Ekaterina Shelest

Dr. Ekaterina Shelest

Systembiologie und Bioinformatik

Forschungsschwerpunkte
  • Transcription factors and their binding sites
  • Mechanisms of transcription regulation and their modeling
  • Comparative genomics and evolution of transcription regulation systems
  • Comparative genomics and evolution of multidomain structures
  • Structure, prediction and evolution of (secondary metabolite) gene clusters
  • Secondary metabolism
  • Epigenetic regulation of secondary metabolism in fungi
  • Functional genome annotation of fungal genomes
  • Algorithms for promoter modeling
Publikationen

Fischer J, Müller SY, Netzker T, Jäger N, Gacek-Matthews A, Scherlach K, Stroe MC, García-Altares M, Pezzini F, Schoeler H, Reichelt M, Gershenzon, Krespach MK, Shelest E, Schroeckh V, Valiante V, Heinzel T, Hertweck C, Strauss J, Brakhage AA (2018) Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites. eLife 7, e40969. Details PubMed

Tauber JP, Gallegos-Monterrosa R, Kovacs AT, Shelest E, Hoffmeister D (2018) Dissimilar pigment regulation in Serpula lacrymans and Paxillus involutus during interkingdom interactions. Microbiology 164(1), 65-77. Details PubMed

Blin K, Wolf T, Chevrette M, Lu X, Schwalen C, Kautsar S, Suarez Duran, H, de los Santos E, Kim HU, Nave M, Dickschat J, Mitchell D, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema M (2017) antiSMASH 4.0 — Improvements in Chemistry Prediction and Gene Cluster Boundary Identification. Nucleic Acids Res 45(W1), W36-W41. Details PubMed Open Access

de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV (2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 18(1), 28. Details PubMed Open Access

Shelest E (2017) Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs. Front Genet 8, 53. Details PubMed Open Access

Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavín JL, Lee SC, Li W, Lindquist E, López-García S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martínez S, Idnurm A, Herrera-Estrella A, Gabaldón T, Grigoriev IV (2016) Expansion of signal transduction pathways in fungi by extensive genome duplication Current Biology 26(12), 1577-1584. Details PubMed

Guthke R, Gerber S, Conrad T, Vlaic S, Durmus S, Cakir T, Sevilgen E, Shelest E, Linde J (2016) Data-based reconstruction of gene regulatory networks of fungal pathogens. Front Microbiol 7, 570. Details PubMed Open Access

Kröber A, Scherlach K, Hortschansky P, Shelest E, Staib P, Kniemeyer O, Brakhage AA (2016) HapX Mediates Iron Homeostasis in the Pathogenic Dermatophyte Arthroderma benhamiae but Is Dispensable for Virulence. PLOS ONE 11(3), e0150701. Details PubMed

Kroll K, Shekhova E, Mattern DJ, Thywissen A, Jacobsen ID, Strassburger M, Heinekamp T, Shelest E, Brakhage AA, Kniemeyer O (2016) The hypoxia-induced dehydrogenase HorA is required for coenzyme Q10 biosynthesis, azole sensitivity and virulence of Aspergillus fumigatus Mol Microbiol 101(1), 92-108. Details PubMed

Penselin D, Münsterkötter M, Kirsten S, Felder M, Taudien S, Platzer M, Asheldford K, Paszkiewicz KH, Harrison R, Hughes DJ, Wolf T, Shelest E, Graap J, Hoffmann J, Wenzel C, Wöltje N, King KM, Fitt BDL, Güldener U, Avrova A, Knogge W (2016) Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses BMC Genomics 17(1), 953. Details Open Access

Rischer M, Klassen J, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C (2016) Draft Genome Sequence of Shewanella sp. P1-14-1, a Bacterial Inducer of Settlement and Morphogenesis in Larvae of the Marine Hydroid Hydractinia Echinata Genome Announc 4(1), e00003-16. Details PubMed

Shelest E, Wingender E (2016) Systems biology of transcription regulation Front. Genet. 7, 124. (Review) Details

Tauber JP, Schroeckh V, Shelest E, Brakhage AA, Hoffmeister D (2016) Bacteria induce pigment formation in the basidiomycete Serpula lacrymans. Environ Microbiol 18, 5218-5227. Details PubMed

Valiante V, Baldin C, Hortschansky P, Jain R, Thywißen A, Straßburger M, Shelest E, Heinekamp T, Brakhage AA (2016) The Aspergillus fumigatus conidial melanin production is regulated by the bifunctional bHLH DevR and MADS-box RlmA transcription factors. Mol Microbiol 102(2), 321-335. Details PubMed

Voigt K, Wolf T, Ochsenreiter K, Nagy G, Kaerger K, Shelest E, Papp T (2016) 15 Genetic and metabolic aspects of primary and secondary metabolism of the Zygomycetes In: Hoffmeister D. (eds) Biochemistry and Molecular Biology (ed.) The Mycota Vol. III: 3rd edition. III, pp. 361-385. Springer Verlag, Berlin, Heidelberg, New York. (Review) Details Open Access PDF

