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Items: 25

1.

Gene expression in chronic granulomatous disease and interferon-γ receptor-deficient cells treated in vitro with interferon-γ.

Frazão JB, Colombo M, Simillion C, Bilican A, Keller I, Wüthrich D, Zhu Z, Okoniewski MJ, Bruggmann R, Condino-Neto A, Newburger PE.

J Cell Biochem. 2019 Mar;120(3):4321-4332. doi: 10.1002/jcb.27718. Epub 2018 Sep 27.

PMID:
30260027
2.

Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures.

Leśniewska A, Zyprych-Walczak J, Szabelska-Beręsewicz A, Okoniewski MJ.

Biol Direct. 2018 Feb 21;13(1):3. doi: 10.1186/s13062-018-0205-x.

3.

Benchmarking distributed data warehouse solutions for storing genomic variant information.

Wiewiórka MS, Wysakowicz DP, Okoniewski MJ, Gambin T.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax049.

4.

Corrigendum: Pramel7 mediates ground-state pluripotency through proteasomal-epigenetic combined pathways.

Graf U, Casanova EA, Wyck S, Dalcher D, Gatti M, Vollenweider E, Okoniewski MJ, Weber FA, Patel SS, Schmid MW, Li J, Sharif J, Wanner GA, Koseki H, Wong J, Pelczar P, Penengo L, Santoro R, Cinelli P.

Nat Cell Biol. 2017 Jul 28;19(8):1003. doi: 10.1038/ncb3572.

PMID:
28752849
5.

Pramel7 mediates ground-state pluripotency through proteasomal-epigenetic combined pathways.

Graf U, Casanova EA, Wyck S, Dalcher D, Gatti M, Vollenweider E, Okoniewski MJ, Weber FA, Patel SS, Schmid MW, Li J, Sharif J, Wanner GA, Koseki H, Wong J, Pelczar P, Penengo L, Santoro R, Cinelli P.

Nat Cell Biol. 2017 Jul;19(7):763-773. doi: 10.1038/ncb3554. Epub 2017 Jun 12. Erratum in: Nat Cell Biol. 2017 Jul 28;19(8):1003.

PMID:
28604677
6.

Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response.

Anjanappa RB, Mehta D, Okoniewski MJ, Szabelska-Berȩsewicz A, Gruissem W, Vanderschuren H.

Mol Plant Pathol. 2018 Feb;19(2):476-489. doi: 10.1111/mpp.12565. Epub 2017 Aug 10.

7.

Identification of Novel Equine (Equus caballus) Tendon Markers Using RNA Sequencing.

Kuemmerle JM, Theiss F, Okoniewski MJ, Weber FA, Hemmi S, Mirsaidi A, Richards PJ, Cinelli P.

Genes (Basel). 2016 Nov 10;7(11). pii: E97.

8.

In vivo profiling reveals immunomodulatory effects of sorafenib and dacarbazine on melanoma.

Urosevic-Maiwald M, Barysch MJ, Cheng PF, Karpova MB, Steinert H, Okoniewski MJ, Dummer R.

Oncoimmunology. 2015 Jan 7;4(2):e988458. eCollection 2015 Feb. Erratum in: Oncoimmunology. 2016 Feb 17;5(1):e1104009.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

High correspondence between Affymetrix exon and standard expression arrays.

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

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

25.

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