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Items: 27

1.

The Proteogenomic Landscape of Curable Prostate Cancer.

Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T, Boutros PC.

Cancer Cell. 2019 Mar 18;35(3):414-427.e6. doi: 10.1016/j.ccell.2019.02.005.

PMID:
30889379
2.

Widespread and Functional RNA Circularization in Localized Prostate Cancer.

Chen S, Huang V, Xu X, Livingstone J, Soares F, Jeon J, Zeng Y, Hua JT, Petricca J, Guo H, Wang M, Yousif F, Zhang Y, Donmez N, Ahmed M, Volik S, Lapuk A, Chua MLK, Heisler LE, Foucal A, Fox NS, Fraser M, Bhandari V, Shiah YJ, Guan J, Li J, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Fradet Y, Têtu B, Liu S, Feng F, Wu X, Shao YW, Komor MA, Sahinalp C, Collins C, Hoogstrate Y, de Jong M, Fijneman RJA, Fei T, Jenster G, van der Kwast T, Bristow RG, Boutros PC, He HH.

Cell. 2019 Feb 7;176(4):831-843.e22. doi: 10.1016/j.cell.2019.01.025.

PMID:
30735634
3.

Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.

Prentice LM, Miller RR, Knaggs J, Mazloomian A, Aguirre Hernandez R, Franchini P, Parsa K, Tessier-Cloutier B, Lapuk A, Huntsman D, Schaeffer DF, Sheffield BS.

PLoS One. 2018 Apr 26;13(4):e0196434. doi: 10.1371/journal.pone.0196434. eCollection 2018.

4.

Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer.

Wyatt AW, Mo F, Wang K, McConeghy B, Brahmbhatt S, Jong L, Mitchell DM, Johnston RL, Haegert A, Li E, Liew J, Yeung J, Shrestha R, Lapuk AV, McPherson A, Shukin R, Bell RH, Anderson S, Bishop J, Hurtado-Coll A, Xiao H, Chinnaiyan AM, Mehra R, Lin D, Wang Y, Fazli L, Gleave ME, Volik SV, Collins CC.

Genome Biol. 2014 Aug 26;15(8):426. doi: 10.1186/s13059-014-0426-y.

5.

A meta-analysis approach for characterizing pan-cancer mechanisms of drug sensitivity in cell lines.

Wang K, Shrestha R, Wyatt AW, Reddy A, Lehár J, Wang Y, Lapuk A, Collins CC.

PLoS One. 2014 Jul 18;9(7):e103050. doi: 10.1371/journal.pone.0103050. eCollection 2014.

6.

The role of mRNA splicing in prostate cancer.

Lapuk AV, Volik SV, Wang Y, Collins CC.

Asian J Androl. 2014 Jul-Aug;16(4):515-21. doi: 10.4103/1008-682X.127825. Review.

7.

Poly-gene fusion transcripts and chromothripsis in prostate cancer.

Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, Shukin R, Lapuk AV, Jones SJ, Zhao Y, Marra MA, Gleave ME, Volik SV, Wang Y, Sahinalp SC, Collins CC.

Genes Chromosomes Cancer. 2012 Dec;51(12):1144-53. doi: 10.1002/gcc.21999. Epub 2012 Aug 25.

PMID:
22927308
8.

From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer.

Lapuk AV, Wu C, Wyatt AW, McPherson A, McConeghy BJ, Brahmbhatt S, Mo F, Zoubeidi A, Anderson S, Bell RH, Haegert A, Shukin R, Wang Y, Fazli L, Hurtado-Coll A, Jones EC, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Zhao Y, Marra MA, Fanjul A, Maher CA, Chinnaiyan AM, Rubin MA, Beltran H, Sahinalp SC, Gleave ME, Volik SV, Collins CC.

J Pathol. 2012 Jul;227(3):286-97. doi: 10.1002/path.4047.

9.

Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer.

Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, Butterfield YS, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Jones SJ, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Sahinalp SC, Gleave ME, Volik SV, Collins CC.

J Pathol. 2012 May;227(1):53-61. doi: 10.1002/path.3987. Epub 2012 Mar 21.

10.

Next generation sequencing of prostate cancer from a patient identifies a deficiency of methylthioadenosine phosphorylase, an exploitable tumor target.

Collins CC, Volik SV, Lapuk AV, Wang Y, Gout PW, Wu C, Xue H, Cheng H, Haegert A, Bell RH, Brahmbhatt S, Anderson S, Fazli L, Hurtado-Coll A, Rubin MA, Demichelis F, Beltran H, Hirst M, Marra M, Maher CA, Chinnaiyan AM, Gleave M, Bertino JR, Lubin M, Wang Y.

Mol Cancer Ther. 2012 Mar;11(3):775-83. doi: 10.1158/1535-7163.MCT-11-0826. Epub 2012 Jan 17.

11.

