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Items: 39

1.

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.

2.

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.

3.

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.

4.

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
5.

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
6.

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
7.

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
8.

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
9.

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

de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV.

Genome Biol. 2017 Feb 14;18(1):28. doi: 10.1186/s13059-017-1151-0.

10.

Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification.

Mäkelä MR, Mansouri S, Wiebenga A, Rytioja J, de Vries RP, Hildén KS.

N Biotechnol. 2016 Dec 25;33(6):834-841. doi: 10.1016/j.nbt.2016.07.014. Epub 2016 Jul 25.

PMID:
27469436
11.

Protease and lipase activities of fungal and bacterial strains derived from an artisanal raw ewe's milk cheese.

Ozturkoglu-Budak S, Wiebenga A, Bron PA, de Vries RP.

Int J Food Microbiol. 2016 Nov 21;237:17-27. doi: 10.1016/j.ijfoodmicro.2016.08.007. Epub 2016 Aug 13.

PMID:
27541978
12.

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.

Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavín JL, Lee SC, Li W, Lindquist E, López-García S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martínez S, Idnurm A, Herrera-Estrella A, Gabaldón T, Grigoriev IV.

Curr Biol. 2016 Jun 20;26(12):1577-1584. doi: 10.1016/j.cub.2016.04.038. Epub 2016 May 26.

13.

Secretion of small proteins is species-specific within Aspergillus sp.

Valette N, Benoit-Gelber I, Falco MD, Wiebenga A, de Vries RP, Gelhaye E, Morel-Rouhier M.

Microb Biotechnol. 2017 Mar;10(2):323-329. doi: 10.1111/1751-7915.12361. Epub 2016 May 7.

14.

Genetic Interaction of Aspergillus nidulans galR, xlnR and araR in Regulating D-Galactose and L-Arabinose Release and Catabolism Gene Expression.

Kowalczyk JE, Gruben BS, Battaglia E, Wiebenga A, Majoor E, de Vries RP.

PLoS One. 2015 Nov 18;10(11):e0143200. doi: 10.1371/journal.pone.0143200. eCollection 2015.

15.

Enhancing saccharification of wheat straw by mixing enzymes from genetically-modified Trichoderma reesei and Aspergillus niger.

Jiang Y, Duarte AV, van den Brink J, Wiebenga A, Zou G, Wang C, de Vries RP, Zhou Z, Benoit I.

Biotechnol Lett. 2016 Jan;38(1):65-70. doi: 10.1007/s10529-015-1951-9. Epub 2015 Sep 9.

16.

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass.

Benoit I, Culleton H, Zhou M, DiFalco M, Aguilar-Osorio G, Battaglia E, Bouzid O, Brouwer CPJM, El-Bushari HBO, Coutinho PM, Gruben BS, Hildén KS, Houbraken J, Barboza LAJ, Levasseur A, Majoor E, Mäkelä MR, Narang HM, Trejo-Aguilar B, van den Brink J, vanKuyk PA, Wiebenga A, McKie V, McCleary B, Tsang A, Henrissat B, de Vries RP.

Biotechnol Biofuels. 2015 Aug 1;8:107. doi: 10.1186/s13068-015-0285-0. eCollection 2015.

17.

Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment.

Veneault-Fourrey C, Commun C, Kohler A, Morin E, Balestrini R, Plett J, Danchin E, Coutinho P, Wiebenga A, de Vries RP, Henrissat B, Martin F.

Fungal Genet Biol. 2014 Nov;72:168-181. doi: 10.1016/j.fgb.2014.08.007. Epub 2014 Aug 28.

PMID:
25173823
18.

A genomic survey of proteases in Aspergilli.

Budak SO, Zhou M, Brouwer C, Wiebenga A, Benoit I, Di Falco M, Tsang A, de Vries RP.

BMC Genomics. 2014 Jun 25;15:523. doi: 10.1186/1471-2164-15-523.

19.

The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown.

