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Items: 50

1.

Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis.

Tafer H, Poyntner C, Lopandic K, Sterflinger K, Piñar G.

Genes (Basel). 2019 May 20;10(5). pii: E381. doi: 10.3390/genes10050381.

2.

Transcriptome Study of an Exophiala dermatitidis PKS1 Mutant on an ex Vivo Skin Model: Is Melanin Important for Infection?

Poyntner C, Mirastschijski U, Sterflinger K, Tafer H.

Front Microbiol. 2018 Jul 3;9:1457. doi: 10.3389/fmicb.2018.01457. eCollection 2018.

3.

Big Sound and Extreme Fungi-Xerophilic, Halotolerant Aspergilli and Penicillia with Low Optimal Temperature as Invaders of Historic Pipe Organs.

Sterflinger K, Voitl C, Lopandic K, Piñar G, Tafer H.

Life (Basel). 2018 Jun 14;8(2). pii: E22. doi: 10.3390/life8020022.

4.

Draft Genome Sequence of the Saccharomyces cerevisiae × Saccharomyces kudriavzevii HA1836 Interspecies Hybrid Yeast.

Lopandic K, Tafer H, Sterflinger K.

Genome Announc. 2018 May 17;6(20). pii: e00343-18. doi: 10.1128/genomeA.00343-18.

5.

Draft Genome Sequence of the Interspecies Hybrid Saccharomyces pastorianus Strain HA2560, Isolated from a Municipal Wastewater Treatment Plant.

Tafer H, Sterflinger K, Lopandic K.

Genome Announc. 2018 Apr 26;6(17). pii: e00341-18. doi: 10.1128/genomeA.00341-18.

6.

Draft Genome Sequences of the Black Rock Fungus Knufia petricola and Its Spontaneous Nonmelanized Mutant.

Tesei D, Tafer H, Poyntner C, Piñar G, Lopandic K, Sterflinger K.

Genome Announc. 2017 Nov 2;5(44). pii: e01242-17. doi: 10.1128/genomeA.01242-17.

7.

Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda.

Blasi B, Tafer H, Kustor C, Poyntner C, Lopandic K, Sterflinger K.

Sci Rep. 2017 Sep 12;7(1):11436. doi: 10.1038/s41598-017-11807-8.

8.

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection.

Poyntner C, Blasi B, Arcalis E, Mirastschijski U, Sterflinger K, Tafer H.

Front Cell Infect Microbiol. 2016 Oct 24;6:136. eCollection 2016.

9.
10.

Pathogenic Yet Environmentally Friendly? Black Fungal Candidates for Bioremediation of Pollutants.

Blasi B, Poyntner C, Rudavsky T, Prenafeta-Boldú FX, Hoog S, Tafer H, Sterflinger K.

Geomicrobiol J. 2016 Mar 15;33(3-4):308-317. Epub 2016 Feb 25.

11.

Protein functional analysis data in support of comparative proteomics of the pathogenic black yeast Exophiala dermatitidis under different temperature conditions.

Tesei D, Marzban G, Marchetti-Deschmann M, Tafer H, Arcalis E, Sterflinger K.

Data Brief. 2015 Sep 2;5:372-5. doi: 10.1016/j.dib.2015.08.008. eCollection 2015 Dec.

12.

Draft Genome of Debaryomyces fabryi CBS 789T, Isolated from a Human Interdigital Mycotic Lesion.

Tafer H, Sterflinger K, Lopandic K.

Genome Announc. 2016 Feb 4;4(1). pii: e01580-15. doi: 10.1128/genomeA.01580-15.

13.

Proteome of tolerance fine-tuning in the human pathogen black yeast Exophiala dermatitidis.

Tesei D, Marzban G, Marchetti-Deschmann M, Tafer H, Arcalis E, Sterflinger K.

J Proteomics. 2015 Oct 14;128:39-57. doi: 10.1016/j.jprot.2015.07.007. Epub 2015 Jul 17.

14.

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster.

Agrisani A, Tafer H, Stadler PF, Furia M.

Noncoding RNA. 2015 Jul 13;1(2):139-150. doi: 10.3390/ncrna1020139.

15.

Amid the possible causes of a very famous foxing: molecular and microscopic insight into Leonardo da Vinci's self-portrait.

Piñar G, Tafer H, Sterflinger K, Pinzari F.

Environ Microbiol Rep. 2015 Dec;7(6):849-59. doi: 10.1111/1758-2229.12313. Epub 2015 Aug 19.

16.

From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response.

Blasi B, Tafer H, Tesei D, Sterflinger K.

