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Results: 1 to 20 of 49

1.

Universality of core promoter elements?

Siebert M, Söding J.

Nature. 2014 Jul 23;511(7510):E11-2. doi: 10.1038/nature13587.

PMID:
25056067
[PubMed - in process]
2.

RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress.

Saponaro M, Kantidakis T, Mitter R, Kelly GP, Heron M, Williams H, Söding J, Stewart A, Svejstrup JQ.

Cell. 2014 May 22;157(5):1037-49. doi: 10.1016/j.cell.2014.03.048. Epub 2014 May 15.

PMID:
24836610
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

In vivo ligands of MDA5 and RIG-I in measles virus-infected cells.

Runge S, Sparrer KM, Lässig C, Hembach K, Baum A, García-Sastre A, Söding J, Conzelmann KK, Hopfner KP.

PLoS Pathog. 2014 Apr 17;10(4):e1004081. doi: 10.1371/journal.ppat.1004081. eCollection 2014 Apr.

PMID:
24743923
[PubMed - in process]
Free PMC Article
4.

Eph receptors and ephrin class B ligands are expressed at tissue boundaries in Hydra vulgaris.

Tischer S, Reineck M, Söding J, Münder S, Böttger A.

Int J Dev Biol. 2013;57(9-10):759-65. doi: 10.1387/ijdb.130158ab.

PMID:
24307295
[PubMed - in process]
Free Article
5.

Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II.

Meinel DM, Burkert-Kautzsch C, Kieser A, O'Duibhir E, Siebert M, Mayer A, Cramer P, Söding J, Holstege FC, Sträßer K.

PLoS Genet. 2013 Nov;9(11):e1003914. doi: 10.1371/journal.pgen.1003914. Epub 2013 Nov 14.

PMID:
24244187
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

kClust: fast and sensitive clustering of large protein sequence databases.

Hauser M, Mayer CE, Söding J.

BMC Bioinformatics. 2013 Aug 15;14:248. doi: 10.1186/1471-2105-14-248.

PMID:
23945046
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Discriminative modelling of context-specific amino acid substitution probabilities.

Angermüller C, Biegert A, Söding J.

Bioinformatics. 2012 Dec 15;28(24):3240-7. doi: 10.1093/bioinformatics/bts622. Epub 2012 Oct 17.

PMID:
23080114
[PubMed - indexed for MEDLINE]
Free Article
8.

P-value-based regulatory motif discovery using positional weight matrices.

Hartmann H, Guthöhrlein EW, Siebert M, Luehr S, Söding J.

Genome Res. 2013 Jan;23(1):181-94. doi: 10.1101/gr.139881.112. Epub 2012 Sep 18.

PMID:
22990209
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences.

Luehr S, Hartmann H, Söding J.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W104-9. doi: 10.1093/nar/gks602. Epub 2012 Jun 12.

PMID:
22693218
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation.

Close P, East P, Dirac-Svejstrup AB, Hartmann H, Heron M, Maslen S, Chariot A, Söding J, Skehel M, Svejstrup JQ.

Nature. 2012 Mar 25;484(7394):386-9. doi: 10.1038/nature10925.

PMID:
22446626
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.

Remmert M, Biegert A, Hauser A, Söding J.

Nat Methods. 2011 Dec 25;9(2):173-5. doi: 10.1038/nmeth.1818.

PMID:
22198341
[PubMed - indexed for MEDLINE]
12.

A conserved GA element in TATA-less RNA polymerase II promoters.

Seizl M, Hartmann H, Hoeg F, Kurth F, Martin DE, Söding J, Cramer P.

PLoS One. 2011;6(11):e27595. doi: 10.1371/journal.pone.0027595. Epub 2011 Nov 16.

PMID:
22110682
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset.

Feller C, Prestel M, Hartmann H, Straub T, Söding J, Becker PB.

Nucleic Acids Res. 2012 Feb;40(4):1509-22. doi: 10.1093/nar/gkr869. Epub 2011 Oct 27.

PMID:
22039099
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.

Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75.

PMID:
21988835
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Protein sequence comparison and fold recognition: progress and good-practice benchmarking.

Söding J, Remmert M.

Curr Opin Struct Biol. 2011 Jun;21(3):404-11. doi: 10.1016/j.sbi.2011.03.005. Epub 2011 Mar 31. Review.

PMID:
21458982
[PubMed - indexed for MEDLINE]
16.

The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair.

Lammens K, Bemeleit DJ, Möckel C, Clausing E, Schele A, Hartung S, Schiller CB, Lucas M, Angermüller C, Söding J, Strässer K, Hopfner KP.

Cell. 2011 Apr 1;145(1):54-66. doi: 10.1016/j.cell.2011.02.038.

PMID:
21458667
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1.

Frauer C, Rottach A, Meilinger D, Bultmann S, Fellinger K, Hasenöder S, Wang M, Qin W, Söding J, Spada F, Leonhardt H.

PLoS One. 2011 Feb 2;6(2):e16627. doi: 10.1371/journal.pone.0016627.

PMID:
21311766
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.

Armache JP, Jarasch A, Anger AM, Villa E, Becker T, Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix B, Söding J, Westhof E, Wilson DN, Beckmann R.

Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19748-53. doi: 10.1073/pnas.1009999107. Epub 2010 Oct 27.

PMID:
20980660
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Of bits and bugs--on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure.

Graebsch A, Roche S, Kostrewa D, Söding J, Niessing D.

PLoS One. 2010 Oct 14;5(10):e13402. doi: 10.1371/journal.pone.0013402.

PMID:
20976240
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.

Armache JP, Jarasch A, Anger AM, Villa E, Becker T, Bhushan S, Jossinet F, Habeck M, Dindar G, Franckenberg S, Marquez V, Mielke T, Thomm M, Berninghausen O, Beatrix B, Söding J, Westhof E, Wilson DN, Beckmann R.

Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19754-9. doi: 10.1073/pnas.1010005107. Epub 2010 Oct 25.

PMID:
20974910
[PubMed - indexed for MEDLINE]
Free PMC Article

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