Jonathan Parra, Sylvia Soldatou, Liam M. Rooney, Katherine R. Duncan (2021), Pseudonocardia abyssalis sp. nov. and Pseudonocardia oceani sp. nov., two novel actinomycetes isolated from the deep Southern Ocean. International Journal of Systematic and Evolutionary Biology. 71(9), https://doi.org/10.1099/ijsem.0.005032
Agustina Undabarrena, Camila F. Pereira, Worarat Kruasuwan, Jonathan Parra, Nelly Sélem-Mojica, Kristiina Vind, Jana K. Schniete (2021), Integrating perspectives in actinomycete research: an ActinoBase review of 2020-2021. Microbiology. 167(9), https://doi.org/10.1099/mic.0.001084
Michelle A Schorn, Stefan Verhoeven, Lars Ridder, Florian Huber, Deepa D Acharya, Alexander A Aksenov, Gajender Aleti, Jamshid Amiri Moghaddam, Allegra T Aron, Saefuddin Aziz, Anelize Bauermeister, Katherine D Bauman, Martin Baunach, Christine Beemelmanns, J Michael Beman, María Victoria Berlanga-Clavero, Alex A Blacutt, Helge B Bode, Anne Boullie, Asker Brejnrod, Tim S Bugni, Alexandra Calteau, Liu Cao, Víctor J Carrión, Raquel Castelo-Branco, Shaurya Chanana, Alexander B Chase, Marc G Chevrette, Leticia V Costa-Lotufo, Jason M Crawford, Cameron R Currie, Bart Cuypers, Tam Dang, Tristan de Rond, Alyssa M Demko, Elke Dittmann, Chao Du, Christopher Drozd, Jean-Claude Dujardin, Rachel J Dutton, Anna Edlund, David P Fewer, Neha Garg, Julia M Gauglitz, Emily C Gentry, Lena Gerwick, Evgenia Glukhov, Harald Gross, Muriel Gugger, Dulce G Guillén Matus, Eric JN Helfrich, Benjamin-Florian Hempel, Jae-Seoun Hur, Marianna Iorio, Paul R Jensen, Kyo Bin Kang, Leonard Kaysser, Neil L Kelleher, Chung Sub Kim, Ki Hyun Kim, Irina Koester, Gabriele M König, Tiago Leao, Seoung Rak Lee, Yi-Yuan Lee, Xuanji Li, Jessica C Little, Katherine N Maloney, Daniel Männle, Andrew C McAvoy, Willam W Metcalf, Hosein Mohimani, Carlos Molina-Santiago, Bradley S Moore, Michael W Mullowney, Mitchell Muskat, Louis-Félix Nothias, Ellis C O’Neill, Elizabeth I Parkinson, Daniel Petras, Jörn Piel, Emily C Pierce, Karine Pires, Raphael Reher, Diego Romero, M Caroline Roper, Michael Rust, Hamada Saad, Carmen Saenz, Laura M Sanchez, Søren Johannes Sørensen, Margherita Sosio, Roderich D Süssmuth, Douglas Sweeney, Kapil Tahlan, Regan J Thomson, Nicholas J Tobias, Amaro E Trindade-Silva, Gilles P van Wezel, Mingxun Wang, Kelly C Weldon, Fan Zhang, Nadine Ziemert, Katherine R Duncan, Max Crüsemann, Simon Rogers, Pieter C Dorrestein, Marnix H Medema, Justin JJ van der Hooft (2021) A community resource for paired genomic and metabolomic data mining. Nature Chemical Biology. 17(4) 363-368 www.nature.com/articles/s41589-020-00724-z
Soldatou, S., Eldjarn, G. H., Ramsey, A., van der Hooft, J. J. J., Hughes, A. H., Rogers, S. & Duncan, K. R,* Comparative metabologenomics analysis of polar actinomycetes (2021) Marine Drugs. 19(2) 103; [*corresponding author]. www.mdpi.com/1660-3397/19/2/103
