The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. - Christoph Steinbeck; Yongquan Han; Stefan Kuhn 001; Oliver Horlacher; Edgar Luttmann; Egon L. Willighagen (J. Chem. Inf. Comput. Sci., 2003)

NMRShiftDB-Constructing a Free Chemical Information System with Open-Source Components. - Christoph Steinbeck; Stefan Krause; Stefan Kuhn 001 (J. Chem. Inf. Comput. Sci., 2003)

Bioclipse: an open source workbench for chemo- and bioinformatics. - Ola Spjuth; Tobias Helmus; Egon L. Willighagen; Stefan Kuhn 001; Martin Eklund; Johannes Wagener; Peter Murray-Rust; Christoph Steinbeck; Jarl E. S. Wikberg (BMC Bioinform., 2007)

Chemical Markup, XML, and the World Wide Web, 7. CMLSpect, an XML Vocabulary for Spectral Data. - Stefan Kuhn 001; Tobias Helmus; Robert J. Lancashire; Peter Murray-Rust; Henry S. Rzepa; Christoph Steinbeck; Egon L. Willighagen (J. Chem. Inf. Model., 2007)

Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction. - Stefan Kuhn 001; Björn Egert; Steffen Neumann; Christoph Steinbeck (BMC Bioinform., 2008)

Bioclipse 2: A scriptable integration platform for the life sciences. - Ola Spjuth; Jonathan Alvarsson; Arvid Berg; Martin Eklund; Stefan Kuhn 001; Carl Mäsak; Gilleain M. Torrance; Johannes Wagener; Egon L. Willighagen; Christoph Steinbeck; Jarl E. S. Wikberg (BMC Bioinform., 2009)

Progress on an open source computer-assisted structure elucidation suite (SENECA). - Stefan Kuhn 001; Christoph Steinbeck (J. Cheminformatics, 2010)

Computational metabolomics - a field at the boundaries of cheminformatics and bioinformatics. - Christoph Steinbeck; Stefan Kuhn 001; Kalai Vanii Jayaseelan; Pablo A. Moreno (J. Cheminformatics, 2011)

Towards Modelling of Local Reversibility. - Stefan Kuhn 001; Irek Ulidowski (RC, 2015)

A Calculus for Local Reversibility. - Stefan Kuhn 001; Irek Ulidowski (RC, 2016)

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. - Egon L. Willighagen; John W. Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn 001; Tomás Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain M. Torrance; Chris T. A. Evelo; et al. (J. Cheminformatics, 2017)

Erratum to: The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. - Egon L. Willighagen; John W. Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn 001; Tomás Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain M. Torrance; Chris T. A. Evelo; et al. (J. Cheminformatics, 2017)

Simulation of Base Excision Repair in the Calculus of Covalent Bonding. - Stefan Kuhn 001 (RC, 2018)

Local reversibility in a Calculus of Covalent Bonding. - Stefan Kuhn 001; Irek Ulidowski (Sci. Comput. Program., 2018)

Puffle-Pod Marine Evacuation System (POMES). - Eda Tumer; Stefan Kuhn 001 (SmartWorld/SCALCOM/UIC/ATC/CBDCom/IOP/SCI, 2019)

Rapid prediction of NMR spectral properties with quantified uncertainty. - Eric Jonas; Stefan Kuhn 001 (J. Cheminformatics, 2019)

Local reversibility and the Calculus of Covalent Bonding. - Stefan Kuhn 001 (2019)

Identifying Parkinson's Disease Through the Classification of Audio Recording Data. - James Bielby; Stefan Kuhn 001; Simon Colreavy-Donnelly; Fabio Caraffini; Stuart O'Connor; Zacharias A. Anastassi (CEC, 2020)

A Neural Network for Interpolating Light-Sources. - Simon Colreavy-Donnelly; Stefan Kuhn 001; Fabio Caraffini; Stuart O'Connor; Zacharias A. Anastassi; Simon Coupland (COMPSAC, 2020)

Shallow buried improvised explosive device detection via convolutional neural networks. - Simon Colreavy-Donnelly; Fabio Caraffini; Stefan Kuhn 001; Mario Gongora 001; Johana Florez-Lozano; Carlos Parra 001 (Integr. Comput. Aided Eng., 2020)

Reversibility in Chemical Reactions. - Stefan Kuhn 001; Bogdan Aman; Gabriel Ciobanu; Anna Philippou; Kyriaki Psara; Irek Ulidowski (Selected Results of the COST Action IC1405, 2020)

Reversibility of Executable Interval Temporal Logic Specifications. - Antonio Cau; Stefan Kuhn 001; James Hoey (RC, 2021)

A Pilot Study For Fragment Identification Using 2D NMR and Deep Learning. - Stefan Kuhn 001; Eda Tumer; Simon Colreavy-Donnelly; Ricardo Moreira Borges (CoRR, 2021)

Executable Interval Temporal Logic Specifications. - Antonio Cau; Stefan Kuhn 001; James Hoey (CoRR, 2021)

SCIPS: A serious game using a guidance mechanic to scaffold effective training for cyber security. - Stuart O'Connor; Salim Hasshu; James Bielby; Simon Colreavy-Donnelly; Stefan Kuhn 001; Fabio Caraffini; Richard Smith 002 (Inf. Sci., 2021)

Dataset Size and Machine Learning - Open NMR Databases as a Case Study. - Stefan Kuhn 001; Ricardo Moreira Borges; Francesco Venturini; Maurizio Sansotera (COMPSAC, 2022)

Direct deduction of chemical class from NMR spectra. - Stefan Kuhn 001; Carlos Cobas; Agustin Barba; Simon Colreavy-Donnelly; Fabio Caraffini; Ricardo Moreira Borges (CoRR, 2022)

Modelling of DNA mismatch repair with a reversible process calculus. - Stefan Kuhn 001; Irek Ulidowski (Theor. Comput. Sci., 2022)

Image Processing Model to Estimate Nutritional Values in Raw and Cooked Vegetables. - Tan Jo Yen; Sivakumar Vengusamy; Fabio Caraffini; Stefan Kuhn 001; Simon Colreavy-Donnelly (FRUCT, 2023)

Extended Reality, Augmented Users, and Design Implications for Virtual Learning Environments. - Lilian Genaro Motti Ader; Katie Crowley; Stefan Kuhn 001; Fabio Caraffini; Turgay Altindag; Simon Colreavy-Donnelly (ISTAS, 2023)

A Reversible Debugger for MPI Applications. - Mihkel Tiks; Ott-Kaarel Martens; Eero Vainikko; Stefan Kuhn 001 (DEBT@ISSTA, 2024)

Implementing Reversible Neural Networks. - Uku Zingel; Stefan Kuhn 001; Eero Vainikko (RC, 2025)