Staff at EMBL

Ivica Letunic

Web Coordinator
Bork Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Publications

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L.J., von Mering, C. & Bork, P. Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. Epub 2011 Nov 16. PubMed

InterPro in 2011: new developments in the family and domain prediction database. Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S., de Castro, E., Coggill, P., Corbett, M., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Fraser, M., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., McMenamin, C., Mi, H., Mutowo-Muellenet, P., Mulder, N., Natale, D., Orengo, C., Pesseat, S., Punta, M., Quinn, A.F., Rivoire, C., Sangrador-Vegas, A., Selengut, J.D., Sigrist, C.J., Scheremetjew, M., Tate, J., Thimmajanarthanan, M., Thomas, P.D., Wu, C.H., Yeats, C. & Yong, S.Y. Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. Epub 2011 Nov 16. PubMed

iPath2.0: interactive pathway explorer. Yamada, T., Letunic, I., Okuda, S., Kanehisa, M. & Bork, P. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W412-5. Epub 2011 May 5. PubMed

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Letunic, I. & Bork, P. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W475-8. Epub 2011 Apr 5. PubMed

SMART 6: recent updates and new developments. Letunic, I., Doerks, T. & Bork, P. Nucleic Acids Res. 2009 Jan;37(Database issue):D229-32. Epub 2008 Oct 31. PubMed

InterPro: the integrative protein signature database. Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, R.D., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. & Yeats, C. Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. Epub 2008 Oct 21. PubMed

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages. Pincus, D., Letunic, I., Bork, P. & Lim, W.A. Proc Natl Acad Sci U S A. 2008 Jul 15;105(28):9680-4. Epub 2008 Jul 3. PubMed

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. King, N., Westbrook, M.J., Young, S.L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., Marr, M., Pincus, D., Putnam, N., Rokas, A., Wright, K.J., Zuzow, R., Dirks, W., Good, M., Goodstein, D., Lemons, D., Li, W., Lyons, J.B., Morris, A., Nichols, S., Richter, D.J., Salamov, A., Sequencing, J.G., Bork, P., Lim, W.A., Manning, G., Miller, W.T., McGinnis, W., Shapiro, H., Tjian, R., Grigoriev, I.V. & Rokhsar, D. Nature. 2008 Feb 14;451(7180):783-8. PubMed

iPath: interactive exploration of biochemical pathways and networks. Letunic, I., Yamada, T., Kanehisa, M. & Bork, P. Trends Biochem Sci. 2008 Feb 12;. PubMed

4DXpress: a database for cross-species expression pattern comparisons. Haudry, Y., Berube, H., Letunic, I., Weeber, P.D., Gagneur, J., Girardot, C., Kapushesky, M., Arendt, D., Bork, P., Brazma, A., Furlong, E., Wittbrodt, J. & Henrich, T. Nucleic Acids Res. 2007 Oct 4;. PubMed

Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Harrington, E.D., Singh, A.H., Doerks, T., Letunic, I., von Mering, C., Jensen, L.J., Raes, J. & Bork, P. Proc Natl Acad Sci U S A. 2007 Aug 28;104(35):13913-8. Epub 2007 Aug 23. PubMed

Insights into social insects from the genome of the honeybee Apis mellifera. Sequencing Consortium, T.H. (Bork, P.) Nature. 2006 Nov 23;444(7118):512. PubMed

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Letunic, I. & Bork, P. Bioinformatics. 2006 Oct 18;. PubMed

SMART 5: domains in the context of genomes and networks. Letunic, I., Copley, R.R., Pils, B., Pinkert, S., Schultz, J. & Bork, P. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D257-60. PubMed

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. Rehwinkel, J., Letunic, I., Raes, J., Bork, P. & Izaurralde, E. RNA 2005 Oct;11(10):1530-44. PubMed

Consistency of genome-based methods in measuring Metazoan evolution. Zdobnov, E.M., von Mering, C., Letunic, I. & Bork, P. FEBS Lett 2005 Jun 13;579(15):3355-61. Epub 2005 Apr 18. PubMed

InterPro, progress and status in 2005. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Pagni, M., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J., Silventoinen, V., Studholme, D.J., Vaughan, R. & Wu, C.H. Nucleic Acids Res 2005 Jan 1;33(Database issue):D201-5. PubMed