Hughes, A. H., Magot, F., Tawfike, A. F., Rad-Menéndez, C., Thomas, N., Young, L. C., Stucchi, L., Carettoni, D., Stanley, M. S., Edrada-Ebel, R., Duncan, K. R.* (2021) Exploring the Chemical Space of Macro- and Micro-Algae Using Comparative Metabolomics. Microorganisms, 9(2), 311; [*corresponding author]. https://doi.org/10.3390/microorganisms9020311
van der Hooft, J. J., Mohimani, H., Bauermeister, A., Dorrestein, P. C., Duncan, K. R.*, Medema, M. H.* (2020) Linking Genomics and Metabolomics to Chart Specialized Metabolite Discovery. Chem. Soc. Rev., 2020,49, 3297-3314 [*co-corresponding author] https://doi.org/10.1039/D0CS00162G
Prudence, S. M. M., Addington, E. , Castaño-Espriu, L., Mark, D. R., Pintor-Escobar, L., Russell, A. H., McLean T. C. Advances in Actinomycete Research: an Actinobase Review of 2019. Microbiology. https://doi.org/10.1099/mic.0.000944
Eldjarn, G. Ramsay, A. van der Hooft, JJJ. Duncan, K. R. Soldatou, S. Rousu, J. Rogers, S*. (2020). Ranking Microbial Metabolomic and Genomic Links Using Correlation-Based and Feature-Based Scoring Functions. [* Corresponding author]. PLoS Computational Biology. 17(5): e1008920. journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008920
Millán-Aguiñaga, N. Soldatou, S., Brozio, S., Munnoch, J. T., Howe, J., Hoskisson, P. A., Duncan, K. R*. (2019) Awakening Ancient Polar Actinobacteria: Diversity, Evolution and Specialized Metabolite Potential. [* Corresponding author]. Microbiology. 165(1), 1169-1180, https://doi.org/10.1099/mic.0.000845
Soltatou, S.+, Eldjarn, G. H.+, Huerta-Uribe, A.+, Rogers, S., Duncan, K. R.* (2019) Linking Biosynthetic and Chemical Space to Accelerate Microbial Secondary Metabolite Discovery. [+ Co-first author and * corresponding author]. FEMS Microbiology Letters. 366(13), fnz142. doi.org/10.1093/femsle/fnz142
Hicks, N. R.*+, Liu, X., Gregory, R., Kenny, J. Lucaci, A., Lenzi, L., Paterson, D. M., Duncan, K. R.*+ (2018) Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Costal Sediments. [+ Co-first author and * Co-corresponding author]. Frontiers in Microbiology. doi: https://doi.org/10.3389/fmicb.2018.01730
Vallet, M., Vanbellingen, Q. P. Fu, T., Le Caer, J-P, Della-Negra, S., Touboul, D., Duncan, K. R., Nay, B., Brunelle, A. and Prado, S. (2017) An integrative approach to decipher the chemical antagonism between the competing endophytes Paraconiothyrium variabile and Bacillus subtilis. Journal of Natural Products doi:10.1021/acs.jnatprod.6b01185
Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A. V., Meehan, M. J., Liu, W-T., Crüseman, M., Boudreau, P. D., Esquenazi, E., Sandoval-Calderón, M., Kersten, R. D., Pace, L. A., Quinn, R. A., Duncan, K. R., Hsu, C-C., Floros, D. J., Gavilan, R. G., Kleigrewe, K., Northen, T., Dutton, R. J., Parrot, D., Carlson, E. E., Aigle, B., Michelsen, C. F., Jelsbak, L., Sohlenkamp, C., Pevzner, P., Edlund, A., McLean, J., Piel, J., Murphy, B. T., Gerwick, L., Liaw, C-C., Yang, Y-L., Humpf, H-U., Maansson, M., Keyzers, R. A., Sims, A. C., Johnson, A. R., Sidebottom, A. M., Sedio, B. E., Klitgaard, A., Larson, C. B., Boya