Dr. Ekaterina Shelest
- 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
(2018) Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites. eLife 7, e40969.
(2018) Dissimilar pigment regulation in Serpula lacrymans and Paxillus involutus during interkingdom interactions. Microbiology 164(1), 65-77.
(2017) antiSMASH 4.0 — Improvements in Chemistry Prediction and Gene Cluster Boundary Identification. Nucleic Acids Res 45(W1), W36-W41.
(2017) Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 18(1), 28.
(2017) Transcription Factors in Fungi: TFome Dynamics, Three Major Families, and Dual-Specificity TFs. Front Genet 8, 53.
(2016) Expansion of signal transduction pathways in fungi by extensive genome duplication Current Biology 26(12), 1577-1584.
(2016) Data-based reconstruction of gene regulatory networks of fungal pathogens. Front Microbiol 7, 570.
(2016) HapX Mediates Iron Homeostasis in the Pathogenic Dermatophyte Arthroderma benhamiae but Is Dispensable for Virulence. PLOS ONE 11(3), e0150701.
(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.
(2016) Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses BMC Genomics 17(1), 953.
(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.
(2016) Systems biology of transcription regulation Front. Genet. 7, 124. (Review)
(2016) Bacteria induce pigment formation in the basidiomycete Serpula lacrymans. Environ Microbiol 18, 5218-5227.
(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.
(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)
(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.
(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.
(2015) Multimodular type I polyketide synthases in algae evolve by module duplications and displacement of AT domains in trans BMC genomics 16(1), 1015.
(2015) Glucocorticoids limit acute lung inflammation in concert with inflammatory stimuli by induction of SphK1 Nature Communications 6, 7796.
(2015) CASSIS and SMIPS: Promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes Bioinformatics 32(8), 1138-1143.
(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.
(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.
(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.
(2014) Terrein Biosynthesis in Aspergillus terreus and Its Impact on Phytotoxicity. Chem Biol 21(6), 719-731.
(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.
(2012) Novel traits of Trichoderma predicted through the analysis of its secretome. FEMS Microbiol Lett 337(1), 1-9.
(2012) Breaking the silence: protein stabilization uncovers silenced biosynthetic gene clusters in the fungus Aspergillus nidulans. Appl Environ Microbiol 78(23), 8234-8244.
(2012) Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection. MBio 3(5), e00259.
(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.
(2010) DistanceScan: a tool for promoter modeling. Bioinformatics 26(11), 1460-1462.
(2009) Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans. Proc Natl Acad Sci U S A 106(34), 14558-14563.
(2008) Transcription factors in fungi. FEMS Microbiol Lett 286(2), 145-151.