Alexander Kanitz

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==Contact Information==
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==Contact information==
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[[Image:Alex.JPG|150px|right]]
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[[Image:Alex.JPG|120px|right]]
*ETH Zurich<br/>
*ETH Zurich<br/>
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*Email: [mailto:alexander.kanitz@pharma.ethz.ch alexander.kanitz@pharma.ethz.ch]
*Email: [mailto:alexander.kanitz@pharma.ethz.ch alexander.kanitz@pharma.ethz.ch]
 +
==Research interests==
 +
*Gene regulatory networks
 +
*Laboratory automation / informatics ("Science 2.0")
 +
*Synthetic biology
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==Education==
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==Current position==
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'''Molecular Life Sciences''', Ph.D., ETH Zurich, Switzerland (December 2011)<br/>
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'''11-2012 – present'''<br/>
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'''Medical Biochemistry''', M.Sc., University of Amsterdam, The Netherlands (March 2007)<br/>
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'''RNA Regulatory Networks group, Institute of Molecular and Life Sciences, University of Zurich, Switzerland'''<br/>
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'''Molecular Biotechnology''', B.Sc., Technical University of Munich, Germany (July 2004)
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Post-doctoral fellow<br/>
 +
Supervision: Mihaela Zavolan
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==Expertise==
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==Research experience==
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Profound knowledge of gene regulatory systems and networks with a particular focus on post-transcriptional gene regulation; strong background in biochemistry, molecular biology, cell biology; familiarity with bioinformatics and biotechnology concepts and methods
+
'''09-2012 – 11-2012'''<br/>
-
 
+
'''Statistical Genomics group, Institute of Molecular and Life Sciences, University of Zurich, Switzerland'''<br/>
-
 
