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Items: 42

1.

Deacetylation Inhibition Reverses PABPN1-Dependent Muscle Wasting.

Olie CS, Riaz M, Konietzny R, Charles PD, Pinto-Fernandez A, Kiełbasa SM, Aartsma-Rus A, Goeman JJ, Kessler BM, Raz V.

iScience. 2019 Jan 22;12:318-332. doi: 10.1016/j.isci.2019.01.024. [Epub ahead of print]

2.

Skewed X-inactivation is common in the general female population.

Shvetsova E, Sofronova A, Monajemi R, Gagalova K, Draisma HHM, White SJ, Santen GWE, Chuva de Sousa Lopes SM, Heijmans BT, van Meurs J, Jansen R, Franke L, Kiełbasa SM, den Dunnen JT, 't Hoen PAC; BIOS consortium; GoNL consortium.

Eur J Hum Genet. 2019 Mar;27(3):455-465. doi: 10.1038/s41431-018-0291-3. Epub 2018 Dec 14.

PMID:
30552425
3.

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage.

Coutinho de Almeida R, Ramos YFM, Mahfouz A, den Hollander W, Lakenberg N, Houtman E, van Hoolwerff M, Suchiman HED, Rodríguez Ruiz A, Slagboom PE, Mei H, Kiełbasa SM, Nelissen RGHH, Reinders M, Meulenbelt I.

Ann Rheum Dis. 2019 Feb;78(2):270-277. doi: 10.1136/annrheumdis-2018-213882. Epub 2018 Dec 1.

4.

The Effect of Corticosteroids on Human Choroidal Endothelial Cells: A Model to Study Central Serous Chorioretinopathy.

Brinks J, van Dijk EHC, Habeeb M, Nikolaou A, Tsonaka R, Peters HAB, Sips HCM, van de Merbel AF, de Jong EK, Notenboom RGE, Kielbasa SM, van der Maarel SM, Quax PHA, Meijer OC, Boon CJF.

Invest Ophthalmol Vis Sci. 2018 Nov 1;59(13):5682-5692. doi: 10.1167/iovs.18-25054.

PMID:
30489628
5.

Selective Glucocorticoid Receptor Modulation Prevents and Reverses Nonalcoholic Fatty Liver Disease in Male Mice.

Koorneef LL, van den Heuvel JK, Kroon J, Boon MR, 't Hoen PAC, Hettne KM, van de Velde NM, Kolenbrander KB, Streefland TCM, Mol IM, Sips HCM, Kielbasa SM, Mei H, Belanoff JK, Pereira AM, Oosterveer MH, Hunt H, Rensen PCN, Meijer OC.

Endocrinology. 2018 Dec 1;159(12):3925-3936. doi: 10.1210/en.2018-00671.

PMID:
30321321
6.

Integrating omics datasets with the OmicsPLS package.

Bouhaddani SE, Uh HW, Jongbloed G, Hayward C, Klarić L, Kiełbasa SM, Houwing-Duistermaat J.

BMC Bioinformatics. 2018 Oct 11;19(1):371. doi: 10.1186/s12859-018-2371-3.

7.

Human Bone Marrow-Resident Natural Killer Cells Have a Unique Transcriptional Profile and Resemble Resident Memory CD8+ T Cells.

Melsen JE, Lugthart G, Vervat C, Kielbasa SM, van der Zeeuw SAJ, Buermans HPJ, van Ostaijen-Ten Dam MM, Lankester AC, Schilham MW.

Front Immunol. 2018 Aug 22;9:1829. doi: 10.3389/fimmu.2018.01829. eCollection 2018.

8.

Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome.

Rovito R, Warnatz HJ, Kiełbasa SM, Mei H, Amstislavskiy V, Arens R, Yaspo ML, Lehrach H, Kroes ACM, Goeman JJ, Vossen ACTM.

PLoS One. 2018 Jul 19;13(7):e0200652. doi: 10.1371/journal.pone.0200652. eCollection 2018.

9.

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model.

Toonen LJA, Overzier M, Evers MM, Leon LG, van der Zeeuw SAJ, Mei H, Kielbasa SM, Goeman JJ, Hettne KM, Magnusson OT, Poirel M, Seyer A, 't Hoen PAC, van Roon-Mom WMC.