P, C. A., Torres-Mendoza, D., Gonzalez, D. J., Silva, D. B., Marques, L. M., Demarque, D. P., Pociute, E., O'Neill, E. C., Briand, E., Helfrich, E. J. N., Granatosky, E. A., Glukhov, E., Ryffel, F., Houson, H., Mohimani, H., Kharbush, J. J., Zeng, Y., Vorholt, J. A., Kurita, K. L., Charusanti, P., McPhail, K. L., Nielsen, K. F., Vuong, L., Elfeki, M., Traxler, M. F., Engene, N., Koyama, N., Vining, O. B., Baric, R., Silva, R. S., Mascuch, S. J., Tomasi, S., Jenkins, S., Macherla, V., Hoffman, T., Agarwal, V., Williams, P. G., Dai, J., Neupane, R., Gurr, J., Rodríguez, A. M. C., Lamsa, A., Zhang, C., Dorrestein, K., Duggan, B. M., Almaliti, J., Allard, P, M., Phapale, P., Nothias, L. F., Alexandrov, T., Litaudon, M., Wolfender, J. L., Kyle, J. E., Metz, T. O., Peryea, T., Nguyen, D-T., VanLeer, D., Shinn, P., Jadhav, A., Müller, R., Waters, K. M., Shi, W., Liu, X., Zhang, L., Knight, R., Jensen, P. R., Palsson, B. O., Pogliano, K., Linington, R. G., Gutiérrez, M., Lopes, N. P., Gerwick, W. H., Moore, B. S., Dorrestein, P. C. Bandeira, N. (2016) Sharing and community curation of mass spectra by GNPS. Nature Biotechnology 34, 828–837. doi:10.1038/nbt.3597
Buchholtz, H. and Duncan, K. R.* (2016) Antarctic Sponge Associated Microbial Chemistry with Biomedical Relevance – the Need for Ecologically Driven Studies. [*Corresponding author] August 2016. Curr. Org. Chem. 21(5): 395-401 doi:10.2174/1385272820666161020122153
Purves, K., MacIntyre, L., Brennan, D., Hreggviosson, G. O., Kuttner, E., Asgeirsdottir, M. E., Young, L. C., Green, D.H. Edrada-Ebel, R, Duncan, K.R.* (2016) Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting. Metabolites 6(1): 2. [*Corresponding author] doi:10.3390/metabo6010002
Duncan, K.R., Crüsemann, M., Lechner, A., Sarkar, A., Li, J., Ziemert, N., Wang, M., Moore, B.S., Dorrestein, P.C. and Jensen, P.R. (2015) Molecular Network and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species. Chem. & Biol. 22: 1-12. http://dx.doi.org/10.1016/j.chembiol.2015.03.010
Patin, N.V., Duncan, K.R., Jensen, P. R. (2015) Competitive Strategies Differentiate Closely-Related Species of Marine Bacteria. ISME J. 10(2): 478-490 doi.org/10.1038/ismej.2015.128
Duncan, K., Haltli, B., Gill, K.A. and Kerr R.G. (2014) Bioprospecing from Marine Sediments of New Brunswick, Canada: Exploring the Relationship Between Total Bacterial Diversity and Actinobacteria Diversity. Mar. Drugs, 12, 899-925; doi:10.3390/md12020899
Duncan, K.R., Haltli, B., Gill, K.A., Correa, H., Berrué, F. and Kerr, R.G. (2014) Exploring the Diversity and Metabolic Potential of Actinomycetes from Temperate Marine Sediments from Newfoundland, Canada. J. Ind. Microbiol. Biotech 42(1): 57-72 doi:10.1007/s10295-014-1529x
Weitz, M., Duncan, K., Pattin, N.V., and Jensen, P.R. (2013) Antagonistic Interactions Mediated by Marine Bacteria, the Role of Small Molecules. J. Chem. Ecol. 39(7): 879-891 doi:10.1007/s10886-013-0316-x
Forner, D., Berrue, F., Correa, H., Duncan, K., Kerr, R.G. (2013) Chemical Dereplication of Marine Actinomycetes by Liquid Chromatography - High Resolution Mass Spectrometry Profiling and Statistical Analysis Anal. Chim. Acta. 12(805): 70-79 doi:10.1016/j.aca.2013.10.029
