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Items: 35

1.

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy.

Föll MC, Moritz L, Wollmann T, Stillger MN, Vockert N, Werner M, Bronsert P, Rohr K, Grüning BA, Schilling O.

Gigascience. 2019 Dec 1;8(12). pii: giz143. doi: 10.1093/gigascience/giz143.

2.

Software engineering for scientific big data analysis.

Grüning BA, Lampa S, Vaudel M, Blankenberg D.

Gigascience. 2019 May 1;8(5). pii: giz054. doi: 10.1093/gigascience/giz054.

3.

Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome.

Nührenberg TG, Cederqvist M, Marini F, Stratz C, Grüning BA, Trenk D, Binder H, Gilsbach R, Neumann FJ, Hein L.

Biomed Res Int. 2018 Nov 1;2018:8989252. doi: 10.1155/2018/8989252. eCollection 2018.

4.

Parkour LIMS: high-quality sample preparation in next generation sequencing.

Anatskiy E, Ryan DP, Grüning BA, Arrigoni L, Manke T, Bönisch U.

Bioinformatics. 2019 Apr 15;35(8):1422-1424. doi: 10.1093/bioinformatics/bty820.

PMID:
30239601
5.

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

Wolff J, Bhardwaj V, Nothjunge S, Richard G, Renschler G, Gilsbach R, Manke T, Backofen R, Ramírez F, Grüning BA.

Nucleic Acids Res. 2018 Jul 2;46(W1):W11-W16. doi: 10.1093/nar/gky504.

6.

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Goecks J, Taylor J, Nekrutenko A, Blankenberg D.

Nucleic Acids Res. 2018 Jul 2;46(W1):W537-W544. doi: 10.1093/nar/gky379.

7.

Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo.

Gilsbach R, Schwaderer M, Preissl S, Grüning BA, Kranzhöfer D, Schneider P, Nührenberg TG, Mulero-Navarro S, Weichenhan D, Braun C, Dreßen M, Jacobs AR, Lahm H, Doenst T, Backofen R, Krane M, Gelb BD, Hein L.

Nat Commun. 2018 Jan 26;9(1):391. doi: 10.1038/s41467-017-02762-z.

8.

High-resolution TADs reveal DNA sequences underlying genome organization in flies.

Ramírez F, Bhardwaj V, Arrigoni L, Lam KC, Grüning BA, Villaveces J, Habermann B, Akhtar A, Manke T.

Nat Commun. 2018 Jan 15;9(1):189. doi: 10.1038/s41467-017-02525-w.

9.

Combinatorial Omics Analysis Reveals Perturbed Lysosomal Homeostasis in Collagen VII-deficient Keratinocytes.

Thriene K, Grüning BA, Bornert O, Erxleben A, Leppert J, Athanasiou I, Weber E, Kiritsi D, Nyström A, Reinheckel T, Backofen R, Has C, Bruckner-Tuderman L, Dengjel J.

Mol Cell Proteomics. 2018 Apr;17(4):565-579. doi: 10.1074/mcp.RA117.000437. Epub 2018 Jan 11.

10.

DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes.

Nothjunge S, Nührenberg TG, Grüning BA, Doppler SA, Preissl S, Schwaderer M, Rommel C, Krane M, Hein L, Gilsbach R.

Nat Commun. 2017 Nov 21;8(1):1667. doi: 10.1038/s41467-017-01724-9.

11.

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R.

Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409.

12.

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

Grüning BA, Rasche E, Rebolledo-Jaramillo B, Eberhard C, Houwaart T, Chilton J, Coraor N, Backofen R, Taylor J, Nekrutenko A.

PLoS Comput Biol. 2017 May 25;13(5):e1005425. doi: 10.1371/journal.pcbi.1005425. eCollection 2017 May.

13.

BioContainers: an open-source and community-driven framework for software standardization.

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y.

Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

14.

5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation.

Kranzhöfer DK, Gilsbach R, Grüning BA, Backofen R, Nührenberg TG, Hein L.

PLoS One. 2016 Nov 16;11(11):e0166575. doi: 10.1371/journal.pone.0166575. eCollection 2016.

15.

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.

Döring K, Grüning BA, Telukunta KK, Thomas P, Günther S.

PLoS One. 2016 Oct 5;11(10):e0163794. doi: 10.1371/journal.pone.0163794. eCollection 2016.

17.

MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing.

Wecker T, Hoffmeier K, Plötner A, Grüning BA, Horres R, Backofen R, Reinhard T, Schlunck G.

Invest Ophthalmol Vis Sci. 2016 Apr;57(4):1706-13. doi: 10.1167/iovs.15-17828.

PMID:
27064390
18.

DOT1L Activity Promotes Proliferation and Protects Cortical Neural Stem Cells from Activation of ATF4-DDIT3-Mediated ER Stress In Vitro.

Roidl D, Hellbach N, Bovio PP, Villarreal A, Heidrich S, Nestel S, Grüning BA, Boenisch U, Vogel T.

Stem Cells. 2016 Jan;34(1):233-45. doi: 10.1002/stem.2187. Epub 2015 Sep 29.

19.

Anatomy of BioJS, an open source community for the life sciences.

Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, Grüning BA, Inupakutika D, Sillitoe I, Thanki AS, Vieira B, Villaveces JM, Schneider MV, Lewis S, Pettifer S, Rost B, Corpas M.

Elife. 2015 Jul 8;4. doi: 10.7554/eLife.07009.

20.

Deciphering the Epigenetic Code of Cardiac Myocyte Transcription.

Preissl S, Schwaderer M, Raulf A, Hesse M, Grüning BA, Köbele C, Backofen R, Fleischmann BK, Hein L, Gilsbach R.