Mol Neurodegener. 2018 Jun 22;13(1):31. doi: 10.1186/s13024-018-0261-9.

10.

Brain Transcriptomic Analysis of Hereditary Cerebral Hemorrhage With Amyloidosis-Dutch Type.

Grand Moursel L, van Roon-Mom WMC, Kiełbasa SM, Mei H, Buermans HPJ, van der Graaf LM, Hettne KM, de Meijer EJ, van Duinen SG, Laros JFJ, van Buchem MA, 't Hoen PAC, van der Maarel SM, van der Weerd L.

Front Aging Neurosci. 2018 Apr 13;10:102. doi: 10.3389/fnagi.2018.00102. eCollection 2018.

11.

Genes associated with venous thromboembolism in colorectal cancer patients.

Ünlü B, van Es N, Arindrarto W, Kiełbasa SM, Mei H, Westerga J, Middeldorp S, Kuppen PJK, Otten JMMB, Cannegieter S, Versteeg HH.

J Thromb Haemost. 2018 Feb;16(2):293-302. doi: 10.1111/jth.13926. Epub 2018 Jan 15.

PMID:
29247594
12.

The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs.

Raz V, Riaz M, Tatum Z, Kielbasa SM, 't Hoen PAC.

FASEB J. 2018 Mar;32(3):1579-1590. doi: 10.1096/fj.201700861R. Epub 2018 Jan 3.

PMID:
29141996
13.

RNA-seq analysis of Lgr6+ stem cells and identification of an Lgr6 isoform.

van de Glind GC, Bastidas Torres AN, Zoutman WH, van der Zeeuw SAJ, Kiełbasa SM, de Gruijl FR, Tensen CP.

Exp Dermatol. 2018 Oct;27(10):1172-1175. doi: 10.1111/exd.13453. Epub 2017 Dec 20.

PMID:
28987003
14.

Disease variants alter transcription factor levels and methylation of their binding sites.

Bonder MJ, Luijk R, Zhernakova DV, Moed M, Deelen P, Vermaat M, van Iterson M, van Dijk F, van Galen M, Bot J, Slieker RC, Jhamai PM, Verbiest M, Suchiman HE, Verkerk M, van der Breggen R, van Rooij J, Lakenberg N, Arindrarto W, Kielbasa SM, Jonkers I, van 't Hof P, Nooren I, Beekman M, Deelen J, van Heemst D, Zhernakova A, Tigchelaar EF, Swertz MA, Hofman A, Uitterlinden AG, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, van den Berg LH, van Zwet EW, Mei H, Li Y, Lemire M, Hudson TJ; BIOS Consortium, Slagboom PE, Wijmenga C, Veldink JH, van Greevenbroek MM, van Duijn CM, Boomsma DI, Isaacs A, Jansen R, van Meurs JB, 't Hoen PA, Franke L, Heijmans BT.

Nat Genet. 2017 Jan;49(1):131-138. doi: 10.1038/ng.3721. Epub 2016 Dec 5.

PMID:
27918535
15.

Identification of context-dependent expression quantitative trait loci in whole blood.

Zhernakova DV, Deelen P, Vermaat M, van Iterson M, van Galen M, Arindrarto W, van 't Hof P, Mei H, van Dijk F, Westra HJ, Bonder MJ, van Rooij J, Verkerk M, Jhamai PM, Moed M, Kielbasa SM, Bot J, Nooren I, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, Zhernakova A, Li Y, Tigchelaar EF, de Klein N, Beekman M, Deelen J, van Heemst D, van den Berg LH, Hofman A, Uitterlinden AG, van Greevenbroek MM, Veldink JH, Boomsma DI, van Duijn CM, Wijmenga C, Slagboom PE, Swertz MA, Isaacs A, van Meurs JB, Jansen R, Heijmans BT, 't Hoen PA, Franke L.

Nat Genet. 2017 Jan;49(1):139-145. doi: 10.1038/ng.3737. Epub 2016 Dec 5.

PMID:
27918533
16.

New function of the myostatin/activin type I receptor (ALK4) as a mediator of muscle atrophy and muscle regeneration.

