Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis.

Autor: Signe Tang Karlsen, Tammi Camilla Vesth, Gunnar Oregaard, Vera Kuzina Poulsen, Ole Lund, Gemma Henderson, Jacob Bælum

Publikováno v: PLoS ONE, Vol 16, Iss 3, p e0246287 (2021)

Lactococcus lactis strains are important components in industrial starter cultures for cheese manufacturing. They have many strain-dependent properties, which affect the final product. Here, we explored the use of machine learning to create systemati

Externí odkaz: https://doaj.org/article/4509328bfb6b40a090ec5fbf52567e40

Genus level analysis of PKS-NRPS and NRPS-PKS hybrids reveals their origin in Aspergilli

Autor: Tammi Camilla Vesth, Mikael Rørdam Andersen, Sebastian Theobald

Publikováno v: BMC Genomics
Theobald, S, Vesth, T C & Andersen, M R 2019, ' Genus level analysis of PKS-NRPS and NRPS-PKS hybrids reveals their origin in Aspergilli ', BMC Genomics, vol. 20, no. 1, 847 . https://doi.org/10.1186/s12864-019-6114-2
BMC Genomics, Vol 20, Iss 1, Pp 1-12 (2019)

Background Filamentous fungi produce a vast amount of bioactive secondary metabolites (SMs) synthesized by e.g. hybrid polyketide synthase-nonribosomal peptide synthetase enzymes (PKS-NRPS; NRPS-PKS). While their domain structure suggests a common an

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4bf511848de7f3ed6483002f280a43d0
http://europepmc.org/articles/PMC6854747

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Autor: Robert Riley, Martin Engelhard Kogle, Jakob Blæsbjerg Hoof, Kerrie Barry, Kimchi Strasser, Ronald P. de Vries, Kurt LaButti, Jon K. Magnuson, Alicia Clum, Pallavi A. Phatale, Tammi Camilla Vesth, Matt Nolan, Ad Wiebenga, John M. Gladden, Scott E. Baker, Sebastian Theobald, Jens Christian Frisvad, Blake A. Simmons, Kristian Fog Nielsen, Miia R. Mäkelä, Sajeet Haridas, Laura Sandor, Ellen Kirstine Lyhne, Asaf Salamov, Mikael Rørdam Andersen, Igor V. Grigoriev, Matthieu Hainaut, Thomas Ostenfeld Larsen, Elodie Drula, Jane L. Nybo, Cindy Chen, Julian Brandl, Anna Lipzen, Bernard Henrissat, Uffe Hasbro Mortensen, Erin McDonnell, Alan Kuo, Morten Thrane Nielsen, Adrian Tsang

Publikováno v: Nature Genetics
Nature Genetics, Nature Publishing Group, 2018, 50 (12), pp.1688-1695. ⟨10.1038/s41588-018-0246-1⟩
Nature Genetics, 50(12), 1688-+. Nature Publishing Group
Nature Genetics, 2018, 50 (12), pp.1688-1695. ⟨10.1038/s41588-018-0246-1⟩
Nature genetics, vol 50, iss 12
Vesth, TC; Nybo, JL; Theobald, S; Frisvad, JC; Larsen, TO; Nielsen, KF; et al.(2018). Investigation of inter-and intraspecies variation through genome sequencing of Aspergillus section Nigri. Nature Genetics. doi: 10.1038/s41588-018-0246-1. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/37c6r9tq
Vesth, T C, Nybo, J L, Theobald, S, Frisvad, J C, Larsen, T O, Nielsen, K F, Hoof, J B, Brandl, J, Salamov, A, Riley, R, Gladden, J M, Phatale, P, Nielsen, M T, Lyhne, E K, Kogle, M E, Strasser, K, McDonnell, E, Barry, K, Clum, A, Chen, C, LaButti, K, Haridas, S, Nolan, M, Sandor, L, Kuo, A, Lipzen, A, Hainaut, M, Drula, E, Tsang, A, Magnuson, J K, Henrissat, B, Wiebenga, A, Simmons, B A, Mäkelä, M R, de Vries, R P, Grigoriev, I V, Mortensen, U H, Baker, S E & Andersen, M R 2018, ' Investigation of inter-and intraspecies variation through genome sequencing of Aspergillus section Nigri ', Nature Genetics, vol. 50, pp. 1688–1695 . https://doi.org/10.1038/s41588-018-0246-1
Nature Genetics, 50, 1688. Nature Publishing Group

