PathMe: merging and exploring mechanistic pathway knowledge. - Daniel Domingo-Fernández; Sarah Mubeen; Josep Marín-Llaó; Charles Tapley Hoyt; Martin Hofmann-Apitius (BMC Bioinform., 2019)

Drug2ways: Reasoning over causal paths in biological networks for drug discovery. - Daniel Rivas-Barragan; Sarah Mubeen; Francesc Guim Bernat; Martin Hofmann-Apitius; Daniel Domingo-Fernández (PLoS Comput. Biol., 2020)

CLEP: a hybrid data- and knowledge-driven framework for generating patient representations. - Vinay Srinivas Bharadhwaj; Mehdi Ali; Colin Birkenbihl; Sarah Mubeen; Jens Lehmann 001; Martin Hofmann-Apitius; Charles Tapley Hoyt; Daniel Domingo-Fernández (Bioinform., 2021)

MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms. - Josep Marín-Llaó; Sarah Mubeen; Alexandre Perera-Lluna; Martin Hofmann-Apitius; Sergio Picart-Armada; Daniel Domingo-Fernández (Bioinform., 2021)

On the influence of several factors on pathway enrichment analysis. - Sarah Mubeen; Alpha Tom Kodamullil; Martin Hofmann-Apitius; Daniel Domingo-Fernández (Briefings Bioinform., 2022)

Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. - Rebeca Queiroz Figueiredo; Sara Díaz del Ser; Tamara Raschka; Martin Hofmann-Apitius; Alpha Tom Kodamullil; Sarah Mubeen; Daniel Domingo-Fernández (BMC Bioinform., 2022)

Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery. - Daniel Domingo-Fernández; Yojana Gadiya; Abhishek Patel; Sarah Mubeen; Daniel Rivas-Barragan; Chris W. Diana; Biswapriya B. Misra; David Healey; John C. Rokicki; Viswa Teja S. S. Colluru (PLoS Comput. Biol., 2022)

Contextualizing and interpreting biological data with pathway knowledge and network algorithms - Sarah Mubeen (2023)

Exploring the known chemical space of the plant kingdom: insights into taxonomic patterns, knowledge gaps, and bioactive regions. - Daniel Domingo-Fernández; Yojana Gadiya; Sarah Mubeen; David Healey; Bryan H. Norman; Viswa Teja S. S. Colluru (J. Cheminformatics, 2023)

Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk. - Sepehr Golriz Khatami; Astghik Sargsyan; Maria Francesca Russo; Daniel Domingo-Fernández; Andrea Zaliani; Abish Kaladharan; Priya Sethumadhavan; Sarah Mubeen; Yojana Gadiya; Reagon Karki; Stephan Gebel; Ram Kumar Ruppa Surulinathan; et al. (Data, 2024)

CLEP. - Vinay Srinivas Bharadhwaj; Mehdi Ali; Colin Birkenbihl; Sarah Mubeen; Jens Lehmann 001; Martin Hofmann-Apitius; Charles Tapley Hoyt; Daniel Domingo-Fernández (Zenodo, 2024)

CLEP. - Vinay Srinivas Bharadhwaj; Mehdi Ali; Colin Birkenbihl; Sarah Mubeen; Jens Lehmann 001; Martin Hofmann-Apitius; Charles Tapley Hoyt; Daniel Domingo-Fernández (Zenodo, 2024)

CLEP. - Vinay Srinivas Bharadhwaj; Mehdi Ali; Colin Birkenbihl; Sarah Mubeen; Jens Lehmann 001; Martin Hofmann-Apitius; Charles Tapley Hoyt; Daniel Domingo-Fernández (Zenodo, 2025)