Publications

  • Meier A. and Söding J.
    Context similarity scoring improves protein sequence alignment in the midnight zone.
    Bioinformatics, doi: 10.1093/bioinformatics/btu697 (2014).

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  • Siebert M., and Söding, J.
    Universality of core promoter motifs?
    Nature
    (Brief Commun. Arising) 511:E11-E12 (2014).

    See also Venters B. and Pugh F., Nature, doi:10.1038/nature13588 (2014).

  • Seemayer S.#, Gruber M.#, and Söding J.
    CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations.
    Bioinformatics, in press. (# Equal contributions.)

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  • Baejen C.#, Torkler P.#, Gressel S., Essig K., Söding J*, and Cramer P*.
    Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition.
    Mol. Cell. 155:1075-1087 (2014). #Equal contributions; *Corresponding authors.

  • Wickles S., Singharoy A., Andreani J., Seemayer S., Bischoff L., Berninghausen O., Söding, J., Schulten K., van der Sluis E., and Beckmann R.
    A structural model of the active ribosome-bound membrane protein insertase YidC.
    eLife 10.7554/eLife.03035 (2014).

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  • Söding J.
    In silico-Funktions- und Strukturvorhersagen bei Proteinen.
    BIOspektrum 02:158-160 (2014). (Invited, not peer reviewed, in German).

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  • Runge S.#, Sparrer K. M. J.#, Lässig C.#, Hembach K, Baum A., Garcia-Sastre A., Söding J., Conzelmann K.-K., Hopfner K.-P.
    In vivo ligands of MDA5 and RIG-I in measles virus-infected cells.
    PLoS Pathogens, in press (2014). (# Equal contributions.)

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  • Saponaro M.#, Mitter R.#, Kantidakis T.#, Kelly G. P.*, Heron M., Williams H., Söoding J., Stewart A. and Svejstrup J. Q.
    RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress.
    Cell 157:1037–104 (2014).  (#Equal contributions.)

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  • Tischer S., Reineck M., Söding J., Münder S., and Böttger A.
    Eph receptors and ephrin class B ligands are expressed at tissue boundaries in Hydra vulgaris.
    Int. J. Dev. Biol.
    , 57:759-765 (2014).

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  • Meinel D., Burkert-Kautzsch C., Kieser A., O’Duibhir E., Siebert M., Mayer A., Cramer P., Söding J., Holstege F.C., Sträßer K.
    Recruitment of TREX to the Transcription Machinery by its Direct Binding to the Phospho-CTD of RNA Polymerase II.
    PLoS Genet.
    , 9:e1003914 (2014).

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  • Schulz D.#, Schwalb B.#, Kiesel A., Baejen C., Torkler P., Gagneur J., Söding J.* and Cramer P.* (2013)
    Transcriptome surveillance by selective termination of non-coding RNA synthesis.
    Cell, 155:1075-1087 (2013).  
    (#Equal contributions. *Corresponding authors.)

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  • Hauser M.#, Mayer C.E.#, and Söding J.
    kClust: fast and sensitive clustering of large protein sequence databases
    BMC Bioinformatics 14:248 (2013). (#Equal contribution)

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  • Hartmann, H., Guthöhrlein, E. W., Siebert, M., Luehr, S., and Söding, J.
    P-value based regulatory motif discovery using positional weight matrices.
    Genome Res.
    , 23:181-194 (2012).
    [Author manuscript incl. Suppl. Mat. (11MB)]

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  • Angermüller C., Biegert A., and Söding J.
    Discriminative modeling of context-specific amino acid substitution probabilities.
    Bioinformatics
    28: 3240-3247 (2012)
    .

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  • Luehr S., Hartmann H., and Söding J.
    The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences
    Nucleic Acids Res.
    40: W104-W109 (2012)
    .

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  • Close P., East P., Dirac-Svejstrup A. B., Hartmann H., Heron M., Maslen S., Chariot A., Söding J., Skehel M., and Svejstrup J. Q.
    DBIRD integrates alternative mRNA splicing with RNA polymerase II transcript elongation.
    Nature
    484:386–389 (2012).