Pasteuning-Vuhman S, Boertje-van der Meulen JW, van Putten M, Overzier M, Ten Dijke P, Kiełbasa SM, Arindrarto W, Wolterbeek R, Lezhnina KV, Ozerov IV, Aliper AM, Hoogaars WM, Aartsma-Rus A, Loomans CJ.

FASEB J. 2017 Jan;31(1):238-255. doi: 10.1096/fj.201600675R. Epub 2016 Oct 12.

17.

ARTISAN PCR: rapid identification of full-length immunoglobulin rearrangements without primer binding bias.

Koning MT, Kiełbasa SM, Boersma V, Buermans HPJ, van der Zeeuw SAJ, van Bergen CAM, Cleven AHG, Kluin PM, Griffioen M, Navarrete MA, Veelken H.

Br J Haematol. 2017 Sep;178(6):983-986. doi: 10.1111/bjh.14180. Epub 2016 Jun 15. No abstract available.

PMID:
27301611
18.

Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression.

de Bruin RG, Shiue L, Prins J, de Boer HC, Singh A, Fagg WS, van Gils JM, Duijs JM, Katzman S, Kraaijeveld AO, Böhringer S, Leung WY, Kielbasa SM, Donahue JP, van der Zande PH, Sijbom R, van Alem CM, Bot I, van Kooten C, Jukema JW, Van Esch H, Rabelink TJ, Kazan H, Biessen EA, Ares M Jr, van Zonneveld AJ, van der Veer EP.

Nat Commun. 2016 Mar 31;7:10846. doi: 10.1038/ncomms10846.

19.

Integrated Whole Genome and Transcriptome Analysis Identified a Therapeutic Minor Histocompatibility Antigen in a Splice Variant of ITGB2.

Pont MJ, van der Lee DI, van der Meijden ED, van Bergen CA, Kester MG, Honders MW, Vermaat M, Eefting M, Marijt EW, Kielbasa SM, Hoen PA, Falkenburg JH, Griffioen M.

Clin Cancer Res. 2016 Aug 15;22(16):4185-96. doi: 10.1158/1078-0432.CCR-15-2307. Epub 2016 Mar 10.

20.

Molecular signatures of age-associated chronic degeneration of shoulder muscles.

Raz Y, Henseler JF, Kolk A, Tatum Z, Groosjohan NK, Verwey NE, Arindrarto W, Kielbasa SM, Nagels J, 't Hoen PA, Nelissen RG, Raz V.

Oncotarget. 2016 Feb 23;7(8):8513-23. doi: 10.18632/oncotarget.7382.

21.

Selection patterns of B-cell receptors and the natural history of follicular lymphoma.

Scherer F, van der Burgt M, Kiełbasa SM, Bertinetti-Lapatki C, Dühren von Minden M, Mikesch K, Zirlik K, de Wreede L, Veelken H, Navarrete MA.

Br J Haematol. 2016 Dec;175(5):972-975. doi: 10.1111/bjh.13901. Epub 2015 Dec 21. No abstract available.

PMID:
26687432
22.

Whole-transcriptome analysis of flow-sorted cervical cancer samples reveals that B cell expressed TCL1A is correlated with improved survival.

Punt S, Corver WE, van der Zeeuw SA, Kielbasa SM, Osse EM, Buermans HP, de Kroon CD, Jordanova ES, Gorter A.

Oncotarget. 2015 Nov 17;6(36):38681-94. doi: 10.18632/oncotarget.4526.

23.

Two Plasmodium 6-Cys family-related proteins have distinct and critical roles in liver-stage development.

Annoura T, van Schaijk BC, Ploemen IH, Sajid M, Lin JW, Vos MW, Dinmohamed AG, Inaoka DK, Rijpma SR, van Gemert GJ, Chevalley-Maurel S, Kiełbasa SM, Scheltinga F, Franke-Fayard B, Klop O, Hermsen CC, Kita K, Gego A, Franetich JF, Mazier D, Hoffman SL, Janse CJ, Sauerwein RW, Khan SM.

FASEB J. 2014 May;28(5):2158-70. doi: 10.1096/fj.13-241570. Epub 2014 Feb 7.

PMID:
24509910
24.

What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform.

Swat M, Kiełbasa SM, Polak S, Olivier B, Bruggeman FJ, Tulloch MQ, Snoep JL, Verhoeven AJ, Westerhoff HV.