+
Supervision: Mark Robinson<br/>
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==Research Experience==
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Project title: "Development of tools and methods for the analysis of ribosomal profiling data in the yeast Saccharomyces cerevisiae."<br/><br/>
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'''11-2007 – 12-2011'''<br/>
+
'''11-2007 – 06-2012'''<br/>
'''Pharmacogenomics Unit, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland'''<br/>
'''Pharmacogenomics Unit, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland'''<br/>
-
Supervision: Prof. Dr. André Gerber, Prof. Dr. Michael Detmar<br/>
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Supervision: André Gerber, Michael Detmar<br/>
Project title: “Tools and strategies for the unraveling of post-transcriptional gene regulatory networks”<br/><br/>
Project title: “Tools and strategies for the unraveling of post-transcriptional gene regulatory networks”<br/><br/>
'''12-2006 – 02-2007'''<br/>
'''12-2006 – 02-2007'''<br/>
'''Swammerdam Institute of Life Sciences, University of Amsterdam, The Netherlands'''<br/>
'''Swammerdam Institute of Life Sciences, University of Amsterdam, The Netherlands'''<br/>
-
Supervision: Prof. Dr. Stanley Brul, Dr. Hans van der Spek<br/>
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Supervision: Stanley Brul, Hans van der Spek<br/>
Project title: “Status, complications and future prospects of highly active antiretroviral therapy”<br/><br/>
Project title: “Status, complications and future prospects of highly active antiretroviral therapy”<br/><br/>
'''02-2006 – 07-2006'''<br/>
'''02-2006 – 07-2006'''<br/>
'''Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore'''<br/>
'''Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore'''<br/>
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Supervision: Prof. Dr. Vinay Tergaonkar<br/>
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Supervision: Vinay Tergaonkar<br/>
Project title: “Characterization of a putative IKK2 in Danio Rerio”<br/><br/>
Project title: “Characterization of a putative IKK2 in Danio Rerio”<br/><br/>
'''10-2004 – 09-2005'''<br/>
'''10-2004 – 09-2005'''<br/>
'''Department of Hepatology, Academic Medical Center, University of Amsterdam, The Netherlands'''<br/>
'''Department of Hepatology, Academic Medical Center, University of Amsterdam, The Netherlands'''<br/>
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Supervision: Prof. Dr. Jurgen Seppen<br/>
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Supervision: Jurgen Seppen<br/>
Project titles: ”Lentiviral gene transfer of chemically inducible hepatocyte growth factor receptor” and “Liver re-targeting of lentiviral particles”<br/><br/>
Project titles: ”Lentiviral gene transfer of chemically inducible hepatocyte growth factor receptor” and “Liver re-targeting of lentiviral particles”<br/><br/>
'''03-2004 – 07-2004'''<br/>
'''03-2004 – 07-2004'''<br/>
'''Institute of Biological Chemistry, Technical University of Munich, Germany'''<br/>
'''Institute of Biological Chemistry, Technical University of Munich, Germany'''<br/>
-
Supervision: Prof. Dr. Arne Skerra, Dr. habil. Ingo Korndörfer<br/>
+
Supervision: Arne Skerra, Ingo Korndörfer<br/>
Project title: ”Production and characterization of the enzymatically active domain of the endolysine Ply500 isolated from Listeria monocytogenes bacteriophage A 500”<br/><br/>
Project title: ”Production and characterization of the enzymatically active domain of the endolysine Ply500 isolated from Listeria monocytogenes bacteriophage A 500”<br/><br/>
'''08-2003 – 10-2003 & 07-2004 – 08-2004'''<br/>
'''08-2003 – 10-2003 & 07-2004 – 08-2004'''<br/>
'''Traineeships Research and Development at Micromet, Inc., Munich, Germany'''
'''Traineeships Research and Development at Micromet, Inc., Munich, Germany'''
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==Current position==
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==Acquired skills==
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I am a grad student in the [http://gerber.openwetware.org/ Gerber Lab] at the ETH Zurich, working on post-transcriptional gene regulation, and was recruited through the [http://www.lifescience-graduateschool.ch/index.php?id=17 Molecular Life Sciences] program of the [http://www.lifescience-graduateschool.ch/ Life Science Zurich Graduate School].<br/><br/>
+
Experienced with transcriptomics (microarray) and proteomics (mass spectrometry) techniques as well as standard biochemical, molecular and cell biological techniques (cell culturing, cloning, Western/Northern blotting, immunopurification, qPCR, FACS, immunofluorescence, in vitro enzymatic and binding assays); used model systems: human cell lines, zebrafish, E. coli, P. pastoris, lentiviral vectors; profound knowledge of statistical and bioinformatics-based analytical methods (Perl, shell scripting & R/Bioconductor); highly developed scientific writing, data preparation, presentation and publication skills
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Tentative title of the project: ''[[Gerber:Projects|"Systematic Analysis of the Crosstalk between Regulatory RNA-Binding Proteins and the MicroRNA Machinery"]]''.<br/><br/>
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I am an initiator of the [http://www.rna.ethz.ch/ RNA Club Zurich] and the (currently defunct) Zurich-based "Web Utilities and Software Seminar". Furthermore I maintain the web presence of the [http://gerber.openwetware.org/ Gerber Lab] (currently moving to the UK).
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==Previous labs==
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*2006 - [http://www.imcb.a-star.edu.sg/php/vinayt.php Tergaonkar Lab], [http://www.imcb.a-star.edu.sg/php/main.php Institute of Molecular and Cell Biology], Biopolis, Singapore: ''"Characterization of a Putative IKK2 in Danio rerio"'' / Supervisor: Prof. Vinay Tergaonkar
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*2004-2005 - Seppen Lab, [http://www.livercenter.nl/ AMC Liver Center], University of Amsterdam, The Netherlands: ''"Lentiviral Gene Transfer of Chemically Inducible Hepatocyte Growth Factor Receptor and Liver Re-Targeting of Lentiviral Particles"'' / Supervisors: Dr. Jurgen Seppen, Prof. Ronald P.J. Oude-Elferink
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-
 
