Maciej Kandula

Maciej Kańduła

phone: +43-732-2468-4520
fax: +43-732-2468-4539

e-mail: [email protected]

Room: S3 327 (Computer Science Building, Science Park 3)

Education

2014-present: Postdoc Researcher, Johannes Kepler University Linz, Austria
2013-2017: PhD in Bioinformatics, BOKU University Vienna, Austria
2015: Marshall Plan Scholarship scholar, Boston University, USA
2010-2012: MEng, Biotechnology, with distinction, BOKU University Vienna, Austria

Employment record

Aug 2017 - present: Research Assistant, Institute of Bioinformatics, Johannes Kepler University, Linz, Austria
Apr 2015 - Nov 2015: Research Scholar, Department of Mathematics and Statistics and Center for Regenerative Medicine, Boston University, USA
Apr 2012 - Aug 2017: Research Assistant, Chair of Bioinformatics Research Group, BOKU University Vienna and VetMed University Vienna, Austria
Mar 2011 - Feb 2012: Research Assistant, Dept of Biotechnology, BOKU University Vienna, Austria
Apr 2010 - Sep 2010: Internship, QM, Nestlé Suisse SA, Vevey, Switzerland
Nov 2006 - Jan 2011: Institute of Applied Genetics and Cell Biology, BOKU University Vienna, Austria

Research Topics

Deep Learning
Convolutional neural networks
Life science data analysis and bioinformatics
Heterogeneous molecular data integration
Scientific workflow systems

Selected Publications

Kańduła, M; Singh, S; Kolaczyk, E; Kreil, D. A Multi-layer network approach to data integration for patient stratification. Biology Direct, extended abstract accepted
Kańduła, M; Kreil, D. Novel benchmark demonstrates: data integration can offset limitations of weak signals in cancer study. Nature Methods, submitted
Shridhar, S; Klanert, G; Auer, N; Hernandez-Lopez, I; Kańduła, M; Hackl, M; Grillari, J; Stralis-Pavese, N; Kreil, D; Borth, N. Transcriptomic changes in CHO cells after adaptation to suspension growth in protein-free medium analysed by a species-specific microarray, J Biotechnology 2017
Dame, K; Cincotta, S; Lang, A; Sanghrajka, R; Zhang, L; Kwok, L; Wilson, T; Choi, J; Kańduła, M; Monti, S; Hollenberg, A; Mehta, P; Kotton, D; Ikonomou, L. Thyroid progenitors are robustly derived from embryonic stem cells through transient, developmental stage-specific overexpression of Nkx2-1, Stem Cell Reports 2017
Spjuth, O; Bongcam-Rudloff, E; Carrasco Hernández, G; Forer, L; Giovacchini, M; Valls Guimera, R; Kallio, A; Korpelainen, E; Kańduła, M; Krachunov, M; Kreil, D; Kulev, O; Labaj, P; Lampa, S; Pireddu, L; Schönherr, S; Siretskiy, A; Vassilev, D. (2015) Experiences with workflows for automating data-intensive bioinformatics. Biology Direct 2015
Sayegh, R; Zotter, S; Roberts, P; Kańduła, M; Sacu, S; Kreil, D; Baumann, B; Pircher, M; Hitzenberger, C; Schmidt-Erfurth, U. (2015) Polarization-sensitive Optical Coherence Tomography and Conventional Retinal Imaging Strategies in Assessing Foveal Integrity in Geographic Atrophy. Investigative Ophthalmology & Visual Science 2015

Honors, Awards and Fellowships

Best Talk Award at CAMDA/ISMB 2017
Marshall Plan Scholarship (Boston, USA) in 2015
ISMB/ECCB 2015 Travel Fellowship
IAESTE Internship (Vevey, Switzerland) in 2010
ERASMUS Scholarship (Copenhagen, Denmark) in 2009

Invited Talks at International Conferences

A multi-layer network approach to data integration for patient stratification, at CAMDA/ISMB 2017, Prague, Czech Republic, Best Talk Award
Balanced benchmarks show simple approaches succeed with growing numbers, at IBSB 2015, Boston, USA
Lightweight contender: Snakemake, at Workshop on e-Infrastructures for Massively Parallel Sequencing 2015, Uppsala, Sweden
A network-based prediction of pathways dysregulated in Kidney Renal Clear Cell Carcinoma (KIRC) - new insights from the integration of multiple data sources, at CAMDA 2014, Boston, USA
A network-based prediction of pathways dysregulated in Kidney Renal Clear Cell Carcinoma (KIRC), at IBSB 2014, Berlin, Germany

Additional Affiliations

Chair of Bioinformatics Research Group, BOKU University Vienna, Austria http://www.bioinf.boku.ac.at/MMKandula.php
Member of the International Society for Computational Biology (ISCB)