Efficient algorithms for extracting biological key pathways with global constraints. - Jan Baumbach; Tobias Friedrich 001; Timo Kötzing; Anton Krohmer; Joachim Müller; Josch Pauling (GECCO, 2012)

CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. - Josch Pauling; Richard Röttger; Andreas Tauch; Vasco Ariston de Carvalho Azevedo; Jan Baumbach (Nucleic Acids Res., 2012)

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. - Nicolas Alcaraz; Josch Pauling; Richa Batra; Eudes Barbosa; Alexander Junge; Anne Christensen; Vasco Ariston de Carvalho Azevedo; Henrik J. Ditzel; Jan Baumbach (BMC Syst. Biol., 2014)

Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks. - Josch Pauling; Edda Klipp (J. Integr. Bioinform., 2016)

Parameter estimation of qualitative biological regulatory networks on high performance computing hardware. - Muhammad Tariq Saeed; Jamil Ahmad; Jan Baumbach; Josch Pauling; Aamir Shafi; Rehan Zafar Paracha; Asad Hayat; Amjad Ali 001 (BMC Syst. Biol., 2018)

Computational Lipidomics. - Josch Pauling (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Success Factors of Artificial Intelligence Implementation in Healthcare. - Justus Wolff; Josch Pauling; Andreas Keck; Jan Baumbach (Frontiers Digit. Health, 2021)

Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies. - Gihanna Galindez; Julian O. Matschinske; Tim D. Rose; Sepideh Sadegh; Marisol Salgado-Albarrán; Julian Späth; Jan Baumbach; Josch Konstantin Pauling (Nat. Comput. Sci., 2021)

Federated machine learning for a facilitated implementation of Artificial Intelligence in healthcare - a proof of concept study for the prediction of coronary artery calcification scores. - Justus Wolff; Julian O. Matschinske; Dietrich Baumgart; Anne Pytlik; Andreas Keck; Arunakiry Natarajan; Claudio E. von Schacky; Josch Pauling; Jan Baumbach (J. Integr. Bioinform., 2022)

Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data. - Tim D. Rose; Nikolai Köhler; Lisa Falk; Lucie Klischat; Olga Lazareva; Josch Konstantin Pauling (Briefings Bioinform., 2023)

Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE. - Lis Arend; Klaudia Adamowicz; Johannes R. Schmidt; Yuliya Burankova; Olga I. Zolotareva; Olga Tsoy; Josch Konstantin Pauling; Stefan Kalkhof; Jan Baumbach; Markus List; Tanja Laske (Briefings Bioinform., 2025)