Interface Focus. 2011 Feb 6;1(1):16-23. doi: 10.1098/rsfs.2010.0011. Epub 2010 Dec 8.

25.

CpG deamination creates transcription factor-binding sites with high efficiency.

Zemojtel T, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M.

Genome Biol Evol. 2011;3:1304-11. doi: 10.1093/gbe/evr107. Epub 2011 Oct 19.

26.

Adaptive seeds tame genomic sequence comparison.

Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC.

Genome Res. 2011 Mar;21(3):487-93. doi: 10.1101/gr.113985.110. Epub 2011 Jan 5.

27.

Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells.

Jürchott K, Kuban RJ, Krech T, Blüthgen N, Stein U, Walther W, Friese C, Kiełbasa SM, Ungethüm U, Lund P, Knösel T, Kemmner W, Morkel M, Fritzmann J, Schlag PM, Birchmeier W, Krueger T, Sperling S, Sers C, Royer HD, Herzel H, Schäfer R.

PLoS Genet. 2010 Dec 2;6(12):e1001231. doi: 10.1371/journal.pgen.1001231.

28.

TransFind--predicting transcriptional regulators for gene sets.

Kiełbasa SM, Klein H, Roider HG, Vingron M, Blüthgen N.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W275-80. doi: 10.1093/nar/gkq438. Epub 2010 May 28.

29.

Targetfinder.org: a resource for systematic discovery of transcription factor target genes.

Kiełbasa SM, Blüthgen N, Fähling M, Mrowka R.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W233-8. doi: 10.1093/nar/gkq374. Epub 2010 May 11.

30.

Regulation of clock-controlled genes in mammals.

Bozek K, Relógio A, Kielbasa SM, Heine M, Dame C, Kramer A, Herzel H.

PLoS One. 2009;4(3):e4882. doi: 10.1371/journal.pone.0004882. Epub 2009 Mar 16.

31.

A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts.

Blüthgen N, Legewie S, Kielbasa SM, Schramme A, Tchernitsa O, Keil J, Solf A, Vingron M, Schäfer R, Herzel H, Sers C.

FEBS J. 2009 Feb;276(4):1024-35. doi: 10.1111/j.1742-4658.2008.06846.x. Epub 2009 Jan 12.

32.

Methylation and deamination of CpGs generate p53-binding sites on a genomic scale.

Zemojtel T, Kielbasa SM, Arndt PF, Chung HR, Vingron M.

Trends Genet. 2009 Feb;25(2):63-6. doi: 10.1016/j.tig.2008.11.005. Epub 2008 Dec 26.

PMID:
19101055
33.

Transcriptional autoregulatory loops are highly conserved in vertebrate evolution.

Kiełbasa SM, Vingron M.

PLoS One. 2008 Sep 15;3(9):e3210. doi: 10.1371/journal.pone.0003210.

34.

Promoter analysis of Mammalian clock controlled genes.

Bozek K, Kiełbasa SM, Kramer A, Herzel H.

Genome Inform. 2007;18:65-74.

PMID:
18546475
35.

Regulatory elements of marine cyanobacteria.

Kiełbasa SM, Herzel H, Axmann IM.

Genome Inform. 2007;18:1-11.

PMID:
18546470
36.

Measuring similarities between transcription factor binding sites.

Kielbasa SM, Gonze D, Herzel H.

BMC Bioinformatics. 2005 Sep 28;6:237.

37.

Inferring combinatorial regulation of transcription in silico.

Blüthgen N, Kiełbasa SM, Herzel H.

Nucleic Acids Res. 2005 Jan 12;33(1):272-9. Print 2005.

38.

HuSiDa--the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells.

Truss M, Swat M, Kielbasa SM, Schäfer R, Herzel H, Hagemeier C.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D108-11.

39.

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.

Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W235-41.

40.

HOMGL-comparing genelists across species and with different accession numbers.

Blüthgen N, Kiełbasa SM, Cajavec B, Herzel H.

Bioinformatics. 2004 Jan 1;20(1):125-6.

PMID:
14693820
41.

Combining frequency and positional information to predict transcription factor binding sites.

Kiełbasa SM, Korbel JO, Beule D, Schuchhardt J, Herzel H.

Bioinformatics. 2001 Nov;17(11):1019-26.

PMID:
11724730
42.

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