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  • Remmert M., Biegert A., Hauser A., and Söding J.
    HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.
    Nat Methods
    9:173-175 (2011)
    .

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  • Seizl M., Hartmann H., Hoeg F., Kurth F., Martin D. E., Söding J., and Cramer P.
    A functional GA element in TATA-less RNA polymerase II promoters.
    PLoS ONE
    6: e27595 (2011).

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  • Feller C., Prestel M., Hartmann H., Straub T., Söding J., and Becker P.
    The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset.
    Nucleic Acids Res. 40:1509-1522 (2011).

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  • Sievers F., Wilm A., Dineen D., Gibson T., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Söding J., Thompson J, and Higgins D.
    Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega.
    Mol Syst Biol.
    7:539 (2011)
    .

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  • Söding J. and Remmert M.  
    Protein sequence comparison and fold recognition: progress and good-practice benchmarking.
    Curr Opin Struct Biol 21:404-411 (2011).

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  • Lammens K., Bemeleit D. J., Möckel C., Clausing E., Schele A., Hartung S., Schiller C. B., Lucas M., Angermüller C., Söding J., Sträßer, and Hopfner K.-P.   
    X-ray structure of a bacterial Mre11:Rad50 complex reveals an ATP dependent molecular clamp in DNA double-strand break repair.
    Cell 145:54-66 (2011).

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  • Frauer C., Rottach A., Meilinger D., Bultmann S., Fellinger K., Hasenoeder S., Söding J., Spada F., Leonhardt H.
    Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1.
    PLoS ONE 6: e16627 (2011).

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  • Armache J. P., Jarasch A., Anger A. M., 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 D. N., Beckmann R.
    Localization of eukaryote-specific ribosomal proteins in a 5.5Å cryo-EM map of the 80S eukaryotic ribosome.
    Proc Natl Acad Sci USA. 107:19754-19759 (2010).

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  • Armache J. P., Jarasch A., Anger A. M., 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 D. N., Beckmann R.
    Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
    Proc Natl Acad Sci USA. 107:19748-19753 (2010).

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  • Graebsch A., Roche S., Kostrewa D., Söding J., and Niessing D.  
    Of Bits and Bugs - on the Use of Bioinformatics and a Bacterial Crystal Structure to Solve a Eukaryotic Repeat-protein Structure.
    PLoS ONE 5:e13402 (2010).

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  • Mayer A*., Lidschreiber M*., Siebert M*., Leike K., Söding J., and Cramer P.
    Uniform transitions of the general RNA polymerase II transcription complex.
    Nat Struct Mol Biol. 17:1272-1278 (2010).  (*) Shared first authors.

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  • Lasi M., Pauly B., Schmidt N., Cikala M., Stiening B., Käsbauer T., Zenner G., Popp T., Wagner A., Knapp R., Hubert A.H., Grunert M., Söding J., David CN., and Böttger A.,
    The molecular cell death machinery in the simple cnidarian hydra includes an extended caspase family, APAF-1 and pro- and antiapoptotic Bcl-2 proteins.
    Cell Res. 20:812-825. (2010).

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  • Remmert M., Biegert A., Linke D., Lupas A. N., and Söding J.
    Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin.
    Mol Biol Evol. 27:1348-1358 (2010).

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  • Siebert M., Lidschreiber M., Hartmann H., and Söding J.
    A Guideline for ChIP - Chip Data Quality Control and Normalization.
    Epigenome Network of Excellence, protocol 47 (2010). (Invited, not peer reviewed).

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  • Alva V., Remmert M., Biegert A., Lupas A. N., and Söding J.
    A galaxy of folds.
    Protein Sci. 19:124-130 (2010).

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  • Biegert A. and Söding J.(invited)
    A boost for sequence searching.
    G.I.T. Laboratory Journal 9-10:22-23 (2009).
    BIOforum Europe. 10:26-27 (2009).

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  • Hildebrand A., Remmert M., Biegert A., and Söding J.
    Fast and accurate automatic structure prediction with HHpred.
    Proteins. 77 Suppl 9:128-132 (2009).

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  • Remmert M., Linke D., Lupas A. N. and Söding J.
    HHomp - Prediction and classification of outer membrane proteins.
    Nucleic Acids Res. 37:W446-451 (2009).

