YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. - Carl G. de Boer; Timothy R. Hughes (Nucleic Acids Res., 2012)

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization. - Carl G. de Boer; Aviv Regev (BMC Bioinform., 2018)

LegNet: a best-in-class deep learning model for short DNA regulatory regions. - Dmitry Penzar; Daria Nogina; Elizaveta Noskova; Arsenii Zinkevich; Georgy Meshcheryakov; Andrey Lando; Abdul Muntakim Rafi; Carl G. de Boer; Ivan V. Kulakovskiy (Bioinform., 2023)