CrossLink: visualization and exploration of sequence relationships between (micro) RNAs. - Tobias Dezulian; Martin H. Schaefer 001; Roland Wiese; Detlef Weigel; Daniel H. Huson (Nucleic Acids Res., 2006)

MedlineRanker: flexible ranking of biomedical literature. - Jean-Fred Fontaine; Adriano Barbosa-Silva; Martin H. Schaefer 001; Matthew R. Huska; Enrique M. Muro; Miguel A. Andrade-Navarro (Nucleic Acids Res., 2009)

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. - Tiago J. S. Lopes; Martin H. Schaefer 001; Jason E. Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Gabriele Neumann; Miguel A. Andrade-Navarro; Yoshihiro Kawaoka; Hiroaki Kitano (Bioinform., 2011)

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. - Joachim von Eichborn; Mathias Dunkel; Björn O. Gohlke; Sarah C. Preissner; Michael F. Hoffmann; Jakob M. J. Bauer; J. Douglas Armstrong; Martin H. Schaefer 001; Miguel A. Andrade-Navarro; Nicolas Le Novère; Michael D. R. Croning; Seth G. N. Grant; et al. (Nucleic Acids Res., 2013)

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions. - Martin H. Schaefer 001; Tiago J. S. Lopes; Nancy Mah; Jason E. Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Caroline Louis-Jeune; Amie J. Eisfeld; Gabriele Neumann; Carol Perez-Iratxeta; Yoshihiro Kawaoka; Hiroaki Kitano; et al. (PLoS Comput. Biol., 2013)

Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways. - Martin H. Schaefer 001; Jae-Seong Yang; Luis Serrano; Christina Kiel (PLoS Comput. Biol., 2014)

Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen. - Apichat Suratanee; Martin H. Schaefer 001; Matthew J. Betts; Zita Soons; Heiko A. Mannsperger; Nathalie Harder; Marcus Oswald; Markus Gipp; Ellen Ramminger; Guillermo Marcus Martinez; Reinhard Männer; Karl Rohr; et al. (PLoS Comput. Biol., 2014)

HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. - Gregorio Alanis-Lobato; Miguel A. Andrade-Navarro; Martin H. Schaefer 001 (Nucleic Acids Res., 2017)

MIPPIE: the mouse integrated protein-protein interaction reference. - Gregorio Alanis-Lobato; Jannik S. Möllmann; Martin H. Schaefer 001; Miguel A. Andrade-Navarro (Database J. Biol. Databases Curation, 2020)

Generation and Interpretation of Context-Specific Human Protein-Protein Interaction Networks with HIPPIE. - Gregorio Alanis-Lobato; Martin H. Schaefer 001 (Protein-Protein Interaction Networks, 2020)

Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer. - Gökçe Senger; Martin H. Schaefer 001 (Frontiers Bioinform., 2021)