Structural Bioinformatics, Publications

Publications

EMBL Publications
bold denotes group members, (1) denotes co-first authorships, * denotes group members as corresponding author(s), + denotes former group members, italics (end) give principle collaborating groups
    2009
  1. S. Kuhner, V. Van Noort, M.J. Betts, A. Leo-Macias, C. Blachier-Batisse, M. Rode, T. Yamada, T. Maier, S. Bader, P. Beltran-Alvarez, W.H. Chen, D. Devos, D.C. Diez, M. Guell Cargol, T. Norambuena, I. Racke, A. Schmidt, E. Yus, R. Aebersold, R. Herrmann, B. Bottcher, A. Frangakis, R. B. Russell, L. Serrano, P. Bork, A.C. Gavin, Proteome organization in a streamlined bacterium, Science, 326, 1235-1240, 2009. Serrano (CRG), Gavin, Bork, Frangakis, Bottcher (EMBL) PubMed 19965468
  2. E. Yus, T. Maier, K. Michalodimitrakis, T. Yamada, M. Guell, J. Wodke, S. Martinez, B. Bourgeois, R. Raineri, R. Herrmann, O.V. Kalinina, S. Kuehner, M. Rode, V. van Noort, R. Gutierrez-Gallego, R.B. Russell, A.C. Gavin, P. Bork, L. Serrano, Integrative analysis of metabolism and its regulation in a small bacterium, Science, 26, 1263-1268. 2009. Serrano (CRG), Bork, Gavin (EMBL) PubMed 19965476
  3. M.J. Betts, R.B. Russell*, A more structured metabolome, Nature Struct. Mol. Biol., 16,1125-1126, 2009. (News & Views) PubMed 19888310
  4. F. Kutlar, L.M. Hilliard, L. Zhuang, N. Patel, B. Eroglu, S.E. Meiler, H. Carmichael, R.B. Russell, A. Kutlar, Hb M Dothan [beta 25/26 (B7/B8)/(GGT/GAG-->GAG//Gly/Glu-->Glu]; a new mechanism of unstable methemoglobin variant and molecular characteristics. Blood Cells Mol Dis., 3, 235-238, 2009 Kutlar, Medical College of Georgia PubMed 19758826
  5. O.V. Kalinina*, M. Gelfand, R.B.Russell, Specificity determining residues improve protein functional site predictions, BMC Bioinformatics, 10, 174, 2009. Gelfand, Moscow PubMed 19508719
  6. E. Petsalaki, A. Stark+, E. Uridales, R.B. Russell*, Accurate prediction of peptide binding sites on protein surfaces, PLoS Comput. Biol., 5, e1000335 2009. PubMed 19325869

    7. 2008
  7. R.B. Russell*, P. Aloy+, Targeting and tinkering with interaction networks, Nature Chem. Biol., 4,666-673, 2008. PubMed 18936751 Aloy, IRB Barcelona
  8. S.A. Solheim, E. Petsalaki E, A.J. Stokka, R.B. Russell, K. Taskén, T. Berge, Interactions between the Fyn SH3-domain and adaptor protein Cbp/PAG derived ligands, effects on kinase activity and affinity. FEBS J. 275, 4863-4874. PMID: 18721137 PubMed 18721137 Berge, University of Oslo
  9. E. Petsalaki, R.B. Russell, Peptide-mediated interactions in biological systems: new discoveries and applications, Curr. Opin. Biotech., 19, 344-350, 2008. PubMed 18602004
  10. T. Taverner, H. Hernandez, M. Sharon, B.T. Rutolo, D. Matak-Vinkovic, D. Devos, R.B. Russell, C.V. Robinson. Subunite architecture of intact protein complexes from mass spectrometry and homology modeling. Acc. Chem. Res., 41, 617-627, 2008. PubMed 18314965 Robinson, University of Cambridge
  11. R.B. Russell & T.J. Gibson, A careful disorderliness in the proteome: sites for interaction and targets for future therapies, FEBS Lett., 582, 1271-1275, 2008. PubMed 18284921 Gibson, EMBL-HD
  12. S. Guenther, M. Kuhn, M. Dunkel, M. Campillos, C. Senger, E. Petsalaki, J. Ahmed, E.G. Urdiales, A. Gewiess, L.J. Jensen, R. Schneider, R. Skoblo, R. B. Russell, P.E. Bourne, P. Bork, R. Preissner. SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res., 36 (Database issue), D919-D922. PubMed 17942422 Bork, Schneider EMBL-HD; Preissner, Charite, Berlin; Bourne, UCSD