Agustina Undabarrena, Camila F. Pereira, Worarat Kruasuwan, Jonathan Parra, Nelly Sélem-Mojica, Kristiina Vind, Jana K. Schniete (2021), Integrating perspectives in actinomycete research: an ActinoBase review of 2020-2021. Microbiology. 167(9), https://doi.org/10.1099/mic.0.001084
Michelle A Schorn, Stefan Verhoeven, Lars Ridder, Florian Huber, Deepa D Acharya, Alexander A Aksenov, Gajender Aleti, Jamshid Amiri Moghaddam, Allegra T Aron, Saefuddin Aziz, Anelize Bauermeister, Katherine D Bauman, Martin Baunach, Christine Beemelmanns, J Michael Beman, María Victoria Berlanga-Clavero, Alex A Blacutt, Helge B Bode, Anne Boullie, Asker Brejnrod, Tim S Bugni, Alexandra Calteau, Liu Cao, Víctor J Carrión, Raquel Castelo-Branco, Shaurya Chanana, Alexander B Chase, Marc G Chevrette, Leticia V Costa-Lotufo, Jason M Crawford, Cameron R Currie, Bart Cuypers, Tam Dang, Tristan de Rond, Alyssa M Demko, Elke Dittmann, Chao Du, Christopher Drozd, Jean-Claude Dujardin, Rachel J Dutton, Anna Edlund, David P Fewer, Neha Garg, Julia M Gauglitz, Emily C Gentry, Lena Gerwick, Evgenia Glukhov, Harald Gross, Muriel Gugger, Dulce G Guillén Matus, Eric JN Helfrich, Benjamin-Florian Hempel, Jae-Seoun Hur, Marianna Iorio, Paul R Jensen, Kyo Bin Kang, Leonard Kaysser, Neil L Kelleher, Chung Sub Kim, Ki Hyun Kim, Irina Koester, Gabriele M König, Tiago Leao, Seoung Rak Lee, Yi-Yuan Lee, Xuanji Li, Jessica C Little, Katherine N Maloney, Daniel Männle, Andrew C McAvoy, Willam W Metcalf, Hosein Mohimani, Carlos Molina-Santiago, Bradley S Moore, Michael W Mullowney, Mitchell Muskat, Louis-Félix Nothias, Ellis C O’Neill, Elizabeth I Parkinson, Daniel Petras, Jörn Piel, Emily C Pierce, Karine Pires, Raphael Reher, Diego Romero, M Caroline Roper, Michael Rust, Hamada Saad, Carmen Saenz, Laura M Sanchez, Søren Johannes Sørensen, Margherita Sosio, Roderich D Süssmuth, Douglas Sweeney, Kapil Tahlan, Regan J Thomson, Nicholas J Tobias, Amaro E Trindade-Silva, Gilles P van Wezel, Mingxun Wang, Kelly C Weldon, Fan Zhang, Nadine Ziemert, Katherine R Duncan, Max Crüsemann, Simon Rogers, Pieter C Dorrestein, Marnix H Medema, Justin JJ van der Hooft (2021) A community resource for paired genomic and metabolomic data mining. Nature Chemical Biology. 17(4) 363-368 www.nature.com/articles/s41589-020-00724-z
Soldatou, S., Eldjarn, G. H., Ramsey, A., van der Hooft, J. J. J., Hughes, A. H., Rogers, S. & Duncan, K. R,* Comparative metabologenomics analysis of polar actinomycetes (2021) Marine Drugs. 19(2) 103; [*corresponding author]. www.mdpi.com/1660-3397/19/2/103
Hughes, A. H., Magot, F., Tawfike, A. F., Rad-Menéndez, C., Thomas, N., Young, L. C., Stucchi, L., Carettoni, D., Stanley, M. S., Edrada-Ebel, R., Duncan, K. R.* (2021) Exploring the Chemical Space of Macro- and Micro-Algae Using Comparative Metabolomics. Microorganisms, 9(2), 311; [*corresponding author]. https://doi.org/10.3390/microorganisms9020311