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  • Biegert A. and Söding J.
    Sequence context-specific profiles for homology searching.
    Proc Natl Acad Sci USA 106:3770-3775 (2009).
    PNAS Editor's Selection 106:3641-3642 (2009).

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  • Bateman A., Finn R. D., Sims P. J., Wiedmer T., Biegert A., and Söding J.
    Phospholipid scramblases and Tubby like proteins belong to a new superfamily of membrane tethered transcription factors.
    Bioinformatics 25:159-162 (2009).

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  • Agarwal V., Remmert M., Biegert A., and Söding J.
    PDBalert: automatic, recurrent remote homology tracking and protein structure prediction.
    BMC Struc. Biol. 8:51 (2008).

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  • Jasiak A. J., Hartmann H., Karakasili E., Marian K., Flatley A., Kremmer E., Sträßer K., Martin D. E., Söding J., and Cramer P.
    Genome-associated RNA polymerase II includes the dissociable RPB4/7 subcomplex.
    J Biol Chem. 283:26423-26427 (2008).

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  • Biegert A. and Söding J.
    De novo identification of highly diverged protein repeats by probabilistic consistency.
    Bioinformatics 24:807-814 (2008).

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  • Fischer J., Mayer C. E., and Söding J.
    Prediction of protein functional residues from sequence by probability density estimation.
    Bioinformatics 24:613-620 (2008).

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  • Chaudhuri I., Söding J., and Lupas A. N.
    Evolution of the beta-propeller fold.
    Proteins 71:795-803 (2008).

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  • Hsiao, N. H., Söding J., Linke, D., Lange, C., Hertweck, C., Wohlleben, W., and Takano, E. ScbA from Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize gamma-butyrolactones.
    Microbiology 153:1394-1404 (2007).

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  • Alva V., Ammelburg M., Söding J., and Lupas A. N.
    On the origin of the histone fold.
    BMC Struct Biol. 7:17 (2007).

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  • Karpenahalli M. R., Lupas A. N., and Söding J.
    TPRpred: a tool for prediction of TPR-, PPR and SEL1-like repeats from protein sequences.
    BMC Bioinformatics 8:2 (2007).

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  • Gruber M., Söding J., and Lupas A. N.
    Comparative analysis of coiled-coil prediction methods.
    J Struct Biol. 155:140-145 (2006).

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  • Söding J., Remmert M., and Biegert A.
    HHrep: de novo protein repeat detection and the origin of TIM barrels.
    Nucleic Acids Res. 34:W137-142 (2006).

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  • Söding J., Remmert M., Biegert A., Lupas A. N.
    HHsenser: exhaustive transitive profile search using HMM-HMM comparison.
    Nucleic Acids Res. 34:W374-378 (2006).

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  • Biegert A., Mayer C., Remmert M., Söding J., Lupas A. N.
    The MPI Bioinformatics Toolkit for protein sequence analysis.
    Nucleic Acids Res. 34:W335-339 (2006).

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  • Albrecht R., Zeth K., Söding J., Lupas A. N., and Linke D.
    Expression, crystallization and preliminary X-ray crystallographic studies of the outer membrane protein OmpW from Escherichia coli.
    Acta Crystallogr Sect F Struct Biol Cryst Commun. 62:415-418 (2006).

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  • Söding J.
    Protein structure and function prediction by pairwise comparison of hidden Markov models.
    For: Heinz-Billing-Preis zur Foerderung des wissenschaftliches Rechnens (2006)
    (not peer-reviewed).

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  • Moussian B., Söding J., Schwarz H., and Nusslein-Volhard C.
    Retroactive, a membrane-anchored extracellular protein related to vertebrate snake neurotoxin-like proteins, is required for cuticle organization in the larva of Drosophila melanogaster.
    Dev Dyn. 233:1056-1063 (2005).

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  • Söding J., Biegert A., and Lupas A. N.
    The HHpred interactive server for protein homology detection and structure prediction.
    Nucleic Acids Res. 33:W244-248 (2005).

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  • Gruber M., Söding J., and Lupas A. N.
    REPPER--repeats and their periodicities in fibrous proteins.
    Nucleic Acids Res. 33:W239-243 (2005).

