Research/art/teacher profile of a person
Name and surname:
doc. Mgr. Tomáš Vinař, PhD.
Document type:
Research/art/teacher profile of a person
The name of the university:
Comenius University Bratislava
The seat of the university:
Šafárikovo námestie 6, 818 06 Bratislava

I. - Basic information

I.1 - Surname
Vinař
I.2 - Name
Tomáš
I.3 - Degrees
doc. Mgr., PhD.
I.4 - Year of birth
1976
I.5 - Name of the workplace
Comenius University in Bratislava, Faculty of Mathematics, Physics and Informatics
I.6 - Address of the workplace
Mlynská dolina, 842 48 Bratislava
I.7 - Position
associate professor
I.8 - E-mail address
tomas.vinar@fmph.uniba.sk
I.9 - Hyperlink to the entry of a person in the Register of university staff
https://www.portalvs.sk/regzam/detail/5517
I.10 - Name of the study field in which a person works at the university
computer science
I.11 - ORCID iD
0000-0003-3898-3447

II. - Higher education and further qualification growth

II.1 - First degree of higher education
II.2 - Second degree of higher education
II.a - Name of the university or institution
Comenius University in Bratislava
II.b - Year
1999
II.c - Study field and programme
computer science
II.3 - Third degree of higher education
II.a - Name of the university or institution
University of Waterloo, Canada
II.b - Year
2006
II.c - Study field and programme
computer science
II.4 - Associate professor
II.a - Name of the university or institution
Comenius University in Bratislava
II.b - Year
2017
II.c - Study field and programme
computer science
II.5 - Professor
II.6 - Doctor of Science (DrSc.)

III. - Current and previous employment

III.a - Occupation-position III.b - Institution III.c - Duration
associate professor (before 06/2017 independent researcher) Comenius University in Bratislava, Slovakia 01/2009-present
postdoctoral researcher Cornell University, USA 08/2006-12/2008
research assistant professor University of Waterloo, Canada 09/2005-07/2006
technical assistant / assistant Comenius University in Bratislava, Slovakia 1994-1999

IV. - Development of pedagogical, professional, language, digital and other skills

IV.a - Activity description, course name, other IV.b - Name of the institution IV.c - Year
Test of English as Foreign Language (TOEFL) ETS 1998
Introductions to methodology of e-learning (short course) Comenius University in Bratislava 2021
Accessibility of the Comenius University web site (short course) Comenius University in Bratislava 2024

V. - Overview of activities within the teaching career at the university

V.1 - Overview of the profile courses taught in the current academic year according to study programmes
V.1.a - Name of the profile course V.1.b - Study programme V.1.c - Degree V.1.d - Field of study
Machine Learning applied informatics; computer science II. computer science
Methods in Bioinformatics bioinformatics; computer science I.; II. computer science, biology; computer science
Principles of Data Science data science I. computer science, mathematics
Efficient Algorithms and Data Structures applied informatics I. computer science
Perspectives of the Current Bioinformatics bioinformatics I. computer science, biology
Data Management data science; bioinformatics I. computer science, mathematics; computer science, biology
Genomics computer science II. computer science
V.2 - Overview of the responsibility for the delivery, development and quality assurance of the study programme or its part at the university in the current academic year
V.2.a - Name of the study programme V.2.b - Degree V.2.c - Field of study
Data Science I. computer science, mathematics (interdiscplinary)
V.3 - Overview of the responsibility for the development and quality of the field of habilitation procedure and inaugural procedure in the current academic year
V.4 - Overview of supervised final theses
V.4.1 - Number of currently supervised theses
V.4.a - Bachelor's (first degree)
2
V.4.b - Diploma (second degree)
2
V.4.c - Dissertation (third degree)
2
V.4.2 - Number of defended theses
V.4.a - Bachelor's (first degree)
15
V.4.b - Diploma (second degree)
18
V.4.c - Dissertation (third degree)
3
V.5 - Overview of other courses taught in the current academic year according to study programmes
V.5.a - Name of the course V.5.b - Study programme V.5.c - Degree V.5.d - Field of study
Bioinformatics Seminar computer science; applied informatics II. computer science
Algorithmics for Hard Problems applied informatics II. computer science

VI. - Overview of the research/artistic/other outputs

VI.1 - Overview of the research/artistic/other outputs and the corresponding citations
VI.1.1 - Number of the research/artistic/other outputs
VI.1.a - Overall
118
VI.1.b - Over the last six years
36
VI.1.2 - Number of the research/artistic/other outputs registered in the Web of Science or Scopus databases
VI.1.a - Overall
118
VI.1.b - Over the last six years
36
VI.1.3 - Number of citations corresponding to the research/artistic/other outputs
VI.1.a - Overall
5207
VI.1.b - Over the last six years
1970
VI.1.4 - Number of citations registered in the Web of Science or Scopus databases
VI.1.a - Overall
5207
VI.1.b - Over the last six years
1970
VI.1.5 - Number of invited lectures at the international, national level
VI.1.a - Overall
2
VI.1.b - Over the last six years
2
VI.2 - The most significant research/artistic/other outputs
1
Richard A Gibbs, Jeffrey Rogers, Michael G Katze, Roger Bumgarner, George M Weinstock, Tomas Vinar et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316(5822):222-234. 2007.
2
Carolin Kosiol, Tomas Vinar, Rute R. da Fonseca, Melissa J. Hubisz, Carlos D. Bustamante, Rasmus Nielsen, Adam Siepel. Patterns of positive selection in six Mammalian genomes. PLoS Genetics, 4(8):e1000144. 2008.
3
Vladimír Boža, Broňa Brejová, Tomáš Vinař. DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PLoS One, 12(6):e0178751. 2017.
4
Brona Brejova, Daniel G. Brown, Tomas Vinar. Vector seeds: an extension to spaced seeds. Journal of Computer and System Sciences, 70(3):364-380. 2005.
5
Vladimir Boza, Peter Peresini, Brona Brejova, Tomas Vinar. DeepNano-blitz: a fast base caller for MinION nanopore sequencers. Bioinformatics, 36(14):4191-4192. 2020.
VI.3 - The most significant research/artistic/other outputs over the last six years
1
Vladimir Boza, Peter Peresini, Brona Brejova, Tomas Vinar. DeepNano-blitz: a fast base caller for MinION nanopore sequencers. Bioinformatics, 36(14):4191-4192. 2020.
2

