Ivica Letunic - Publications

Affiliations: 
Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
Website:
http://www.embl.de/research/units/scb/bork/members/index.php?s_personId=1790

62 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, ... ... Letunic I, et al. Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature Communications. 11: 6448. PMID 33349634 DOI: 10.1038/s41467-020-20412-9  1
2020 Molinaro A, Bel Lassen P, Henricsson M, Wu H, Adriouch S, Belda E, Chakaroun R, Nielsen T, Bergh PO, Rouault C, André S, Marquet F, Andreelli F, Salem JE, Assmann K, ... ... Letunic I, et al. Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature Communications. 11: 5881. PMID 33208748 DOI: 10.1038/s41467-020-19589-w  1
2020 Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, ... ... Letunic I, et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Research. PMID 33156333 DOI: 10.1093/nar/gkaa977  1
2020 Letunic I, Khedkar S, Bork P. SMART: recent updates, new developments and status in 2020. Nucleic Acids Research. PMID 33104802 DOI: 10.1093/nar/gkaa937  1
2020 Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, ... ... Letunic I, et al. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature. 581: 310-315. PMID 32433607 DOI: 10.1038/s41586-020-2269-x  1
2019 Mende DR, Letunic I, Maistrenko OM, Schmidt TSB, Milanese A, Paoli L, Hernández-Plaza A, Orakov AN, Forslund SK, Sunagawa S, Zeller G, Huerta-Cepas J, Coelho LP, Bork P. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. Nucleic Acids Research. PMID 31647096 DOI: 10.1093/nar/gkz1002  1
2019 Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Research. PMID 30931475 DOI: 10.1093/nar/gkz239  1
2018 Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research. PMID 30418610 DOI: 10.1093/nar/gky1085  1
2018 Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Research. PMID 30398656 DOI: 10.1093/nar/gky1100  1
2018 Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, ... Letunic I, et al. Metagenomic analysis of gut microbial communities from a Central Asian population. Bmj Open. 8: e021682. PMID 30056386 DOI: 10.1136/bmjopen-2018-021682  1
2018 Darzi Y, Letunic I, Bork P, Yamada T. iPath3.0: interactive pathways explorer v3. Nucleic Acids Research. PMID 29718427 DOI: 10.1093/nar/gky299  1
2017 Letunic I, Bork P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Research. PMID 29040681 DOI: 10.1093/nar/gkx922  1
2017 Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P. proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Research. 45: D529-D534. PMID 28053165 DOI: 10.1093/nar/gkw989  1
2016 Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, ... Letunic I, et al. InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Research. PMID 27899635 DOI: 10.1093/nar/gkw1107  1
2016 Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research. PMID 27095192 DOI: 10.1093/nar/gkw290  1
2015 Kuhn M, Letunic I, Jensen LJ, Bork P. The SIDER database of drugs and side effects. Nucleic Acids Research. PMID 26481350 DOI: 10.1093/nar/gkv1075  1
2015 Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, ... ... Letunic I, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Research. 43: D213-21. PMID 25428371 DOI: 10.1093/nar/gku1243  1
2015 Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Research. 43: D494-502. PMID 25361965 DOI: 10.1093/nar/gku1081  1
2015 Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Research. 43: D257-60. PMID 25300481 DOI: 10.1093/nar/gku949  1
2013 Minguez P, Letunic I, Parca L, Bork P. PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic Acids Research. 41: D306-11. PMID 23193284 DOI: 10.1093/nar/gks1230  1
2012 Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research. 40: D284-9. PMID 22096231 DOI: 10.1093/nar/gkr1060  1
2012 Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, ... ... Letunic I, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research. 40: D306-12. PMID 22096229 DOI: 10.1093/nar/gkr948  1
2012 Letunic I, Doerks T, Bork P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Research. 40: D302-5. PMID 22053084 DOI: 10.1093/nar/gkr931  1
2011 Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P. iPath2.0: interactive pathway explorer. Nucleic Acids Research. 39: W412-5. PMID 21546551 DOI: 10.1093/nar/gkr313  1
2011 Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Research. 39: W475-8. PMID 21470960 DOI: 10.1093/nar/gkr201  1
2011 Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology. 7: 473. PMID 21407210 DOI: 10.1038/msb.2011.6  1
2010 Procter JB, Thompson J, Letunic I, Creevey C, Jossinet F, Barton GJ. Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods. 7: S16-25. PMID 20195253 DOI: 10.1038/nmeth.1434  1
2010 Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology. 6: 343. PMID 20087340 DOI: 10.1038/msb.2009.98  1
2010 Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Research. 38: D190-5. PMID 19900971 DOI: 10.1093/nar/gkp951  1
2009 Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, et al. Impact of genome reduction on bacterial metabolism and its regulation. Science (New York, N.Y.). 326: 1263-8. PMID 19965476 DOI: 10.1126/science.1177263  1
2009 Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings of the National Academy of Sciences of the United States of America. 106: 1374-9. PMID 19164758 DOI: 10.1073/pnas.0808022106  1
2009 Letunic I, Doerks T, Bork P. SMART 6: recent updates and new developments. Nucleic Acids Research. 37: D229-32. PMID 18978020 DOI: 10.1093/nar/gkn808  1
2009 Whitaker JW, Letunic I, McConkey GA, Westhead DR. metaTIGER: a metabolic evolution resource. Nucleic Acids Research. 37: D531-8. PMID 18953037 DOI: 10.1093/nar/gkn826  1
