Research interests
- Bioinformatics and computational biology: DNA regulatory elements, chromatin architecture
- Machine learning: feature selection
Current projects
- “Algorithms for inferring multi-contact interactions from chromosome conformation capture data” aiming to develop new algorithms to interpret three-dimensional organization of the genome. Funded by the Polish National Agency for Academic Exchange.
- Integration of multiple types of single-cell genomics data, in particular single cell RNA-seq, ATAC-seq and Hi-C data.
Open positions
- Ph.D. positions in bioinformatics – application deadline is June 15th, 2020
Teaching
- Teaching archive (in Polish)
Software
- Code used for the analysis in Ghavi-Helm et al., 2019
- Romulus: Robust multi-state identification of transcription factor binding sites from DNase-seq data
- TACO: Transcription factor Association from Complex Overrepresentation, predicting overrepresented motif complexes in genome-wide sets of regulatory regions
Talks, theses, notes etc.
- Uncoupling gene expression and chromatin organization during embryogenesis by genomic rearrangements – talk at the EMBL Genome Biology Unit seminar, 2018
- Multi-state identification of transcription factor binding sites from DNase-seq data – talk at the EMBL Centre for Biological Modelling seminar, 2018
- Modeling transcription factor complex binding to eukaryotic genomes – Ph.D. thesis in computer science
- Predicting cell type-specific transcription factor cooperative binding – talk at the RECOMB Regulatory Genomics 2011 conference
- 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 talk
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
Brief CV
Employment and education
- 2020–present: Assistant professor of computer science at the University of Warsaw
- 2014–2019: Postdoctoral fellow at the European Molecular Biology Laboratory in Heidelberg, Germany
- 2009–2014: Ph.D. student in computer science at the University of Warsaw and Genome Institute of Singapore
Grants and fellowships
- 2020–2024: Polish Returns grant, Polish National Agency for Academic Exchange
- 2017–2018: Marie Skłodowska-Curie Individual Fellowship, Horizon 2020
- 2012–2014: Individual pre-doctoral grant PRELUDIUM, National Science Centre, Poland
Publications
Contact
E-mail: ajank(at)mimuw.edu.pl
Skype: aleksander_jankowski
Public PGP key
Address: University of Warsaw, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, 02-097 Warsaw, Poland
Room: 5850
Phone: +48 225544585