    13. 2007
  13. A. Al-Amoudi, D.C. Díez, M.J. Betts, A.S. Frangakis AS. The molecular architecture of cadherins in native epidermal desmosomes. Nature, 450, 832-837. PubMed 18064004 Frangakis, EMBL-HD
  14. D. Devos, R.B. Russell* A more complete, complexed & structured interactome, Curr. Opin. Struct. Biol. 17, 370-377, 2007. PubMed 17574831
  15. R. Linding+, L.J. Jensen, G.J. Ostheimer, M.A.T.M. van Vugt, C. Jorgensen, I.M. Miron, F. Diella, K. Colwill, L. Taylor, K. Elder, P. Metalinikov, V. Nguyen, A. Pasculescu, J. Jin, J.G. Park, L.D. Samson, J.R. Woodgett, R.B. Russell, P. Bork, M.B. Yaffe, T. Pawson, Systematic Discovery of In Vivo Phosphorylation Networks, Cell, 129, 1415-1426, 2007.Bork, EMBL-HD; Yaffe, MIT; Pawson, Toronto PubMed 17570479
  16. M.J. Betts, R.B. Russell* The hard cell: from proteomics to a whole cell model, FEBS Lett., 129, 1415-1426, 2007. PubMed 17555749
  17. J. Moelleken, J. Malsam, M.J. Betts, A. Movafeghi, I. Reckmann, I. Meissner, A. Hellwig, R.B. Russell, T. Sollner, B. Brugger, F. Wieland, Differential localization of isoformic coatomer complexes within the Golgi Apparatus, Proc. Natl. Acad. Sci. USA, 104, 4425-4430, 2007. PubMed 17360540 Wieland, University of Heidelberg
  18. G. Apic, R.B. Russell*, A shortcut to peptides to modulate platelets Nature Chem. Biol., 3, 83-84, 2007. PubMed 17235341 (News & Views)
  19. V. Neduva, R.B. Russell*, Proline-rich regions in transcriptional complexes: heading in many directions, Science STKE, 369 2007. PubMed 17228057

    20. 2006
  20. D. Devos, O.V. Kalinina, R.B. Russell*, Harry Potter and the Structural Biologist's (Key)stone Genome Biol., 7,333, 2006. PubMed 17201936
  21. V. Neduva, R.B. Russell*, Peptides mediating interaction networks: new leads at last Curr. Opin. Biotech., 17,465-471, 2006. PubMed 16962311
  22. V. Neduva, R.B. Russell*, DILIMOT: Discovery of Linear Motifs in Proteins Nucleic Acids Res., 34, W350-355, 2006. PubMed 16845024
  23. P. Aloy, R.B. Russell*, Structural Systems Biology: modelling protein-protein interactions, Nature Rev. Mol. Cell. Biol., 7, 188-197, 2006. PubMed 16496021
  24. A.C. Gavin(1), P. Aloy(1), P. Grandi, R. Krause, M. Boesche, M. Marzioch, C. Rau, L. Juhl-Jensen, S. Bastuck, B. Dumpelfeld, A. Edelmann, M. Heurtier, V. Hoffman, C. Hoefert, K. Klein, M. Hudak, A. Michon, M. Schelder, M. Remor, T. Rudi, S. Hooper, A. Bauer, T. Bouwmeester, G. Casari, G. Drewes, B. Kuster, G. Neubauer, J. Rick, P. Bork, R.B. Russell*, G. Superti-Furga, Proteome survey reveals modularity of the yeast cell machinery Nature, 440, 631-636, 2006. PubMed 16429126 Cellzome AG & Bork, EMBL-HD


