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Items: 1 to 50 of 176

1.

CRISPR-Cas Systems in Multicellular Cyanobacteria.

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

RNA Biol. 2018 Jul 11. doi: 10.1080/15476286.2018.1493330. [Epub ahead of print]

PMID:
29995583
2.

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.

PMID:
29953864
3.

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.

4.

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. 2018 Jun 19:1-13. doi: 10.1080/15476286.2018.1483685. [Epub ahead of print]

PMID:
29911924
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.

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.

7.

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.

PMID:
29808028
8.

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.

9.

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.

10.

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.

PMID:
29676245
11.

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. 2018 May 21:1-12. doi: 10.1080/15476286.2018.1460994. [Epub ahead of print]

PMID:
29649958
12.

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.

PMID:
29643205
13.

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 Apr 3. doi: 10.1093/bioinformatics/bty208. [Epub ahead of print]

PMID:
29617966
14.

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.

15.

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.

16.

CMV - Visualization for RNA and Protein family models and their comparisons.

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

Bioinformatics. 2018 Mar 15. doi: 10.1093/bioinformatics/bty158. [Epub ahead of print]

PMID:
29554223
17.

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.

18.

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.

19.

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.

PMID:
29326176
20.

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.

21.

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
22.

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.

23.

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.

24.

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.

25.

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
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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
35.

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.

36.

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.

37.

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
38.

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.

39.

Mechanism of β-actin mRNA Recognition by ZBP1.

Nicastro G, Candel AM, Uhl M, Oregioni A, Hollingworth D, Backofen R, Martin SR, Ramos A.

Cell Rep. 2017 Jan 31;18(5):1187-1199. doi: 10.1016/j.celrep.2016.12.091.

40.

GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders.

Hornig T, Grüning B, Kundu K, Houwaart T, Backofen R, Biber K, Normann C.

Genet Res (Camb). 2017 Jan 30;99:e1. doi: 10.1017/S0016672316000148.

PMID:
28132660
41.

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.

de Araujo Oliveira JV, Costa F, Backofen R, Stadler PF, Machado Telles Walter ME, Hertel J.

BMC Bioinformatics. 2016 Dec 15;17(Suppl 18):464. doi: 10.1186/s12859-016-1345-6.

42.

An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions.

Kundu K, Backofen R.

Methods Mol Biol. 2017;1555:83-97. doi: 10.1007/978-1-4939-6762-9_6.

PMID:
28092029
43.

Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M.

Sci Rep. 2017 Jan 11;7:39421. doi: 10.1038/srep39421. No abstract available.

44.

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.

45.

Plasticity of archaeal C/D box sRNA biogenesis.

Tripp V, Martin R, Orell A, Alkhnbashi OS, Backofen R, Randau L.

Mol Microbiol. 2017 Jan;103(1):151-164. doi: 10.1111/mmi.13549. Epub 2016 Oct 29.

46.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M.

Sci Rep. 2016 Oct 7;6:34589. doi: 10.1038/srep34589. Erratum in: Sci Rep. 2017 Jan 11;7:39421.

47.

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression.

Niknafs YS, Han S, Ma T, Speers C, Zhang C, Wilder-Romans K, Iyer MK, Pitchiaya S, Malik R, Hosono Y, Prensner JR, Poliakov A, Singhal U, Xiao L, Kregel S, Siebenaler RF, Zhao SG, Uhl M, Gawronski A, Hayes DF, Pierce LJ, Cao X, Collins C, Backofen R, Sahinalp CS, Rae JM, Chinnaiyan AM, Feng FY.

Nat Commun. 2016 Sep 26;7:12791. doi: 10.1038/ncomms12791.

48.

GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS.

Hoppmann AS, Schlosser P, Backofen R, Lausch E, Köttgen A.

PLoS One. 2016 Sep 9;11(9):e0162466. doi: 10.1371/journal.pone.0162466. eCollection 2016.

49.

Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs.

Reimann V, Alkhnbashi OS, Saunders SJ, Scholz I, Hein S, Backofen R, Hess WR.

Nucleic Acids Res. 2017 Jan 25;45(2):915-925. doi: 10.1093/nar/gkw786. Epub 2016 Sep 5.

50.

Characterizing leader sequences of CRISPR loci.

Alkhnbashi OS, Shah SA, Garrett RA, Saunders SJ, Costa F, Backofen R.

Bioinformatics. 2016 Sep 1;32(17):i576-i585. doi: 10.1093/bioinformatics/btw454.

PMID:
27587677

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