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*2004 - [http://www.lrz-muenchen.de/~Biologische-Chemie/ Skerra Lab], [http://www.lrz-muenchen.de/~Biologische-Chemie/ Institute of Biological Chemistry], Technical University of Munich, Germany: ''"Production and characterization of the enzymatically active domain of the endolysine Ply500 isolated from Listeria monocytogenes-bacteriophage A 500"'' / Supervisors: Dr. Ingo P. Korndörfer, Prof. Arne Skerra
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==Education==
==Education==
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<!--Include info about your educational background-->
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'''Molecular Life Sciences''', Ph.D., ETH Zurich, Switzerland (December 2011)<br/>
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*since 2007: PhD student, [http://www.lifescience-graduateschool.ch/index.php?id=17 Life Science Zurich Graduate School], [http://www.ethz.ch/index_EN ETH Zurich]
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'''Medical Biochemistry''', M.Sc., University of Amsterdam, The Netherlands (March 2007)<br/>
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*2004-2007: [http://www.studeren.uva.nl/msc_medical_biochemistry MSc Medical Biochemistry], [http://www.uva.nl/start.cfm/la=en/th=main University of Amsterdam]
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'''Molecular Biotechnology''', B.Sc., Technical University of Munich, Germany (July 2004)
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*2001-2004: [http://www.lrz-muenchen.de/~Molekulare-Biotechnologie/ BSc Molecular Biotechnology], [http://portal.mytum.de/welcome_en/document_view? Technical University of Munich]
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 +
==Expertise==
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Profound knowledge of gene regulatory systems and networks with a particular focus on post-transcriptional gene regulation; strong background in biochemistry, molecular biology, cell biology; familiarity with bioinformatics and biotechnology concepts and methods
==Publications==
==Publications==
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications.  You can add or remove lines as needed -->
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications.  You can add or remove lines as needed -->
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<biblio>
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*<u>Kanitz A</u>. (2013). '''Post-Transcriptional Gene Regulation: Tools and Strategies for the Unraveling of Post-Transcriptional Gene Regulatory Networks'''. Based on dissertation #20147 at ETH Zurich. ''Südwestdeutscher Verlag für Hochschulschriften. ISBN-13: 978-3838136707''
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#Paper4 Kanitz A and Gerber AP. [http://dx.doi.org/10.1002/wsbm.55 ''Circuitry of mRNA regulation.''] Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2009 Sep 30. doi: 10.1002/wsbm.55
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#Paper3 pmid=18776931
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#Paper2 pmid=18560152
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#Paper1 pmid=17630838
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</biblio>
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==Useful links==
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*<u>Kanitz A</u>, Imig J, Dziunycz PJ, Primorac A, Galgano A, Hofbauer GFL, Gerber AP^, Detmar M^. (2012). '''The Expression Levels of MicroRNA-361-5p and Its Target VEGFA Are Inversely Correlated in Human Cutaneous Squamous Cell Carcinoma'''. ''PLoS One. 7(11):e49568''
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*[http://gerber.openwetware.org Gerber Lab on OWW]
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*[http://www.pharma.ethz.ch/institute_groups/pharmacogenomics/research_gerber/index Gerber Lab @ Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland]
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*<u>Kanitz A</u>^, Imig J^, Gerber AP. (2012). '''RNA regulons and the RNA-protein interaction network'''. ''Biomol Concepts 3(5):403-414''
 +
 
 +
*<u>Kanitz A</u>, Gerber AP. (2010). '''Circuitry of mRNA regulation'''. ''Wiley Interdiscip Rev Syst Biol Med. 2(2):245-51''
 +
 
 +
*Galgano A, Forrer M, Jaskiewicz L, <u>Kanitz A</u>, Zavolan M, Gerber AP. (2008). '''Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system'''. ''PLoS One. 3(9):e3164''
 +
 
 +
*Korndörder IP, <u>Kanitz A</u>, Danzer J, Zimmer M, Loessner MJ, Skerra A. (2008). '''Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a member of the LAS peptidase family'''. ''Acta Crystallogr D Biol Crystallogr. 64(Pt 6):644-50''
 +
 
 +
*Markusic DM, <u>Kanitz A</u>, Oude-Elferink RP, Seppen J. (2007). '''Preferential gene transfer of lentiviral vectors to liver-derived cells, using a hepatitis B peptide displayed on GP64'''. ''Hum Gene Ther. 18(7):673-9''
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 +
^ equal contribution
 +
 
 +
==Links==
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*[http://www.biozentrum.unibas.ch/research/groups-platforms/overview/unit/zavolan/ Zavolan Lab, Biozentrum, University of Basel, Switzerland]
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*[http://www.imls.uzh.ch/research/robinson.html Robinson Lab, Institute of Molecular and Life Sciences, University of Zurich, Switzerland]
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*[http://gerber.openwetware.org Gerber Lab, Institute of Biosciences and Medicine, University of Surrey, UK]
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*[http://www.pharma.ethz.ch/institute_groups/pharmacogenomics/ Detmar Lab, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland]
*[http://www.lifescience-graduateschool.ch/ Life Science Zurich Graduate School]
*[http://www.lifescience-graduateschool.ch/ Life Science Zurich Graduate School]
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*[http://www.imcb.a-star.edu.sg/php/vinayt.php Tergaonkar Lab @ Institute of Molecular and Cell Biology, Biopolis, Singapore]
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*[http://www.imcb.a-star.edu.sg/php/vinayt.php Tergaonkar Lab, Institute of Molecular and Cell Biology, Singapore]
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*[http://www.lrz-muenchen.de/~Biologische-Chemie/ Skerra Lab @ Institute of Biological Chemistry, Technical University of Munich, Germany (German only)]
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*[http://www.lrz-muenchen.de/~Biologische-Chemie/ Skerra Lab, Institute of Biological Chemistry, Technical University of Munich, Germany (German only)]
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Revision as of 08:38, 16 May 2013

Contact information

  • ETH Zurich

     Department of Chemistry and Applied Biosciences
     Institute of Pharmaceutical Sciences / Pharmacogenomics Unit
     Wolfgang Pauli-Strasse 10
     8093 Zurich
     Switzerland
     Google Maps link

Research interests

  • Gene regulatory networks
  • Laboratory automation / informatics ("Science 2.0")
  • Synthetic biology

Current position

11-2012 – present
RNA Regulatory Networks group, Institute of Molecular and Life Sciences, University of Zurich, Switzerland
Post-doctoral fellow
Supervision: Mihaela Zavolan

Research experience

09-2012 – 11-2012
Statistical Genomics group, Institute of Molecular and Life Sciences, University of Zurich, Switzerland
Supervision: Mark Robinson
Project title: "Development of tools and methods for the analysis of ribosomal profiling data in the yeast Saccharomyces cerevisiae."

