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Items: 1 to 50 of 188

1.

uORF-Tools-Workflow for the determination of translation-regulatory upstream open reading frames.

Scholz A, Eggenhofer F, Gelhausen R, Grüning B, Zarnack K, Brüne B, Backofen R, Schmid T.

PLoS One. 2019 Sep 12;14(9):e0222459. doi: 10.1371/journal.pone.0222459. eCollection 2019.

2.

ShaKer: RNA SHAPE prediction using graph kernel.

Mautner S, Montaseri S, Miladi M, Raden M, Costa F, Backofen R.

Bioinformatics. 2019 Jul 15;35(14):i354-i359. doi: 10.1093/bioinformatics/btz395.

3.

CRISPR-Cas bioinformatics.

Alkhnbashi OS, Meier T, Mitrofanov A, Backofen R, Voß B.

Methods. 2019 Jul 19. pii: S1046-2023(18)30471-7. doi: 10.1016/j.ymeth.2019.07.013. [Epub ahead of print] Review.

PMID:
31326596
4.

A pan-cancer analysis of synonymous mutations.

Sharma Y, Miladi M, Dukare S, Boulay K, Caudron-Herger M, Groß M, Backofen R, Diederichs S.

Nat Commun. 2019 Jun 12;10(1):2569. doi: 10.1038/s41467-019-10489-2.

5.

The RNA workbench 2.0: next generation RNA data analysis.

Fallmann J, Videm P, Bagnacani A, Batut B, Doyle MA, Klingstrom T, Eggenhofer F, Stadler PF, Backofen R, Grüning B.

Nucleic Acids Res. 2019 Jul 2;47(W1):W511-W515. doi: 10.1093/nar/gkz353.

6.

Controlling Grain Boundaries by Magnetic Fields.

Backofen R, Elder KR, Voigt A.

Phys Rev Lett. 2019 Mar 29;122(12):126103. doi: 10.1103/PhysRevLett.122.126103.

PMID:
30978082
7.

Integration of accessibility data from structure probing into RNA-RNA interaction prediction.

Miladi M, Montaseri S, Backofen R, Raden M.

Bioinformatics. 2019 Aug 15;35(16):2862-2864. doi: 10.1093/bioinformatics/bty1029.

8.

FOXG1 Regulates PRKAR2B Transcriptionally and Posttranscriptionally via miR200 in the Adult Hippocampus.

Weise SC, Arumugam G, Villarreal A, Videm P, Heidrich S, Nebel N, Dumit VI, Sananbenesi F, Reimann V, Craske M, Schilling O, Hess WR, Fischer A, Backofen R, Vogel T.

Mol Neurobiol. 2019 Jul;56(7):5188-5201. doi: 10.1007/s12035-018-1444-7. Epub 2018 Dec 11.

9.

DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex.

Franz H, Villarreal A, Heidrich S, Videm P, Kilpert F, Mestres I, Calegari F, Backofen R, Manke T, Vogel T.

Nucleic Acids Res. 2019 Jan 10;47(1):168-183. doi: 10.1093/nar/gky953.

10.

GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge.

Costa F, Grün D, Backofen R.

Nat Commun. 2018 Sep 11;9(1):3685. doi: 10.1038/s41467-018-05988-7.

11.

Interactive implementations of thermodynamics-based RNA structure and RNA-RNA interaction prediction approaches for example-driven teaching.

Raden M, Mohamed MM, Ali SM, Backofen R.

PLoS Comput Biol. 2018 Aug 30;14(8):e1006341. doi: 10.1371/journal.pcbi.1006341. eCollection 2018 Aug.

12.

Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1.

Nickel L, Ulbricht A, Alkhnbashi OS, Förstner KU, Cassidy L, Weidenbach K, Backofen R, Schmitz RA.

RNA Biol. 2019 Apr;16(4):492-503. doi: 10.1080/15476286.2018.1514234. Epub 2018 Sep 13.

13.

CRISPR-Cas systems in multicellular cyanobacteria.

Hou S, Brenes-Álvarez M, Reimann V, Alkhnbashi OS, Backofen R, Muro-Pastor AM, Hess WR.

RNA Biol. 2019 Apr;16(4):518-529. doi: 10.1080/15476286.2018.1493330. Epub 2018 Aug 15.

14.

Community-Driven Data Analysis Training for Biology.

Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D; Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B.

Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012.

15.

Practical Computational Reproducibility in the Life Sciences.

Grüning B, Chilton J, Köster J, Dale R, Soranzo N, van den Beek M, Goecks J, Backofen R, Nekrutenko A, Taylor J.

Cell Syst. 2018 Jun 27;6(6):631-635. doi: 10.1016/j.cels.2018.03.014.

16.

Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families.

