CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. - Jan Baumbach; Karina Brinkrolf; Tobias Wittkop; Andreas Tauch; Sven Rahmann (J. Integr. Bioinform., 2006)

Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing. - Tobias Wittkop; Jan Baumbach; Francisco Pereira Lobo; Sven Rahmann (BMC Bioinform., 2007)

MoRAine - A web server for fast computational transcription factor binding motif re-annotation. - Jan Baumbach; Tobias Wittkop; Jochen Weile; Thomas Kohl; Sven Rahmann (J. Integr. Bioinform., 2008)

Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. - Tobias Wittkop; Sven Rahmann; Jan Baumbach (J. Integr. Bioinform., 2010)

Clustering biological data by unraveling hidden transitive substructures. - Tobias Wittkop (2010)

clusterMaker: a multi-algorithm clustering plugin for Cytoscape. - John H. Morris; Leonard Apeltsin; Aaron M. Newman; Jan Baumbach; Tobias Wittkop; Gang Su; Gary D. Bader; Thomas E. Ferrin (BMC Bioinform., 2011)

Extension and Robustness of Transitivity Clustering for Protein-Protein Interaction Network Analysis. - Tobias Wittkop; Sven Rahmann; Richard Röttger; Sebastian Böcker; Jan Baumbach (Internet Math., 2011)

Introduction: Advances in Computational Systems Bioinformatics. - Tobias Wittkop; Sean D. Mooney (J. Bioinform. Comput. Biol., 2011)

Online Transitivity Clustering of Biological Data with Missing Values. - Richard Röttger; Christoph Kreutzer; Thuy Duong Vu; Tobias Wittkop; Jan Baumbach (GCB, 2012)

Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles. - Richard Röttger; Prabhav Kalaghatgi; Peng Sun 008; Siomar de Castro Soares; Vasco Ariston de Carvalho Azevedo; Tobias Wittkop; Jan Baumbach (Bioinform., 2013)

STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. - Tobias Wittkop; Emily TerAvest; Uday S. Evani; K. Mathew Fleisch; Ari E. Berman; Corey Powell; Nigam H. Shah; Sean D. Mooney (BMC Bioinform., 2013)