BORYS WRÓBEL, CURRICULUM VITAE



Name: Borys Wróbel

Date and place of birth: 13 January 1976, Gdansk, Poland

Nationality: Polish

Current affiliation:

Systems Modelling Laboratory, Department of Marine Genetics and Biotechnology, Institute of Oceanology, Polish Academy of Sciences and

Evolutionary Systems Laboratory, Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, Poland

Degrees:

28 May 1997: MSc in biotechnology (Polish: magister biotechnologii), Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk (joint program).

11 Dec 1998: PhD in biology (Polish: doktor nauk biologicznych w zakresie biologii), Faculty of Biology, Geography and Oceanology, University of Gdansk, Poland.

29 Oct 2008: Habilitation to Direct Research in biology (Polish: doktor habilitowany nauk biologicznych w zakresie biologii), Faculty of Biology, University of Gdansk, Poland.

Courses:

1996: Chromatography Course, University of Bremen, Germany.

1996: Radiation Safety in the Laboratory, US National Institutes of Health, Bethesda, Maryland, USA.

1999: Bioinformatics Training Workshop, International Center for Cooperation in Bioinformatics-Israel National Node, Wiezmann Institute of Science, Rehovot, Israel.

2001: Bioinformatics: From genome sequences to protein structures, European Molecular Biology Organization, University of Uppsala, Uppsala Sweden.

2002: RNA Structure and Function, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.

2002: Bioinformatics and Computational Biology, Foundation BBVA, Madrid, Spain.

2002: Methods and applications of molecular phylogeny, Sevilla, Spain.

2002: Administration of Linux systems, Valencia, Spain.

2002: Evolution of Structure and Function in Biology, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.

2003: Relating molecular evolution and protein function, Valencia, Spain.

2003: Mathematics of Evolution and Phylogeny, Paris, France.

2002-2005: Courses at the Department of Computer Science, University of Valencia, Spain: Technology of Programming Methodology of Programming (C++) Theory of Information and Codification Robotics Artificial Intelligence and Knowledge Engineering Operating Systems Theory of Automata and Formal Languages Programming Languages (Java, Prolog and Lisp) Advanced Concepts of Operating Systems Computer Networks Theory of Complexity Advanced Algorithms and Data Structures (Java) Databases Adaptive Systems Parallel Algorithms

2005: Courses at the Department of Statistics and Operative Investigation, University of Valencia, Spain: Bayesian Inference Model Selection (a course in a PhD programme on Bayesian Methods, Industrial Statistics and Optimization)

2005: An Introduction to Bayesian inference and MCMC, Technical University of Valencia, Spain.

2006: Summer School in Theoretical Neuroscience and Complex Systems, Frankfurt Institute for Advanced Studies, Germany.

2008: Introduction to Mathematica, Interdisciplinary Center for Mathematical and Computational Modelling, University of Warsaw, Poland.

2010: European Molecular Biology Organisation Practical Course: In silico systems biology network reconstruction, analysis and network based modelling, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.

2010: Complex Systems Summer School 2010, Santa Fe Institute, Santa Fe, New Mexico, USA.
Natural languages: Proficiency in: English, Polish (native) and Spanish.

Understanding of: French, Portuguese, Russian

Computer languages/environments:

C, C++, Java, MATLAB, R, HTML; basic skills in Mathematica, Prolog and Lisp.

Teaching:

1998: Computer methods in molecular biology (lectures and lab supervision)

2001: Molecular genetics lab

2001: Undergraduate seminar

2001: Principles of bioinformatics (lectures)

2007: Principles of modern biology (lectures)

2009: Embodied artificial intelligence (lectures)

2010: Modelling of biological processes (lectures and lab supervision)

2011: Introduction to systems biology (lectures)


Scholarships and Fellowships:

1994-1998: Department of Molecular Biology, University of Gdansk, Poland, Polish National Fund for Gifted Children (1993-1994), City of Gdansk (1994-1995), Polish Minister for National Education (1995-1997), University of Gdansk Postgraduate Scholarship (1997-1998).

1996: Laboratory of Molecular Genetics, US National Institute of Child Health and Human Development, Bethesda, Maryland, USA, Research Fellowship (one month).

1997-1998: Laboratory of Genetics, the Salk Institute for Biological Studies, La Jolla, California, USA, Fulbright Visiting Researcher.

1999-2001: Laboratory of Molecular Genetics and Biotechnology, The Hebrew University of Jerusalem, Israel, The Hebrew University Postdoctoral Fellowship (1999), Federation of European Biochemical Societies Long-Term Fellowship (1999-2000), European Molecular Biology Organization Long-Term Fellowship (2000-2001).

2002-2005: Department of Evolutionary Genetics, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Spain, Marie Curie Fellowship (2002-2004).

Awards:

1997: Procter & Gamble Poland Award for the best MSc thesis.

1999: Prime Minster Award for an exceptional PhD thesis.

2001: Polish Genetical Society Award for a collection of papers published in 1998-2000.

2001: Rector of the University of Gdansk Award.

2006: Foundation for Polish Science Fellowship.

2007: Foundation for Polish Science Fellowship (extension).

