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Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences.

Siebert M, Söding J.

Nucleic Acids Res. 2016 Jul 27;44(13):6055-69. doi: 10.1093/nar/gkw521. Epub 2016 Jun 9.


The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.

Alva V, Nam SZ, Söding J, Lupas AN.

Nucleic Acids Res. 2016 Jul 8;44(W1):W410-5. doi: 10.1093/nar/gkw348. Epub 2016 Apr 29.


Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails.

Stützer A, Liokatis S, Kiesel A, Schwarzer D, Sprangers R, Söding J, Selenko P, Fischle W.

Mol Cell. 2016 Jan 21;61(2):247-59. doi: 10.1016/j.molcel.2015.12.015. Epub 2016 Jan 14.


MMseqs software suite for fast and deep clustering and searching of large protein sequence sets.

Hauser M, Steinegger M, Söding J.

Bioinformatics. 2016 May 1;32(9):1323-30. doi: 10.1093/bioinformatics/btw006. Epub 2016 Jan 6.


A vocabulary of ancient peptides at the origin of folded proteins.

Alva V, Söding J, Lupas AN.

Elife. 2015 Dec 14;4:e09410. doi: 10.7554/eLife.09410.


Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.

Meier A, Söding J.

PLoS Comput Biol. 2015 Oct 23;11(10):e1004343. doi: 10.1371/journal.pcbi.1004343. eCollection 2015 Oct.


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

Andreani J, Söding J.

Bioinformatics. 2015 Jun 1;31(11):1729-37. doi: 10.1093/bioinformatics/btv041. Epub 2015 Jan 23.


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.


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.


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.


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.


Universality of core promoter elements?

Siebert M, Söding J.

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


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.


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.


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.


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.


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.


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.


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.


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.

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