Publications by authors named "Hakim Tafer"

52Publications

Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value.

Environ Microbiol 2020 Aug 29;22(8):3218-3233. Epub 2020 May 29.

Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, A-1190, Vienna, Austria.

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http://dx.doi.org/10.1111/1462-2920.15064DOI Listing
August 2020

Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas.

BMC Genomics 2020 Apr 9;21(1):290. Epub 2020 Apr 9.

Plant Biotechnology Unit, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.

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http://dx.doi.org/10.1186/s12864-020-6666-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7146973PMC
April 2020

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

Genes (Basel) 2019 05 20;10(5). Epub 2019 May 20.

VIBT EQ Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.

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http://dx.doi.org/10.3390/genes10050381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6563132PMC
May 2019

Transcriptome Study of an Mutant on an Skin Model: Is Melanin Important for Infection?

Front Microbiol 2018 3;9:1457. Epub 2018 Jul 3.

Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria.

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http://dx.doi.org/10.3389/fmicb.2018.01457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037837PMC
July 2018

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

Life (Basel) 2018 Jun 14;8(2). Epub 2018 Jun 14.

VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria.

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http://www.mdpi.com/2075-1729/8/2/22
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http://dx.doi.org/10.3390/life8020022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027336PMC
June 2018

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

Genome Announc 2018 May 17;6(20). Epub 2018 May 17.

VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.

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http://dx.doi.org/10.1128/genomeA.00343-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5958256PMC
May 2018

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

Genome Announc 2018 Apr 26;6(17). Epub 2018 Apr 26.

VIBT-Extremophile Center, University of Natural Resources and Life Sciences Vienna, Vienna, Austria

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.00341-18
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http://dx.doi.org/10.1128/genomeA.00341-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920194PMC
April 2018

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

Genome Announc 2017 Nov 2;5(44). Epub 2017 Nov 2.

VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria.

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http://dx.doi.org/10.1128/genomeA.01242-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668551PMC
November 2017

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

Sci Rep 2017 09 12;7(1):11436. Epub 2017 Sep 12.

Department of Biotechnology, VIBT-EQ Extremophile Center, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.

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http://dx.doi.org/10.1038/s41598-017-11807-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5595782PMC
September 2017

The Transcriptome of during Skin Model Infection.

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

Department of Biotechnology, VIBT EQ Extremophile Center, University of Natural Resources and Life Sciences Vienna, Austria.

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http://dx.doi.org/10.3389/fcimb.2016.00136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075926PMC
September 2017

Genome sequence of the filamentous soil fungus Chaetomium cochliodes reveals abundance of genes for heme enzymes from all peroxidase and catalase superfamilies.

BMC Genomics 2016 Sep 29;17(1):763. Epub 2016 Sep 29.

Department of Chemistry, Division of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190, Vienna, Austria.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041501PMC
http://dx.doi.org/10.1186/s12864-016-3111-6DOI Listing
September 2016

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

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

University of Natural Resources and Life Sciences Vienna, VIBT-Extremophile Center , Vienna , Austria.

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http://dx.doi.org/10.1080/01490451.2015.1052118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4786828PMC
March 2016

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

Data Brief 2015 Dec 2;5:372-5. Epub 2015 Sep 2.

VIBT Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.

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http://dx.doi.org/10.1016/j.dib.2015.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773397PMC
December 2015

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

Genome Announc 2016 Feb 4;4(1). Epub 2016 Feb 4.

University of Natural Resources and Life Sciences Vienna, VIBT-Extremophile Center, Vienna, Austria

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http://dx.doi.org/10.1128/genomeA.01580-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742678PMC
February 2016

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

J Proteomics 2015 Oct 17;128:39-57. Epub 2015 Jul 17.

VIBT Extremophile Center, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.

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http://dx.doi.org/10.1016/j.jprot.2015.07.007DOI Listing
October 2015

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster.

Noncoding RNA 2015 Jul 13;1(2):139-150. Epub 2015 Jul 13.

Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, I-80126 Napoli, Italy.

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http://dx.doi.org/10.3390/ncrna1020139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932544PMC
July 2015

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

Environ Microbiol Rep 2015 Dec 19;7(6):849-59. Epub 2015 Aug 19.

Istituto Centrale per il Restauro e la Conservazione del Patrimonio Archivistico e Librario (ICRCPAL), Ministero per i Beni e le Attivita Culturali, Via Milano 76, Rome, 00184, Italy.

