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Article

Omidi, Saeed and Zavolan, Mihaela and Pachkov, Mikhail and Breda, Jeremie and Berger, Severin and van Nimwegen, Erik. (2017) Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Computational Biology, 13 (7). e1005176.

Swiss Institute of Bioinformatics Members, SIB. (2016) The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44 (D1). D27-D37.

Artimo, Panu and Duvaud, Séverine and Pachkov, Mikhail and Ioannidis, Vassilios and van Nimwegen, Erik and Stockinger, Heinz. (2016) The ISMARA client. F1000Research, 5 (Elixir). p. 2851.

Pemberton-Ross, Peter J. and Pachkov, Mikhail and van Nimwegen, Erik. (2015) ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data. Methods, Vol. 85. pp. 62-74.

Bertels, Frederic and Silander, Olin K. and Pachkov, Mikhail and Rainey, Paul B. and van Nimwegen, Erik. (2014) Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular biology and evolution, Vol. 31, no. 5. pp. 1077-1088.

Balwierz, Piotr J. and Pachkov, Mikhail and Arnold, Phild and Gruber, Andreas J. and Zavolan, Mihaela and van Nimwegen, Erik. (2014) ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs. Genome research, Vol. 24, H. 5. pp. 869-884.

Gruber, Andreas J. and Grandy, William A. and Balwierz, Piotr J. and Dimitrova, Yoana A. and Pachkov, Mikhail and Ciaudo, Constance and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Research, 42 (14). pp. 9313-9326.