2009: Prime Minster Award for an exceptional habilitation thesis.

2010: Polish Genetical Society Award for a collection of papers published in 2007-2009 .

Papers (peer-reviewed only):

  1. Wróbel B. (1994) Pamiec na poziomie komórkowym i molekularnym [Memory on the cellular and molecular level]. Kosmos, 43, 231-244.
  2. Neubauer P., Wróbel B., Wegrzyn G. (1996) DNA degradation at elevated temperatures after plasmid amplification in amino acid-starved Escherichia coli cells. Biotech. Lett., 18, 321-326.
  3. Wróbel B., Wegrzyn G. (1997) Replication and amplification of lambda plasmids in Escherichia coli during amino acid starvation and limitation. FEMS Microbiol. Lett., 153, 151-157.
  4. Wróbel B., Wegrzyn G. (1997) Replication of plasmids derived from P1, F, R1, R6K and RK2 replicons in amino acid-starved Escherichia coli stringent and relaxed strains. J. Basic Microbiol., 37, 451-462.
  5. Wróbel B., Wegrzyn G. (1997) Differential amplification efficiency of pMB1 and p15A (ColE1-type) replicons in Escherichia coli stringent and relaxed strains starved for particular amino acids. Microbiol. Res.,152, 251-255.
  6. Wróbel B., Wegrzyn G, (1997) Amplification of pSC101 replicons in Escherichia coli during amino acid limitation. J. Biotechnol., 58, 205-208.
  7. Mikiewicz D., Wróbel B., Wegrzyn G., Plucienniczak A. (1997) Isolation and characterization of a ColE1-like plasmid from Enterobacter agglomerans with a novel variant of rom gene. Plasmid, 38, 210-219.
  8. Wróbel B., Wegrzyn G. (1998) Replication regulation of ColE1-like plasmids in amino acid-starved Escherichia coli. Plasmid, 39, 48-62.
  9. Wróbel B., Murphy H., Cashel M., Wegrzyn G. (1998) Guanosine tetraphosphate (ppGpp)-mediated inhibition of the bacteriophage lpR promoter activity in Escherichia coli. Mol. Gen. Genetics, 257, 490-495.
  10. Wróbel B., Srutkowska S., Wegrzyn G. (1998) A lambdoid phage isolated from cultures of the commonly used Escherichia coli K-12 stringent/relaxed strains CP78/CP79 after spontaneous prophage induction. Acta Biochim. Pol., 45, 251-259.
  11. Wróbel B., Herman-Antosiewicz A., Szalewska-Palasz A., Wegrzyn G. (1998) Polyadenylation of oop RNA in the regulation of bacteriophage l development. Gene, 212, 57-65.
  12. Szalewska-Palasz A., Wróbel B., Wegrzyn G. (1998) Rapid degradation of polyadenylated oop RNA. FEBS Lett., 43,70-72.
  13. Wegrzyn A., Wróbel B., Wegrzyn G. (1999) Altered biological properties of cell membranes in Escherichia coli dnaA and seqA mutants. Mol. Gen. Genetics, 261, 762-769.
  14. Czyz A., Wróbel B., Wegrzyn G. (2000) Vibrio harveyi bioluminescence plays a role in stimulation of DNA repair. Microbiology, 146, 283-288.
  15. Potrykus K., Wróbel B., Wegrzyn A., Wegrzyn G. (2000) Replication of oriJ-based plasmid DNA during the stringent and relaxed responses of Escherichia coli. Plasmid, 44, 111-126.
  16. Wróbel B., Yosef Y., Oppenheim A.B., Oppenheim A. (2000) Production and purification of SV40 major capsid protein (VP1) in Escherichia coli strains deficient for the GroELS chaperone machine. J. Biotechnol., 28, 285-289.
  17. Czyz A., Los M., Wróbel B., Wegrzyn G. (2001) Inhibition of spontaneous induction of lambdoid prophages in Escherichia coli cultures: simple procedures with possible biotechnologial applications.BMC Biotechnology, 1:1.
  18. Wróbel B., Wegrzyn G. (2002) Evolution of lambdoid replication modules. Virus Genes, 24, 163-171.
  19. Czyz A., Los M., Wróbel B., Wegrzyn G. (2002) Alleviation of problems with lambdoid prophage induction in Escherichia coli cultures. In: Life Sciences Technology, World Markets Research Centre, London, UK.
  20. Wang Z., Le G., Shi Y., Wegrzyn G., Wróbel B. (2002) A model for regulation of ColE1-like plasmid replication by uncharged tRNAs in amino acid starved Escherichia coli cells. Plasmid, 47, 69-78.
  21. Wróbel B. (2002) Replikacja plazmidów [Replication of plasmids]. Kosmos, 51, 255-257.
  22. Wróbel B., Slominski B., Wegrzyn G. (2003) The optimal eukaryotic signal for translation initiation from non-AUG codons, present upstream of bacteriophage lambda P cistron, is inactive in Escherichia coli. Cell. Mol. Biol. Lett., 8, 305-310.
  23. Sanjuan R.,Wróbel B., (2005) Weighted Least-Squares Likelihood Ratio Test for branch testing in phylogenies reconstructed from distance measures. Syst. Biol., 54, 218-229.