© 2018, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply. Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To le

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a11ff4506d0cc40cbfeb88507ec955b0
https://hal-amu.archives-ouvertes.fr/hal-02094492

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Autor: Giancarlo Perrone, Anna Lipzen, Igor V. Grigoriev, Ana Ramón, Claudio Scazzocchio, Karin M. Overkamp, David Cánovas, Alan Kuo, George Diallinas, Kristiina Hildén, Tabea Schütze, Asaf Salamov, Patricia A. vanKuyk, Anthony Levasseur, Cindy Choi, Tamás Emri, Bernard Henrissat, Erzsébet Sándor, Gerhard H. Braus, Evy Battaglia, Camila Caldana, María Harispe, Kurt LaButti, Nadhira Salih, Andrew MacCabe, Renato Augusto Corrêa dos Santos, Stefan Rauscher, Guillermo Aguilar-Osorio, François Piumi, Ellen Lagendijk, Axel A. Brakhage, Giuseppina Mulè, David B. Archer, Cristiane Uchima, André Damasio, Nada Kraševec, Tammi Camilla Vesth, Petter Melin, Rob Habgood, Susanna A. Braus-Stromeyer, Gavin Sherlock, Mojtaba Asadollahi, Marion Askin, Abeer Hossain, Miia R. Mäkelä, Fusheng Chen, Erzsébet Fekete, Natalia Mielnichuk, Márton Miskei, Jennifer R. Wortman, Diego Mauricio Riaño-Pachón, Manuel Sanguinetti, Ákos Molnár, Alicia Clum, Jaap Visser, Scott E. Baker, Jos Houbraken, Eric Record, Reinhard Fischer, Rob Samson, Isabelle Benoit, Christos Gournas, Kristina Sepčić, Harald Kusch, Paul S. Dyer, Diana van Rossen-Uffink, Nathalie van de Wiele, Antonio F. Logrieco, Eugenia Karabika, Jean Paul Ouedraogo, Roberto Ruller, Juliana Velasco de Castro Oliveira, Alla Lapidus, Gustavo C. Cerqueira, Margarita Orejas, Miaomiao Zhou, Vicky Sophianopoulou, Vera Meyer, Chew Yee Ngan, Levente Karaffa, Shiela E. Unkles, Hee-Soo Park, Iran Malavazi, Antonia Gallo, Sotiris Amillis, Adrian Tsang, Julian Röhrig, Ekaterina Shelest, Jens Christian Frisvad, Bernhard Seiboth, Tiziano Benocci, Ad Wiebenga, Erzsébet Orosz, Erika Lindquist, Gregor Anderluh, Vincent Robert, Ryan Hope, Matthieu Hainaut, Robert Riley, Ronald P. de Vries, Gustavo H. Goldman, Mikael Rørdam Andersen, István Pócsi, Zsolt Karányi, Hui Sun, Richard B. Todd, Jae-Hyuk Yu, Wanping Chen, Özgür Bayram, Berl R. Oakley, Antonia Susca, Michel Flipphi, Fabio M. Squina, Susanne Freyberg, Arthur F. J. Ram, Peter J. Punt, Kerrie Barry