11-2007 – 06-2012
Pharmacogenomics Unit, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
Supervision: André Gerber, Michael Detmar
Project title: “Tools and strategies for the unraveling of post-transcriptional gene regulatory networks”

12-2006 – 02-2007
Swammerdam Institute of Life Sciences, University of Amsterdam, The Netherlands
Supervision: Stanley Brul, Hans van der Spek
Project title: “Status, complications and future prospects of highly active antiretroviral therapy”

02-2006 – 07-2006
Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
Supervision: Vinay Tergaonkar
Project title: “Characterization of a putative IKK2 in Danio Rerio”

10-2004 – 09-2005
Department of Hepatology, Academic Medical Center, University of Amsterdam, The Netherlands
Supervision: Jurgen Seppen
Project titles: ”Lentiviral gene transfer of chemically inducible hepatocyte growth factor receptor” and “Liver re-targeting of lentiviral particles”

03-2004 – 07-2004
Institute of Biological Chemistry, Technical University of Munich, Germany
Supervision: Arne Skerra, Ingo Korndörfer
Project title: ”Production and characterization of the enzymatically active domain of the endolysine Ply500 isolated from Listeria monocytogenes bacteriophage A 500”

08-2003 – 10-2003 & 07-2004 – 08-2004
Traineeships Research and Development at Micromet, Inc., Munich, Germany

Acquired skills

Experienced with transcriptomics (microarray) and proteomics (mass spectrometry) techniques as well as standard biochemical, molecular and cell biological techniques (cell culturing, cloning, Western/Northern blotting, immunopurification, qPCR, FACS, immunofluorescence, in vitro enzymatic and binding assays); used model systems: human cell lines, zebrafish, E. coli, P. pastoris, lentiviral vectors; profound knowledge of statistical and bioinformatics-based analytical methods (Perl, shell scripting & R/Bioconductor); highly developed scientific writing, data preparation, presentation and publication skills

Education

Molecular Life Sciences, Ph.D., ETH Zurich, Switzerland (December 2011)
Medical Biochemistry, M.Sc., University of Amsterdam, The Netherlands (March 2007)
Molecular Biotechnology, B.Sc., Technical University of Munich, Germany (July 2004)

Expertise

Profound knowledge of gene regulatory systems and networks with a particular focus on post-transcriptional gene regulation; strong background in biochemistry, molecular biology, cell biology; familiarity with bioinformatics and biotechnology concepts and methods

Publications

  • Kanitz A. (2013). Post-Transcriptional Gene Regulation: Tools and Strategies for the Unraveling of Post-Transcriptional Gene Regulatory Networks. Based on dissertation #20147 at ETH Zurich. Südwestdeutscher Verlag für Hochschulschriften. ISBN-13: 978-3838136707
  • Kanitz A, Imig J, Dziunycz PJ, Primorac A, Galgano A, Hofbauer GFL, Gerber AP^, Detmar M^. (2012). The Expression Levels of MicroRNA-361-5p and Its Target VEGFA Are Inversely Correlated in Human Cutaneous Squamous Cell Carcinoma. PLoS One. 7(11):e49568
  • Kanitz A^, Imig J^, Gerber AP. (2012). RNA regulons and the RNA-protein interaction network. Biomol Concepts 3(5):403-414
  • Kanitz A, Gerber AP. (2010). Circuitry of mRNA regulation. Wiley Interdiscip Rev Syst Biol Med. 2(2):245-51
  • Galgano A, Forrer M, Jaskiewicz L, Kanitz A, Zavolan M, Gerber AP. (2008). Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One. 3(9):e3164
  • Korndörder IP, Kanitz A, Danzer J, Zimmer M, Loessner MJ, Skerra A. (2008). Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a member of the LAS peptidase family. Acta Crystallogr D Biol Crystallogr. 64(Pt 6):644-50
  • Markusic DM, Kanitz A, Oude-Elferink RP, Seppen J. (2007). Preferential gene transfer of lentiviral vectors to liver-derived cells, using a hepatitis B peptide displayed on GP64. Hum Gene Ther. 18(7):673-9

^ equal contribution

Links


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