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Items: 1 to 50 of 225

1.

Enhanced Inhibition of Influenza A Virus Adhesion by Di- and Trivalent Hemagglutinin Inhibitors.

Lu W, Du W, Somovilla VJ, Yu G, Haksar D, de Vries E, Boons GJ, de Vries RP, de Haan CAM, Pieters RJ.

J Med Chem. 2019 Jul 11;62(13):6398-6404. doi: 10.1021/acs.jmedchem.9b00303. Epub 2019 Jun 28.

2.

N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses.

Broszeit F, Tzarum N, Zhu X, Nemanichvili N, Eggink D, Leenders T, Li Z, Liu L, Wolfert MA, Papanikolaou A, Martínez-Romero C, Gagarinov IA, Yu W, García-Sastre A, Wennekes T, Okamatsu M, Verheije MH, Wilson IA, Boons GJ, de Vries RP.

Cell Rep. 2019 Jun 11;27(11):3284-3294.e6. doi: 10.1016/j.celrep.2019.05.048.

3.

Protecting-Group-Controlled Enzymatic Glycosylation of Oligo-N-Acetyllactosamine Derivatives.

Gagarinov IA, Li T, Wei N, Sastre Toraño J, de Vries RP, Wolfert MA, Boons GJ.

Angew Chem Int Ed Engl. 2019 Jul 29;58(31):10547-10552. doi: 10.1002/anie.201903140. Epub 2019 Jul 1.

PMID:
31108002
4.

A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi.

Lubbers RJM, Dilokpimol A, Visser J, Mäkelä MR, Hildén KS, de Vries RP.

Biotechnol Adv. 2019 May 7. pii: S0734-9750(19)30077-1. doi: 10.1016/j.biotechadv.2019.05.002. [Epub ahead of print] Review.

PMID:
31075306
5.

Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens.

Casado López S, Peng M, Daly P, Andreopoulos B, Pangilinan J, Lipzen A, Riley R, Ahrendt S, Ng V, Barry K, Daum C, Grigoriev IV, Hildén KS, Mäkelä MR, de Vries RP.

Microbiol Resour Announc. 2019 May 2;8(18). pii: e00264-19. doi: 10.1128/MRA.00264-19.

6.

Deletion of either the regulatory gene ara1 or metabolic gene xki1 in Trichoderma reesei leads to increased CAZyme gene expression on crude plant biomass.

Benocci T, Aguilar-Pontes MV, Kun RS, Lubbers RJM, Lail K, Wang M, Lipzen A, Ng V, Grigoriev IV, Seiboth B, Daly P, de Vries RP.

Biotechnol Biofuels. 2019 Apr 9;12:81. doi: 10.1186/s13068-019-1422-y. eCollection 2019.

7.

Glycosylation of the viral attachment protein of avian coronavirus is essential for host cell and receptor binding.

Parsons LM, Bouwman KM, Azurmendi H, de Vries RP, Cipollo JF, Verheije MH.

J Biol Chem. 2019 May 10;294(19):7797-7809. doi: 10.1074/jbc.RA119.007532. Epub 2019 Mar 22.

PMID:
30902814
8.

Virus recognition of glycan receptors.

Thompson AJ, de Vries RP, Paulson JC.

Curr Opin Virol. 2019 Feb;34:117-129. doi: 10.1016/j.coviro.2019.01.004. Epub 2019 Mar 5. Review.

PMID:
30849709
9.

Guinea Fowl Coronavirus Diversity Has Phenotypic Consequences for Glycan and Tissue Binding.

Bouwman KM, Delpont M, Broszeit F, Berger R, Weerts EAWS, Lucas MN, Delverdier M, Belkasmi S, Papanikolaou A, Boons GJ, Guérin JL, de Vries RP, Ducatez MF, Verheije MH.

J Virol. 2019 May 1;93(10). pii: e00067-19. doi: 10.1128/JVI.00067-19. Print 2019 May 15.

10.

Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation.

Kun RS, Gomes ACS, Hildén KS, Salazar Cerezo S, Mäkelä MR, de Vries RP.

Biotechnol Adv. 2019 Nov 1;37(6):107361. doi: 10.1016/j.biotechadv.2019.02.017. Epub 2019 Feb 27. Review.

PMID:
30825514
11.

Liposome-targeted recombinant human acid sphingomyelinase: Production, formulation, and in vitro evaluation.

Aldosari MH, de Vries RP, Rodriguez LR, Hesen NA, Beztsinna N, van Kuilenburg ABP, Hollak CEM, Schellekens H, Mastrobattista E.

Eur J Pharm Biopharm. 2019 Apr;137:185-195. doi: 10.1016/j.ejpb.2019.02.019. Epub 2019 Feb 25.

PMID:
30818011
12.

The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum.

Coconi Linares N, Di Falco M, Benoit-Gelber I, Gruben BS, Peng M, Tsang A, Mäkelä MR, de Vries RP.

N Biotechnol. 2019 Jul 25;51:57-66. doi: 10.1016/j.nbt.2019.02.005. Epub 2019 Feb 20.

PMID:
30797054
13.

Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales).

Urquhart AS, Mondo SJ, Mäkelä MR, Hane JK, Wiebenga A, He G, Mihaltcheva S, Pangilinan J, Lipzen A, Barry K, de Vries RP, Grigoriev IV, Idnurm A.

Front Microbiol. 2018 Dec 13;9:3058. doi: 10.3389/fmicb.2018.03058. eCollection 2018.

14.

Fluorescent Trimeric Hemagglutinins Reveal Multivalent Receptor Binding Properties.

Nemanichvili N, Tomris I, Turner HL, McBride R, Grant OC, van der Woude R, Aldosari MH, Pieters RJ, Woods RJ, Paulson JC, Boons GJ, Ward AB, Verheije MH, de Vries RP.

J Mol Biol. 2019 Feb 15;431(4):842-856. doi: 10.1016/j.jmb.2018.12.014. Epub 2018 Dec 29.

15.

l-Arabinose induces d-galactose catabolism via the Leloir pathway in Aspergillus nidulans.

Németh Z, Kulcsár L, Flipphi M, Orosz A, Aguilar-Pontes MV, de Vries RP, Karaffa L, Fekete E.

Fungal Genet Biol. 2019 Feb;123:53-59. doi: 10.1016/j.fgb.2018.11.004. Epub 2018 Nov 26.

PMID:
30496805
16.

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli.

Mäkelä MR, DiFalco M, McDonnell E, Nguyen TTM, Wiebenga A, Hildén K, Peng M, Grigoriev IV, Tsang A, de Vries RP.

Stud Mycol. 2018 Sep;91:79-99. doi: 10.1016/j.simyco.2018.09.001. Epub 2018 Oct 29.

17.

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.

Aguilar-Pontes MV, Brandl J, McDonnell E, Strasser K, Nguyen TTM, Riley R, Mondo S, Salamov A, Nybo JL, Vesth TC, Grigoriev IV, Andersen MR, Tsang A, de Vries RP.

Stud Mycol. 2018 Sep;91:61-78. doi: 10.1016/j.simyco.2018.10.001. Epub 2018 Oct 7.

18.

Duplications and losses of genes encoding known elements of the stress defence system of the Aspergilli contribute to the evolution of these filamentous fungi but do not directly influence their environmental stress tolerance.

Emri T, Antal K, Riley R, Karányi Z, Miskei M, Orosz E, Baker SE, Wiebenga A, de Vries RP, Pócsi I.

Stud Mycol. 2018 Sep;91:23-36. doi: 10.1016/j.simyco.2018.10.003. Epub 2018 Oct 11.

19.

The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet.