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http://dx.doi.org/10.1111/1758-2229.12313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959533PMC
December 2015

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

Genome Announc 2015 Apr 9;3(2). Epub 2015 Apr 9.

VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.00203-15
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http://dx.doi.org/10.1128/genomeA.00203-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392147PMC
April 2015

Developmentally regulated expression and expression strategies of Drosophila snoRNAs.

Insect Biochem Mol Biol 2015 Jun 29;61:69-78. Epub 2015 Jan 29.

Department of Biology, University of Naples "Federico II", Complesso Universitario Monte Santangelo, via Cinthia, 80126 Napoli, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.ibmb.2015.01.013DOI Listing
June 2015

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

Genome Announc 2015 Jan 29;3(1). Epub 2015 Jan 29.

VIBT-Extremophile Center, University of Natural Resources and Life Sciences, Vienna, Austria.

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http://dx.doi.org/10.1128/genomeA.01283-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4319495PMC
January 2015

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

Wiley Interdiscip Rev RNA 2014 Sep-Oct;5(5):591-600. Epub 2014 Jul 9.

Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1002/wrna.1243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233971PMC
April 2015

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

Front Microbiol 2014 28;5:262. Epub 2014 May 28.

Department of Biotechnology, Vienna Institute of Biotechnology, University of Natural Resources and Life Sciences Vienna, Austria.

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http://dx.doi.org/10.3389/fmicb.2014.00262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035567PMC
June 2014

Bioinformatics of siRNA design.

Authors:
Hakim Tafer

Methods Mol Biol 2014 ;1097:477-90

Institut fur Informatik, Universitat Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1007/978-1-62703-709-9_22DOI Listing
November 2014

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

Nature 2014 Jan 18;505(7484):546-9. Epub 2013 Dec 18.

1] Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany [2] Centre for Genomic Regulation (CRG), C. Dr. Aiguader 88, 08003 Barcelona, Spain [3] Universitat Pompeu Fabra (UPF), C. Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1038/nature12817DOI Listing
January 2014

snoStrip: a snoRNA annotation pipeline.

Bioinformatics 2014 Jan 29;30(1):115-6. Epub 2013 Oct 29.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btt604DOI Listing
January 2014

Atypical RNAs in the coelacanth transcriptome.

J Exp Zool B Mol Dev Evol 2014 Sep 30;322(6):342-51. Epub 2013 Oct 30.

Department of Computer Science, Bioinformatics Group, University of Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1002/jez.b.22542DOI Listing
September 2014

Matching of Soulmates: coevolution of snoRNAs and their targets.

Mol Biol Evol 2014 Feb 24;31(2):455-67. Epub 2013 Oct 24.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1093/molbev/mst209DOI Listing
February 2014

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

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

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkt291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977658PMC
July 2013

The African coelacanth genome provides insights into tetrapod evolution.

Nature 2013 Apr;496(7445):311-6

Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA.

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http://dx.doi.org/10.1038/nature12027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633110PMC
April 2013

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

Hum Mutat 2013 Apr;34(4):546-56

Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.

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http://dx.doi.org/10.1002/humu.22273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708107PMC
April 2013

