| Prediction of plant lncRNA by ensemble machine learning classifiers CMA Simopoulos, EA Weretilnyk, GB Golding BMC genomics 19, 1-11, 2018 | 58 | 2018 |
| Metabolic and co-expression network-based analyses associated with nitrate response in rice V Coneva, C Simopoulos, JA Casaretto, A El-Kereamy, DR Guevara, ... BMC genomics 15, 1-14, 2014 | 46 | 2014 |
| Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics L Li, T Wang, Z Ning, X Zhang, J Butcher, JM Serrana, CMA Simopoulos, ... Nature Communications 14 (1), 3428, 2023 | 16 | 2023 |
| Molecular traits of long non-protein coding RNAs from diverse plant species show little evidence of phylogenetic relationships CMA Simopoulos, EA Weretilnyk, GB Golding G3: Genes, Genomes, Genetics 9 (8), 2511-2520, 2019 | 16 | 2019 |
| Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water … CMA Simopoulos, MJR MacLeod, S Irani, WWL Sung, MJ Champigny, ... BMC genomics 21, 1-16, 2020 | 10 | 2020 |
| pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies CMA Simopoulos, Z Ning, X Zhang, L Li, K Walker, M Lavallée-Adam, ... Bioinformatics 36 (14), 4171-4179, 2020 | 10 | 2020 |
| iMetaLab Suite: A one‐stop toolset for metaproteomics L Li, Z Ning, K Cheng, X Zhang, CMA Simopoulos, D Figeys Imeta 1 (2), e25, 2022 | 8 | 2022 |
| MetaProClust-MS1: an MS1 profiling approach for large-scale microbiome screening CMA Simopoulos, Z Ning, L Li, MM Khamis, X Zhang, M Lavallée-Adam, ... MSystems 7 (4), e00381-22, 2022 | 4 | 2022 |
| Using machine learning to predict long non-coding RNAs and exploring their evolutionary patterns and prevalence in plant transcriptomes C Simopoulos | 1 | 2019 |
| PhyloFunc: Phylogeny-informed Functional Distance as a New Ecological Metric for Metaproteomic Data Analysis L Wang, CMA Simopoulos, JM Serrana, Z Ning, B Sun, J Yuan, D Figeys, ... bioRxiv, 2024.05. 28.596184, 2024 | | 2024 |
| Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies CMA Simopoulos, D Figeys, M Lavallée-Adam Proteomics in Systems Biology: Methods and Protocols, 319-338, 2022 | | 2022 |
| MetaProClust-MS1: A tool for clustering metaproteomes using rapid MS1 profiling CMA Simopoulos, Z Ning, L Li, MM Khamis, X Zhang, M Lavallée-Adam, ... bioRxiv, 2021.03. 31.437863, 2021 | | 2021 |
| Local adaptation in the extremophile Eutrema salsugineum: Exploring the role of putative lncRNAs C Simopoulos, M MacLeod, E Weretilnyk, B Golding IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT 54, S10-S11, 2018 | | 2018 |
| pepFunk, a tool for peptide-centric functional analysis in CMA Simopoulos, Z Ning, X Zhang, L Li, K Walker, M Lavallée-Adam, ... | | |
