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Items: 1 to 20 of 25

1.

Combining dependent P-values with an empirical adaptation of Brown's method.

Poole W, Gibbs DL, Shmulevich I, Bernard B, Knijnenburg TA.

Bioinformatics. 2016 Sep 1;32(17):i430-i436. doi: 10.1093/bioinformatics/btw438.

PMID:
27587659
2.

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.

Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MC, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA; Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RG.

Cancer Cell. 2016 Aug 8;30(2):363. doi: 10.1016/j.ccell.2016.07.013. No abstract available.

PMID:
27505681
3.

A Landscape of Pharmacogenomic Interactions in Cancer.

Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LF, Saez-Rodriguez J, McDermott U, Garnett MJ.

Cell. 2016 Jul 28;166(3):740-54. doi: 10.1016/j.cell.2016.06.017. Epub 2016 Jul 7.

4.

Loss of ARID1A activates ANXA1, which serves as a predictive biomarker for trastuzumab resistance.

Berns K, Sonnenblick A, Gennissen A, Brohée S, Hijmans ME, Evers B, Fumagalli D, Desmedt C, Loibl S, Denkert C, Neven P, Guo W, Zhang F, Knijnenburg TA, Bosse T, van der Heijden MS, Hindriksen S, Nijkamp W, Wessels LF, Joensuu H, Mills GB, Beijersbergen RL, Sotiriou C, Bernards R.

Clin Cancer Res. 2016 May 12. pii: clincanres.2996.2015. [Epub ahead of print]

PMID:
27172896
5.

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.

Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MC, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA; Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RG.

Cancer Cell. 2016 May 9;29(5):723-36. doi: 10.1016/j.ccell.2016.04.002.

6.

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data.

Bressler R, Kreisberg RB, Bernard B, Niederhuber JE, Vockley JG, Shmulevich I, Knijnenburg TA.

PLoS One. 2015 Dec 17;10(12):e0144820. doi: 10.1371/journal.pone.0144820. eCollection 2015.

PMID:
26679347
Free PMC Article
7.

A multilevel pan-cancer map links gene mutations to cancer hallmarks.

Knijnenburg TA, Bismeijer T, Wessels LF, Shmulevich I.

Chin J Cancer. 2015 Sep 14;34(10):439-49. doi: 10.1186/s40880-015-0050-6.

8.

SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer.

Papadakis AI, Sun C, Knijnenburg TA, Xue Y, Grernrum W, Hölzel M, Nijkamp W, Wessels LF, Beijersbergen RL, Bernards R, Huang S.

Cell Res. 2015 Apr;25(4):445-58. doi: 10.1038/cr.2015.16. Epub 2015 Feb 6.

9.

Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose.

Romagnoli G, Knijnenburg TA, Liti G, Louis EJ, Pronk JT, Daran JM.

Yeast. 2015 Jan;32(1):29-45. doi: 10.1002/yea.3015. Epub 2014 May 13.

10.

Multiscale representation of genomic signals.

Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I.

Nat Methods. 2014 Jun;11(6):689-94. doi: 10.1038/nmeth.2924. Epub 2014 Apr 13.

11.

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.

Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3645-50. doi: 10.1073/pnas.1216918110. Epub 2013 Feb 6.

12.

EPEPT: a web service for enhanced P-value estimation in permutation tests.

Knijnenburg TA, Lin J, Rovira H, Boyle J, Shmulevich I.

BMC Bioinformatics. 2011 Oct 24;12:411. doi: 10.1186/1471-2105-12-411.

13.

A regression model approach to enable cell morphology correction in high-throughput flow cytometry.

Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I.

Mol Syst Biol. 2011 Sep 27;7:531. doi: 10.1038/msb.2011.64.

14.

Genome-wide analysis of effectors of peroxisome biogenesis.

Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemistö A, Boyle J, Rachubinski RA, Shmulevich I, Aitchison JD.

PLoS One. 2010 Aug 4;5(8):e11953. doi: 10.1371/journal.pone.0011953.

15.

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.

Ramsey SA, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, Shmulevich I.

Bioinformatics. 2010 Sep 1;26(17):2071-5. doi: 10.1093/bioinformatics/btq405. Epub 2010 Jul 27.

16.

Fewer permutations, more accurate P-values.

Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I.

Bioinformatics. 2009 Jun 15;25(12):i161-8. doi: 10.1093/bioinformatics/btp211.

17.

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data.

Knijnenburg TA, Daran JM, van den Broek MA, Daran-Lapujade PA, de Winde JH, Pronk JT, Reinders MJ, Wessels LF.

BMC Genomics. 2009 Jan 27;10:53. doi: 10.1186/1471-2164-10-53.

18.

Creating gene set activity profiles with time-series expression data.

Knijnenburg TA, Wessels LF, Reinders MJ.

Int J Bioinform Res Appl. 2008;4(3):306-23.

PMID:
18640906
19.

Combinatorial influence of environmental parameters on transcription factor activity.

Knijnenburg TA, Wessels LF, Reinders MJ.

Bioinformatics. 2008 Jul 1;24(13):i172-81. doi: 10.1093/bioinformatics/btn155.

20.

Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes.

de Groot MJ, Daran-Lapujade P, van Breukelen B, Knijnenburg TA, de Hulster EA, Reinders MJ, Pronk JT, Heck AJ, Slijper M.

Microbiology. 2007 Nov;153(Pt 11):3864-78.

PMID:
17975095
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