169
Hadjithomas M, Chen IMA, Chu K, Ratner A, Palaniappan K, Szeto E et al (2015) IMG-ABC: a
knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. MBio 6:e00932-15
Halabalaki M, Vougogiannopoulou K, Mikros E, Skaltsounis AL (2014) Recent advances and new
strategies in the NMR-based identification of natural products. Current opinion in biotechnology 25 pp.1–7
Hasin Y, Seldin M, Lusis A (2017) Multiomics approaches to disease. Genome Biol 18:83
Hider R (1984) Siderophore mediated absorption of iron. Struct Bond 58:25–87
Hillman ET, Readnour LR, Solomon KV (2017) Exploiting the natural product potential of fungi
with integratedomics and synthetic biology approaches. Curr Opin Syst Biol 5:50–56
Johnson LJ, Koulman A, Christensen M, Lane GA, Fraser K, Forester N et al (2013) An extracellular siderophore is required to maintain the mutualistic interaction of Epichloë festucae with
Lolium perenne. PLoS Pathog 9:e1003332
Johnston CW, Skinnider MA, Wyatt MA, Li X, Ranieri MR, Yang L et al (2015) An automated
Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products.
Nat Commun 6:8421
Kersten RD, Yang YL, Xu Y, Cimermancic P, Nam SJ, Fenical W et al (2011) A mass spectrometry–guided genome mining approach for natural product peptidogenomics. Nat Chem Biol
7:794
Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND (2010) SMURF:
genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 47:736–741
Khater S, Gupta M, Agrawal P, Sain N, Prava J, Gupta P et al (2017) SBSPKSv2: structure-based
sequence analysis of polyketide synthases and non-ribosomal peptide synthetases. Nucleic
Acids Res 45:W72–W79
Kim HU, Charusanti P, Lee SY, Weber T (2016) Metabolic engineering with systems biology tools
to optimize production of prokaryotic secondary metabolites. Nat Prod Rep 33:933–941
Knudsen M, Søndergaard D, Tofting-Olesen C, Hansen FT, Brodersen DE, Pedersen CN (2015)
Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases.
Bioinformatics 32:325–329
Komaki H, Sakurai K, Hosoyama A, Kimura A, Igarashi Y, Tamura T (2018) Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close
Streptomyces strains. Sci Rep 8:6888
Krug D, Müller R (2014) Secondary metabolomics: the impact of mass spectrometry-based
approaches on the discovery and characterization of microbial natural products. Nat Prod Rep
31:768–783
Lambertz C, Garvey M, Klinger J, Heesel D, Klose H, Fischer R, Commandeur U (2014)
Challenges and advances in the heterologous expression of cellulolytic enzymes: a review.
Biotechnol Biofuels 7:135
Lasocki S, Gaillard T, Rineau E (2014) Iron is essential for living! Crit Care 18:678
Liu R, Chen L, Jiang Y, Zhou Z, Zou G (2015) Efficient genome editing in filamentous fungus
Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov 1:15007
Lotz K, Hartmann A, Grafahrend-Belau E, Schreiber F, Junker BH (2014) Elementary flux modes,
flux balance analysis, and their application to plant metabolism. In: Sriram G (ed) Plant metabolism. Humana Press, Totowa, pp 231–252
Martínez-Núñez MA, López VEL (2016) Nonribosomal peptides synthetases and their applications in industry. Sustainable Chem Processes 4:13
Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA et al (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis
gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346
Medema MH, Paalvast Y, Nguyen DD, Melnik A, Dorrestein PC, Takano E, Breitling R (2014)
Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.
PLoS Comput Biol 10(9):e1003822
10 Bioinformatics Applications in Fungal Siderophores: Omics Implications
Hadjithomas M, Chen IMA, Chu K, Ratner A, Palaniappan K, Szeto E et al (2015) IMG-ABC: a
knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. MBio 6:e00932-15
Halabalaki M, Vougogiannopoulou K, Mikros E, Skaltsounis AL (2014) Recent advances and new
strategies in the NMR-based identification of natural products. Current opinion in biotechnology 25 pp.1–7
Hasin Y, Seldin M, Lusis A (2017) Multiomics approaches to disease. Genome Biol 18:83
Hider R (1984) Siderophore mediated absorption of iron. Struct Bond 58:25–87
Hillman ET, Readnour LR, Solomon KV (2017) Exploiting the natural product potential of fungi
with integratedomics and synthetic biology approaches. Curr Opin Syst Biol 5:50–56
Johnson LJ, Koulman A, Christensen M, Lane GA, Fraser K, Forester N et al (2013) An extracellular siderophore is required to maintain the mutualistic interaction of Epichloë festucae with
Lolium perenne. PLoS Pathog 9:e1003332
Johnston CW, Skinnider MA, Wyatt MA, Li X, Ranieri MR, Yang L et al (2015) An automated
Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products.
Nat Commun 6:8421
Kersten RD, Yang YL, Xu Y, Cimermancic P, Nam SJ, Fenical W et al (2011) A mass spectrometry–guided genome mining approach for natural product peptidogenomics. Nat Chem Biol
7:794
Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND (2010) SMURF:
genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol 47:736–741
Khater S, Gupta M, Agrawal P, Sain N, Prava J, Gupta P et al (2017) SBSPKSv2: structure-based
sequence analysis of polyketide synthases and non-ribosomal peptide synthetases. Nucleic
Acids Res 45:W72–W79
Kim HU, Charusanti P, Lee SY, Weber T (2016) Metabolic engineering with systems biology tools
to optimize production of prokaryotic secondary metabolites. Nat Prod Rep 33:933–941
Knudsen M, Søndergaard D, Tofting-Olesen C, Hansen FT, Brodersen DE, Pedersen CN (2015)
Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases.
Bioinformatics 32:325–329
Komaki H, Sakurai K, Hosoyama A, Kimura A, Igarashi Y, Tamura T (2018) Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close
Streptomyces strains. Sci Rep 8:6888
Krug D, Müller R (2014) Secondary metabolomics: the impact of mass spectrometry-based
approaches on the discovery and characterization of microbial natural products. Nat Prod Rep
31:768–783
Lambertz C, Garvey M, Klinger J, Heesel D, Klose H, Fischer R, Commandeur U (2014)
Challenges and advances in the heterologous expression of cellulolytic enzymes: a review.
Biotechnol Biofuels 7:135
Lasocki S, Gaillard T, Rineau E (2014) Iron is essential for living! Crit Care 18:678
Liu R, Chen L, Jiang Y, Zhou Z, Zou G (2015) Efficient genome editing in filamentous fungus
Trichoderma reesei using the CRISPR/Cas9 system. Cell Discov 1:15007
Lotz K, Hartmann A, Grafahrend-Belau E, Schreiber F, Junker BH (2014) Elementary flux modes,
flux balance analysis, and their application to plant metabolism. In: Sriram G (ed) Plant metabolism. Humana Press, Totowa, pp 231–252
Martínez-Núñez MA, López VEL (2016) Nonribosomal peptides synthetases and their applications in industry. Sustainable Chem Processes 4:13
Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA et al (2011) antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis
gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346
Medema MH, Paalvast Y, Nguyen DD, Melnik A, Dorrestein PC, Takano E, Breitling R (2014)
Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products.
PLoS Comput Biol 10(9):e1003822
10 Bioinformatics Applications in Fungal Siderophores: Omics Implications