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Items: 1 to 20 of 34

1.

Ensembl 2012.

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM.

Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90. doi: 10.1093/nar/gkr991. Epub 2011 Nov 15.

2.

Tumor suppressor genes FHIT and WWOX are deleted in primary effusion lymphoma (PEL) cell lines.

Roy D, Sin SH, Damania B, Dittmer DP.

Blood. 2011 Aug 18;118(7):e32-9. doi: 10.1182/blood-2010-12-323659. Epub 2011 Jun 17.

3.

NCBI GEO: archive for functional genomics data sets--10 years on.

Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1005-10. doi: 10.1093/nar/gkq1184. Epub 2010 Nov 21.

4.

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.

Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1002-4. doi: 10.1093/nar/gkq1040. Epub 2010 Nov 10.

5.

Algorithm-driven artifacts in median polish summarization of microarray data.

Giorgi FM, Bolger AM, Lohse M, Usadel B.

BMC Bioinformatics. 2010 Nov 11;11:553. doi: 10.1186/1471-2105-11-553.

6.

waviCGH: a web application for the analysis and visualization of genomic copy number alterations.

Carro A, Rico D, Rueda OM, Díaz-Uriarte R, Pisano DG.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W182-7. doi: 10.1093/nar/gkq441. Epub 2010 May 27.

7.

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.

Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W210-3. doi: 10.1093/nar/gkq388. Epub 2010 May 16.

8.

Networking of differentially expressed genes in human cancer cells resistant to methotrexate.

Selga E, Oleaga C, Ramírez S, de Almagro MC, Noé V, Ciudad CJ.

Genome Med. 2009 Sep 4;1(9):83. doi: 10.1186/gm83.

9.

CGHregions: dimension reduction for array CGH data with minimal information loss.

van de Wiel MA, Wieringen WN.

Cancer Inform. 2007 Feb 8;3:55-63.

10.

RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.

Rueda OM, Diaz-Uriarte R.

Bioinformatics. 2009 Aug 1;25(15):1959-60. doi: 10.1093/bioinformatics/btp307. Epub 2009 May 6.

11.

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.

Kauffmann A, Gentleman R, Huber W.

Bioinformatics. 2009 Feb 1;25(3):415-6. doi: 10.1093/bioinformatics/btn647. Epub 2008 Dec 23.

12.

Power enhancement via multivariate outlier testing with gene expression arrays.

Asare AL, Gao Z, Carey VJ, Wang R, Seyfert-Margolis V.

Bioinformatics. 2009 Jan 1;25(1):48-53. doi: 10.1093/bioinformatics/btn591. Epub 2008 Nov 16.

13.

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.

Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. doi: 10.1093/nar/gkn889. Epub 2008 Nov 10.

14.

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation.

Wingender E.

Brief Bioinform. 2008 Jul;9(4):326-32. doi: 10.1093/bib/bbn016. Epub 2008 Apr 24.

15.

CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.

Lai W, Choudhary V, Park PJ.

Bioinformatics. 2008 Apr 1;24(7):1014-5. doi: 10.1093/bioinformatics/btn067. Epub 2008 Feb 22.

16.

Estimation and assessment of raw copy numbers at the single locus level.

Bengtsson H, Irizarry R, Carvalho B, Speed TP.

Bioinformatics. 2008 Mar 15;24(6):759-67. doi: 10.1093/bioinformatics/btn016. Epub 2008 Jan 19.

17.

The vertebrate genome annotation (Vega) database.

Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL.

Nucleic Acids Res. 2008 Jan;36(Database issue):D753-60. Epub 2007 Nov 14.

18.

miRBase: tools for microRNA genomics.

Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.

Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8. Epub 2007 Nov 8.

19.

Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays.

Guttman M, Mies C, Dudycz-Sulicz K, Diskin SJ, Baldwin DA, Stoeckert CJ Jr, Grant GR.

PLoS Genet. 2007 Aug;3(8):e143.

20.

MicroRNA targeting specificity in mammals: determinants beyond seed pairing.

Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP.

Mol Cell. 2007 Jul 6;27(1):91-105.

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