van der Hooft, J. J., Mohimani, H., Bauermeister, A., Dorrestein, P. C., Duncan, K. R.*, Medema, M. H.* (2020) Linking Genomics and Metabolomics to Chart Specialized Metabolite Discovery. Chem. Soc. Rev., 2020,49, 3297-3314 [*co-corresponding author] https://doi.org/10.1039/D0CS00162G
Prudence, S. M. M., Addington, E. , Castaño-Espriu, L., Mark, D. R., Pintor-Escobar, L., Russell, A. H., McLean T. C. Advances in Actinomycete Research: an Actinobase Review of 2019. Microbiology. https://doi.org/10.1099/mic.0.000944
Eldjarn, G. Ramsay, A. van der Hooft, JJJ. Duncan, K. R. Soldatou, S. Rousu, J. Rogers, S*. (2020). Ranking Microbial Metabolomic and Genomic Links Using Correlation-Based and Feature-Based Scoring Functions. [* Corresponding author]. PLoS Computational Biology. 17(5): e1008920. journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008920
Millán-Aguiñaga, N. Soldatou, S., Brozio, S., Munnoch, J. T., Howe, J., Hoskisson, P. A., Duncan, K. R*. (2019) Awakening Ancient Polar Actinobacteria: Diversity, Evolution and Specialized Metabolite Potential. [* Corresponding author]. Microbiology. 165(1), 1169-1180, https://doi.org/10.1099/mic.0.000845
Soltatou, S.+, Eldjarn, G. H.+, Huerta-Uribe, A.+, Rogers, S., Duncan, K. R.* (2019) Linking Biosynthetic and Chemical Space to Accelerate Microbial Secondary Metabolite Discovery. [+ Co-first author and * corresponding author]. FEMS Microbiology Letters. 366(13), fnz142. doi.org/10.1093/femsle/fnz142
Hicks, N. R.*+, Liu, X., Gregory, R., Kenny, J. Lucaci, A., Lenzi, L., Paterson, D. M., Duncan, K. R.*+ (2018) Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Costal Sediments. [+ Co-first author and * Co-corresponding author]. Frontiers in Microbiology. doi: https://doi.org/10.3389/fmicb.2018.01730
Vallet, M., Vanbellingen, Q. P. Fu, T., Le Caer, J-P, Della-Negra, S., Touboul, D., Duncan, K. R., Nay, B., Brunelle, A. and Prado, S. (2017) An integrative approach to decipher the chemical antagonism between the competing endophytes Paraconiothyrium variabile and Bacillus subtilis. Journal of Natural Products doi:10.1021/acs.jnatprod.6b01185
Wang, M., Carver, J. J., Phelan, V. V., Sanchez, L. M., Garg, N., Peng, Y., Nguyen, D. D., Watrous, J., Kapono, C. A., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A. V., Meehan, M. J., Liu, W-T., Crüseman, M., Boudreau, P. D., Esquenazi, E., Sandoval-Calderón, M., Kersten, R. D., Pace, L. A., Quinn, R. A., Duncan, K. R., Hsu, C-C., Floros, D. J., Gavilan, R. G., Kleigrewe, K., Northen, T., Dutton, R. J., Parrot, D., Carlson, E. E., Aigle, B., Michelsen, C. F., Jelsbak, L., Sohlenkamp, C., Pevzner, P., Edlund, A., McLean, J., Piel, J., Murphy, B. T., Gerwick, L., Liaw, C-C., Yang, Y-L., Humpf, H-U., Maansson, M., Keyzers, R. A., Sims, A. C., Johnson, A. R., Sidebottom, A. M., Sedio, B. E., Klitgaard, A., Larson, C. B., Boya