Genome Gerrymandering: Optimal Division of the Genome into Regions with Cancer Type SpecificDifferences in Mutation Rates. - Adamo Young; Jacob Chmura; Yoon-Sik Park; Quaid Morris; Gurnit Atwal (PSB, 2020)

MassFormer: Tandem Mass Spectrum Prediction with Graph Transformers. - Adamo Young; Bo Wang 044; Hannes L. Röst (CoRR, 2021)

Supervised topic modeling for predicting molecular substructure from mass spectrometry. - Gabriel Reder; Adamo Young; Jaan Altosaar; Jakub Rajniak; Noémie Elhadad; Michael Fischbach; Susan Holmes (F1000Research, 2021)

A graph neural network approach for molecule carcinogenicity prediction. - Philip Fradkin; Adamo Young; Lazar Atanackovic; Brendan J. Frey; Leo J. Lee; Bo Wang 044 (Bioinform., 2022)

SELFIES and the future of molecular string representations. - Mario Krenn; Qianxiang Ai; Senja Barthel; Nessa Carson; Angelo Frei; Nathan C. Frey; Pascal Friederich; Théophile Gaudin; Alberto Alexander Gayle; Kevin Maik Jablonka; Rafael F. Lameiro; Dominik Lemm; et al. (Patterns, 2022)

Unleashing the Strengths of Unlabeled Data in Pan-cancer Abdominal Organ Quantification: the FLARE22 Challenge. - Jun Ma 016; Yao Zhang 010; Song Gu; Cheng Ge; Shihao Ma; Adamo Young; Cheng Zhu; Kangkang Meng; Xin Yang 009; Ziyan Huang; Fan Zhang; Wentao Liu; et al. (CoRR, 2023)

MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

FraGNNet: A Deep Probabilistic Model for Mass Spectrum Prediction. - Adamo Young; Fei Wang 062; David S. Wishart; Bo Wang 044; Hannes L. Röst; Russ Greiner (CoRR, 2024)

Tandem mass spectrum prediction for small molecules using graph transformers. - Adamo Young; Hannes L. Röst; Bo Wang 044 (Nat. Mac. Intell., 2024)

FraGNNet: A Deep Probabilistic Model for Tandem Mass Spectrum Prediction. - Adamo Young; Fei Wang 062; David S. Wishart; Bo Wang 044; Russell Greiner; Hannes Rost (Trans. Mach. Learn. Res., 2025)

ChemPile: A 250GB Diverse and Curated Dataset for Chemical Foundation Models. - Adrian Mirza; Nawaf Alampara; Martiño Ríos-García; Mohamed Abdelalim; Jack Butler; Bethany Connolly; Tunca Dogan; Marianna Nezhurina; Bünyamin Sen; Santosh Tirunagari; Mark Worrall; Adamo Young; et al. (CoRR, 2025)