome profiling of thyroid nodules identifies expression-based signatures for accurate thyroid cancer diagnosis.

Wiseman SM, Haddad Z, Walker B, Vergara IA, Sierocinski T, Crisan A, Ghadessi M, Dao P, Zimmermann B, Triche TJ, Erho N, Davicioni E.

J Clin Endocrinol Metab. 2013 Oct;98(10):4072-9. doi: 10.1210/jc.2013-1991. Epub 2013 Aug 8.

PMID:
23928671
20.

Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy.

Erho N, Crisan A, Vergara IA, Mitra AP, Ghadessi M, Buerki C, Bergstralh EJ, Kollmeyer T, Fink S, Haddad Z, Zimmermann B, Sierocinski T, Ballman KV, Triche TJ, Black PC, Karnes RJ, Klee G, Davicioni E, Jenkins RB.

PLoS One. 2013 Jun 24;8(6):e66855. doi: 10.1371/journal.pone.0066855. Print 2013.

21.

Validation of a genomic classifier that predicts metastasis following radical prostatectomy in an at risk patient population.

Karnes RJ, Bergstralh EJ, Davicioni E, Ghadessi M, Buerki C, Mitra AP, Crisan A, Erho N, Vergara IA, Lam LL, Carlson R, Thompson DJ, Haddad Z, Zimmermann B, Sierocinski T, Triche TJ, Kollmeyer T, Ballman KV, Black PC, Klee GG, Jenkins RB.

J Urol. 2013 Dec;190(6):2047-53. doi: 10.1016/j.juro.2013.06.017. Epub 2013 Jun 11.

22.

CooVar: co-occurring variant analyzer.

Vergara IA, Frech C, Chen N.

BMC Res Notes. 2012 Nov 1;5:615. doi: 10.1186/1756-0500-5-615.

23.

Transcriptome-wide detection of differentially expressed coding and non-coding transcripts and their clinical significance in prostate cancer.

Erho N, Buerki C, Triche TJ, Davicioni E, Vergara IA.

J Oncol. 2012;2012:541353. doi: 10.1155/2012/541353. Epub 2012 Aug 16.

24.

Secreted protein, acidic and rich in cysteine-like 1 (SPARCL1) is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome.

Hurley PJ, Marchionni L, Simons BW, Ross AE, Peskoe SB, Miller RM, Erho N, Vergara IA, Ghadessi M, Huang Z, Gurel B, Park BH, Davicioni E, Jenkins RB, Platz EA, Berman DM, Schaeffer EM.

Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):14977-82. doi: 10.1073/pnas.1203525109. Epub 2012 Aug 27.

25.

RNA-seq analysis of the C. briggsae transcriptome.

Uyar B, Chu JS, Vergara IA, Chua SY, Jones MR, Wong T, Baillie DL, Chen N.

Genome Res. 2012 Aug;22(8):1567-80. doi: 10.1101/gr.134601.111. Epub 2012 Jul 6.

26.

Genomic "Dark Matter" in Prostate Cancer: Exploring the Clinical Utility of ncRNA as Biomarkers.

Vergara IA, Erho N, Triche TJ, Ghadessi M, Crisan A, Sierocinski T, Black PC, Buerki C, Davicioni E.

Front Genet. 2012 Feb 22;3:23. doi: 10.3389/fgene.2012.00023. eCollection 2012.

27.

Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile.

Vergara IA, Villouta P, Herrera S, Melo F.

Forensic Sci Int Genet. 2012 May;6(3):e83-5. doi: 10.1016/j.fsigen.2011.07.002. Epub 2011 Aug 2.

PMID:
21813345
28.

Quantitative trait locus (QTL) mapping reveals a role for unstudied genes in Aspergillus virulence.

Christians JK, Cheema MS, Vergara IA, Watt CA, Pinto LJ, Chen N, Moore MM.

PLoS One. 2011 Apr 29;6(4):e19325. doi: 10.1371/journal.pone.0019325.

29.

Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster.

Vergara IA, Chen N.

BMC Genomics. 2010 Sep 24;11:516. doi: 10.1186/1471-2164-11-516.

30.

Using the Generic Synteny Browser (GBrowse_syn).

McKay SJ, Vergara IA, Stajich JE.

Curr Protoc Bioinformatics. 2010 Sep;Chapter 9:Unit 9.12. doi: 10.1002/0471250953.bi0912s31.

31.

Using OrthoCluster for the detection of synteny blocks among multiple genomes.

Vergara IA, Chen N.

Curr Protoc Bioinformatics. 2009 Sep;Chapter 6:Unit 6.10 6.10.1-18. doi: 10.1002/0471250953.bi0610s27.

PMID:
19728289
32.

Polymorphic segmental duplication in the nematode Caenorhabditis elegans.

Vergara IA, Mah AK, Huang JC, Tarailo-Graovac M, Johnsen RC, Baillie DL, Chen N.

BMC Genomics. 2009 Jul 21;10:329. doi: 10.1186/1471-2164-10-329.

33.

OrthoClusterDB: an online platform for synteny blocks.

Ng MP, Vergara IA, Frech C, Chen Q, Zeng X, Pei J, Chen N.

BMC Bioinformatics. 2009 Jun 23;10:192. doi: 10.1186/1471-2105-10-192.

34.

Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression.

Faunes F, Sánchez N, Castellanos J, Vergara IA, Melo F, Larraín J.

Genome Biol. 2009 Feb 11;10(2):R15. doi: 10.1186/gb-2009-10-2-r15.

35.

StAR: a simple tool for the statistical comparison of ROC curves.

Vergara IA, Norambuena T, Ferrada E, Slater AW, Melo F.

BMC Bioinformatics. 2008 Jun 5;9:265. doi: 10.1186/1471-2105-9-265.

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