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

Authors:
Martien A M Groenen Alan L Archibald Hirohide Uenishi Christopher K Tuggle Yasuhiro Takeuchi Max F Rothschild Claire Rogel-Gaillard Chankyu Park Denis Milan Hendrik-Jan Megens Shengting Li Denis M Larkin Heebal Kim Laurent A F Frantz Mario Caccamo Hyeonju Ahn Bronwen L Aken Anna Anselmo Christian Anthon Loretta Auvil Bouabid Badaoui Craig W Beattie Christian Bendixen Daniel Berman Frank Blecha Jonas Blomberg Lars Bolund Mirte Bosse Sara Botti Zhan Bujie Megan Bystrom Boris Capitanu Denise Carvalho-Silva Patrick Chardon Celine Chen Ryan Cheng Sang-Haeng Choi William Chow Richard C Clark Christopher Clee Richard P M A Crooijmans Harry D Dawson Patrice Dehais Fioravante De Sapio Bert Dibbits Nizar Drou Zhi-Qiang Du Kellye Eversole João Fadista Susan Fairley Thomas Faraut Geoffrey J Faulkner Katie E Fowler Merete Fredholm Eric Fritz James G R Gilbert Elisabetta Giuffra Jan Gorodkin Darren K Griffin Jennifer L Harrow Alexander Hayward Kerstin Howe Zhi-Liang Hu Sean J Humphray Toby Hunt Henrik Hornshøj Jin-Tae Jeon Patric Jern Matthew Jones Jerzy Jurka Hiroyuki Kanamori Ronan Kapetanovic Jaebum Kim Jae-Hwan Kim Kyu-Won Kim Tae-Hun Kim Greger Larson Kyooyeol Lee Kyung-Tai Lee Richard Leggett Harris A Lewin Yingrui Li Wansheng Liu Jane E Loveland Yao Lu Joan K Lunney Jian Ma Ole Madsen Katherine Mann Lucy Matthews Stuart McLaren Takeya Morozumi Michael P Murtaugh Jitendra Narayan Dinh Truong Nguyen Peixiang Ni Song-Jung Oh Suneel Onteru Frank Panitz Eung-Woo Park Hong-Seog Park Geraldine Pascal Yogesh Paudel Miguel Perez-Enciso Ricardo Ramirez-Gonzalez James M Reecy Sandra Rodriguez-Zas Gary A Rohrer Lauretta Rund Yongming Sang Kyle Schachtschneider Joshua G Schraiber John Schwartz Linda Scobie Carol Scott Stephen Searle Bertrand Servin Bruce R Southey Goran Sperber Peter Stadler Jonathan V Sweedler Hakim Tafer Bo Thomsen Rashmi Wali Jian Wang Jun Wang Simon White Xun Xu Martine Yerle Guojie Zhang Jianguo Zhang Jie Zhang Shuhong Zhao Jane Rogers Carol Churcher Lawrence B Schook

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

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http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
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http://www.nature.com/doifinder/10.1038/nature11622
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http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

ViennaRNA Package 2.0.

Algorithms Mol Biol 2011 Nov 24;6:26. Epub 2011 Nov 24.

Institute for Theoretical Chemistry and Structural Biology, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1186/1748-7188-6-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319429PMC
November 2011

RNApredator: fast accessibility-based prediction of sRNA targets.

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

Institute of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkr467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125805PMC
July 2011

Fast accessibility-based prediction of RNA-RNA interactions.

Bioinformatics 2011 Jul 18;27(14):1934-40. Epub 2011 May 18.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr281DOI Listing
July 2011

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

Bioinformatics 2011 Jan 13;27(2):279-80. Epub 2010 Nov 13.

Department of Computer Science, University of Leipzig, Leipzig, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq642DOI Listing
January 2011

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

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

Designing optimal siRNA based on target site accessibility.

Methods Mol Biol 2010 ;623:137-54

Institute for Theoretical Chemistry, University Vienna, Vienna, Austria.

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http://dx.doi.org/10.1007/978-1-60761-588-0_9DOI Listing
May 2010

RNAsnoop: efficient target prediction for H/ACA snoRNAs.

Bioinformatics 2010 Mar 16;26(5):610-6. Epub 2009 Dec 16.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btp680DOI Listing
March 2010

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

Nucleic Acids Res 2009 Apr 16;37(5):1602-15. Epub 2009 Jan 16.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/nar/gkn1084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655684PMC
April 2009

Target site effects in the RNA interference and microRNA pathways.

Biochem Soc Trans 2008 Dec;36(Pt 6):1216-9

Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna, Austria.

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http://dx.doi.org/10.1042/BST0361216DOI Listing
December 2008

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

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

Institute of Theoretical Biochemistry (TBI), University of Vienna, Austria.

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http://dx.doi.org/10.1038/nbt1404DOI Listing
May 2008

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

Bioinformatics 2008 Nov 23;24(22):2657-63. Epub 2008 Apr 23.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btn193DOI Listing
November 2008

Invertebrate 7SK snRNAs.

J Mol Evol 2008 Feb 12;66(2):107-15. Epub 2008 Jan 12.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1007/s00239-007-9052-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755741PMC
February 2008

Partition function and base pairing probabilities of RNA heterodimers.

Algorithms Mol Biol 2006 Mar 16;1(1). Epub 2006 Mar 16.

Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, Vienna, Austria.

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http://dx.doi.org/10.1186/1748-7188-1-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459172PMC
March 2006

Thermodynamics of RNA-RNA binding.

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

Institute for Theoretical Chemistry, University of Vienna Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btl024DOI Listing
May 2006

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

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

Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland.

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http://dx.doi.org/10.1021/bi0356606DOI Listing
February 2004