Grum-Grzhimaylo AA, Falkoski DL, van den Heuvel J, Valero-Jiménez CA, Min B, Choi IG, Lipzen A, Daum CG, Aanen DK, Tsang A, Henrissat B, Bilanenko EN, de Vries RP, van Kan JAL, Grigoriev IV, Debets AJM.

Mol Ecol. 2018 Dec;27(23):4808-4819. doi: 10.1111/mec.14912. Epub 2018 Nov 22.

PMID:
30368956
20.

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

Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, 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 JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR.

Nat Genet. 2018 Dec;50(12):1688-1695. doi: 10.1038/s41588-018-0246-1. Epub 2018 Oct 22.

PMID:
30349117
21.

A community-driven reconstruction of the Aspergillus niger metabolic network.

Brandl J, Aguilar-Pontes MV, Schäpe P, Noerregaard A, Arvas M, Ram AFJ, Meyer V, Tsang A, de Vries RP, Andersen MR.

Fungal Biol Biotechnol. 2018 Sep 26;5:16. doi: 10.1186/s40694-018-0060-7. eCollection 2018.

22.

Selective Cleavage of Lignin β-O-4 Aryl Ether Bond by β-Etherase of the White-Rot Fungus Dichomitus squalens.

Marinović M, Nousiainen P, Dilokpimol A, Kontro J, Moore R, Sipilä J, de Vries RP, Mäkelä MR, Hildén K.

ACS Sustain Chem Eng. 2018 Mar 5;6(3):2878-2882. doi: 10.1021/acssuschemeng.7b03619. Epub 2018 Jan 25.

23.

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood.

Daly P, López SC, Peng M, Lancefield CS, Purvine SO, Kim YM, Zink EM, Dohnalkova A, Singan VR, Lipzen A, Dilworth D, Wang M, Ng V, Robinson E, Orr G, Baker SE, Bruijnincx PCA, Hildén KS, Grigoriev IV, Mäkelä MR, de Vries RP.

Environ Microbiol. 2018 Nov;20(11):4141-4156. doi: 10.1111/1462-2920.14416. Epub 2018 Oct 18.

PMID:
30246402
24.

Enzymatic Adaptation of Podospora anserina to Different Plant Biomass Provides Leads to Optimized Commercial Enzyme Cocktails.

Benocci T, Daly P, Aguilar-Pontes MV, Lail K, Wang M, Lipzen A, Ng V, Grigoriev IV, de Vries RP.

Biotechnol J. 2019 Apr;14(4):e1800185. doi: 10.1002/biot.201800185. Epub 2018 Oct 8.

25.

Physiological background of the remarkably high Cd2+ tolerance of the Aspergillus fumigatus Af293 strain.

Kurucz V, Kiss B, Szigeti ZM, Nagy G, Orosz E, Hargitai Z, Harangi S, Wiebenga A, de Vries RP, Pócsi I, Emri T.

J Basic Microbiol. 2018 Nov;58(11):957-967. doi: 10.1002/jobm.201800200. Epub 2018 Aug 31.

PMID:
30168857
26.

Evolutionary Adaptation to Generate Mutants.

de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I.

Methods Mol Biol. 2018;1775:133-137. doi: 10.1007/978-1-4939-7804-5_12.

PMID:
29876815
27.

Introduction: Overview of Fungal Genomics.

de Vries RP, Grigoriev IV, Tsang A.

Methods Mol Biol. 2018;1775:1-7. doi: 10.1007/978-1-4939-7804-5_1.

PMID:
29876804
28.

In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics.

Peng M, Aguilar-Pontes MV, de Vries RP, Mäkelä MR.

Front Microbiol. 2018 May 18;9:1045. doi: 10.3389/fmicb.2018.01045. eCollection 2018.

29.

Talaromyces borbonicus, sp. nov., a novel fungus from biodegraded Arundo donax with potential abilities in lignocellulose conversion.

Varriale S, Houbraken J, Granchi Z, Pepe O, Cerullo G, Ventorino V, Chin-A-Woeng T, Meijer M, Riley R, Grigoriev IV, Henrissat B, de Vries RP, Faraco V.