Publikováno v: Genome Biology
Genome Biology, 2017, 18, ⟨10.1186/s13059-017-1151-0⟩
Genome Biology (18), . (2017)
Digital.CSIC. Repositorio Institucional del CSIC
instname
de Vries, R P, Riley, R, Wiebenga, A, Aguilar-Osorio, G, Amillis, S, Uchima, C A, Anderluh, G, Asadollahi, M, Askin, M, Barry, K, Battaglia, E, Bayram, Ö, Benocci, T, Braus-Stromeyer, S A, Caldana, C, Cánovas, D, Cerqueira, G C, Chen, F, Chen, W, Choi, C, Clum, A, dos Santos, R A C, de Lima Damásio, A R, Diallinas, G, Emri, T, Fekete, E, Flipphi, M, Freyberg, S, Gallo, A, Gournas, C, Habgood, R, Hainaut, M, Harispe, M L, Henrissat, B, Hildén, K S, Hope, R, Hossain, A, Karabika, E, Karaffa, L, Karányi, Z, Kraševec, N, Kuo, A, Kusch, H, LaButti, K, Lagendijk, E L, Lapidus, A, Levasseur, A, Lindquist, E, Lipzen, A, Logrieco, A F, MacCabe, A, Mäkelä, M R, Malavazi, I, Melin, P, Meyer, V, Mielnichuk, N, Miskei, M, Molnár, Á P, Mulé, G, Ngan, C Y, Orejas, M, Orosz, E, Ouedraogo, J P, Overkamp, K M, Park, H-S, Perrone, G, Piumi, F, Punt, P J, Ram, A F J, Ramón, A, Rauscher, S, Record, E, Riaño-Pachón, D M, Robert, V, Röhrig, J, Ruller, R, Salamov, A, Salih, N S, Samson, R A, Sándor, E, Sanguinetti, M, Schütze, T, Sepčić, K, Shelest, E, Sherlock, G, Sophianopoulou, V, Squina, F M, Sun, H, Susca, A, Todd, R B, Tsang, A, Unkles, S E, van de Wiele, N, van Rossen-Uffink, D, de Castro Oliveira, J V, Vesth, T C, Visser, J, Yu, J-H, Zhou, M, Andersen, M R, Archer, D B, Baker, S E, Benoit, I, Brakhage, A A, Braus, G H, Fischer, R, Frisvad, J C, Goldman, G H, Houbraken, J, Oakley, B, Pócsi, I, Scazzocchio, C, Seiboth, B, vanKuyk, P A, Wortman, J, Dyer, P S & Grigoriev, I V 2017, ' Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus ', Genome Biology, vol. 18, no. 1, 28 . https://doi.org/10.1186/s13059-017-1151-0
Genome biology (Online) 18 (2017): 2–45. doi:10.1186/s13059-017-1151-0
info:cnr-pdr/source/autori:Ronald P. de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia,.. Antonia Gallo, Antonio F. Logrieco, ....Giuseppina Mulé, ...Giancarlo Perrone, .... Antonia Susca, ...Jennifer Wortman, Paul S. Dyer, Igor V. Grigoriev/titolo:Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus/doi:10.1186%2Fs13059-017-1151-0/rivista:Genome biology (Online)/anno:2017/pagina_da:2/pagina_a:45/intervallo_pagine:2–45/volume:18
Genome Biology, 18. BioMed Central
Genome Biology, 18, 28
Genome Biology, BioMed Central, 2017, 18, ⟨10.1186/s13059-017-1151-0⟩
De Vries, R P, Riley, R, Wiebenga, A, Aguilar-Osorio, G, Amillis, S, Uchima, C A, Anderluh, G, Asadollahi, M, Askin, M, Barry, K, Battaglia, E, Bayram, Ö, Benocci, T, Braus-Stromeyer, S A, Caldana, C, Cánovas, D, Cerqueira, G C, Chen, F, Chen, W, Choi, C, Clum, A, dos Santos, R A C, Damásio, A R D L, Diallinas, G, Emri, T, Fekete, E, Flipphi, M, Freyberg, S, Gallo, A, Gournas, C, Habgood, R, Hainaut, M, Harispe, M L, Henrissat, B, Hildén, K S, Hope, R, Hossain, A, Karabika, E, Karaffa, L, Karányi, Z, Kraševec, N, Kuo, A, Kusch, H, Labutti, K, Lagendijk, E L, Lapidus, A, Levasseur, A, Lindquist, E, Lipzen, A, Logrieco, A F, Maccabe, A, Mäkelä, M R, Malavazi, I, Melin, P, Meyer, V, Mielnichuk, N, Miskei, M, Molnár, Á P, Mulé, G, Ngan, C Y, Orejas, M, Orosz, E, Ouedraogo, J P, Overkamp, K M, Park, H-S, Perrone, G, Piumi, F, Punt, P J, Ram, A F J, Ramón, A, Rauscher, S, Record, E, Riaño-Pachón, D M, Robert, V, Röhrig, J, Ruller, R, Salamov, A, Salih, N S, Samson, R A, Sándor, E, Sanguinetti, M, Schütze, T, Sepčić, K, Shelest, E, Sherlock, G, Sophianopoulou, V, Squina, F M, Sun, H, Susca, A, Todd, R B, Tsang, A, Unkles, S E, van de Wiele, N, Van Rossen-Uffink, D, Oliveira, J V D C, Vesth, T C, Visser, J, Yu, J-H, Zhou, M, Andersen, M R, Archer, D B, Baker, S E, Benoit, I, Brakhage, A A, Braus, G H, Fischer, R, Frisvad, J C, Goldman, G H, Houbraken, J, Oakley, B, Pócsi, I, Scazzocchio, C, Seiboth, B, Vankuyk, P A, Wortman, J, Dyer, P S & Grigoriev, I V 2017, ' Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus ', Genome Biology, vol. 18, no. 1, 28, pp. 1-45 . https://doi.org/10.1186/s13059-017-1151-0