PLoS One. 2015 Jun 10;10(6):e0127103. doi: 10.1371/journal.pone.0127103. eCollection 2015. Erratum in: PLoS One. 2018 Nov 26;13(11):e0208360.

17.

Draft Genome Sequence of Exophiala mesophila, a Black Yeast with High Bioremediation Potential.

Tafer H, Lopandic K, Blasi B, Poyntner C, Sterflinger K.

Genome Announc. 2015 Apr 9;3(2). pii: e00203-15. doi: 10.1128/genomeA.00203-15.

18.

Developmentally regulated expression and expression strategies of Drosophila snoRNAs.

Angrisani A, Tafer H, Stadler PF, Furia M.

Insect Biochem Mol Biol. 2015 Jun;61:69-78. doi: 10.1016/j.ibmb.2015.01.013. Epub 2015 Jan 29.

PMID:
25641266
19.

Draft Genome of Cladophialophora immunda, a Black Yeast and Efficient Degrader of Polyaromatic Hydrocarbons.

Sterflinger K, Lopandic K, Blasi B, Poynter C, de Hoog S, Tafer H.

Genome Announc. 2015 Jan 29;3(1). pii: e01283-14. doi: 10.1128/genomeA.01283-14.

20.

Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs.

Matylla-Kulinska K, Tafer H, Weiss A, Schroeder R.

Wiley Interdiscip Rev RNA. 2014 Sep-Oct;5(5):591-600. doi: 10.1002/wrna.1243. Epub 2014 Jul 9.

21.

Structured RNAs and synteny regions in the pig genome.

Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J.

BMC Genomics. 2014 Jun 10;15:459. doi: 10.1186/1471-2164-15-459.

22.

Quantification of fungal abundance on cultural heritage using real time PCR targeting the β-actin gene.

Ettenauer J, Piñar G, Tafer H, Sterflinger K.

Front Microbiol. 2014 May 28;5:262. doi: 10.3389/fmicb.2014.00262. eCollection 2014.

23.

Bioinformatics of siRNA design.

Tafer H.

Methods Mol Biol. 2014;1097:477-90. doi: 10.1007/978-1-62703-709-9_22. Review.

PMID:
24639173
24.

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).

Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H.

Nature. 2014 Jan 23;505(7484):546-9. doi: 10.1038/nature12817. Epub 2013 Dec 18.

PMID:
24352233
25.

snoStrip: a snoRNA annotation pipeline.

Bartschat S, Kehr S, Tafer H, Stadler PF, Hertel J.

Bioinformatics. 2014 Jan 1;30(1):115-6. doi: 10.1093/bioinformatics/btt604. Epub 2013 Oct 29.

PMID:
24174566
26.

Atypical RNAs in the coelacanth transcriptome.

Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF.

J Exp Zool B Mol Dev Evol. 2014 Sep;322(6):342-51. doi: 10.1002/jez.b.22542. Epub 2013 Oct 30.

PMID:
24174405
27.

Matching of Soulmates: coevolution of snoRNAs and their targets.

Kehr S, Bartschat S, Tafer H, Stadler PF, Hertel J.

Mol Biol Evol. 2014 Feb;31(2):455-67. doi: 10.1093/molbev/mst209. Epub 2013 Oct 24.

PMID:
24162733
28.

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species.

Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim KW, Sheng Z, An Y, Searle S, Herrero J, Groenen MAM, Crooijmans RPMA, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RHS, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N.

Nat Genet. 2013 Jul;45(7):776-783. doi: 10.1038/ng.2657. Epub 2013 Jun 9.

29.

The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W475-9. doi: 10.1093/nar/gkt291. Epub 2013 Apr 29.

30.

The African coelacanth genome provides insights into tetrapod evolution.

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K.

Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.

31.

RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.

Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.

Hum Mutat. 2013 Apr;34(4):546-56. doi: 10.1002/humu.22273. Erratum in: Hum Mutat. 2013 Jun;34(6):925.

32.

Analyses of pig genomes provide insight into porcine demography and evolution.

Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB.

Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.

33.

Genomic and morphological evidence converge to resolve the enigma of Strepsiptera.

Niehuis O, Hartig G, Grath S, Pohl H, Lehmann J, Tafer H, Donath A, Krauss V, Eisenhardt C, Hertel J, Petersen M, Mayer C, Meusemann K, Peters RS, Stadler PF, Beutel RG, Bornberg-Bauer E, McKenna DD, Misof B.

Curr Biol. 2012 Jul 24;22(14):1309-13. doi: 10.1016/j.cub.2012.05.018. Epub 2012 Jun 14. Erratum in: Curr Biol. 2013 Jul 22;23(14):1388.