Klassen JL, Rischer M, Wolf T, Guo H, Shelest E, Clardy J, Beemelmanns C (2015) Genome Sequences of Three Pseudoalteromonas Strains P1-8, P1-11 and P1-30 Isolated from the Marine Hydroid Hydractinia echinata Genome Announc. 3(6), e01380-15. Details PubMed

Klassen JL, Wolf T, Rischer M, Guo H, Shelest E, Clardy J, Beemelmanns C (2015) Draft Genome Sequences of Six Pseudoalteromonas sp. Strains P1-7a, P1-9, P1-13-1a, P1-16-1b, P1-25 and P1-26, which Induce Larval Settlement and Metamorphosis in Hydractinia echinata Genome Announc. 3(6), e01477-15. Details PubMed

Shelest E, Heimerl N, Fichtner M, Sasso S (2015) Multimodular type I polyketide synthases in algae evolve by module duplications and displacement of AT domains in trans BMC genomics 16(1), 1015. Details PubMed Open Access

Vettorazzi S, Bode C, Dejager L, Frappart L, Shelest E, Klaßen C, Tasdogan A, Reichardt HM, Libert C, Schneider M, Weih F, Uhlenhaut H, David J-P, Gräler M, Kleiman A, Tuckermann JP (2015) Glucocorticoids limit acute lung inflammation in concert with inflammatory stimuli by induction of SphK1 Nature Communications 6, 7796. Details PubMed

Wolf T, Shelest V, Nath N, Shelest E (2015) CASSIS and SMIPS: Promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes Bioinformatics 32(8), 1138-1143. Details PubMed Open Access

Sasso S, Shelest E, Hoffmeister D (2014) Comments on the distribution and phylogeny of type I polyketide synthases and nonribosomal peptide synthetases in eukaryotes. Proc Natl Acad Sci U S A 111, E3946. Details PubMed

Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K (2014) Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial Mucorales (Mucoromycotina). PLOS Genetics 10(8), e1004496. Details PubMed Open Access

Shelest E, Voigt K (2014) Genomics to study basal lineage fungal biology: phylogenomics suggest a common origin In: Alistair J.B. Brown (ed.) The Mycota XIII, Fungal Genomics 2. edition. 13, pp. 31-60. Springer, Berlin, Heidelberg. Details

Zaehle C, Gressler M, Shelest E, Geib E, Hertweck C, Brock M (2014) Terrein Biosynthesis in Aspergillus terreus and Its Impact on Phytotoxicity. Chem Biol 21(6), 719-731. Details PubMed

Wolf T, Shelest V, Shelest E (2013) Motif-based method for genome-wide prediction of eukaryotic gene clusters In: A. Petrosino, L. Maddalena, P. Pala (eds.) Lecture Notes in Computer Science (LNCS) 2nd International Workshop on Pattern Recognition in Proteomics, Structural Biology and Bioinformatics, Naples, Italien, 09/09/2013-09/10/2013, 8158, pp. 389-398.Springer-Verlag, Berlin, Heidelberg. Details

Druzhinina IS, Shelest E, Kubicek CP (2012) Novel traits of Trichoderma predicted through the analysis of its secretome. FEMS Microbiol Lett 337(1), 1-9. Details PubMed

Gerke J, Bayram O, Feussner K, Landesfeind M, Shelest E, Feussner I, Braus GH (2012) Breaking the silence: protein stabilization uncovers silenced biosynthetic gene clusters in the fungus Aspergillus nidulans. Appl Environ Microbiol 78(23), 8234-8244. Details PubMed

Martinez DA, Oliver BG, Gräser Y, Goldberg JM, Li W, Martinez-Rossi NM, Monod M, Shelest E, Barton RC, Birch E, Brakhage AA, Chen Z, Gurr SJ, Heiman D, Heitman J, Kosti I, Rossi A, Saif S, Samalova M, Saunders CW, Shea T, Summerbell RC, Xu J, Young S, Zeng Q, Birren BW, Cuomo CA, White TC (2012) Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. MBio 3(5), e00259. Details PubMed

Bergmann S, Funk AN, Scherlach K, Schroeckh V, Shelest E, Horn U, Hertweck C, Brakhage AA (2010) Activation of a silent fungal polyketide biosynthesis pathway through regulatory cross talk with a cryptic nonribosomal peptide synthetase gene cluster. Appl Environ Microbiol 76(24), 8143-8149. Details PubMed Open Access PDF Supplement

Shelest V, Albrecht D, Shelest E (2010) DistanceScan: a tool for promoter modeling. Bioinformatics 26(11), 1460-1462. Details PubMed

Schroeckh V, Scherlach K, Nützmann HW, Shelest E, Schmidt-Heck W, Schuemann J, Martin K, Hertweck C, Brakhage AA (2009) Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans. Proc Natl Acad Sci U S A 106(34), 14558-14563. Details PubMed

Shelest E (2008) Transcription factors in fungi. FEMS Microbiol Lett 286(2), 145-151. Details PubMed