| Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites N Hadadi, H MohammadiPeyhani, L Miskovic, M Seijo, V Hatzimanikatis Proceedings of the National Academy of Sciences 116 (15), 7298-7307, 2019 | 94 | 2019 |
| A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives J Hafner, J Payne, H MohammadiPeyhani, V Hatzimanikatis, C Smolke Nature Communications 12 (1), 1760, 2021 | 59 | 2021 |
| Updated ATLAS of biochemistry with new metabolites and improved enzyme prediction power J Hafner, H MohammadiPeyhani, A Sveshnikova, A Scheidegger, ... ACS synthetic biology 9 (6), 1479-1482, 2020 | 46 | 2020 |
| Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx H MohammadiPeyhani, J Hafner, A Sveshnikova, V Viterbo, ... Nature Communications 13 (1), 1560, 2022 | 39 | 2022 |
| Computational tools and resources for designing new pathways to small molecules A Sveshnikova, H MohammadiPeyhani, V Hatzimanikatis Current Opinion in Biotechnology 76, 102722, 2022 | 20 | 2022 |
| A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions E Vayena, A Chiappino-Pepe, H MohammadiPeyhani, Y Francioli, ... Proceedings of the National Academy of Sciences 119 (46), e2211197119, 2022 | 15 | 2022 |
| NICEdrug. ch, a workflow for rational drug design and systems-level analysis of drug metabolism H MohammadiPeyhani, A Chiappino-Pepe, K Haddadi, J Hafner, ... Elife 10, e65543, 2021 | 10 | 2021 |
| ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds A Sveshnikova, H MohammadiPeyhani, V Hatzimanikatis Metabolic Engineering 72, 259-274, 2022 | 8 | 2022 |
| ATLASx: a computational map for the exploration of biochemical space H Mohammadi-Peyhani, J Hafner, A Sveshnikova, V Viterbo, ... BioRxiv, 2021.02. 17.431583, 2021 | 8 | 2021 |
| Knowledge of the neighborhood of the reactive site up to three atoms can predict biochemistry and protein sequences N Hadadi, H MohamadiPeyhani, L Miskovic, M Seijo, V Hatzimanikatis bioRxiv, 210039, 2017 | 2 | 2017 |
| Enzyme promiscuous profiles for protein sequence and reaction annotation H MohammadiPeyhani, A Sveshnikova, L Miskovic, V Hatzimanikatis bioRxiv, 2023.09. 13.557547, 2023 | 1 | 2023 |
| NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions E Vayena, A Chiappino-Pepe, H MohammadiPeyhani, Y Francioli, ... bioRxiv, 2022.02. 10.479881, 2022 | 1 | 2022 |
| Pathway Design J Hafner, H Mohammadi‐Peyhani, V Hatzimanikatis Metabolic Engineering: Concepts and Applications 13, 237-257, 2021 | 1 | 2021 |
| Lab-in-the-loop therapeutic antibody design with deep learning NC Frey, I Hotzel, SD Stanton, RL Kelly, RG Alberstein, EK Makowski, ... bioRxiv, 2025.02. 19.639050, 2025 | | 2025 |
| deepNGS Navigator: Exploring antibody NGS datasets using deep contrastive learning H MohammadiPeyhani, E Lee, R Bonneau, V Gligorijevic, JH Lee bioRxiv, 2025.01. 27.634805, 2025 | | 2025 |
| Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation H Mohammadi Peyhani, A Sveshnikova, L Miskovic, V Hatzimanikatis Zenodo, 2023 | | 2023 |
| Bridging the gap between rule-based expert systems and machine learning in computer-aided retrosynthetic design D Probst, A Sveshnikova, HM Peyhani, V Hatzimanikatis, T Laino American Chemical Society (ACS) Fall Meeting, 2022 | | 2022 |
| Supplementary datasets for" ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds" A Sveshnikova, H Mohammadi Peyhani, V Hatzimanikatis Zenodo, 2022 | | 2022 |
| Pathway Design H Jasmin, MP Homa, H Vassily Metabolic Engineering: Concepts and Applications 13, 2021 | | 2021 |
| Database for drug metabolism and comparisons, NICEdrug. ch, aids discovery and design H MohammadiPeyhani, A Chiappino-Pepe, K Haddadi, J Hafner, ... bioRxiv, 2020.05. 28.120782, 2020 | | 2020 |
