Website: boskovav.github.io
Email: boskovav57(AT)univie.ac.at
Phone: ++43 +1 / 4277 - 74330

Postal address:
Center for Integrative Bioinformatics Vienna (CIBIV)
Max Perutz Labs
Campus Vienna Biocenter 5 (VBC5)
A-1030 Wien, Austria

Research interests

• Phylodynamics
• Bayesian statistics
• Next-generation sequencing
• Computational biology

Education

• Oct 2013 - Aug 2017: PhD at ETH Zurich, Switzerland
  Thesis title: Pathogen phylodynamics: better, smarter and faster
  Advisor: Prof. Dr. Tanja Stadler
• Sept 2011 - Aug 2013: MSc ETH UZH in Computational Biology and Bioinformatics, ETH Zurich and University of Zurich, Switzerland
  
• Jan 2010 - Aug 2010: Visiting graduate research student, Harvard Medical School and Broad Institute, USA
  
• Sept 2008 - Feb 2011: MSc in Biomedical Sciences, Utrecht University, The Netherlands
  
• Sept 2007 - Dec 2007: Exchange semester student, Univerisity of California Irvine, USA
  
• Sept 2005 - May 2008: BSc in Liberal Arts and Sciences, Utrecht University, The Netherlands
  

Professional Experience

• Jan 2019 - now: Postdoctoral researcher (Swiss National Science Foundation Fellow), Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Austria
  
• Oct 2017 - Aug 2018: Postdoctoral researcher, Computational Evolution and Theoretical Biology, ETH Zurich, Switzerland
  
• Oct 2013 - Aug 2017: Doctoral researcher, Computational Evolution, ETH Zurich, Switzerland
  
• Mar 2011 - Aug 2011: Research Analyst, Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
  

Teaching Activities

Semester Courses

• Fall Semester 2016: Teaching assistant, Computational Biology, ETH Zurich, Switzerland
  
• Fall Semester 2015: Teaching assistant, Molecular Evolution, Phylogenetics and Phylodynamics, ETH Zurich, Switzerland
  

Workshops

• 2018: Lecturer and teaching assistant, Introduction to Molecular Phylogenetics, Hong Kong
  
• 2018, 2017, 2016: Lecturer and teaching assistant, Taming the BEAST workshop, Switzerland and New Zealand
  
• 2016: Teaching assistant, Computational Biology for Infectious Diseases, Hanoi, Vietnam
  

Guest Lecturer

• 2017 Semester course in Special Track 1: ”Genome Oriented”, Zurich University of Applied Sciences (ZHAW), Switzerland
  Title: “Introduction to epidemiological inference from phylogenies”

• 2015 Workshop in Genomics and Evolution of Microbial Pathogens, Zurich University of Applied Sciences (ZHAW), Switzerland
  Title: “BEAST 2 How to”

Invited Talks

2017

• Whole genome sequencing for clinical microbiology: Translation into routine applications, Basel, Switzerland
  Title: “Next-generation phylodynamic”

2016

• Infectious Disease Epidemiology seminar at Imperial College London, United Kingdom
  Title: “Investigating the dynamics of Zika virus in the Americas”

Software contributions

• BEAST 2: package developer - http://www.beast2.org

Publications

2020

• V. Boskova and T. Stadler (2020) PIQMEE: Bayesian phylodynamic method for analysis of large datasets with duplicate sequences. Mol. Biol. Evol., 37, 3061-3075. (DOI: 10.1093/molbev/msaa136, PMID: 32492139, software)

2018

• V. Boskova, T. Stadler, and C. Magnus (2018) The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic. Virus Evolution, 4(1): vex044. (DOI: 10.1093/ve/vex044 )

2017

• J. Barido-Sottani^e, V. Boskova^e, L. Du Plessis^e, D. Kühnert^e, C. Magnus^e, V. Mitov^e, N. F. Müller^e, J. Pečerska^e, D. A. Rasmussen^e, C. Zhang^e, A. J. Drummond, T. A. Heath, O. G. Pybus, T. G. Vaughan, and T. Stadler (2017) Taming the BEAST - A Community Teaching Material Resource for BEAST 2. Systematic Biology, 67(1) 170-174. (DOI: 10.1093/sysbio/syx060)
  ^e contributed equally

2016

• D. M. Meinel, R. Kuehl, R. Zbinden, V. Boskova, C. Garzoni, D. Fadini, M. Dolina, B. Blümel, T. Weibel, S. Tschudin-Sutter, A. F. Widmer, J. A. Bielicki, A. Dierig, U. Heininger, R. Konrad, A. Berger, V. Hinic, D. Goldenberger, A. Blaich, T. Stadler, M. Battegay, A. Sing, and A. Egli (2016) Outbreak investigation for toxigenic Corynebacterium diphtheriae wound infections in refugees from Northeast Africa and Syria in Switzerland and Germany by whole genome sequencing. Clinical Microbiology and Infection, 22(12): 1003.e1-1003.e8. (DOI: 10.1016/j.cmi.2016.08.010)

2015

• D. Vijaykrishna, E. C. Holmes, U. Joseph, M. Fourment, Y. C.F. Su, R. Halpin, R. T.C. Lee, Y. M. Deng, V. Gunalan, X. Lin, T. B. Stockwell, N. B. Fedorova, B. Zhou, N. Spirason, D. Kühnert, V. Boskova, T. Stadler, A.-M. Costa, D. E. Dwyer, Q. S. Huang, L. C Jennings, W. Rawlinson, S. G. Sullivan, A. C Hurt, S. Maurer-Stroh, D. E Wentworth, G. J.D. Smith, and I. G. Barr (2015) The contrasting phylodynamics of human influenza B viruses. eLife, 4: e05055. (DOI: 10.7554/eLife.05055)
• S. Zoller, V. Boskova, and M. Anisimova (2015) Maximum-likelihood tree estimation using codon substitution models with multiple partitions. Molecular Biology and Evolution, 32(8): 2208-2216. (DOI: 10.1093/molbev/msv097)

2014

• V. Boskova, S. Bonhoeffer, and T. Stadler (2014) Inference of epidemiological dynamics based on simulated phylogenies using birth-death and coalescent models. PLoS Computational Biology, 10(11): e1003913. (DOI: 10.1371/journal.pcbi.1003913)

2013

• S. van Heesch, M. Mokry, V. Boskova, W. Junker, R. Mehon, P. Toonen, E. de Bruijn, J. D. Shull, T. J. Aitman, E. Cuppen, and V. Guryev (2013) Systematic biases in DNA copy number originate from isolation procedures. Genome biology, 14(4): R33. (DOI: 10.1186/gb-2013-14-4-r33)