Circ Res. 2015 Aug 14;117(5):413-23. doi: 10.1161/CIRCRESAHA.115.306337. Epub 2015 Jun 23.

PMID:
26105955
21.

The purchasable chemical space: a detailed picture.

Lucas X, Grüning BA, Bleher S, Günther S.

J Chem Inf Model. 2015 May 26;55(5):915-24. doi: 10.1021/acs.jcim.5b00116. Epub 2015 Apr 30.

PMID:
25894297
22.

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.

Gilsbach R, Preissl S, Grüning BA, Schnick T, Burger L, Benes V, Würch A, Bönisch U, Günther S, Backofen R, Fleischmann BK, Schübeler D, Hein L.

Nat Commun. 2014 Oct 22;5:5288. doi: 10.1038/ncomms6288.

23.

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations.

Schubert D, Bode C, Kenefeck R, Hou TZ, Wing JB, Kennedy A, Bulashevska A, Petersen BS, Schäffer AA, Grüning BA, Unger S, Frede N, Baumann U, Witte T, Schmidt RE, Dueckers G, Niehues T, Seneviratne S, Kanariou M, Speckmann C, Ehl S, Rensing-Ehl A, Warnatz K, Rakhmanov M, Thimme R, Hasselblatt P, Emmerich F, Cathomen T, Backofen R, Fisch P, Seidl M, May A, Schmitt-Graeff A, Ikemizu S, Salzer U, Franke A, Sakaguchi S, Walker LSK, Sansom DM, Grimbacher B.

Nat Med. 2014 Dec;20(12):1410-1416. doi: 10.1038/nm.3746. Epub 2014 Oct 20.

24.

PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering.

Patel H, Grüning BA, Günther S, Merfort I.

Bioinformatics. 2014 Oct 15;30(20):2978-80. doi: 10.1093/bioinformatics/btu424. Epub 2014 Jul 1.

PMID:
24990608
25.

deepTools: a flexible platform for exploring deep-sequencing data.

Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91. doi: 10.1093/nar/gku365. Epub 2014 May 5.

26.

Regio- and stereoselective intermolecular oxidative phenol coupling in Streptomyces.

Präg A, Grüning BA, Häckh M, Lüdeke S, Wilde M, Luzhetskyy A, Richter M, Luzhetska M, Günther S, Müller M.

J Am Chem Soc. 2014 Apr 30;136(17):6195-8. doi: 10.1021/ja501630w. Epub 2014 Apr 18.

PMID:
24746278
27.

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

Cock PJ, Grüning BA, Paszkiewicz K, Pritchard L.

PeerJ. 2013 Sep 17;1:e167. doi: 10.7717/peerj.167. eCollection 2013.

28.

Characterization and phylogenetic analysis of the mitochondrial genome of Glarea lozoyensis indicates high diversity within the order Helotiales.

Youssar L, Grüning BA, Günther S, Hüttel W.

PLoS One. 2013 Sep 25;8(9):e74792. doi: 10.1371/journal.pone.0074792. eCollection 2013.

29.

Draft Genome Sequence of Streptomyces viridochromogenes Strain Tu57, Producer of Avilamycin.

Grüning BA, Erxleben A, Hähnlein A, Günther S.

Genome Announc. 2013 Jun 20;1(3). pii: e00384-13. doi: 10.1128/genomeA.00384-13.

30.

StreptomeDB: a resource for natural compounds isolated from Streptomyces species.

Lucas X, Senger C, Erxleben A, Grüning BA, Döring K, Mosch J, Flemming S, Günther S.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1130-6. doi: 10.1093/nar/gks1253. Epub 2012 Nov 28.

31.

Genome sequence of the fungus Glarea lozoyensis: the first genome sequence of a species from the Helotiaceae family.

Youssar L, Grüning BA, Erxleben A, Günther S, Hüttel W.

Eukaryot Cell. 2012 Feb;11(2):250. doi: 10.1128/EC.05302-11. Erratum in: Eukaryot Cell. 2012 Jun;11(6):829.

32.

Mining and evaluation of molecular relationships in literature.

Senger C, Grüning BA, Erxleben A, Döring K, Patel H, Flemming S, Merfort I, Günther S.

Bioinformatics. 2012 Mar 1;28(5):709-14. doi: 10.1093/bioinformatics/bts026. Epub 2012 Jan 13.

PMID:
22247277
33.

Small-molecule conversion of toxic oligomers to nontoxic β-sheet-rich amyloid fibrils.

Bieschke J, Herbst M, Wiglenda T, Friedrich RP, Boeddrich A, Schiele F, Kleckers D, Lopez del Amo JM, Grüning BA, Wang Q, Schmidt MR, Lurz R, Anwyl R, Schnoegl S, Fändrich M, Frank RF, Reif B, Günther S, Walsh DM, Wanker EE.

Nat Chem Biol. 2011 Nov 20;8(1):93-101. doi: 10.1038/nchembio.719.

PMID:
22101602
34.

Genome sequence of Streptomyces sp. strain Tü6071.

Erxleben A, Wunsch-Palasis J, Grüning BA, Luzhetska M, Bechthold A, Günther S.

J Bacteriol. 2011 Aug;193(16):4278-9. doi: 10.1128/JB.00377-11. Epub 2011 Jun 24.

35.

Compounds In Literature (CIL): screening for compounds and relatives in PubMed.

Grüning BA, Senger C, Erxleben A, Flemming S, Günther S.

Bioinformatics. 2011 May 1;27(9):1341-2. doi: 10.1093/bioinformatics/btr130. Epub 2011 Mar 16.

PMID:
21414988

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