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Visualizing Genomic Data Using Gviz and Bioconductor.

Hahne F, Ivanek R.

Methods Mol Biol. 2016;1418:335-51. doi: 10.1007/978-1-4939-3578-9_16.


Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome.

Brasa S, Mueller A, Jacquemont S, Hahne F, Rozenberg I, Peters T, He Y, McCormack C, Gasparini F, Chibout SD, Grenet O, Moggs J, Gomez-Mancilla B, Terranova R.

Clin Epigenetics. 2016 Feb 5;8:15. doi: 10.1186/s13148-016-0181-x. eCollection 2016.


Orchestrating high-throughput genomic analysis with Bioconductor.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.


QuasR: quantification and annotation of short reads in R.

Gaidatzis D, Lerch A, Hahne F, Stadler MB.

Bioinformatics. 2015 Apr 1;31(7):1130-2. doi: 10.1093/bioinformatics/btu781. Epub 2014 Nov 21.


Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

Vacchi-Suzzi C, Hahne F, Scheubel P, Marcellin M, Dubost V, Westphal M, Boeglen C, Büchmann-Møller S, Cheung MS, Cordier A, De Benedetto C, Deurinck M, Frei M, Moulin P, Oakeley E, Grenet O, Grevot A, Stull R, Theil D, Moggs JG, Marrer E, Couttet P.

PLoS One. 2013;8(1):e52442. doi: 10.1371/journal.pone.0052442. Epub 2013 Jan 2.


Identification of Dlk1-Dio3 imprinted gene cluster noncoding RNAs as novel candidate biomarkers for liver tumor promotion.

Lempiäinen H, Couttet P, Bolognani F, Müller A, Dubost V, Luisier R, Del Rio Espinola A, Vitry V, Unterberger EB, Thomson JP, Treindl F, Metzger U, Wrzodek C, Hahne F, Zollinger T, Brasa S, Kalteis M, Marcellin M, Giudicelli F, Braeuning A, Morawiec L, Zamurovic N, Längle U, Scheer N, Schübeler D, Goodman J, Chibout SD, Marlowe J, Theil D, Heard DJ, Grenet O, Zell A, Templin MF, Meehan RR, Wolf RC, Elcombe CR, Schwarz M, Moulin P, Terranova R, Moggs JG.

Toxicol Sci. 2013 Feb;131(2):375-86. doi: 10.1093/toxsci/kfs303. Epub 2012 Oct 22.


Different collector types for sampling deposition of polycyclic aromatic hydrocarbons--comparison of measurement results and their uncertainty.

Gladtke D, Bakker F, Biaudet H, Brennfleck A, Coleman P, Creutznacher H, Van Egmond BF, Hafkenscheid T, Hahne F, Houtzager MM, Leoz-Garziandia E, Menichini E, Olschewski A, Remesch T.

J Environ Monit. 2012 Aug;14(8):2054-62. doi: 10.1039/c2em30119a. Epub 2012 Jun 29.


Computational methods for early predictive safety assessment from biological and chemical data.

Nigsch F, Lounkine E, McCarren P, Cornett B, Glick M, Azzaoui K, Urban L, Marc P, Müller A, Hahne F, Heard DJ, Jenkins JL.

Expert Opin Drug Metab Toxicol. 2011 Dec;7(12):1497-511. doi: 10.1517/17425255.2011.632632. Epub 2011 Nov 4. Review.


iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor.

Lee K, Hahne F, Sarkar D, Gentleman R.

Adv Bioinformatics. 2009:103839. doi: 10.1155/2009/103839. Epub 2009 Nov 12.


Analysis of High-Throughput Flow Cytometry Data Using plateCore.

Strain E, Hahne F, Brinkman RR, Haaland P.

Adv Bioinformatics. 2009:356141. doi: 10.1155/2009/356141. Epub 2009 Oct 11.


Per-channel basis normalization methods for flow cytometry data.

Hahne F, Khodabakhshi AH, Bashashati A, Wong CJ, Gascoyne RD, Weng AP, Seyfert-Margolis V, Bourcier K, Asare A, Lumley T, Gentleman R, Brinkman RR.

Cytometry A. 2010 Feb;77(2):121-31. doi: 10.1002/cyto.a.20823.


flowClust: a Bioconductor package for automated gating of flow cytometry data.

Lo K, Hahne F, Brinkman RR, Gottardo R.

BMC Bioinformatics. 2009 May 14;10:145. doi: 10.1186/1471-2105-10-145.


flowCore: a Bioconductor package for high throughput flow cytometry.

Hahne F, LeMeur N, Brinkman RR, Ellis B, Haaland P, Sarkar D, Spidlen J, Strain E, Gentleman R.

BMC Bioinformatics. 2009 Apr 9;10:106. doi: 10.1186/1471-2105-10-106.


Extending pathways based on gene lists using InterPro domain signatures.

Hahne F, Mehrle A, Arlt D, Poustka A, Wiemann S, Beissbarth T.

BMC Bioinformatics. 2008 Jan 4;9:3. doi: 10.1186/1471-2105-9-3.


Modeling breast cell cycle regulation--overcoming drug resistance.

Arlt D, Sahin O, Korf U, Loebke C, Beissbarth T, Hahne F, Wiemann S, Poustka A.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:40-3. No abstract available.


Reduced expression of vacuole membrane protein 1 affects the invasion capacity of tumor cells.

Sauermann M, Sahin O, Sültmann H, Hahne F, Blaszkiewicz S, Majety M, Zatloukal K, Füzesi L, Poustka A, Wiemann S, Arlt D.

Oncogene. 2008 Feb 21;27(9):1320-6. Epub 2007 Aug 27.


High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins.

Sauermann M, Hahne F, Schmidt C, Majety M, Rosenfelder H, Bechtel S, Huber W, Poustka A, Arlt D, Wiemann S.

J Biomol Screen. 2007 Jun;12(4):510-20. Epub 2007 May 3.


Statistical methods and software for the analysis of highthroughput reverse genetic assays using flow cytometry readouts.

Hahne F, Arlt D, Sauermann M, Majety M, Poustka A, Wiemann S, Huber W.

Genome Biol. 2006;7(8):R77. Epub 2006 Aug 17.


The LIFEdb database in 2006.

Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A, Wiemann S.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D415-8.


Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle.

Arlt D, Huber W, Liebel U, Schmidt C, Majety M, Sauermann M, Rosenfelder H, Bechtel S, Mehrle A, Bannasch D, Schupp I, Seiler M, Simpson JC, Hahne F, Moosmayer P, Ruschhaupt M, Guilleaume B, Wellenreuther R, Pepperkok R, Sültmann H, Poustka A, Wiemann S.

Cancer Res. 2005 Sep 1;65(17):7733-42.

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