Shah SA, Alkhnbashi OS, Behler J, Han W, She Q, Hess WR, Garrett RA, Backofen R.

RNA Biol. 2019 Apr;16(4):530-542. doi: 10.1080/15476286.2018.1483685. Epub 2018 Jun 19.

17.

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.

18.

AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments.

Hoinka J, Backofen R, Przytycka TM.

Mol Ther Nucleic Acids. 2018 Jun 1;11:515-517. doi: 10.1016/j.omtn.2018.04.006. Epub 2018 Apr 22. No abstract available.

19.

Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression.

Zhang Y, Pitchiaya S, Cieślik M, Niknafs YS, Tien JC, Hosono Y, Iyer MK, Yazdani S, Subramaniam S, Shukla SK, Jiang X, Wang L, Liu TY, Uhl M, Gawronski AR, Qiao Y, Xiao L, Dhanasekaran SM, Juckette KM, Kunju LP, Cao X, Patel U, Batish M, Shukla GC, Paulsen MT, Ljungman M, Jiang H, Mehra R, Backofen R, Sahinalp CS, Freier SM, Watt AT, Guo S, Wei JT, Feng FY, Malik R, Chinnaiyan AM.

Nat Genet. 2018 Jun;50(6):814-824. doi: 10.1038/s41588-018-0120-1. Epub 2018 May 28.

20.

Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR, Backofen R.

Nucleic Acids Res. 2018 Jul 2;46(W1):W25-W29. doi: 10.1093/nar/gky329.

21.

GLASSgo - Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence.

Lott SC, Schäfer RA, Mann M, Backofen R, Hess WR, Voß B, Georg J.

Front Genet. 2018 Apr 17;9:124. doi: 10.3389/fgene.2018.00124. eCollection 2018.

22.

Structure and Interaction Prediction in Prokaryotic RNA Biology.

Wright PR, Mann M, Backofen R.

Microbiol Spectr. 2018 Apr;6(2). doi: 10.1128/microbiolspec.RWR-0001-2017. Review.

PMID:
29676245
23.

The nuts and bolts of the Haloferax CRISPR-Cas system I-B.

Maier LK, Stachler AE, Brendel J, Stoll B, Fischer S, Haas KA, Schwarz TS, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Gophna U, Marchfelder A.

RNA Biol. 2019 Apr;16(4):469-480. doi: 10.1080/15476286.2018.1460994. Epub 2018 May 21.

24.

In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors.

Sutandy FXR, Ebersberger S, Huang L, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S, König J.

Genome Res. 2018 May;28(5):699-713. doi: 10.1101/gr.229757.117. Epub 2018 Apr 11.

25.

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions.

Gawronski AR, Uhl M, Zhang Y, Lin YY, Niknafs YS, Ramnarine VR, Malik R, Feng F, Chinnaiyan AM, Collins CC, Sahinalp SC, Backofen R.

Bioinformatics. 2018 Sep 15;34(18):3101-3110. doi: 10.1093/bioinformatics/bty208.

26.

The RNA-binding protein ARPP21 controls dendritic branching by functionally opposing the miRNA it hosts.

Rehfeld F, Maticzka D, Grosser S, Knauff P, Eravci M, Vida I, Backofen R, Wulczyn FG.

Nat Commun. 2018 Mar 26;9(1):1235. doi: 10.1038/s41467-018-03681-3.

27.

uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins.

Maticzka D, Ilik IA, Aktas T, Backofen R, Akhtar A.

Nat Commun. 2018 Mar 20;9(1):1142. doi: 10.1038/s41467-018-03575-4.

28.

CMV: visualization for RNA and protein family models and their comparisons.

Eggenhofer F, Hofacker IL, Backofen R, Höner Zu Siederdissen C.

Bioinformatics. 2018 Aug 1;34(15):2676-2678. doi: 10.1093/bioinformatics/bty158.

29.

hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons.

Briese M, Saal-Bauernschubert L, Ji C, Moradi M, Ghanawi H, Uhl M, Appenzeller S, Backofen R, Sendtner M.

Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):E2859-E2868. doi: 10.1073/pnas.1721670115. Epub 2018 Mar 5.

30.

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.

31.

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.

32.

Complex dewetting scenarios of ultrathin silicon films for large-scale nanoarchitectures.

Naffouti M, Backofen R, Salvalaglio M, Bottein T, Lodari M, Voigt A, David T, Benkouider A, Fraj I, Favre L, Ronda A, Berbezier I, Grosso D, Abbarchi M, Bollani M.

Sci Adv. 2017 Nov 10;3(11):eaao1472. doi: 10.1126/sciadv.aao1472. eCollection 2017 Nov.

33.

Comparative RNA Genomics.

Backofen R, Gorodkin J, Hofacker IL, Stadler PF.