Mycologia. 2018 Mar-Apr;110(2):316-324. doi: 10.1080/00275514.2018.1456835. Epub 2018 May 29.

PMID:
29843575
30.

The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA.

Mäkelä MR, Aguilar-Pontes MV, van Rossen-Uffink D, Peng M, de Vries RP.

Sci Rep. 2018 Apr 27;8(1):6655. doi: 10.1038/s41598-018-25152-x.

31.

Characterization of a feruloyl esterase from Aspergillus terreus facilitates the division of fungal enzymes from Carbohydrate Esterase family 1 of the carbohydrate-active enzymes (CAZy) database.

Mäkelä MR, Dilokpimol A, Koskela SM, Kuuskeri J, de Vries RP, Hildén K.

Microb Biotechnol. 2018 Sep;11(5):869-880. doi: 10.1111/1751-7915.13273. Epub 2018 Apr 26.

32.

Fungal Stress Database (FSD)--a repository of fungal stress physiological data.

Orosz E, van de Wiele N, Emri T, Zhou M, Robert V, de Vries RP, Pócsi I.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay009.

33.

On the origin of vanillyl alcohol oxidases.

Gygli G, de Vries RP, van Berkel WJH.

Fungal Genet Biol. 2018 Jul;116:24-32. doi: 10.1016/j.fgb.2018.04.003. Epub 2018 Apr 5.

34.

Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga.

Mäkelä MR, Peng M, Granchi Z, Chin-A-Woeng T, Hegi R, van Pelt SI, Ahrendt S, Riley R, Hainaut M, Henrissat B, Grigoriev IV, de Vries RP, Hildén KS.

Genome Announc. 2018 Apr 5;6(14). pii: e01414-17. doi: 10.1128/genomeA.01414-17.

35.

Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot Fungus Dichomitus squalens.

Casado López S, Peng M, Issak TY, Daly P, de Vries RP, Mäkelä MR.

Appl Environ Microbiol. 2018 May 17;84(11). pii: e00403-18. doi: 10.1128/AEM.00403-18. Print 2018 Jun 1.

36.

Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans.

Khosravi C, Battaglia E, Kun RS, Dalhuijsen S, Visser J, Aguilar-Pontes MV, Zhou M, Heyman HM, Kim YM, Baker SE, de Vries RP.

BMC Genomics. 2018 Mar 22;19(1):214. doi: 10.1186/s12864-018-4609-x.

37.

Enhanced Human-Type Receptor Binding by Ferret-Transmissible H5N1 with a K193T Mutation.

Peng W, Bouwman KM, McBride R, Grant OC, Woods RJ, Verheije MH, Paulson JC, de Vries RP.

J Virol. 2018 Apr 27;92(10). pii: e02016-17. doi: 10.1128/JVI.02016-17. Print 2018 May 15.

38.

A senescence-delaying pre-culture medium for transcriptomics of Podospora anserina.

Benocci T, de Vries RP, Daly P.

J Microbiol Methods. 2018 Mar;146:33-36. doi: 10.1016/j.mimet.2018.01.010. Epub 2018 Feb 3.

39.

Draft Genome Sequence of Talaromyces adpressus.

Cerullo G, Houbraken J, Granchi Z, Pepe O, Varriale S, Ventorino V, Chin-A-Woeng T, Meijer M, de Vries RP, Faraco V.

Genome Announc. 2018 Jan 11;6(2). pii: e01430-17. doi: 10.1128/genomeA.01430-17.

40.

The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates.

Pontes MVA, Patyshakuliyeva A, Post H, Jurak E, Hildén K, Altelaar M, Heck A, Kabel MA, de Vries RP, Mäkelä MR.

Fungal Genet Biol. 2018 Mar;112:12-20. doi: 10.1016/j.fgb.2017.12.004. Epub 2017 Dec 22.

41.

