A Clustering Approach to Generalized Tree Alignment with Application to Alu Repeats. - Benno Schwikowski; Martin Vingron (German Conference on Bioinformatics - Selected Papers, 1996)

Attacking Generalized tree Alignment by a Deferred Path Heuristic. - Benno Schwikowski; Martin Vingron (German Conference on Bioinformatics, 1996)

The Deferred Path Heuristic for the Generalized Tree Alignment Problem. - Benno Schwikowski; Martin Vingron (J. Comput. Biol., 1997)

An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. - Mathieu Blanchette; Benno Schwikowski; Martin Tompa (ISMB, 2000)

Universal DNA Tag Systems: A Combinatorial Design Scheme. - Amir Ben-Dor; Richard M. Karp; Benno Schwikowski; Zohar Yakhini (J. Comput. Biol., 2000)

Algorithmic Challenges in Mass Spectrometry and Systems Biology. - Benno Schwikowski (GI Jahrestagung (Ergänzungsband), 2002)

Discovering regulatory and signalling circuits in molecular interaction networks. - Trey Ideker; Owen Ozier; Benno Schwikowski; Andrew F. Siegel (ISMB, 2002)

On enumerating all minimal solutions of feedback problems. - Benno Schwikowski; Ewald Speckenmeyer (Discret. Appl. Math., 2002)

Algorithms for Phylogenetic Footprinting. - Mathieu Blanchette; Benno Schwikowski; Martin Tompa (J. Comput. Biol., 2002)

Towards optimally multiplexed applications of universal DNA tag systems. - Amir Ben-Dor; Tzvika Hartman; Benno Schwikowski; Roded Sharan; Zohar Yakhini (RECOMB, 2003)

Weighted sequence graphs: boosting iterated dynamic programming using locally suboptimal solutions. - Benno Schwikowski; Martin Vingron (Discret. Appl. Math., 2003)

The Restriction Scaffold Problem. - Amir Ben-Dor; Richard M. Karp; Benno Schwikowski; Ron Shamir (J. Comput. Biol., 2003)

Predicting protein-peptide interactions via a network-based motif sampler. - David J. Reiss; Benno Schwikowski (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Towards Optimally Multiplexed Applications of Universal Arrays. - Amir Ben-Dor; Tzvika Hartman; Richard M. Karp; Benno Schwikowski; Roded Sharan; Zohar Yakhini (J. Comput. Biol., 2004)

Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C virus infection. - David J. Reiss; Iliana Avila-Campillo; Vesteinn Thorsson; Benno Schwikowski; Timothy Galitski (BMC Bioinform., 2005)

Graph-based methods for analysing networks in cell biology. - Tero Aittokallio; Benno Schwikowski (Briefings Bioinform., 2006)

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. - Olivier Garcia; Cosmin Saveanu; Melissa S. Cline; Micheline Fromont-Racine; Alain Jacquier; Benno Schwikowski; Tero Aittokallio (Bioinform., 2007)

Phylogenetic distances are encoded in networks of interacting pathways. - Aurélien Mazurie; Danail Bonchev; Benno Schwikowski; Gregory A. Buck (Bioinform., 2008)

Indexing and Searching a Mass Spectrometry Database. - Søren Besenbacher; Benno Schwikowski; Jens Stoye (Algorithms and Applications, 2010)

Evolution of metabolic network organization. - Aurélien Mazurie; Danail Bonchev; Benno Schwikowski; Gregory A. Buck (BMC Syst. Biol., 2010)

Feature Detection with Controlled Error Rates in LC/MS Images. - Sébastien Li-Thiao-Té; Benno Schwikowski (J. Comput. Biol., 2012)

Mining proteomic data for biomedical research. - Laura Elo; Benno Schwikowski (WIREs Data Mining Knowl. Discov., 2012)

The Cytoscape app article collection. - Alexander R. Pico; Gary D. Bader; Barry Demchak; Oriol Guitart Pla; Timothy Hull; William J. R. Longabaugh; Christian Tannus Lopes; Samad Lotia; Piet Molenaar; Jason Montojo; John H. Morris; Keiichiro Ono; et al. (F1000Research, 2014)

The Cyni framework for network inference in Cytoscape. - Oriol Guitart-Pla; Manjunath Kustagi; Frank Rügheimer; Andrea Califano; Benno Schwikowski (Bioinform., 2015)

Detecting multi-way epistasis in family-based association studies. - Cheikh Loucoubar; Audrey V. Grant; Jean-François Bureau; Isabelle Casademont; Ndjido Ardo Bar; Avner Bar-Hen; Mamadou Diop; Joseph Faye; Fatoumata Diene Sarr; Abdoulaye Badiane; Adama Tall; Jean-François Trape; et al. (Briefings Bioinform., 2017)

Network-based analysis of omics data: the LEAN method. - Frederik Gwinner; Gwénola Boulday; Claire Vandiedonck; Minh Arnould; Cécile Cardoso; Iryna Nikolayeva; Oriol Guitart-Pla; Cécile V. Denis; Olivier D. Christophe; Johann Beghain; Elisabeth Tournier-Lasserve; Benno Schwikowski (Bioinform., 2017)

The Cytoscape Automation app article collection. - Barry Demchak; David Otasek; Alexander R. Pico; Gary D. Bader; Keiichiro Ono; Brett Settle; Eric Sage; John H. Morris; William J. R. Longabaugh; Christian Tannus Lopes; Michael Kucera; Adam Treister; et al. (F1000Research, 2018)

An overview of machine learning methods for monotherapy drug response prediction. - Farzaneh Firoozbakht; Behnam Yousefi; Benno Schwikowski (Briefings Bioinform., 2022)

Reproducible Mapping of Tabular Data into Semantic Knowledge Graphs with OntoWeaver and BioCypher. - Johann Dréo; Claire Laudy; Sebastian Lobentanzer; Marko Baric; Ekaterina Gaydukova; Benno Schwikowski (FUSION, 2024)