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Results: 16

1.

SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision.

Wiewiórka MS, Messina A, Pacholewska A, Maffioletti S, Gawrysiak P, Okoniewski MJ.

Bioinformatics. 2014 Sep 15;30(18):2652-3. doi: 10.1093/bioinformatics/btu343. Epub 2014 May 19.

PMID:
24845651
[PubMed - in process]
2.

A comprehensive look at transcription factor gene expression changes in colorectal adenomas.

Vonlanthen J, Okoniewski MJ, Menigatti M, Cattaneo E, Pellegrini-Ochsner D, Haider R, Jiricny J, Staiano T, Buffoli F, Marra G.

BMC Cancer. 2014 Jan 29;14:46. doi: 10.1186/1471-2407-14-46.

PMID:
24472434
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Early insights into the function of KIAA1199, a markedly overexpressed protein in human colorectal tumors.

Tiwari A, Schneider M, Fiorino A, Haider R, Okoniewski MJ, Roschitzki B, Uzozie A, Menigatti M, Jiricny J, Marra G.

PLoS One. 2013 Jul 23;8(7):e69473. doi: 10.1371/journal.pone.0069473. Print 2013.

PMID:
23936024
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Precise breakpoint localization of large genomic deletions using PacBio and Illumina next-generation sequencers.

Okoniewski MJ, Meienberg J, Patrignani A, Szabelska A, Matyas G, Schlapbach R.

Biotechniques. 2013 Feb;54(2):98-100. doi: 10.2144/000113992.

PMID:
23384181
[PubMed - indexed for MEDLINE]
Free Article
5.

Cross-species genome wide expression analysis during pluripotent cell determination in mouse and rat preimplantation embryos.

Casanova EA, Okoniewski MJ, Cinelli P.

PLoS One. 2012;7(10):e47107. doi: 10.1371/journal.pone.0047107. Epub 2012 Oct 15.

PMID:
23077551
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

PGC-1α determines light damage susceptibility of the murine retina.

Egger A, Samardzija M, Sothilingam V, Tanimoto N, Lange C, Salatino S, Fang L, Garcia-Garrido M, Beck S, Okoniewski MJ, Neutzner A, Seeliger MW, Grimm C, Handschin C.

PLoS One. 2012;7(2):e31272. doi: 10.1371/journal.pone.0031272. Epub 2012 Feb 13.

PMID:
22348062
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage.

Okoniewski MJ, Leśniewska A, Szabelska A, Zyprych-Walczak J, Ryan M, Wachtel M, Morzy T, Schäfer B, Schlapbach R.

Nucleic Acids Res. 2012 May;40(9):e63. doi: 10.1093/nar/gkr1249. Epub 2011 Dec 30.

PMID:
22210855
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

rnaSeqMap: a Bioconductor package for RNA sequencing data exploration.

Leśniewska A, Okoniewski MJ.

BMC Bioinformatics. 2011 May 25;12:200. doi: 10.1186/1471-2105-12-200.

PMID:
21612622
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis.

Sims AH, Smethurst GJ, Hey Y, Okoniewski MJ, Pepper SD, Howell A, Miller CJ, Clarke RB.

BMC Med Genomics. 2008 Sep 21;1:42. doi: 10.1186/1755-8794-1-42.

PMID:
18803878
[PubMed]
Free PMC Article
10.

Comprehensive analysis of affymetrix exon arrays using BioConductor.

Okoniewski MJ, Miller CJ.

PLoS Comput Biol. 2008 Feb;4(2):e6. doi: 10.1371/journal.pcbi.0040006. Review. No abstract available.

PMID:
18463711
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Exon level integration of proteomics and microarray data.

Bitton DA, Okoniewski MJ, Connolly Y, Miller CJ.

BMC Bioinformatics. 2008 Feb 25;9:118. doi: 10.1186/1471-2105-9-118.

PMID:
18298841
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases.

Pierce A, Unwin RD, Evans CA, Griffiths S, Carney L, Zhang L, Jaworska E, Lee CF, Blinco D, Okoniewski MJ, Miller CJ, Bitton DA, Spooncer E, Whetton AD.

Mol Cell Proteomics. 2008 May;7(5):853-63. Epub 2007 Oct 21.

PMID:
17951628
[PubMed - indexed for MEDLINE]
Free Article
13.

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Yates T, Okoniewski MJ, Miller CJ.

Nucleic Acids Res. 2008 Jan;36(Database issue):D780-6. Epub 2007 Oct 11.

PMID:
17932061
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data.

Okoniewski MJ, Yates T, Dibben S, Miller CJ.

Genome Biol. 2007;8(5):R79.

PMID:
17498294
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

High correspondence between Affymetrix exon and standard expression arrays.

Okoniewski MJ, Hey Y, Pepper SD, Miller CJ.

Biotechniques. 2007 Feb;42(2):181-5.

PMID:
17373482
[PubMed - indexed for MEDLINE]
Free Article
16.

Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations.

Okoniewski MJ, Miller CJ.

BMC Bioinformatics. 2006 Jun 2;7:276.

PMID:
16749918
[PubMed - indexed for MEDLINE]
Free PMC Article

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