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. During that time, I spent two years at the Genome Institute of Singapore.

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

Publications

• Wang, X., Srivastava, Y., Jankowski, A., Malik, V., Wei, Y., del Rosario, R. C.-H., Cojocaru, V., Prabhakar, S. and Jauch, R. DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1 Nucleic Acids Research 46, 5470–5486 (2018)
• Jankowski, A., Tiuryn, J. and Prabhakar, S. Romulus: Robust multi-state identification of transcription factor binding sites from DNase-seq data Bioinformatics 32, 2419–2426 (2016)
• 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