2009 Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, ... ... Letunic I, et al. InterPro: the integrative protein signature database. Nucleic Acids Research. 37: D211-5. PMID 18940856 DOI: 10.1093/nar/gkn785  1
2009 Singh AH, Doerks T, Letunic I, Raes J, Bork P. Discovering functional novelty in metagenomes: examples from light-mediated processes. Journal of Bacteriology. 191: 32-41. PMID 18849420 DOI: 10.1128/JB.01084-08  1
2008 Pincus D, Letunic I, Bork P, Lim WA. Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages. Proceedings of the National Academy of Sciences of the United States of America. 105: 9680-4. PMID 18599463 DOI: 10.1073/pnas.0803161105  1
2008 Letunic I, Yamada T, Kanehisa M, Bork P. iPath: interactive exploration of biochemical pathways and networks. Trends in Biochemical Sciences. 33: 101-3. PMID 18276143 DOI: 10.1016/j.tibs.2008.01.001  1
2008 King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 451: 783-8. PMID 18273011 DOI: 10.1038/nature06617  1
2008 Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research. 36: D847-53. PMID 17916571 DOI: 10.1093/nar/gkm797  1
2008 Haudry Y, Ong CK, Ettwiller L, Berube H, Letunic I, Kapushesky M, Weeber PD, Wang X, Gagneur J, Girardot C, Arendt D, Bork P, Brazma A, Furlong E, Wittbrodt J, et al. Comparing and analysing gene expression patterns across animal species using 4DXpress Series On Advances in Bioinformatics and Computational Biology. 6: 373-382.  1
2007 Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ, Raes J, Bork P. Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proceedings of the National Academy of Sciences of the United States of America. 104: 13913-8. PMID 17717083 DOI: 10.1073/pnas.0702636104  1
2007 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, ... ... Letunic I, et al. New developments in the InterPro database. Nucleic Acids Research. 35: D224-8. PMID 17202162 DOI: 10.1093/nar/gkl841  1
2007 Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (Oxford, England). 23: 127-8. PMID 17050570 DOI: 10.1093/bioinformatics/btl529  1
2006 Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P. SMART 5: domains in the context of genomes and networks. Nucleic Acids Research. 34: D257-60. PMID 16381859 DOI: 10.1093/nar/gkj079  1
2005 Rehwinkel J, Letunic I, Raes J, Bork P, Izaurralde E. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. Rna (New York, N.Y.). 11: 1530-44. PMID 16199763 DOI: 10.1261/rna.2160905  1
2005 Zdobnov EM, von Mering C, Letunic I, Bork P. Consistency of genome-based methods in measuring Metazoan evolution. Febs Letters. 579: 3355-61. PMID 15943981 DOI: 10.1016/j.febslet.2005.04.006  1
2005 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, ... ... Letunic I, et al. InterPro, progress and status in 2005. Nucleic Acids Research. 33: D201-5. PMID 15608177 DOI: 10.1093/nar/gki106  1
2004 Koehl A, Schmidt N, Rieger A, Pilgram SM, Letunic I, Bork P, Soto F, Friauf E, Nothwang HG. Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression. The European Journal of Neuroscience. 20: 3244-58. PMID 15610157 DOI: 10.1111/j.1460-9568.2004.03791.x  1
2004 Scheich C, Leitner D, Sievert V, Leidert M, Schlegel B, Simon B, Letunic I, Büssow K, Diehl A. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis. Bmc Structural Biology. 4: 4. PMID 15113422 DOI: 10.1186/1472-6807-4-4  1
2004 Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P. SMART 4.0: towards genomic data integration. Nucleic Acids Research. 32: D142-4. PMID 14681379 DOI: 10.1093/nar/gkh088  1
2003 Boue S, Letunic I, Bork P. Alternative splicing and evolution. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 25: 1031-4. PMID 14579243 DOI: 10.1002/bies.10371  1
2003 Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, ... ... Letunic I, et al. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research. 31: 3625-30. PMID 12824381 DOI: 10.1093/nar/gkg545  1
2003 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, ... ... Letunic I, et al. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research. 31: 315-8. PMID 12520011 DOI: 10.1093/nar/gkg046  1
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Letunic I, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/nature01262  1
2002 Christophides GK, Zdobnov E, Barillas-Mury C, Birney E, Blandin S, Blass C, Brey PT, Collins FH, Danielli A, Dimopoulos G, Hetru C, Hoa NT, Hoffmann JA, Kanzok SM, Letunic I, et al. Immunity-related genes and gene families in Anopheles gambiae. Science (New York, N.Y.). 298: 159-65. PMID 12364793 DOI: 10.1126/science.1077136  1
2002 Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (New York, N.Y.). 298: 149-59. PMID 12364792 DOI: 10.1126/science.1077061  1
2002 Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, ... ... Letunic I, et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, N.Y.). 298: 129-49. PMID 12364791 DOI: 10.1126/science.1076181  1
2002 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, ... ... Letunic I, et al. InterPro: an integrated documentation resource for protein families, domains and functional sites. Briefings in Bioinformatics. 3: 225-35. PMID 12230031  1
2002 Letunic I, Copley RR, Bork P. Common exon duplication in animals and its role in alternative splicing. Human Molecular Genetics. 11: 1561-7. PMID 12045209  1
2002 Copley RR, Doerks T, Letunic I, Bork P. Protein domain analysis in the era of complete genomes. Febs Letters. 513: 129-34. PMID 11911892 DOI: 10.1016/S0014-5793(01)03289-6  1
2002 Copley RR, Letunic I, Bork P. Genome and protein evolution in eukaryotes. Current Opinion in Chemical Biology. 6: 39-45. PMID 11827821 DOI: 10.1016/S1367-5931(01)00278-2  1
2002 Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Research. 30: 242-4. PMID 11752305  1
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