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Results: 1 to 20 of 54

1.

bbcontacts: prediction of β-strand pairing from direct coupling patterns.

Andreani J, Söding J.

Bioinformatics. 2015 Jan 23. pii: btv041. [Epub ahead of print]

PMID:
25618863
2.

Implementation of renal key performance indicators: promoting improved clinical practice.

Toussaint ND, McMahon LP, Dowling G, Soding J, Safe M, Knight R, Fair K, Linehan L, Walker RG, Power DA.

Nephrology (Carlton). 2015 Mar;20(3):184-93. doi: 10.1111/nep.12366.

PMID:
25400123
3.

Context similarity scoring improves protein sequence alignments in the midnight zone.

Meier A, Söding J.

Bioinformatics. 2015 Mar 1;31(5):674-81. doi: 10.1093/bioinformatics/btu697. Epub 2014 Oct 22.

PMID:
25338715
4.

Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition.

Baejen C, Torkler P, Gressel S, Essig K, Söding J, Cramer P.

Mol Cell. 2014 Sep 4;55(5):745-57. doi: 10.1016/j.molcel.2014.08.005.

PMID:
25192364
5.

CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations.

Seemayer S, Gruber M, Söding J.

Bioinformatics. 2014 Nov 1;30(21):3128-30. doi: 10.1093/bioinformatics/btu500. Epub 2014 Jul 26.

6.

Universality of core promoter elements?

Siebert M, Söding J.

Nature. 2014 Jul 24;511(7510):E11-2. doi: 10.1038/nature13587. No abstract available.

PMID:
25056067
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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
17.

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.

18.

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.

19.

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.

20.

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
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