    25. 2005
  25. A. Stark(1), J. Brennecke(1), N. Bushati, R.B. Russell, S.M. Cohen, Animal miRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution, Cell, 123, 1133-1146, 2005. PubMed 16337999 Cohen EMBL-HD
  26. V. Neduva, R. Linding, I. Su-Angrand, A. Stark, F. de Massi, T.J. Gibson, J. Lewis, L. Serrano, R.B. Russell*, Systematic discovery of peptides mediating protein interaction networks PLoS Biology, 3, e405, 2005. PubMed 16279839 Gibson, Lewis, Serrano, EMBL-HD
  27. J. Brennecke, A. Stark, S. Cohen, Not miR-ly muscular: microRNAs and muscle development, Genes Dev, 19, 2261-2264, 2005. PubMed 16204177 Cohen, EMBL-HD
  28. V. Neduva, R.B. Russell*, Linear motifs: evolutionary interaction switches, FEBS Lett., 579, 3342-3345, 2005 PubMed 15943979 (FEBS Budapest Conference Issue).
  29. P. Shah, P. Aloy, P. Bork, R.B. Russell*, Structure similarity to bridge sequence space: new families on the bridges, Protein Sci, 14, 1305-1314, 2005. PubMed 15840833. Bork, EMBL-HD
  30. P. Aloy*, R.B. Russell Structure-based systems biology: A zoom lens for the cell, FEBS Lett., 579, 1854-1858, 2005. PubMed 15763563 (FEBS Systems Biology Issue).
  31. G. Apic, T. Ignjatovic, S. Boyer, R.B. Russell Illuminating drug discovery with biological pathways FEBS Lett., 579, 1872-1877, 2005. PubMed 15763566 (FEBS Systems Biology Issue). Cambridge Cell Networks Ltd & AstraZeneca Plc
  32. J. Brennecke(1), A. Stark(1), R.B. Russell, S.M. Cohen, Principles of microRNA/target recognition PLoS Biology, 3, e85, 2005. PubMed 15723116. Cohen, EMBL-HD
  33. P. Aloy, M. Pichaud, R.B. Russell*, Protein Complexes: Structure Predictions for the 21st Century, Curr. Opin. Struct. Biol. 15, 15-22, 2005. PubMed 15718128
  34. A. Stein, R.B. Russell, P. Aloy*, 3did: interacting domains of known three-dimensional structure. Nucleic Acids Res. 33, D413-417, 2005. PubMed 15608228


    35. 2004
  35. M. Hothorn, S. Wolf, P. Aloy, S. Greiner, K. Scheffzek. Structural insights into the target-specificity of plant invertase and pectin methylesterase inhibitory proteins. Plant Cell. 16, 3437-3447, 2004. PubMed 15528298Scheffzek, EMBL-HD
  36. P. Aloy, R.B. Russell*, Ten thousand interactions for the molecular biologist, Nature Biotech. 22, 1317-1321, 2004. PubMed 15470473
  37. A. Stark, A. Shkumatov, R.B. Russell* Finding functional sites in structural genomics proteins, Structure, 12, 1405-1412 , 2004. PubMed 15296734
  38. B. Bottcher, S. Unseld, H. Ceulemans, R.B. Russell, H. Jeske, Geminate structures of African cassava mosaic virus. J. Virol., 78, 6758-6765, 2004. PubMed 15194750 Bottcher, EMBL-HD
  39. R.B. Russell, F. Alber, P. Aloy, F. P. Davis, D. Korkin, M. Pichaud, M. Topf, A. Sali, A structural perspective on protein-protein interactions and complexes. Curr. Opin. Struct. Biol., 14, 313-324, 2004. PubMed 15193311 Sali, UCSF
  40. R.R. Copley, P. Aloy, R.B. Russell, M.J. Telford, Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for idiosyncratic nematode, Evol. Dev., 6,164-169, 2004. PubMed 15099303 Telford, Cambs & Copley, Oxford
  41. H. Ceulemans, R.B. Russell* Fast fitting of atomic structures to low resolution electron density maps by surface overlap maximisation. J. Mol. Biol., 338, 783-793, 2004. PubMed 15099745
  42. P. Aloy*, R.B. Russell, Taking the mystery out of biological networks. EMBO Reports, 5, 349-350, 2004. PubMed 15060570
  43. P. Aloy, B.Bottcher, H. Ceulemans, C. Leutwein, C. Mellwig, S. Fischer, A.C. Gavin, P. Bork, G. Superti-Furga, L. Serrano, R.B. Russell*, Structure-based assembly of protein complexes in yeast, Science, 303, 2026-2029, 2004. PubMed 15044803 Boettcher, Bork, Serrano, EMBL-HD & Cellzome AG
  44. P. Aloy. Secondary structure prediction, protein interactions & complexes, In Dictionary of bioinformatics and computational biology, J. Hancock & M. Zvelebil, ed. John Wiley & Sons, 2004


