Research/art/teacher profile of a person
Name and surname:
doc. Mgr. Bronislava Brejová, 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
Brejová
I.2 - Name
Bronislava
I.3 - Degrees
doc. Mgr. PhD.
I.4 - Year of birth
1976
I.5 - Name of the workplace
Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava
I.6 - Address of the workplace
FMFI UK, Mlynská dolina, 84248 Bratislava, Slovakia
I.7 - Position
Professor
I.8 - E-mail address
bronislava.brejova@fmph.uniba.sk
I.9 - Hyperlink to the entry of a person in the Register of university staff
https://www.portalvs.sk/regzam/detail/5516
I.10 - Name of the study field in which a person works at the university
Computer science
I.11 - ORCID iD
0000-0002-9483-1766

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
2014
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
professor Comenius University in Bratislava July 2022 - present
associate professor Comenius University in Bratislava 2014-2022
researcher Comenius University in Bratislava 2009-2014
researcher Cornell University, USA 2006-2008
research assistant professor University of Waterloo, Canada 2005-2006
assistant Comenius University in Bratislava 1996-1999

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
Research stay at a foreign institution Simon Fraser University, Canada 2022 6 months, 2023 2 months, 2024 1 month
Online course Accessibility of the Comenius University website Comenius University 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
Programming (1) in C/C++ computer science I. computer science
Bachelor thesis seminar (1), (2) bioinformatics, data science I. computer science and biology, computer science and mathematics
Methods in bioinformatics computer science, bioinformatics I., II. computer science, computer science and biology
Data management computer science, bioinformatics, data science I., II. computer science, computer science and biology, computer science and mathematics
Genomics computer science II. computer science
Theory and Methodology of Informatics computer science III. computer science
Data visualization bioinformatics, data science I. computer science and biology, computer science and mathematics
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
Bioinformatics I. computer science and biology
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)
3
V.4.b - Diploma (second degree)
0
V.4.c - Dissertation (third degree)
1
V.4.2 - Number of defended theses
V.4.a - Bachelor's (first degree)
17
V.4.b - Diploma (second degree)
24
V.4.c - Dissertation (third degree)
5
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
Seminar in bioinformatics computer science 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
82
VI.1.b - Over the last six years
28
VI.1.2 - Number of the research/artistic/other outputs registered in the Web of Science or Scopus databases
VI.1.a - Overall
82
VI.1.b - Over the last six years
28
VI.1.3 - Number of citations corresponding to the research/artistic/other outputs
VI.1.a - Overall
2115
VI.1.b - Over the last six years
885
VI.1.4 - Number of citations registered in the Web of Science or Scopus databases
VI.1.a - Overall
2115
VI.1.b - Over the last six years
885
VI.1.5 - Number of invited lectures at the international, national level
VI.1.a - Overall
18
VI.1.b - Over the last six years
2
VI.2 - The most significant research/artistic/other outputs
1

Brejova B., Brown D.G., Li M., Vinar T. ExonHunter: A comprehensive approach to gene finding 2005, Bioinformatics, (SUPPL. 1) pp. i57-i65.

2

B. Brejova, D. G. Brown, T. Vinar. Vector seeds: an extension to spaced seeds. Journal of Computer and System Sciences, 70(3):364-380. 2005.

3

Worley K.C, Warren W.C., Rogers J. (...) Brejova B. et al. The common marmoset genome provides insight into primate biology and evolution. Nature genetics. 2014 Aug;46(8):850.

4

V. Boža, B. Brejová, T. Vinař. DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PloS One, 12(6):e0178751. 2017

5

R.R. Da Fonseca, A. Couto A, A.M. Machado, B. Brejova et al. A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience. 2020 Jan;9(1):giz152.

VI.3 - The most significant research/artistic/other outputs over the last six years
1

Sitarčík, J., Vinař, T., Brejová, B., Krampl, W., Budiš, J., Radvánszky, J. and Lucká, M., 2023. WarpSTR: Determining tandem repeat lengths using raw nanopore signals. Bioinformatics, 39(6), p.btad388

2

Mane, A., Faizrahnemoon, M., Vinař, T., Brejová, B. and Chauve, C., 2023. PlasBin-flow: a flow- based MILP algorithm for plasmid contigs binning. Bioinformatics, 39(Supplement_1), pp.i288-i296.

