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HH-suite3 for fast remote homology detection and deep protein annotation.

Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J.

BMC Bioinformatics. 2019 Sep 14;20(1):473. doi: 10.1186/s12859-019-3019-7.


Lysine/RNA-interactions drive and regulate biomolecular condensation.

Ukmar-Godec T, Hutten S, Grieshop MP, Rezaei-Ghaleh N, Cima-Omori MS, Biernat J, Mandelkow E, Söding J, Dormann D, Zweckstetter M.

Nat Commun. 2019 Jul 2;10(1):2909. doi: 10.1038/s41467-019-10792-y.


Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold.

Steinegger M, Mirdita M, Söding J.

Nat Methods. 2019 Jul;16(7):603-606. doi: 10.1038/s41592-019-0437-4. Epub 2019 Jun 24.


PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes.

Papadopoulos N, Gonzalo PR, Söding J.

Bioinformatics. 2019 Sep 15;35(18):3517-3519. doi: 10.1093/bioinformatics/btz078.


MMseqs2 desktop and local web server app for fast, interactive sequence searches.

Mirdita M, Steinegger M, Söding J.

Bioinformatics. 2019 Aug 15;35(16):2856-2858. doi: 10.1093/bioinformatics/bty1057.


Bayesian multiple logistic regression for case-control GWAS.

Banerjee S, Zeng L, Schunkert H, Söding J.

PLoS Genet. 2018 Dec 31;14(12):e1007856. doi: 10.1371/journal.pgen.1007856. eCollection 2018 Dec.


Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction.

Vorberg S, Seemayer S, Söding J.

PLoS Comput Biol. 2018 Nov 5;14(11):e1006526. doi: 10.1371/journal.pcbi.1006526. eCollection 2018 Nov.


An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium, Crivelli SN.

Sci Rep. 2018 Jul 2;8(1):9939. doi: 10.1038/s41598-018-26812-8.


Clustering huge protein sequence sets in linear time.

Steinegger M, Söding J.

Nat Commun. 2018 Jun 29;9(1):2542. doi: 10.1038/s41467-018-04964-5.


The BaMM web server for de-novo motif discovery and regulatory sequence analysis.

Kiesel A, Roth C, Ge W, Wess M, Meier M, Söding J.

Nucleic Acids Res. 2018 Jul 2;46(W1):W215-W220. doi: 10.1093/nar/gky431.


A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.

Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V.

J Mol Biol. 2018 Jul 20;430(15):2237-2243. doi: 10.1016/j.jmb.2017.12.007. Epub 2017 Dec 16.


MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.

Steinegger M, Söding J.

Nat Biotechnol. 2017 Nov;35(11):1026-1028. doi: 10.1038/nbt.3988. Epub 2017 Oct 16. No abstract available.


WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs.

Galiez C, Siebert M, Enault F, Vincent J, Söding J.

Bioinformatics. 2017 Oct 1;33(19):3113-3114. doi: 10.1093/bioinformatics/btx383.


Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes.

Baejen C, Andreani J, Torkler P, Battaglia S, Schwalb B, Lidschreiber M, Maier KC, Boltendahl A, Rus P, Esslinger S, Söding J, Cramer P.

Mol Cell. 2017 Apr 6;66(1):38-49.e6. doi: 10.1016/j.molcel.2017.02.009. Epub 2017 Mar 16.


Big-data approaches to protein structure prediction.

Söding J.

Science. 2017 Jan 20;355(6322):248-249. doi: 10.1126/science.aal4512. No abstract available.


Uniclust databases of clustered and deeply annotated protein sequences and alignments.

Mirdita M, von den Driesch L, Galiez C, Martin MJ, Söding J, Steinegger M.

Nucleic Acids Res. 2017 Jan 4;45(D1):D170-D176. doi: 10.1093/nar/gkw1081. Epub 2016 Nov 28.


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.


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.


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.


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.


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.


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.


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/ Epub 2011 Mar 31. Review.


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.


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.


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.


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.


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.


Uniform transitions of the general RNA polymerase II transcription complex.

Mayer A, Lidschreiber M, Siebert M, Leike K, Söding J, Cramer P.

Nat Struct Mol Biol. 2010 Oct;17(10):1272-8. doi: 10.1038/nsmb.1903. Epub 2010 Sep 5.


The molecular cell death machinery in the simple cnidarian Hydra includes an expanded caspase family and pro- and anti-apoptotic Bcl-2 proteins.

Lasi M, Pauly B, Schmidt N, Cikala M, Stiening B, Käsbauer T, Zenner G, Popp T, Wagner A, Knapp RT, Huber AH, Grunert M, Söding J, David CN, Böttger A.

Cell Res. 2010 Jul;20(7):812-25. doi: 10.1038/cr.2010.66. Epub 2010 May 18.


Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin.

Remmert M, Biegert A, Linke D, Lupas AN, Söding J.

Mol Biol Evol. 2010 Jun;27(6):1348-58. doi: 10.1093/molbev/msq017. Epub 2010 Jan 27.


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