| A Deep Learning Approach to Antibiotic Discovery JM Stokes, K Yang*, K Swanson*, W Jin, A Cubillos-Ruiz, NM Donghia, ... Cell 180 (4), 688-702. e13, 2020 | 2030 | 2020 |
| Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii G Liu*, DB Catacutan*, K Rathod*, K Swanson, W Jin, JC Mohammed, ... Nature Chemical Biology, 1-9, 2023 | 178 | 2023 |
| Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage RR Stanway*, E Bushell*, A Chiappino-Pepe*, M Roques*, T Sanderson, ... Cell 179 (5), 1112-1128. e26, 2019 | 111 | 2019 |
| Functional and computational genomics reveal unprecedented flexibility in stage-specific Toxoplasma metabolism A Krishnan, J Kloehn*, M Lunghi*, A Chiappino-Pepe, BS Waldman, ... Cell Host & Microbe 27 (2), 290-306. e11, 2020 | 98 | 2020 |
| Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks A Chiappino-Pepe, S Tymoshenko, M Ataman, D Soldati-Favre, ... PLOS Computational Biology 13 (3), e1005397, 2017 | 64 | 2017 |
| The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases SIB Swiss Institute of Bioinformatics Members Nucleic acids research 44 (D1), D27-D37, 2016 | 51 | 2016 |
| A swapped genetic code prevents viral infections and gene transfer A Nyerges, S Vinke, R Flynn, SV Owen, EA Rand, B Budnik, E Keen, ... Nature 615 (7953), 720-727, 2023 | 47 | 2023 |
| Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models N Hadadi, V Pandey, A Chiappino-Pepe, M Morales, H Gallart-Ayala, ... NPJ systems biology and applications 6 (1), 1, 2020 | 41 | 2020 |
| Integration of metabolic, regulatory and signaling networks towards analysis of perturbation and dynamic responses A Chiappino-Pepe, V Pandey, M Ataman, V Hatzimanikatis Current Opinion in Systems Biology 2, 59-66, 2017 | 20 | 2017 |
| Synthetic genomes with altered genetic codes N Ostrov, A Nyerges, A Chiappino-Pepe, A Rudolph, M Baas-Thomas, ... Current Opinion in Systems Biology 24, 32-40, 2020 | 17 | 2020 |
| 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 |
| TEX-FBA: A constraint-based method for integrating gene expression, thermodynamics, and metabolomics data into genome-scale metabolic models V Pandey, DH Gardiol, A Chiappino-Pepe, V Hatzimanikatis bioRxiv, 536235, 2019 | 9 | 2019 |
| Genetic Design Automation for Autonomous Formation of Multicellular Shapes from a Single Cell Progenitor E Appleton*, N Mehdipour*, T Daifuku*, D Briers*, I Haghighi*, M Moret, ... bioRxiv, 807107, 2019 | 5 | 2019 |
| PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models A Chiappino-Pepe#, V Hatzimanikatis STAR Protocols 2 (1), 100280, 2021 | 4 | 2021 |
| Synthetic genomes unveil the effects of synonymous recoding A Nyerges, A Chiappino-Pepe, B Budnik, M Baas-Thomas, R Flynn, ... bioRxiv, 2024.06. 16.599206, 2024 | 3 | 2024 |
| Strategies to identify and edit improvements in synthetic genome segments episomally A Rudolph, A Nyerges, A Chiappino-Pepe, M Landon, M Baas-Thomas, ... Nucleic Acids Research 51 (18), 10094-10106, 2023 | 2 | 2023 |
| Genome reconstructions of metabolism of Plasmodium RBC and liver stages A Chiappino-Pepe, V Pandey, O Billker Current Opinion in Microbiology 63, 259-266, 2021 | 2 | 2021 |
| NADPH composite index analysis quantifies the relationship between compartmentalized NADPH dynamics and growth rates in cancer cells SJ Moon, A Chiappino-Pepe, W Dong, JK Kelleher, M Vander Heiden, ... bioRxiv, 2024.04. 27.591477, 2024 | 1 | 2024 |
| Swapped genetic code blocks viral infections and gene transfer A Nyerges, S Vinke, R Flynn, SV Owen, EA Rand, B Budnik, E Keen, ... bioRxiv, 2022.07. 08.499367, 2022 | 1 | 2022 |
George ChurchHarvard Medical SchoolVerified email at harvard.edu