Levasseur A, Lomascolo A, Chabrol O, Ruiz-Dueñas FJ, Boukhris-Uzan E, Piumi F, Kües U, Ram AF, Murat C, Haon M, Benoit I, Arfi Y, Chevret D, Drula E, Kwon MJ, Gouret P, Lesage-Meessen L, Lombard V, Mariette J, Noirot C, Park J, Patyshakuliyeva A, Sigoillot JC, Wiebenga A, Wösten HA, Martin F, Coutinho PM, de Vries RP, Martínez AT, Klopp C, Pontarotti P, Henrissat B, Record E.

BMC Genomics. 2014 Jun 18;15:486. doi: 10.1186/1471-2164-15-486.

20.

Aspergillus niger RhaR, a regulator involved in L-rhamnose release and catabolism.

Gruben BS, Zhou M, Wiebenga A, Ballering J, Overkamp KM, Punt PJ, de Vries RP.

Appl Microbiol Biotechnol. 2014 Jun;98(12):5531-40. doi: 10.1007/s00253-014-5607-9. Epub 2014 Feb 28.

PMID:
24682478
21.

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus.

Patyshakuliyeva A, Jurak E, Kohler A, Baker A, Battaglia E, de Bruijn W, Burton KS, Challen MP, Coutinho PM, Eastwood DC, Gruben BS, Mäkelä MR, Martin F, Nadal M, van den Brink J, Wiebenga A, Zhou M, Henrissat B, Kabel M, Gruppen H, de Vries RP.

BMC Genomics. 2013 Sep 30;14:663. doi: 10.1186/1471-2164-14-663.

22.

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.

Suzuki H, MacDonald J, Syed K, Salamov A, Hori C, Aerts A, Henrissat B, Wiebenga A, VanKuyk PA, Barry K, Lindquist E, LaButti K, Lapidus A, Lucas S, Coutinho P, Gong Y, Samejima M, Mahadevan R, Abou-Zaid M, de Vries RP, Igarashi K, Yadav JS, Grigoriev IV, Master ER.

BMC Genomics. 2012 Sep 2;13:444. doi: 10.1186/1471-2164-13-444.

23.

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.

Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Górecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kües U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Dueñas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS.

Science. 2012 Jun 29;336(6089):1715-9. doi: 10.1126/science.1221748.

24.

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen.

Olson A, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canbäck B, Coutinho PM, Cullen D, Dalman K, Deflorio G, van Diepen LT, Dunand C, Duplessis S, Durling M, Gonthier P, Grimwood J, Fossdal CG, Hansson D, Henrissat B, Hietala A, Himmelstrand K, Hoffmeister D, Högberg N, James TY, Karlsson M, Kohler A, Kües U, Lee YH, Lin YC, Lind M, Lindquist E, Lombard V, Lucas S, Lundén K, Morin E, Murat C, Park J, Raffaello T, Rouzé P, Salamov A, Schmutz J, Solheim H, Ståhlberg J, Vélëz H, de Vries RP, Wiebenga A, Woodward S, Yakovlev I, Garbelotto M, Martin F, Grigoriev IV, Stenlid J.

New Phytol. 2012 Jun;194(4):1001-13. doi: 10.1111/j.1469-8137.2012.04128.x. Epub 2012 Mar 28.

25.

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.

Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavín JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kües U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5458-63. doi: 10.1073/pnas.1119912109. Epub 2012 Mar 20. Erratum in: Proc Natl Acad Sci U S A. 2012 May 22;109(21):8352. San, Ryu Jae [corrected to Ryu, Jae San].

26.

The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi.

Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC.

Science. 2011 Aug 5;333(6043):762-5. doi: 10.1126/science.1205411. Epub 2011 Jul 14. Erratum in: Science. 2011 Sep 30;333(6051):1825.

27.