ARA1 regulates not only l-arabinose but also d-galactose catabolism in Trichoderma reesei.

Benocci T, Aguilar-Pontes MV, Kun RS, Seiboth B, de Vries RP, Daly P.

FEBS Lett. 2018 Jan;592(1):60-70. doi: 10.1002/1873-3468.12932. Epub 2017 Dec 19.

42.

Fungal feruloyl esterases: Functional validation of genome mining based enzyme discovery including uncharacterized subfamilies.

Dilokpimol A, Mäkelä MR, Varriale S, Zhou M, Cerullo G, Gidijala L, Hinkka H, Brás JLA, Jütten P, Piechot A, Verhaert R, Hildén KS, Faraco V, de Vries RP.

N Biotechnol. 2018 Mar 25;41:9-14. doi: 10.1016/j.nbt.2017.11.004. Epub 2017 Nov 23.

PMID:
29174720
43.

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger.

Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP.

BMC Genomics. 2017 Nov 23;18(1):900. doi: 10.1186/s12864-017-4164-x.

44.

In vivo functional analysis of L-rhamnose metabolic pathway in Aspergillus niger: a tool to identify the potential inducer of RhaR.

Khosravi C, Kun RS, Visser J, Aguilar-Pontes MV, de Vries RP, Battaglia E.

BMC Microbiol. 2017 Nov 6;17(1):214. doi: 10.1186/s12866-017-1118-z.

45.

Fungal glucuronoyl esterases: Genome mining based enzyme discovery and biochemical characterization.

Dilokpimol A, Mäkelä MR, Cerullo G, Zhou M, Varriale S, Gidijala L, Brás JLA, Jütten P, Piechot A, Verhaert R, Faraco V, Hilden KS, de Vries RP.

N Biotechnol. 2018 Jan 25;40(Pt B):282-287. doi: 10.1016/j.nbt.2017.10.003. Epub 2017 Oct 16.

PMID:
29051046
46.

High resolution visualization and exo-proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger.

Kowalczyk JE, Khosravi C, Purvine S, Dohnalkova A, Chrisler WB, Orr G, Robinson E, Zink E, Wiebenga A, Peng M, Battaglia E, Baker S, de Vries RP.

Environ Microbiol. 2017 Nov;19(11):4587-4598. doi: 10.1111/1462-2920.13923. Epub 2017 Oct 20.

PMID:
29027734
47.

Genetic transformation of the white-rot fungus Dichomitus squalens using a new commercial protoplasting cocktail.

Daly P, Slaghek GG, Casado López S, Wiebenga A, Hilden KS, de Vries RP, Mäkelä MR.

J Microbiol Methods. 2017 Dec;143:38-43. doi: 10.1016/j.mimet.2017.10.001. Epub 2017 Oct 4.

PMID:
28987554
48.

Current challenges of research on filamentous fungi in relation to human welfare and a sustainable bio-economy: a white paper.

Meyer V, Andersen MR, Brakhage AA, Braus GH, Caddick MX, Cairns TC, de Vries RP, Haarmann T, Hansen K, Hertz-Fowler C, Krappmann S, Mortensen UH, Peñalva MA, Ram AFJ, Head RM.

Fungal Biol Biotechnol. 2016 Aug 31;3:6. doi: 10.1186/s40694-016-0024-8. eCollection 2016.

49.

Combinatorial control of gene expression in Aspergillus niger grown on sugar beet pectin.

Kowalczyk JE, Lubbers RJM, Peng M, Battaglia E, Visser J, de Vries RP.

Sci Rep. 2017 Sep 27;7(1):12356. doi: 10.1038/s41598-017-12362-y.

50.

Functional diversity in Dichomitus squalens monokaryons.

Casado López S, Theelen B, Manserra S, Issak TY, Rytioja J, Mäkelä MR, de Vries RP.

IMA Fungus. 2017 Jun;8(1):17-25. doi: 10.5598/imafungus.2017.08.01.02. Epub 2017 Mar 8.

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