Genome biology, 18 (1
Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
idUS. Depósito de Investigación de la Universidad de Sevilla
Genome biology, 18 (1), 18:28
Genome Biology, 2017, 18, 〈10.1186/s13059-017-1151-0〉
de Vries, R P, Riley, R, Wiebenga, A, Aguilar-Osorio, G, Amillis, S, Uchima, C A, Anderluh, G, Asadollahi, M, Askin, M, Barry, K, Battaglia, E, Bayram, Ö, Benocci, T, Braus-Stromeyer, S A, Caldana, C, Cánovas, D, Cerqueira, G C, Chen, F, Chen, W, Choi, C, Clum, A, dos Santos, R A C, de Lima Damásio, A R, Diallinas, G, Emri, T, Fekete, E, Flipphi, M, Freyberg, S, Gallo, A, Gournas, C, Habgood, R, Hainaut, M, Harispe, M L, Henrissat, B, Hildén, K S, Hope, R, Hossain, A, Karabika, E, Karaffa, L, Karányi, Z, Kraševec, N, Kuo, A, Kusch, H, LaButti, K, Lagendijk, E L, Lapidus, A, Levasseur, A, Lindquist, E, Lipzen, A, Logrieco, A F, MacCabe, A, Mäkelä, M R, Malavazi, I, Melin, P, Meyer, V, Mielnichuk, N, Miskei, M, Molnár, Á P, Mulé, G, Ngan, C Y, Orejas, M, Orosz, E, Ouedraogo, J P, Overkamp, K M, Park, H S, Perrone, G, Piumi, F, Punt, P J, Ram, A F J, Ramón, A, Rauscher, S, Record, E, Riaño-Pachón, D M, Robert, V A R G, Röhrig, J, Ruller, R, Salamov, A, Salih, N S, Samson, R A, Sándor, E, Sanguinetti, M, Schütze, T, Sepčić, K, Shelest, E, Sherlock, G, Sophianopoulou, V, Squina, F M, Sun, J-H, Susca, A, Todd, R B, Tsang, A, Unkles, S E, van de Wiele, N, van Rossen-Uffink, D, de Castro Oliveira, J V, Vesth, T C, Visser, J, Yu, J-H, Zhou, M, Andersen, M R, Archer, D B, Baker, S E, Benoit, I, Brakhage, A A, Braus, G H, Fischer, R, Frisvad, J C, Goldman, G H, Houbraken, J, Oakley, B R, Pócsi, I, Scazzocchio, C, Seiboth, B, vanKuyk, P A, Wortman, J R, Dyer, P S & Grigoriev, I V 2017, ' Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus ', Genome Biology (Online Edition), vol. 18, 28 . https://doi.org/10.1186/s13059-017-1151-0

[Background] The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an impor

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::519303b98e4e1e5539002b2da2f950e0
https://hal.science/hal-01496186

Ortholog prediction of the Aspergillus genus applicable for synthetic biology

Autor: Jane Nybo, Tammi Camilla Vesth, Sebastian Theobald, Jens Frisvad, Grigoriev, Igor V., Baker, Scott E., Mikael Rørdam Andersen

Publikováno v: Rasmussen, J L N, Vesth, T C, Theobald, S, Frisvad, J C, Grigoriev, I V, Baker, S E & Andersen, M R 2016, ' Ortholog prediction of the Aspergillus genus applicable for synthetic biology ' Cell Symposia: Technology. Biology. Data Science 2016, Berkeley, United States, 09/10/2016-11/10/2016, .
Technical University of Denmark Orbit

The Aspergillus genus contains leading industrial microorganisms, excelling in producing bioactive compounds and enzymes. Using synthetic biology and bioinformatics, we aim to re-engineer these organisms for applications within human health, pharmace

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::2cf8abb52d4c10b4db0da159893153e6
http://orbit.dtu.dk/ws/files/127466595/Abstract_CSYN2016_submittet.pdf