  24. Wróbel B., Torres-Puente M., Jimenez N., Bracho M., Garcia-Robles I., Moya A., Gonzalez-Candelas F. (2006) Analysis of the overdispersed clock in the short term evolution of Hepatitis C Virus: using the E1/E2 gene sequences to infer infection dates in a single source outbreak. Mol. Biol. Evol., 23, 1242-1251.
  25. Wysocka A., Konopa G., Wegrzyn G., Wróbel B. (2006) Genomic DNA hybridization as an attempt to evaluate phylogenetic relationships of Ostracoda. Crustaceana, 79, 1309-1322.
  26. Czarna A., Sanjuan R., Gonzalez-Candelas F., Wróbel B. (2006) Topology testing of phylogenies using least squares methods. BMC Evol. Biol., 6, 105.
  27. Slominski B., Calkiewicz J., Golec P., Wegrzyn G., Wróbel B. (2007) Plasmids derived from Gifsy-1/Gifsy-2, lambdoid prophages contributing to the virulence of Salmonella enterica serovar Typhimurium: implications for the evolution of replication initiation proteins of lambdoid phages and enterobacteria. Microbiology, 153, 1884-1896.
  28. Torres-Puente M., Cuevas J. M., Jiménez-Hernández N., Bracho M. A., García-Robles I., Wrobel B., Carnicer F., del Olmo J., Ortega E., Moya A., González-Candelas F. (2008) Genetic variability in Hepatitis C Virus and its role in antiviral treatment response. J. Viral Hepatitis, 15,188-199.
  29. Torres-Puente M., Cuevas J. M., Jiménez-Hernández N., Bracho M. A., García-Robles I., Wrobel B., Carnicer F., del Olmo J., Ortega E., Moya A., González-Candelas F. (2008) Using evolutionary tools to refine the new hypervariable region 3 within the envelope 2 protein of Hepatitis C Virus. Infection, Genetics and Evolution, 8,74-82.
  30. Wróbel B. (2008) Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences using model-based methods. J. Appl. Genetics, 49, 49-67.
  31. Kijewska, A., Czarna A., Fernández M., Zdzitowiecki K., Rokicki J., Wróbel B. (2008) Analysis of 5.8S rDNA and internal transcribed spacer 1 (ITS1) sequences of ascaridoid nematodes: phylogenetic signal and hypothesis testing. Genes and Genomics, 30, 291-306.
  32. Cuevas J. M., Torres-Puente M., Jiménez-Hernández N., Bracho M. A., García-Robles I., Wrobel B., Carnicer F., del Olmo J., Ortega E., Moya A., González-Candelas F. (2008) Genetic variability of Hepatitis C Virus before and after combined therapy of interferon plus ribavirin PLoS ONE, 26, e3058.
  33. Wysocka A., Kostoski G., Kilikowska A., Wróbel B., Sell J. (2008) A molecular framework for the phylogenetic relationships of the Proasellus (Crustacea, Isopoda) species group, endemic to the Balkan Lake Ohrid. Fundam. Appl. Limnol., 172, 301-313.
  34. Joachimczak M., Wróbel B. (2008) Evolution of 3D development controlled by a gene regulatory network: the complexity of the search space and evolvability. In: Proceedings of the GWAL-8, Leipzig, Germany (Edited by: K. Klemm, D. Merkle and E. Olbrich), IOS Press, Amsterdam, NL.
  35. Joachimczak M., Wróbel B. (2008) Evo-devo in silico: a model of a gene network regulating multicellular development in 3D space with artificial physics. In: Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems (Edited by: S. Bullock, J. Noble, R. Watson, M. Bedau), MIT Press, Boston, MA.
  36. Joachimczak M., Wróbel B.(2009) Evolution of 3D development controlled by a gene regulatory network: the complexity of the search space and evolvability. Adv. Complex Syst., 12, 347-369.
  37. Glinkowska M., £oœ J.M., Szambowska A., Czy¿ A., Ca³kiewicz J., Herman-Antosiewicz A., Wróbel B., Wêgrzyn G., Wêgrzyn A., £oœ M. (2010) Influence of the Escherichia coli oxyR gene on lambda prophage maintenance. Arch. Microbiol., 192, 673-83.
  38. Joachimczak M., Wróbel B. (2010) Processing signals with evolving artificial gene regulatory networks. In: Artificial Life XII: Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems (Edited by: H. Fellermann, M. Dörr, M.M. Hanczyc, L.L. Laursen, S. Maurer, D. Merkle, P.-A. Monnard, K. Stoy, S. Rasmussen), MIT Press, Boston, MA.
  39. Joachimczak M., Wróbel B. (2010) Evolving gene regulatory networks for real time control of foraging behaviours In: Artificial Life XII: Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems (Edited by: H. Fellermann, M. Dörr, M.M. Hanczyc, L.L. Laursen, S. Maurer, D. Merkle, P.-A. Monnard, K. Stoy, S. Rasmussen), MIT Press, Boston, MA.