    45. 2003
  45. A. Stark (1), J. Brennecke(1), R.B. Russell, S.M. Cohen, Identification of Drosophila MicroRNA Targets, PLoS Biology, 1, 397-409, 2003. PubMed 14691535 Cohen, EMBL-HD
  46. R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson, R.B. Russell, Prediction of protein disorder: implications for structural proteomics, Structure, 11, 1453-1459, 2003. PubMed 14604535 Gibson & Bork, EMBL-HD
  47. P. Aloy, A. Stark, C. Hadley, R.B. Russell*, Predictions without templates: New folds, secondary structure and contacts in CASP5. PROTEINS: Struct. Funct. Genet., 53, 436-456, 2003 (CASP5 special issue) PubMed 14579333 .
  48. E. Lorentzen, E. Pohl, P. Zwart, A. Stark, R.B. Russell, T. Knura, R. Hensel, B. Siebers Crystal structure of an archaeal class I aldolase and the evolution of (beta alpha)8 barrel proteins. J. Biol. Chem., 278, 47253-47260, 2003. PubMed 12941964 Pohl, EMBL-HH
  49. P. Aloy, H. Ceulemans, A. Stark, R.B. Russell*, The relationship between sequence and inteaction divergence in proteins. J. Mol. Biol., 332, 989-998, 2003. PubMed 14499603
  50. P. Aloy*, R.B. Russell, Understanding and predicting protein assemblies with 3D structures. Comp Funct Genom, 4, 410-415, 2003. (Review)
  51. A. Stark, R.B. Russell*, Annotation in three dimensions. PINTS: Patterns In Non-homologous Tertiary Structures Nucleic Acids Res , 31, 3341-3344, 2003. PubMed 12824322
  52. R. Linding, R.B. Russell, V. Neduva, T.J. Gibson. Globplot: Exploring protein sequences for globularity and disorder Nucleic Acids Res , 31, 3701-3708, 2003. PubMed 12824398 Gibson, EMBL-HD
  53. J. Brennecke, D.R. Hipfner, A. Stark, R.B. Russell, S.M. Cohen, Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the pro-apoptotic gene hid in Drosophila, Cell, 113, 25-36 , 2003. PubMed 12679032 Cohen, EMBL-HD
  54. A. Stark, S. Sunyaev, R.B. Russell*, A model for statistical significance of local similarities in structure, J. Mol. Biol, 326, 1307-1316, 2003. PubMed 12595245 Bork, EMBL-HD
  55. P. Aloy*, R.B. Russell, InterPreTS: Protein interaction prediction through tertiary structure. Bioinformatics, 19, 161-162, 2003. PubMed 12499311
  56. P. Aloy*, B. Oliva, R.B. Russell. Structural Genomics & Structural Bioinformatics, In Bioinformatics and Genomes: Current Prespectives, M. Andrade, ed. Horizon Scientific Press, 2003. Oliva, IMIM Barcelona
  57. R.R Copley, R.B. Russell* Getting the most from your protein sequence, In Protein Sequencing Protocols, B. Smith, ed. Humana Press, 2003 PubMed 12489448 Bork, EMBL-HD