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Hillier, L.W., Miller, W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A., Delany, M.E., Dodgson, J.B., Chinwalla, A.T., Cliften, P.F., Clifton, S.W., Delehaunty, K.D., Fronick, C., Fulton, R.S., Graves, T.A., Kremitzki, C., Layman, D., Magrini, V., McPherson, J.D., Miner, T.L., Minx, P., Nash, W.E., Nhan, M.N., Nelson, J.O., Oddy, L.G., Pohl, C.S., Randall-Maher, J., Smith, S.M., Wallis, J.W., Yang, S.P., Romanov, M.N., Rondelli, C.M., Paton, B., Smith, J., Morrice, D., Daniels, L., Tempest, H.G., Robertson, L., Masabanda, J.S., Griffin, D.K., Vignal, A., Fillon, V., Jacobbson, L., Kerje, S., Andersson, L., Crooijmans, R.P., Aerts, J., van der Poel, J.J., Ellegren, H., Caldwell, R.B., Hubbard, S.J., Grafham, D.V., Kierzek, A.M., McLaren, S.R., Overton, I.M., Arakawa, H., Beattie, K.J., Bezzubov, Y., Boardman, P.E., Bonfield, J.K., Croning, M.D., Davies, R.M., Francis, M.D., Humphray, S.J., Scott, C.E., Taylor, R.G., Tickle, C., Brown, W.R., Rogers, J., Buerstedde, J.M., Wilson, S.A., Stubbs, L., Ovcharenko, I., Gordon, L., Lucas, S., Miller, M.M., Inoko, H., Shiina, T., Kaufman, J., Salomonsen, J., Skjoedt, K., Wong, G.K., Wang, J., Liu, B., Wang, J., Yu, J., Yang, H., Nefedov, M., Koriabine, M., Dejong, P.J., Goodstadt, L., Webber, C., Dickens, N.J., Letunic, I., Suyama, M., Torrents, D., von Mering, C., Zdobnov, E.M., Makova, K., Nekrutenko, A., Elnitski, L., Eswara, P., King, D.C., Yang, S., Tyekucheva, S., Radakrishnan, A., Harris, R.S., Chiaromonte, F., Taylor, J., He, J., Rijnkels, M., Griffiths-Jones, S., Ureta-Vidal, A., Hoffman, M.M., Severin, J., Searle, S.M., Law, A.S., Speed, D., Waddington, D., Cheng, Z., Tuzun, E., Eichler, E., Bao, Z., Flicek, P., Shteynberg, D.D., Brent, M.R., Bye, J.M., Huckle, E.J., Chatterji, S., Dewey, C., Pachter, L., Kouranov, A., Mourelatos, Z., Hatzigeorgiou, A.G., Paterson, A.H., Ivarie, R., Brandstrom, M., Axelsson, E., Backstrom, N., Berlin, S., Webster, M.T., Pourquie, O., Reymond, A., Ucla, C., Antonarakis, S.E., Long, M., Emerson, J.J., Betran, E., Dupanloup, I., Kaessmann, H., Hinrichs, A.S., Bejerano, G., Furey, T.S., Harte, R.A., Raney, B., Siepel, A., Kent, W.J., Haussler, D., Eyras, E., Castelo, R., Abril, J.F., Castellano, S., Camara, F., Parra, G., Guigo, R., Bourque, G., Tesler, G., Pevzner, P.A., Smit, A., Fulton, L.A., Mardis, E.R. & Wilson, R.K. Nature 2004 Dec 9;432(7018):695-716. PubMed

Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression. Koehl, A., Schmidt, N., Rieger, A., Pilgram, S.M., Letunic, I., Bork, P., Soto, F., Friauf, E. & Nothwang, H.G. Eur J Neurosci 2004 Dec;20(12):3244-58. PubMed

Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis. Scheich, C., Leitner, D., Sievert, V., Leidert, M., Schlegel, B., Simon, B., Letunic, I., Bussow, K. & Diehl, A. BMC Struct Biol 2004 Mar 8;4(1):4. PubMed

SMART 4.0: towards genomic data integration. Letunic, I., Copley, R.R., Schmidt, S., Ciccarelli, F.D., Doerks, T., Schultz, J., Ponting, C.P. & Bork, P. Nucleic Acids Res 2004 Jan 1;32(1):D142-4. PubMed

Alternative splicing and evolution. Boue, S., Letunic, I. & Bork, P. Bioessays 2003 Nov;25(11):1031-4. PubMed

The InterPro Database, 2003 brings increased coverage and new features. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R.R., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S.E., Pagni, M., Peyruc, D., Ponting, C.P., Selengut, J.D., Servant, F., Sigrist, C.J., Vaughan, R. & Zdobnov, E.M. Nucleic Acids Res 2003 Jan 1;31(1):315-8. PubMed

Initial sequencing and comparative analysis of the mouse genome. Waterston, R.H., Lindblad-Toh, K., Birney, E., et al. Nature 2002 Dec 5;420(6915):520-62. PubMed

