Downloads

Software

• 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 and theses in bioinformatics and computational biology

• 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

Talks and notes in mathematics

• 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
• Public PGP key