Kristina Borsova, Evan D. Paul, Viera Kovacova, Monika Radvanszka, Roman Hajdu, Viktoria Cabanova, Monika Slavikova, Martina Lickova, Lubomira Lukacikova, Andrej Belak, Lucia Roussier, Michaela Kosticova, Anna Liskova, Lucia Madarova, Maria Stefkovicova, Lenka Reizigova, Elena Novakova, Peter Sabaka, Alena Koscalova, Brona Brejova, Edita Staronova, Matej Misik, Tomas Vinar, Jozef Nosek, Pavol Cekan, Boris Klempa. Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexedRT-qPCR assay. Scientific Reports, 11(1):20494. 2021.

3

Peter Peresini, Vladimir Boza, Brona Brejova, Tomas Vinar. Nanopore Base Calling on the Edge. Bioinformatics, 37(24):4661-4667. 2021.

4

Jozef Sitarcik, Tomas Vinar, Brona Brejova, Werner Krampl, Jaroslav Budis, Jan Radvanszky, Maria Lucka. WarpSTR: determining tandem repeat lengths using raw nanopore signals. Bioinformatics, 39(6). 2023.

5

Askar Gafurov, Andrej Balaz, Fabian Amman, Kristina Borsova, Viktoria Cabanova, Boris Klempa, Andreas Bergthaler, Tomas Vinar, Brona Brejova. VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples. BMC Bioinformatics, 23(1):551. 2022.

VI.4 - The most significant citations corresponding to the research/artistic/other outputs
1
Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J. and Birol, I., 2009. ABySS: a parallel assembler for short read sequence data. Genome research, 19(6), pp.1117-1123.
2
Yang, Z. and Dos Reis, M., 2010. Statistical properties of the branch-site test of positive selection. Molecular biology and evolution, 28(3), pp.1217-1228.
3
Ching, T., Himmelstein, D.S., Beaulieu-Jones, B.K., Kalinin, A.A., Do, B.T., Way, G.P., Ferrero, E., Agapow, P.M., Zietz, M., Hoffman, M.M. and Xie, W., 2018. Opportunities and obstacles for deep learning in biology and medicine. Journal of The Royal Society Interface, 15(141), p.20170387.
4
Gertz, E.M., Yu, Y.K., Agarwala, R., Schäffer, A.A. and Altschul, S.F., 2006. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC biology, 4(1), pp.1-14.
5
Silvestre-Ryan, J. and Holmes, I., 2021. Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing. Genome biology, 22(1), pp.1-6.
VI.5 - Participation in conducting (leading) the most important research projects or art projects over the last six years
1

2021-2024: ALgorithms for PAngenome Computational Analysis, H2020 956229 (MSCA-ITN), ALPACA (principal investigator for the faculty)

2

2020-2025: Pan-genome Graph Algorithms and Data Integration, H2020 872539 (MSCA-RISE), PANGAIA (principal investigator for the faculty)

3

2018-2021: Chyby a neurčitosť v sekvenovaní DNA: Algoritmy a modely, VEGA 1/0458/18 (principal investigator)

4

2019-2023: Non-conventional applications of emerging sequencing technologies in comparative and functional genomics, APVV-18-0239 (principal investigator for the faculty)

5

2014-2017: Algoritmy a modely pre analýzu komplexných biologických sekvencií, VEGA 1/0719/14 (principal investigator)

6

2022-2025: Bioinformatika patogénov a pangenómov, VEGA 1/0538/22 (principal investigator)

7

2021-2023: Pangenomics for personalized clinical management of infected patients based on viral genome and human exome, Operational Program Integrated Infrastructure ITMS2014: 313011ATL7

VII. - Overview of organizational experience related to higher education and research/artistic/other activities

VII.a - Activity, position VII.b - Name of the institution, board VII.c - Duration
Student Research Conference, chair / member of the organization committee Comenius University in Bratislava 2010-present
Director of the Data Science Study Porgram Comenius University in Bratislava 2020-present

VIII. - Overview of international mobilities and visits oriented on education and research/artistic/other activities in the given field of study

VIII.a - Name of the institution VIII.b - Address of the institution VIII.c - Duration (indicate the duration of stay) VIII.d - Mobility scheme, employment contract, other (describe)
University of Waterloo 200 University Ave W, Waterloo, ON, N2L 3G1, Canada 09/1999-11/2005 doctoral studies
Simon Fraser University 8888 University Dr, Burnaby, BC, V5A 1S6, Canada 02/2022-08/2022 MSCA RISE

IX. - Other relevant facts

Date of last update
2026-03-02