Methods Mol Biol. 2018;1704:363-400. doi: 10.1007/978-1-4939-7463-4_14.

PMID:
29277874
34.

A mutually exclusive stem-loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila.

Ilik IA, Maticzka D, Georgiev P, Gutierrez NM, Backofen R, Akhtar A.

Genes Dev. 2017 Oct 1;31(19):1973-1987. doi: 10.1101/gad.304600.117. Epub 2017 Oct 24.

35.

EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells.

Glaser LV, Rieger S, Thumann S, Beer S, Kuklik-Roos C, Martin DE, Maier KC, Harth-Hertle ML, Grüning B, Backofen R, Krebs S, Blum H, Zimmer R, Erhard F, Kempkes B.

PLoS Pathog. 2017 Oct 2;13(10):e1006664. doi: 10.1371/journal.ppat.1006664. eCollection 2017 Oct.

36.

Morphological Evolution of Pit-Patterned Si(001) Substrates Driven by Surface-Energy Reduction.

Salvalaglio M, Backofen R, Voigt A, Montalenti F.

Nanoscale Res Lett. 2017 Sep 29;12(1):554. doi: 10.1186/s11671-017-2320-5.

37.

Controlling the energy of defects and interfaces in the amplitude expansion of the phase-field crystal model.

Salvalaglio M, Backofen R, Voigt A, Elder KR.

Phys Rev E. 2017 Aug;96(2-1):023301. doi: 10.1103/PhysRevE.96.023301. Epub 2017 Aug 1.

PMID:
28950454
38.

Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data.

Davis JA, Saunders SJ, Mann M, Backofen R.

Nucleic Acids Res. 2017 Sep 6;45(15):8745-8757. doi: 10.1093/nar/gkx605.

39.

Methanosarcina Spherical Virus, a Novel Archaeal Lytic Virus Targeting Methanosarcina Strains.

Weidenbach K, Nickel L, Neve H, Alkhnbashi OS, Künzel S, Kupczok A, Bauersachs T, Cassidy L, Tholey A, Backofen R, Schmitz RA.

J Virol. 2017 Oct 27;91(22). pii: e00955-17. doi: 10.1128/JVI.00955-17. Print 2017 Nov 15.

40.

RIP-Seq Suggests Translational Regulation by L7Ae in Archaea.

Daume M, Uhl M, Backofen R, Randau L.

MBio. 2017 Aug 1;8(4). pii: e00730-17. doi: 10.1128/mBio.00730-17.

41.

Recent advances in RNA folding.

Fallmann J, Will S, Engelhardt J, Grüning B, Backofen R, Stadler PF.

J Biotechnol. 2017 Nov 10;261:97-104. doi: 10.1016/j.jbiotec.2017.07.007. Epub 2017 Jul 8. Review.

42.

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.

43.

RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation.

Backofen R, Engelhardt J, Erxleben A, Fallmann J, Grüning B, Ohler U, Rajewsky N, Stadler PF.

J Biotechnol. 2017 Nov 10;261:76-84. doi: 10.1016/j.jbiotec.2017.05.019. Epub 2017 May 26. Review.

44.

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.

45.

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions.

Mann M, Wright PR, Backofen R.

Nucleic Acids Res. 2017 Jul 3;45(W1):W435-W439. doi: 10.1093/nar/gkx279.

46.

DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome.

Aktaş T, Avşar Ilık İ, Maticzka D, Bhardwaj V, Pessoa Rodrigues C, Mittler G, Manke T, Backofen R, Akhtar A.

Nature. 2017 Apr 6;544(7648):115-119. doi: 10.1038/nature21715. Epub 2017 Mar 29.

PMID:
28355180
47.

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs.

Miladi M, Junge A, Costa F, Seemann SE, Havgaard JH, Gorodkin J, Backofen R.

Bioinformatics. 2017 Jul 15;33(14):2089-2096. doi: 10.1093/bioinformatics/btx114.

48.

sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1.

Prasse D, Förstner KU, Jäger D, Backofen R, Schmitz RA.

RNA Biol. 2017 Nov 2;14(11):1544-1558. doi: 10.1080/15476286.2017.1306170. Epub 2017 Apr 27.

49.

Computational analysis of CLIP-seq data.

Uhl M, Houwaart T, Corrado G, Wright PR, Backofen R.

Methods. 2017 Apr 15;118-119:60-72. doi: 10.1016/j.ymeth.2017.02.006. Epub 2017 Feb 22. Review.

PMID:
28254606
50.

Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP.

Neuhaus K, Landstorfer R, Simon S, Schober S, Wright PR, Smith C, Backofen R, Wecko R, Keim DA, Scherer S.

BMC Genomics. 2017 Feb 28;18(1):216. doi: 10.1186/s12864-017-3586-9.

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