3

A. Gafurov, B. Brejová, P. Medvedev. Markov chains improve the significance computation of overlapping genome annotations. Bioinformatics. 2022 38(I203-I211).

4

Gafurov, A., Baláž, A., Amman, F., Boršová, K., Čabanová, V., Klempa, B., Bergthaler, A., Vinař, T. and Brejová, B., 2022. VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples. BMC Bioinformatics, 23(1), p.551.

5

R.R. Da Fonseca, A. Couto A, A.M. Machado, B. Brejova et al. A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience. 2020 Jan;9(1):giz152.

VI.4 - The most significant citations corresponding to the research/artistic/other outputs
1

Brejova B., Brown D.G., Li M., Vinar T. ExonHunter: A comprehensive approach to gene finding 2005, Bioinformatics, (SUPPL. 1) pp. i57-i65.

Citované v / cited in:

Rätsch G, Sonnenburg S, Srinivasan J, Witte H, Müller KR, Sommer RJ, Schölkopf B. Improving the Caenorhabditis elegans genome annotation using machine learning. PLoS Computational Biology. 2007 Feb;3(2):e20.

2

B. Brejova, D. G. Brown, T. Vinar. Vector seeds: an extension to spaced seeds. Journal of Computer and System Sciences, 70(3):364-380. 2005.

Citované v / cited in:

Csuros, M. and Ma, B., 2007. Rapid homology search with neighbor seeds. Algorithmica, 48(2), pp.187-202.

3

Worley K.C, Warren W.C., Rogers J. (...) Brejova B. et al. The common marmoset genome provides insight into primate biology and evolution. Nature genetics. 2014 Aug;46(8):850.

Citované v / cited in:

Sundaram L, Gao H, Padigepati SR, McRae JF, Li Y, Kosmicki JA, Fritzilas N, Hakenberg J, Dutta A, Shon J, Xu J. Predicting the clinical impact of human mutation with deep neural networks. Nature genetics. 2018 Aug;50(8):1161-70.

4

V. Boža, B. Brejová, T. Vinař. DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PloS One, 12(6):e0178751. 2017

Citované v / cited in:

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.

5

R.R. Da Fonseca, A. Couto A, A.M. Machado, B. Brejova et al. A draft genome sequence of the elusive giant squid, Architeuthis dux. GigaScience. 2020 Jan;9(1):giz152.

Citované v / cited in:

Davison A, Neiman M. Mobilizing molluscan models and genomes in biology. Philosophical Transactions of the Royal Society B. 2021 May 24;376(1825):20200163.

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 (team member)

2

2020-2023: Pan-genome Graph Algorithms and Data Integration, H2020 872539 (MSCA-RISE), PANGAIA (team member)

3

2020-2023 Alternative Representations of Big Genomic Data, VEGA 1/0463/20 (principal investigator)

4

2023-2027: Comparative transcriptomics as a window to the world of fundamental biological processes APVV-22-0144 (riešiteľka)

5

2016-2019 Algorithms for heterogeneous next generation sequencing data VEGA 1/0684/16 (principal investigator)

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
Panel member of VEGA grant agency Scientific Grant Agency 2021-present
Editor of the Journal of Bioinformatics and Computational Biology World Scientific 2015-present
Program committee member of international conferences SPIRE 2021 (String processing and information retrieval), RECOMB – Comparative Genomics 2021 a 2022, MFCS 2020 (Mathematical Foundations of Computer Science) 2020, 2021, 2022
Member of the Scientific Board of the Faculty of Mathematics, Physics and Informatics, Comenius University Faculty of Mathematics, Physics and Informatics, Comenius University 2022-present
Member of the ethic committee Faculty of Mathematics, Physics and Informatics, Comenius University 2021-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 Waterloo, Ontario, Canada 09/1999-11/2005 PhD study
Cornell University Ithaca, New York, USA 08/2006-12/2008 postdoctoral researcher
University of Wroclaw Wroclaw, Poland 03/2015 instructor of a doctoral course, 6 days
Simon Fraser University Burnaby, British Columbia, Canada 02/2022 - 08/2022, , 07/2023-08/2023, 08/2024 Research stays within PANGAIA project

IX. - Other relevant facts

Date of last update
2025-01-09