| COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology D Domingo-Fernández, S Baksi, B Schultz, Y Gadiya, R Karki, T Raschka, ... Bioinformatics 37 (9), 1332-1334, 2021 | 127 | 2021 |
| Deep learning for clustering of multivariate clinical patient trajectories with missing values J de Jong, MA Emon, P Wu, R Karki, M Sood, P Godard, A Ahmad, ... GigaScience 8 (11), giz134, 2019 | 61 | 2019 |
| Comorbidity analysis between Alzheimer’s disease and type 2 diabetes mellitus (T2DM) based on shared pathways and the role of T2DM drugs R Karki, M Hofmann-Apitius Journal of Alzheimer's Disease 60 (2), 721-731, 2017 | 59 | 2017 |
| Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment D Domingo-Fernández, AT Kodamullil, A Iyappan, M Naz, MA Emon, ... Bioinformatics 33 (22), 3679-3681, 2017 | 44 | 2017 |
| Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL) J Fluck, S Madan, S Ansari, AT Kodamullil, R Karki, M Rastegar-Mojarad, ... Database 2016, baw113, 2016 | 34 | 2016 |
| Of mice and men: comparative analysis of neuro-inflammatory mechanisms in human and mouse using cause-and-effect models AT Kodamullil, A Iyappan, R Karki, S Madan, E Younesi, ... Journal of Alzheimer’s disease 59 (3), 1045-1055, 2017 | 25 | 2017 |
| Using drugs as molecular probes: a computational chemical biology approach in neurodegenerative diseases MAEK Emon, R Karki, E Younesi, M Hofmann-Apitius Journal of Alzheimer's Disease 56 (2), 677-686, 2017 | 18 | 2017 |
| Comprehensive fragment screening of the SARS‐CoV‐2 proteome explores novel chemical space for drug development H Berg, MA Wirtz Martin, N Altincekic, I Alshamleh, J Kaur Bains, ... Angewandte Chemie International Edition 61 (46), e202205858, 2022 | 16 | 2022 |
| A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization B Schultz, A Zaliani, C Ebeling, J Reinshagen, D Bojkova, ... Scientific reports 11 (1), 11049, 2021 | 16 | 2021 |
| Data-driven modeling of knowledge assemblies in understanding comorbidity between type 2 diabetes mellitus and Alzheimer’s Disease R Karki, S Madan, Y Gadiya, D Domingo-Fernández, M Hofmann-Apitius Journal of Alzheimer's Disease 78 (1), 87-95, 2020 | 15 | 2020 |
| Realistic simulation of virtual multi-scale, multi-modal patient trajectories using Bayesian networks and sparse auto-encoders M Sood, A Sahay, R Karki, MA Emon, H Vrooman, M Hofmann-Apitius, ... Scientific reports 10 (1), 10971, 2020 | 12 | 2020 |
| Pharmacophore-Based Machine Learning Model To Predict Ligand Selectivity for E3 Ligase Binders R Karki, Y Gadiya, P Gribbon, A Zaliani ACS omega 8 (33), 30177-30185, 2023 | 6 | 2023 |
| Mpox Knowledge Graph: a comprehensive representation embedding chemical entities and associated biology of Mpox R Karki, Y Gadiya, A Zaliani, P Gribbon Bioinformatics Advances 3 (1), vbad045, 2023 | 4 | 2023 |
| The COVID-19 PHARMACOME: A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization B Schultz, A Zaliani, C Ebeling, J Reinshagen, D Bojkova, ... bioRxiv, 2020.09. 23.308239, 2020 | 4 | 2020 |
| A systems biology approach for hypothesizing the effect of genetic variants on neuroimaging features in Alzheimer’s disease S Golriz Khatami, D Domingo-Fernandez, S Mubeen, CT Hoyt, ... Journal of Alzheimer’S Disease 80 (2), 831-840, 2021 | 3 | 2021 |
| Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm R Karki, AT Kodamullil, CT Hoyt, M Hofmann-Apitius BMC bioinformatics 20, 1-8, 2019 | 3 | 2019 |
| Pharmacological Profiles of Neglected Tropical Disease Drugs A Greco, R Karki, Y Gadiya, C Deecke, A Zaliani, S Gul Artificial Intelligence in the Life Sciences, 100116, 2024 | | 2024 |
| Curating, collecting, and cataloguing global COVID-19 datasets for the aim of predicting personalized risk SG Khatami, A Sargsyan, MF Russo, D Domingo-Fernández, A Zaliani, ... Data 9 (2), 25, 2024 | | 2024 |
| Curating, Collecting, and Cataloguing Global COVID-19 Datasets for the Aim of Predicting Personalized Risk S Golriz Khatami, A Sargsyan, MF Russo, D Domingo Fernández, ... | | 2024 |
| Pharmacophore-based ML model to filter candidate E3 ligands and predict E3 Ligase binding probabilities R Karki, Y Gadiya, S Shetty, P Gribbon, A Zaliani Informatics in Medicine Unlocked 44, 101424, 2024 | | 2024 |