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Institute for Machine Learning
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Dipl.-Ing. Maciej Kańduła


  • 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