P, C. A., Torres-Mendoza, D., Gonzalez, D. J., Silva, D. B., Marques, L. M., Demarque, D. P., Pociute, E., O'Neill, E. C., Briand, E., Helfrich, E. J. N., Granatosky, E. A., Glukhov, E., Ryffel, F., Houson, H., Mohimani, H., Kharbush, J. J., Zeng, Y., Vorholt, J. A., Kurita, K. L., Charusanti, P., McPhail, K. L., Nielsen, K. F., Vuong, L., Elfeki, M., Traxler, M. F., Engene, N., Koyama, N., Vining, O. B., Baric, R., Silva, R. S., Mascuch, S. J., Tomasi, S., Jenkins, S., Macherla, V., Hoffman, T., Agarwal, V., Williams, P. G., Dai, J., Neupane, R., Gurr, J., Rodríguez, A. M. C., Lamsa, A., Zhang, C., Dorrestein, K., Duggan, B. M., Almaliti, J., Allard, P, M., Phapale, P., Nothias, L. F., Alexandrov, T., Litaudon, M., Wolfender, J. L., Kyle, J. E., Metz, T. O., Peryea, T., Nguyen, D-T., VanLeer, D., Shinn, P., Jadhav, A., Müller, R., Waters, K. M., Shi, W., Liu, X., Zhang, L., Knight, R., Jensen, P. R., Palsson, B. O., Pogliano, K., Linington, R. G., Gutiérrez, M., Lopes, N. P., Gerwick, W. H., Moore, B. S., Dorrestein, P. C. Bandeira, N. (2016) Sharing and community curation of mass spectra by GNPS. Nature Biotechnology 34, 828–837. doi:10.1038/nbt.3597
Buchholtz, H. and Duncan, K. R.* (2016) Antarctic Sponge Associated Microbial Chemistry with Biomedical Relevance – the Need for Ecologically Driven Studies. [*Corresponding author] August 2016. Curr. Org. Chem. 21(5): 395-401 doi:10.2174/1385272820666161020122153
Purves, K., MacIntyre, L., Brennan, D., Hreggviosson, G. O., Kuttner, E., Asgeirsdottir, M. E., Young, L. C., Green, D.H. Edrada-Ebel, R, Duncan, K.R.* (2016) Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting. Metabolites 6(1): 2. [*Corresponding author] doi:10.3390/metabo6010002
Duncan, K.R., Crüsemann, M., Lechner, A., Sarkar, A., Li, J., Ziemert, N., Wang, M., Moore, B.S., Dorrestein, P.C. and Jensen, P.R. (2015) Molecular Network and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species. Chem. & Biol. 22: 1-12. http://dx.doi.org/10.1016/j.chembiol.2015.03.010
Patin, N.V., Duncan, K.R., Jensen, P. R. (2015) Competitive Strategies Differentiate Closely-Related Species of Marine Bacteria. ISME J. 10(2): 478-490 doi.org/10.1038/ismej.2015.128
Duncan, K., Haltli, B., Gill, K.A. and Kerr R.G. (2014) Bioprospecing from Marine Sediments of New Brunswick, Canada: Exploring the Relationship Between Total Bacterial Diversity and Actinobacteria Diversity. Mar. Drugs, 12, 899-925; doi:10.3390/md12020899
Duncan, K.R., Haltli, B., Gill, K.A., Correa, H., Berrué, F. and Kerr, R.G. (2014) Exploring the Diversity and Metabolic Potential of Actinomycetes from Temperate Marine Sediments from Newfoundland, Canada. J. Ind. Microbiol. Biotech 42(1): 57-72 doi:10.1007/s10295-014-1529x
Weitz, M., Duncan, K., Pattin, N.V., and Jensen, P.R. (2013) Antagonistic Interactions Mediated by Marine Bacteria, the Role of Small Molecules. J. Chem. Ecol. 39(7): 879-891 doi:10.1007/s10886-013-0316-x
Forner, D., Berrue, F., Correa, H., Duncan, K., Kerr, R.G. (2013) Chemical Dereplication of Marine Actinomycetes by Liquid Chromatography - High Resolution Mass Spectrometry Profiling and Statistical Analysis Anal. Chim. Acta. 12(805): 70-79 doi:10.1016/j.aca.2013.10.029