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  • Coles M., Djuranovic S., Söding J., Frickey T., Koretke K., Truffault V., Martin J., and Lupas A. N.
    AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels.
    Structure 13:919-928 (2005).

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  • Söding J.
    Protein homology detection by HMM-HMM comparison.
    Bioinformatics 21:951-960 (2005).

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  • Söding J. and Lupas A. N.
    More than the sum of their parts: on the evolution of proteins from peptides.
    Bioessays 25:837-846 (2003). Review.

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  • Söding, J., Guery-Odelin, D., Desbiolles, P., Chevy, F., Inamori, H., and Dalibard, J.  
    Three body decay of a rubidium Bose-Einstein condensate.
    Appl. Phys. B 69: 257-261 (1999).

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  • Guery-Odelin, D., Söding, J., Desbiolles, P., and Dalibard, J.   
    Is Bose-Einstein condensation of atomic cesium possible?
    Europhys. Lett. 44:25-30 (1998).

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  • Guery-Odelin, D., Söding, J., Desbiolles, P., and Dalibard, J.   
    Strong evaporative cooling of a trapped cesium gas.
    Optics Express 2:323-329 (1998).

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  • Söding, J., Guery-Odelin, D., Desbiolles, P., Ferrari, G., and Dalibard, J.    
    Giant spin relaxation of an ultracold cesium gas.
    Phys Rev Lett. 80:1869-1872 (1998).

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  • Söding, J., Grimm, R., Ovchinnikov, Y. B., Bouyer, P., and Salomon, C.    
    Short-distance atomic beam deceleration with a stimulated light force.
    Phys Rev Lett. 78:1420-1423 (1997).

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  • Söding, J.
    Atomstrahlabbremsung auf kuerzester Distanz mit der stimulierten bichromatischen Lichtkraft, Dissertation.
    Max-Planck-Institute for Nuclear Physics Report No. MPIH-V22-1996 (1996).

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  • Grimm, R., Wasik, G., Söding, J., Ovchinnikov, Y.B.    
    Laser cooling and trapping with rectified optical dipole forces. .
    in Coherent and Collective Interactions of Particle Beams, Proceedings of the International School of Physics "Enrico Fermi", Course CXXXI, A. Aspect, W. Barletta, and R. Bonifacio, eds., 131:481-502 (1996).

  • Söding, J., Grimm, R., and Ovchinnikov, Y. B.    
    Gravitational laser trap for atoms with evanescentwave cooling.
    Optics Commun. 119:652-662 (1995).

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  • Grimm, R., Söding, J., and Ovchinnikov, Y. B. (1995)    
    Trapping atoms by rectified forces in bichromatic optical superlattices.
    JETP Lett. 61:367-372.

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  • Ovchinnikov, Y. B., Söding, J., and Grimm, R.    
    Cooling atoms in dark gravitational laser traps.
    JETP Lett. 61:21-26 (1995).

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  • Ovchinnikov, Y. B., Söding, J., and Grimm, R.   
    A magnetooptical biprism for an atomic interferometer.
    Laser Physics 4:1011-1016 (1994).

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  • Söding, J. and Grimm, R.    
    Stimulated magneto-optical force in the dressed-atom picture.
    Phys Rev A 50:2517-2527 (1994).

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  • Grimm, R., Söding, J., and Ovchinnikov, Y. B.    
    Coherent beam splitter for atoms based on a bichromatic standing light-wave.
    Optics Lett. 19:658-660 (1994).

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  • Ovchinnikov, Y. B., Grimm, R., and Söding, J.    
    Magnetooptic biprism for atomic interferometry.
    JETP Lett. 58:328-332 (1993).

  • Grimm, R., Söding, J., Ovchinnikov, Y. B., and Sidorov, A. I.    
    Sub-doppler manifestation of the magnetooptical radiation force.
    Optics Commun. 98:54-60 (1993).

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  • Söding, J., Grimm, R., Kowalski, J., Ovchinnikov, Y. B., and Sidorov, A. I.
    Observation of the magnetooptical radiation force by laser spectroscopy.
    Europhys Lett. 20:101-106 (1992).

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