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

Goodwin SB, M'barek SB, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J, Aerts A, Antoniw J, Bailey A, Bluhm B, Bowler J, Bristow J, van der Burgt A, Canto-Canché B, Churchill AC, Conde-Ferràez L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De Wit P, Donzelli B, van de Geest HC, van Ham RC, Hammond-Kosack KE, Henrissat B, Kilian A, Kobayashi AK, Koopmann E, Kourmpetis Y, Kuzniar A, Lindquist E, Lombard V, Maliepaard C, Martins N, Mehrabi R, Nap JP, Ponomarenko A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ, Shapiro H, Stergiopoulos I, Torriani SF, Tu H, de Vries RP, Waalwijk C, Ware SB, Wiebenga A, Zwiers LH, Oliver RP, Grigoriev IV, Kema GH.

PLoS Genet. 2011 Jun;7(6):e1002070. doi: 10.1371/journal.pgen.1002070. Epub 2011 Jun 9.

28.

Carbohydrate-active enzymes from the zygomycete fungus Rhizopus oryzae: a highly specialized approach to carbohydrate degradation depicted at genome level.

Battaglia E, Benoit I, van den Brink J, Wiebenga A, Coutinho PM, Henrissat B, de Vries RP.

BMC Genomics. 2011 Jan 17;12:38. doi: 10.1186/1471-2164-12-38.

29.

An enzyme cocktail for efficient protoplast formation in Aspergillus niger.

de Bekker C, Wiebenga A, Aguilar G, Wösten HA.

J Microbiol Methods. 2009 Mar;76(3):305-6. doi: 10.1016/j.mimet.2008.11.001. Epub 2008 Nov 14.

PMID:
19041907
30.

[The value of sigmoido-colonoscopy compared with recto-colonic radiography].

Dekker W, Wiebenga AH, Teng KH, Tytgat GN.

Tijdschr Gastroenterol. 1972;15(1):65-76. Dutch. No abstract available.

PMID:
5030138
31.

Initial experience with sigmoido-coloscopy.

Dekker W, Wiebenga AH, Teng KH, Tytgat GN.

Folia Med Neerl. 1972;15(6):276-8. No abstract available.

PMID:
4640883
32.

[Diagnostic possibilities of the flexible dirigible fiberscopes].

Wiebenga AH, Wittebol P, Ingenhousz R, Boerema I, Pape KS, Oushoorn HH.

Ned Tijdschr Geneeskd. 1971 Nov 20;115(47):1999-2001. Dutch. No abstract available.

PMID:
5317047
33.

[Persistent sutures in the stump of the stomach after resection].

WIEBENGA AH, ten THYE O.

Ned Tijdschr Geneeskd. 1961 Sep 16;105:1853-5. Dutch. No abstract available.

PMID:
14006748
34.

[Giant folds of the stomach].

WIEBENGA AH, IMHOF JW.

Ned Tijdschr Geneeskd. 1961 Sep 16;105:1855-6. Dutch. No abstract available.

PMID:
14006747
35.

[Gastrophotography].

ten THIJE O, WIEBENGA AH, IMHOF JW.

Ned Tijdschr Geneeskd. 1960 Jul 23;104:1412-4. Dutch. No abstract available.

PMID:
13837855
36.

[Case of pancreatic fibrosis in an 18 year old youth].

LIPS JB, WIEBENGA AH.

Ned Tijdschr Geneeskd. 1954 Sep 4;98(36):2500-7. Dutch. No abstract available.

PMID:
13214161
37.

[Gastric biopsy].

WIEBENGA AH, JANSSEN CA, VERDONK GJ.

Sem Hop. 1951 Jun 26;27(47):2032-5. Undetermined Language. No abstract available.

PMID:
14866321
38.

[The significance of gastroscopy in the diagnosis of acute gastric hemorrhage].

WIEBENGA AH.

Ned Tijdschr Geneeskd. 1951 Jan 27;95(4):328-30. Undetermined Language. No abstract available.

PMID:
14806729
39.

[The value of gastroscopy in diagnosis].

WIEBENGA AH.

Ned Tijdschr Geneeskd. 1951 Jan 6;95(1):68-72. Undetermined Language. No abstract available.

PMID:
14806666

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