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Curriculum Vitae

Phone:   (+420) 221 914 227
Fax:       (+420) 221 914 323
E-mail:   hoksza (at) ksi (dot) mff (dot) cuni (dot) cz

Charles University in Prague, Czech Republic
Faculty of Mathematics and Physics, School of Computer Science 

  • Ph.D., Software Systems, September 2010
  • Thesis: Similarity Search in Protein Databases
  • Advisor: Tomáš Skopal, PhD.
  • RNDr., Software Systems, September 2008
  • M.Sc., Data Engineering, August 2006
  • Thesis: Multidimensional Indexing in Relational Databases
  • Advisor: Tomáš Skopal, PhD.


  • databases : indexing, metric indexing, non-metric indexing
  • bioinformatics : structural bioinformatics, protein sequence and structure databases, rna sequence and structure databases
  • cheminformatics : chemical space exploration, chemical space visualization

Researcher (September 2010 - present)
Department of Software Engineering, School of Computer Science, FMP,
Charles University in Prague

Assistant Professor (September 2010 - present)
Lecturer (September 2006 - August 2008)
Department of Computer Science and Mathematics, 


Helmholtz Zentrum MunchenInstitute of Bioinformatics and Systems Biology
Chemoinformatics & Chemical Biology group

January 2012 – April 2012


Application of similarity search in protein active sites databases to the drug side effects prediciton


  • Founding member of SIRET Research Group
  • Member of CSBMB (Czech Society For Biochemistry and Molecular Biology)
  • Member of FOBIA (Czech Free & Open BioInformatic Association)
  • Member of CSCH (Czech Chemical Society)


  •  ADBIS 2011
  •  DKE Journal 2009
  •  SISAP 2008, 2009, 2010, 2012
  •  DATESO 2008, 2012
  •  Journal of Molecular Graphics and Modelling
  •  ENBIK 2012 — National Bioinformatics Conference
  •  CSPUG seminars 2011, 2012 — co-organizing seminars of the Czech and Slovak PostgreSQL Group
  •  DATESO 2007

Charles University in Prague, Prague, Czech Republic
Teaching Asistant (September 2006 – present)

  • Administration of MS SQL Server
  • Database Systems
  • Database Applications
Institute of Chemical Technology, Prague, Czech Republic
Teaching Asistant (September 2011 – present)
  • Bioinformatics Algorithms
  • Database Systems
Czech Technical University in Prague, Prague, Czech Republic
Teaching Asistant (September 2009 – September 2011)
  • Database Systems
  • Retrieval of Multimedia Content on the Web
  • Searching Web and Multimedia Databases
Lecturer (September 2006 - August 2008)
  • Introduction to Unix


Bernard Bolzano Foundation in Computer science Award

Awarded for the paper Density-Based Classification of Protein Structures Using Iterative TM-score, 2010

Werner Von Siemens Excellence Award

Honorable mention for the PhD thesis Similarity Search in Protein Databases, 2010

Programming Languages:

  •  C, C++, C#, ASP.NET, Java, JavaScript, PHP, UNIX shell scripting, SQL
  •  Microsoft SQL Server (TSQL programming, administration), Oracle(PL/SQL programming, administration), PostgreSQL (PG/SQL programming), Firebird (SQL programming), MySQL (SQL programming)