    58. 2002
  58. P. Aloy, R.B. Russell*, The third dimension for protein interactions and complexes. Trends Biochem. Sci., 27, 633-638, 2002. PubMed 12468233 (Review)
  59. R. Metivier, A. Stark, G. Flouriot, M.R. Huebner, H. Brand, G. Penot, D. Manu, S. Denger, G. Reid, M. Kos, R.B. Russell, O. Kah, F. Pakdel, F. Gannon, A Dynamic Structural Model for Estrogen Receptor-alpha Activation by Ligands, Emphasizing the Role of Interactions between Distant A and E Domains. Molecular Cell, 10, 1019-1032, 2002. PubMed 12453411 Gannon, EMBL-HD
  60. R.B. Russell* Genomics, Proteomics & Bioinformatics: All in the same boat Genome Biol., 3, reports4034.1 - 4034.2, 2002. (Conference Report) PubMed 12374575
  61. P. Aloy, R.B. Russell*, Potential artefacts in protein-interaction networks FEBS Lett., 530 , 253-254, 2002 PubMed 12387902
  62. E. Torrents, P. Aloy, I. Gibert & F. Rodriguez-Trelles. Ribonucleotide reductases: divergent evolution of an ancient enzyme. J Mol Evol. 55,138-152, 2002 PubMed 12107591
  63. P. Aloy, F.D. Ciccarelli, C. Leutwein, A.C. Gavin, G. Superti-Furga, P. Bork, B. Boettcher, R.B. Russell* A complex prediction: three-dimensional model of the yeast exosome. EMBO reports, 3, 628-635, 2002 PubMed 12101094 Bork, Boettcher, EMBL-HD & Cellzome AG
  64. M.J. Betts, R.B. Russell*. Amino acid properties and consequences of subsitutionsIn Bioinformatics for Geneticists, M.R. Barnes, I.C. Gray eds, Wiley, 2003
  65. C. P. Ponting, R.B. Russell* The Natural History of Protein Domains Ann. Rev. Biophys. Biomol. Str.. 31, 45-71, 2002 PubMed 11988462 (Review) Ponting, Oxford
  66. P. Aloy, R.B. Russell* Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. USA, 99, 5896-5901, 2002.PubMed 11972061
  67. R.B. Russell*, J.A. Marquez, W. Hengstenberg, K. Scheffzek. Evolutionary relationship between the bacterial HPr kinase and the ubiquitous PEP-carboxykinase: expanding the P-loop nucelotidyl transferase superfamily FEBS Lett. 517, 1-6, 2002.PubMed 12062398 Scheffzek, EMBL-HD
  68. P. Aloy, B. Oliva, E. Querol, F.X. Aviles, R.B. Russell* Structural Similarity to Link Sequence Space: New Potential Superfamilies and Implications for Structural Genomics. Protein Sci. 11, 1101-1116, 2002. PubMed 11967367 Aviles & Querol, UAB, Barcelona
  69. J.A. Marquez, S. Hasenbein, B. Koch, S. Fieulaine, S. Nessler, R.B. Russell, W. Hengstenberg, K. Scheffzek. Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 angstroms resolution: Mimicking the product/substrate of the phospho transfer reactions. Proc. Nat. Acad. Sci. USA. 99, 3458-3463, 2002.PubMed 11904409 Scheffzek, EMBL-HD
  70. F.D. Ciccarelli, R.R. Copley, T.Doerks, R.B. Russell, P. Bork CASH - a beta-helix domain widespread among carboyhdrate-binding proteins Trends. Biochem. Sci.. 27, 59-62, 2002 PubMed 11852237 Bork, EMBL-HD


    71. 2001
  71. M. J. Betts, R. Guigo, P. Agarwal, R.B. Russell* Exon structure conservation in the absense of protein sequence similarity: a relic of dramatic events in evolution? EMBO J. 20, 5354-5360, 2001. PubMed 11574467 Agarwal, Glaxo SmithKline & Guigo, IMIM Barcelona
  72. A.N. Lupas, C.P. Ponting, R.B. Russell* On the Evolution of Protein Folds: Are similar motifs in different protein folds the result of convergence, insertion or relics of an ancient peptide world? J. Struct. Biol., 134,191-203, 2001. PubMed 11551179 Ponting, Oxford & Lupas, MPI Tuebingen

Other Publications (including pre-EMBL):