| Mapping single-cell data to reference atlases by transfer learning M Lotfollahi, M Naghipourfar, MD Luecken, M Khajavi, M Büttner, ... Nature biotechnology 40 (1), 121-130, 2022 | 573 | 2022 |
| Predicting cellular responses to complex perturbations in high‐throughput screens M Lotfollahi, A Klimovskaia Susmelj, C De Donno, L Hetzel, Y Ji, IL Ibarra, ... Molecular systems biology 19 (6), e11517, 2023 | 272 | 2023 |
| Genome modeling and design across all domains of life with Evo 2 G Brixi, MG Durrant, J Ku, M Poli, G Brockman, D Chang, GA Gonzalez, ... BioRxiv, 2025.02. 18.638918, 2025 | 213 | 2025 |
| Conditional out-of-distribution generation for unpaired data using transfer VAE M Lotfollahi, M Naghipourfar, FJ Theis, FA Wolf Bioinformatics 36 (Supplement_2), i610-i617, 2020 | 131 | 2020 |
| Query to reference single-cell integration with transfer learning M Lotfollahi, M Naghipourfar, MD Luecken, M Khajavi, M Büttner, Z Avsec, ... bioRxiv, 2020.07. 16.205997, 2020 | 43 | 2020 |
| Predicting cellular responses to perturbation across diverse contexts with State AK Adduri, D Gautam, B Bevilacqua, A Imran, R Shah, M Naghipourfar, ... BioRxiv, 2025.06. 26.661135, 2025 | 32 | 2025 |
| Conditional out-of-sample generation for unpaired data using trVAE M Lotfollahi, M Naghipourfar, FJ Theis, FA Wolf arXiv preprint arXiv:1910.01791, 2019 | 31 | 2019 |
| Cyrus 2D Simulation Team Description Paper 2016 N Zare, A Keshavarzi, SE Beheshtian, H Mowla, A Akbarpour, H Jafari, ... arXiv preprint arXiv:2202.03726, 2022 | 24 | 2022 |
| A suite of foundation models captures the contextual interplay between codons M Naghipourfar, S Chen, MK Howard, CB Macdonald, A Saberi, T Hagen, ... bioRxiv, 2024 | 8 | 2024 |
| A long-context RNA foundation model for predicting transcriptome architecture A Saberi, B Choi, S Wang, A Hernández-Corchado, M Naghipourfar, ... BioRxiv, 2024.08. 26.609813, 2024 | 4 | 2024 |
| Revealing the grammar of small RNA secretion using interpretable machine learning B Zirak, M Naghipourfar, A Saberi, D Pouyabahar, A Zarezadeh, L Luo, ... Cell Genomics 4 (4), 2024 | 4 | 2024 |
| KODA: An agentic framework for KEGG orthology-driven discovery of antimicrobial drug targets in gut microbiome JA Dehkordi, MS Parsa, M Naghipourfar, M Mofrad ICML 2025 Generative AI and Biology (GenBio) Workshop, 2025 | 3 | 2025 |
| KODA: An Agentic Framework for KEGG Orthology-Driven Discovery of Antimicrobial Drug Targets in Gut Microbiome J Aminian-Dehkordi, M Parsa, M Naghipourfar, MRK Mofrad bioRxiv, 2025.05. 27.656480, 2025 | | 2025 |
| CYRUS 2D Simulation Team Description Paper 2017 Nader Zare, Ali Najimi, Mahtab Sarvmaili, Aryan Akbarpour, Mohsen ... https://www.robocup2017.org/file/symposium/soccer_sim_2D/TDP_CYRUS.pdf, 2017 | | 2017 |
| Learning the Language of Codon Translation with CodonFM S Darabi, F Cao, M Naghipourfar, S Rabhi, A Sethia, K Gion, J Grewal, ... | | |
Fabian J TheisHelmholtz Munich, Technical University of MunichVerified email at helmholtz-muenchen.de
