I am a postdoctoral fellow in Furlong Group at the European Molecular Biology Laboratory in Heidelberg, Germany.

Formerly, I was a Ph.D. student within the Computational Biology Group at the Faculty of Mathematics, Informatics and Mechanics at the University of Warsaw.

My research is focused on computational biology, regulatory genomics and machine learning.

Publications

• Jankowski, A., Tiuryn, J. and Prabhakar, S. Romulus: Robust multi-state identification of transcription factor binding sites from DNase-seq data Bioinformatics (2016) doi: 10.1093/bioinformatics/btw209
• Jankowski, A., Obara, P., Mathur, U. and Tiuryn, J. Enhanceosome transcription factors preferentially dimerize with high mobility group proteins BMC Systems Biology 10, 14 (2016)
• Huang, Y.-H., Jankowski, A., Cheah, K.S., Prabhakar, S. and Jauch, R. SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains. Scientific Reports 5, 10398 (2015)
• Jankowski, A., Prabhakar, S. and Tiuryn, J. TACO: a general-purpose tool for predicting cell-type–specific transcription factor dimers. BMC Genomics 15, 208 (2014)
• Jankowski, A., Szczurek, E., Jauch, R., Tiuryn, J. and Prabhakar, S. Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Genome Research 23, 1307-1318 (2013)
• Kursa, M.B., Jankowski, A. and Rudnicki, W.R. Boruta – a system for feature selection. Fundamenta Informaticae 101, 271-285 (2010)
• Rudnicki, W.R., Jankowski, A., Modzelewski, A., Piotrowski, A. and Zadrożny, A. The new SIMD implementation of the Smith-Waterman algorithm on Cell microprocessor. Fundamenta Informaticae 96, 181-194 (2009)
• My list of publications on Google Scholar
• My profile on ResearchGate

Software

• TACO: Transcription factor Association from Complex Overrepresentation, predicting overrepresented motif complexes in genome-wide sets of regulatory regions
• Romulus: Robust multi-state identification of transcription factor binding sites from DNase-seq data

Teaching

• Teaching archive (in Polish)

Slides, notes, etc.

• Modeling transcription factor complex binding to eukaryotic genomes – Ph.D. thesis in computer science
• Predicting nucleosome binding sites in yeast genome – Master's thesis in mathematics (see also slides in Polish)
• Modelowanie motywów łańcuchami Markowa wyższego rzędu
• Odkrywanie cis-regulatorowych RNA w prokariotach with an appendix Ukryte modele Markowa i algorytm Bauma-Welcha
• Metryzacja struktur zgrubnych – Bachelor's thesis in mathematics
• Metryzacja struktur zgrubnych i hiperbolizacja przestrzeni metrycznych – notes to the seminar talks
• Wirtualizacja – slides on virtualization, Operating Systems course

Varia

• Kwatermistrzostwo obozów wędrownych – a handbook for hiking camp organizers
• Compasses and Ruler – Polish translation of this geometry program
• Conway's Game of Life – an example of cellular automata