Next-generation sequencing of prostate tumors provides independent evidence of xenotropic murine leukemia virus-related gammaretrovirus contamination.

Mo F, Wyatt AW, Wu C, Lapuk AV, Marra MA, Gleave ME, Volik SV, Collins CC.

J Clin Microbiol. 2012 Feb;50(2):536-7. doi: 10.1128/JCM.06170-11. Epub 2011 Dec 7. No abstract available.

12.

Optimally discriminative subnetwork markers predict response to chemotherapy.

Dao P, Wang K, Collins C, Ester M, Lapuk A, Sahinalp SC.

Bioinformatics. 2011 Jul 1;27(13):i205-13. doi: 10.1093/bioinformatics/btr245.

13.

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.

McPherson A, Wu C, Hajirasouliha I, Hormozdiari F, Hach F, Lapuk A, Volik S, Shah S, Collins C, Sahinalp SC.

Bioinformatics. 2011 Jun 1;27(11):1481-8. doi: 10.1093/bioinformatics/btr184. Epub 2011 Apr 9.

PMID:
21478487
14.

Exon-level microarray analyses identify alternative splicing programs in breast cancer.

Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark TA, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray JW.

Mol Cancer Res. 2010 Jul;8(7):961-74. doi: 10.1158/1541-7786.MCR-09-0528. Epub 2010 Jul 6.

15.

FIRMA: a method for detection of alternative splicing from exon array data.

Purdom E, Simpson KM, Robinson MD, Conboy JG, Lapuk AV, Speed TP.

Bioinformatics. 2008 Aug 1;24(15):1707-14. doi: 10.1093/bioinformatics/btn284. Epub 2008 Jun 23.

16.

Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer.

Guan Y, Kuo WL, Stilwell JL, Takano H, Lapuk AV, Fridlyand J, Mao JH, Yu M, Miller MA, Santos JL, Kalloger SE, Carlson JW, Ginzinger DG, Celniker SE, Mills GB, Huntsman DG, Gray JW.

Clin Cancer Res. 2007 Oct 1;13(19):5745-55.

17.

Genomic and transcriptional aberrations linked to breast cancer pathophysiologies.

Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW.

Cancer Cell. 2006 Dec;10(6):529-41.

18.

A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.

Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW.

Cancer Cell. 2006 Dec;10(6):515-27.

19.

Organic cation transporters are determinants of oxaliplatin cytotoxicity.

Zhang S, Lovejoy KS, Shima JE, Lagpacan LL, Shu Y, Lapuk A, Chen Y, Komori T, Gray JW, Chen X, Lippard SJ, Giacomini KM.

Cancer Res. 2006 Sep 1;66(17):8847-57.

20.

Decoding the fine-scale structure of a breast cancer genome and transcriptome.

Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C.

Genome Res. 2006 Mar;16(3):394-404. Epub 2006 Feb 3.

21.

Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization.

van Duin M, van Marion R, Watson JE, Paris PL, Lapuk A, Brown N, Oseroff VV, Albertson DG, Pinkel D, de Jong P, Nacheva EP, Dinjens W, van Dekken H, Collins C.

Cytometry A. 2005;63(1):10-9.

22.

The RAB25 small GTPase determines aggressiveness of ovarian and breast cancers.

Cheng KW, Lahad JP, Kuo WL, Lapuk A, Yamada K, Auersperg N, Liu J, Smith-McCune K, Lu KH, Fishman D, Gray JW, Mills GB.

Nat Med. 2004 Nov;10(11):1251-6. Epub 2004 Oct 24.

PMID:
15502842
23.

Computational BAC clone contig assembly for comprehensive genome analysis.

Lapuk A, Volik S, Vincent R, Chin K, Kuo WL, de Jong P, Collins C, Gray JW.

Genes Chromosomes Cancer. 2004 May;40(1):66-71.

PMID:
15034871
24.

End-sequence profiling: sequence-based analysis of aberrant genomes.

Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, Tao Q, Kowbel D, Huang G, Lapuk A, Kuo WL, Magrane G, De Jong P, Gray JW, Collins C.

Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7696-701. Epub 2003 Jun 4.

25.

Human endogenous retrovirus HERV-K/HERV-H evolution in the genome of primates.

Lapuk AV, Lebedev YuB, Sverdlov ED.

Dokl Biochem. 2000 Jul-Aug;373(1-6):150-2. No abstract available.

PMID:
11002847
27.

Subfamilies and nearest-neighbour dendrogram for the LTRs of human endogenous retroviruses HERV-K mapped on human chromosome 19: physical neighbourhood does not correlate with identity level.

Lavrentieva I, Khil P, Vinogradova T, Akhmedov A, Lapuk A, Shakhova O, Lebedev Y, Monastyrskaya G, Sverdlov ED.

Hum Genet. 1998 Jan;102(1):107-16.

PMID:
9490288

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