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Zdobnov, E.M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D., Holt, R.A., Subramanian, G.M., Mueller, H.M., Dimopoulos, G., Law, J.H., Wells, M.A., Birney, E., Charlab, R., Halpern, A.L., Kokoza, E., Kraft, C.L., Lai, Z., Lewis, S., Louis, C., Barillas-Mury, C., Nusskern, D., Rubin, G.M., Salzberg, S.L., Sutton, G.G., Topalis, P., Wides, R., Wincker, P., Yandell, M., Collins, F.H., Ribeiro, J., Gelbart, W.M., Kafatos, F.C. & Bork, P. Science 2002 Oct 4;298(5591):149-59. PubMed

The genome sequence of the malaria mosquito Anopheles gambiae. Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M., Wides, R., Salzberg, S.L., Loftus, B., Yandell, M., Majoros, W.H., Rusch, D.B., Lai, Z., Kraft, C.L., Abril, J.F., Anthouard, V., Arensburger, P., Atkinson, P.W., Baden, H., de Berardinis, V., Baldwin, D., Benes, V., Biedler, J., Blass, C., Bolanos, R., Boscus, D., Barnstead, M., Cai, S., Center, A., Chatuverdi, K., Christophides, G.K., Chrystal, M.A., Clamp, M., Cravchik, A., Curwen, V., Dana, A., Delcher, A., Dew, I., Evans, C.A., Flanigan, M., Grundschober-Freimoser, A., Friedli, L., Gu, Z., Guan, P., Guigo, R., Hillenmeyer, M.E., Hladun, S.L., Hogan, J.R., Hong, Y.S., Hoover, J., Jaillon, O., Ke, Z., Kodira, C., Kokoza, E., Koutsos, A., Letunic, I., Levitsky, A., Liang, Y., Lin, J.J., Lobo, N.F., Lopez, J.R., Malek, J.A., McIntosh, T.C., Meister, S., Miller, J., Mobarry, C., Mongin, E., Murphy, S.D., O'Brochta, D.A., Pfannkoch, C., Qi, R., Regier, M.A., Remington, K., Shao, H., Sharakhova, M.V., Sitter, C.D., Shetty, J., Smith, T.J., Strong, R., Sun, J., Thomasova, D., Ton, L.Q., Topalis, P., Tu, Z., Unger, M.F., Walenz, B., Wang, A., Wang, J., Wang, M., Wang, X., Woodford, K.J., Wortman, J.R., Wu, M., Yao, A., Zdobnov, E.M., Zhang, H., Zhao, Q., Zhao, S., Zhu, S.C., Zhimulev, I., Coluzzi, M., della Torre, A., Roth, C.W., Louis, C., Kalush, F., Mural, R.J., Myers, E.W., Adams, M.D., Smith, H.O., Broder, S., Gardner, M.J., Fraser, C.M., Birney, E., Bork, P., Brey, P.T., Venter, J.C., Weissenbach, J., Kafatos, F.C., Collins, F.H. & Hoffman, S.L. Science 2002 Oct 4;298(5591):129-49. PubMed

Immunity-related genes and gene families in Anopheles gambiae. Christophides, G.K., Zdobnov, E., Barillas-Mury, C., Birney, E., Blandin, S., Blass, C., Brey, P.T., Collins, F.H., Danielli, A., Dimopoulos, G., Hetru, C., Hoa, N.T., Hoffmann, J.A., Kanzok, S.M., Letunic, I., Levashina, E.A., Loukeris, T.G., Lycett, G., Meister, S., Michel, K., Moita, L.F., Muller, H.M., Osta, M.A., Paskewitz, S.M., Reichhart, J.M., Rzhetsky, A., Troxler, L., Vernick, K.D., Vlachou, D., Volz, J., von Mering, C., Xu, J., Zheng, L., Bork, P. & Kafatos, F.C. Science 2002 Oct 4;298(5591):159-65. PubMed

InterPro: an integrated documentation resource for protein families, domains and functional sites. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R., Courcelle, E., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Griffith-Jones, S., Haft, D., Hermjakob, H., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Orchard, S., Pagni, M., Peyruc, D., Ponting, C.P., Servant, F. & Sigrist, C.J. Brief Bioinform 2002 Sep;3(3):225-35. PubMed

Protein domain analysis in the era of complete genomes. Copley, R.R., Doerks, T., Letunic, I. & Bork, P. FEBS Lett 2002 Feb 20;513(1):129-34. PubMed

Genome and protein evolution in eukaryotes. Copley, R.R., Letunic, I. & Bork, P. Curr Opin Chem Biol 2002 Feb;6(1):39-45. PubMed

Recent improvements to the SMART domain-based sequence annotation resource. Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P. & Bork, P. Nucleic Acids Res 2002 Jan 1;30(1):242-4. PubMed

Exon duplication: A driving force in eukaryotic gene evolution Letunic, I., Copley, R. and Bork, P. Hum.Mol.Genet., 11, 1561-1567