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Items: 1 to 20 of 113


Improved discovery of molecular interactions in genome-scale data with adaptive model-based normalization.

Salzman J, Klass DM, Brown PO.

PLoS One. 2013;8(1):e53930. doi: 10.1371/journal.pone.0053930. Epub 2013 Jan 22.


Genome-wide analysis of RNA-protein interactions in plants.

Barkan A.

Methods Mol Biol. 2009;553:13-37. doi: 10.1007/978-1-60327-563-7_2. Review.


Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments.

Ghosh S, Hirsch HA, Sekinger E, Struhl K, Gingeras TR.

BMC Bioinformatics. 2006 Oct 5;7:434.


Effect of various normalization methods on Applied Biosystems expression array system data.

Barbacioru CC, Wang Y, Canales RD, Sun YA, Keys DN, Chan F, Poulter KA, Samaha RR.

BMC Bioinformatics. 2006 Dec 15;7:533.


Normalization and experimental design for ChIP-chip data.

Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ.

BMC Bioinformatics. 2007 Jun 25;8:219.


PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T.

J Vis Exp. 2010 Jul 2;(41). pii: 2034. doi: 10.3791/2034.


An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies.

Adriaens ME, Jaillard M, Eijssen LM, Mayer CD, Evelo CT.

BMC Genomics. 2012 Jan 25;13:42. doi: 10.1186/1471-2164-13-42.


The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison.

Sioson AA, Mane SP, Li P, Sha W, Heath LS, Bohnert HJ, Grene R.

BMC Bioinformatics. 2006 Apr 20;7:215.


Is this the right normalization? A diagnostic tool for ChIP-seq normalization.

Angelini C, Heller R, Volkinshtein R, Yekutieli D.

BMC Bioinformatics. 2015 May 9;16:150. doi: 10.1186/s12859-015-0579-z.


Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalization.

Binder H, Brücker J, Burden CJ.

J Phys Chem B. 2009 Mar 5;113(9):2874-95. doi: 10.1021/jp808118m.


Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.

Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M.

BMC Bioinformatics. 2007 Aug 3;8:283.


Normalization of oligonucleotide arrays based on the least-variant set of genes.

Calza S, Valentini D, Pawitan Y.

BMC Bioinformatics. 2008 Mar 5;9:140. doi: 10.1186/1471-2105-9-140.


Can Zipf's law be adapted to normalize microarrays?

Lu T, Costello CM, Croucher PJ, Häsler R, Deuschl G, Schreiber S.

BMC Bioinformatics. 2005 Feb 23;6:37.


Pre-processing optimization of RNA immunoprecipitation microarray data.

Barreto-Hernadez E, Gama-Carvalho M, Sousa L.

J Comput Biol. 2011 Oct;18(10):1319-28. doi: 10.1089/cmb.2010.0020. Epub 2011 Jul 21.


A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data.

Han Z, Tian L, Pécot T, Huang T, Machiraju R, Huang K.

BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S2. doi: 10.1186/1471-2105-13-S2-S2.


Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data.

Xiong H, Zhang D, Martyniuk CJ, Trudeau VL, Xia X.

BMC Bioinformatics. 2008 Jan 16;9:25. doi: 10.1186/1471-2105-9-25.


QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions.

Liu B, Yi J, Sv A, Lan X, Ma Y, Huang TH, Leone G, Jin VX.

BMC Genomics. 2013;14 Suppl 8:S3. doi: 10.1186/1471-2164-14-S8-S3. Epub 2013 Dec 9.


A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.


A robust two-way semi-linear model for normalization of cDNA microarray data.

Wang D, Huang J, Xie H, Manzella L, Soares MB.

BMC Bioinformatics. 2005 Jan 21;6:14.


Empirical Bayes screening of many p-values with applications to microarray studies.

Datta S, Datta S.

Bioinformatics. 2005 May 1;21(9):1987-94. Epub 2005 Feb 2.

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