34.

ViennaRNA Package 2.0.

Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL.

Algorithms Mol Biol. 2011 Nov 24;6:26. doi: 10.1186/1748-7188-6-26.

35.

Animal snoRNAs and scaRNAs with exceptional structures.

Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF.

RNA Biol. 2011 Nov-Dec;8(6):938-46. doi: 10.4161/rna.8.6.16603. Epub 2011 Nov 1.

36.

RNApredator: fast accessibility-based prediction of sRNA targets.

Eggenhofer F, Tafer H, Stadler PF, Hofacker IL.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W149-54. doi: 10.1093/nar/gkr467. Epub 2011 Jun 14.

37.

Fast accessibility-based prediction of RNA-RNA interactions.

Tafer H, Amman F, Eggenhofer F, Stadler PF, Hofacker IL.

Bioinformatics. 2011 Jul 15;27(14):1934-40. doi: 10.1093/bioinformatics/btr281. Epub 2011 May 18.

PMID:
21593134
38.

PLEXY: efficient target prediction for box C/D snoRNAs.

Kehr S, Bartschat S, Stadler PF, Tafer H.

Bioinformatics. 2011 Jan 15;27(2):279-80. doi: 10.1093/bioinformatics/btq642. Epub 2010 Nov 13.

PMID:
21076148
39.

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.

PLoS Biol. 2010 Sep 7;8(9). pii: e1000475. doi: 10.1371/journal.pbio.1000475.

40.

Designing optimal siRNA based on target site accessibility.

Hofacker IL, Tafer H.

Methods Mol Biol. 2010;623:137-54. doi: 10.1007/978-1-60761-588-0_9.

PMID:
20217549
41.

RNAsnoop: efficient target prediction for H/ACA snoRNAs.

Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF.

Bioinformatics. 2010 Mar 1;26(5):610-6. doi: 10.1093/bioinformatics/btp680. Epub 2009 Dec 16.

PMID:
20015949
42.

Non-coding RNA annotation of the genome of Trichoplax adhaerens.

Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF.

Nucleic Acids Res. 2009 Apr;37(5):1602-15. doi: 10.1093/nar/gkn1084. Epub 2009 Jan 16.

43.

Target site effects in the RNA interference and microRNA pathways.

Obernosterer G, Tafer H, Martinez J.

Biochem Soc Trans. 2008 Dec;36(Pt 6):1216-9. doi: 10.1042/BST0361216.

PMID:
19021528
44.

The impact of target site accessibility on the design of effective siRNAs.

Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL.

Nat Biotechnol. 2008 May;26(5):578-83. doi: 10.1038/nbt1404. Epub 2008 Apr 27.

PMID:
18438400
45.

RNAplex: a fast tool for RNA-RNA interaction search.

Tafer H, Hofacker IL.

Bioinformatics. 2008 Nov 15;24(22):2657-63. doi: 10.1093/bioinformatics/btn193. Epub 2008 Apr 23.

PMID:
18434344
46.

www.rnaworkbench.com: A new program for analyzing RNA interference.

Vareková RS, Bradác I, Plchút M, Skrdla M, Wacenovsky M, Mahr H, Mayer G, Tanner H, Brugger H, Withalm J, Lederer P, Huber H, Gierlinger G, Graf R, Tafer H, Hofacker I, Schuster P, Polcík M.

Comput Methods Programs Biomed. 2008 Apr;90(1):89-94. doi: 10.1016/j.cmpb.2007.12.001. Epub 2008 Jan 22.

PMID:
18207283
47.

Invertebrate 7SK snRNAs.

Gruber AR, Koper-Emde D, Marz M, Tafer H, Bernhart S, Obernosterer G, Mosig A, Hofacker IL, Stadler PF, Benecke BJ.

J Mol Evol. 2008 Feb;66(2):107-15. doi: 10.1007/s00239-007-9052-6. Epub 2008 Jan 12.

48.

Partition function and base pairing probabilities of RNA heterodimers.

Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL.

Algorithms Mol Biol. 2006 Mar 16;1(1):3.

49.

Thermodynamics of RNA-RNA binding.

Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL.

Bioinformatics. 2006 May 15;22(10):1177-82. Epub 2006 Jan 29.

PMID:
16446276
50.

Nonrandom structure in the urea-unfolded Escherichia coli outer membrane protein X (OmpX).

Tafer H, Hiller S, Hilty C, Fernández C, Wüthrich K.

Biochemistry. 2004 Feb 3;43(4):860-9.

PMID:
14744128

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