TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes. - V. Matys; Olga V. Kel-Margoulis; Ellen Fricke; Ines Liebich; Sigrid Land; A. Barre-Dirrie; Ingmar Reuter; D. Chekmenev; Mathias Krull; Klaus Hornischer; Nico Voss; Philip Stegmaier; et al. (Nucleic Acids Res., 2006)

Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. - T. Waleev; Dmitry Shtokalo; Tatiana Konovalova; Nico Voss; Evgeny Cheremushkin; Philip Stegmaier; Olga V. Kel-Margoulis; Edgar Wingender; Alexander E. Kel (Nucleic Acids Res., 2006)

Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. - Denitsa Alamanova; Philip Stegmaier; Alexander E. Kel (BMC Bioinform., 2010)

Molecular mechanistic associations of human diseases. - Philip Stegmaier; Mathias Krull; Nico Voss; Alexander E. Kel; Edgar Wingender (BMC Syst. Biol., 2010)

3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. - Razif R. Gabdoulline; Denitsa Eckweiler; Alexander E. Kel; Philip Stegmaier (Nucleic Acids Res., 2012)

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs. - Philip Stegmaier; Alexander E. Kel; Edgar Wingender; Jürgen Borlak (PLoS Comput. Biol., 2013)

geneXplainR: An R interface for the geneXplain platform. - Philip Stegmaier; Alexander E. Kel; Edgar Wingender (J. Open Source Softw., 2017)

Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. - Alexander E. Kel; Ulyana Boyarskikh; Philip Stegmaier; Leonid S. Leskov; Andrey V. Sokolov; Ivan S. Yevshin; Nikita Mandrik; Daria Stelmashenko; Jeannette Koschmann; Olga V. Kel-Margoulis; Mathias Krull; Anna Martínez-Cardús; et al. (BMC Bioinform., 2019)