Publications

Caitlin Simopoulos, Zhibin Ning, Leyuan Li, Xu Zhang, Mathieu Lavallée-Adam, Daniel Figeys (2022). MetaProClust-MS1: A tool for clustering metaproteomes using rapid MS1 profiling. mSystems.

Caitlin Simopoulos, Zhibin Ning, Xu Zhang, Leyuan Li, Krystal Walker, Mathieu Lavallée-Adam, Daniel Figeys (2020). pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies. Bioinformatics.

Caitlin Simopoulos, Mitchell JR MacLeod, Solmaz Irani, Wilson WL Sung, Marc J Champigny, Peter S Summers, G Brian Golding, Elizabeth A Weretilnyk (2020). Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress. BMC Genomics.

Caitlin Simopoulos, Elizabeth A Weretilnyk, G Brian Golding (2019). Molecular traits of long non-protein coding RNAs from diverse plant species show little evidence of phylogenetic relationships. G3: Genes, Genomes, Genetics.

Caitlin Simopoulos (2019). Using machine learning to predict long non-coding RNAs and exploring their evolutionary patterns and prevalence in plant transcriptomes. McMaster University.

Caitlin Simopoulos, Elizabeth A Weretilnyk, G Brian Golding (2018). Prediction of plant lncRNA by ensemble machine learning classifiers. BMC Genomics.

Caitlin Simopoulos, Mitchell MacLeod, Elizabeth Weretilnyk, Brian Golding (2018). Local adaptation in the extremophile Eutrema salsugineum: Exploring the role of putative lncRNAs. In Vitro Cellular & Devlopmental Biology-Plant.

Viktoriya Coneva, Caitlin Simopoulos, José A Casaretto, Ashraf El-kereamy, David R Guevara, Jonathan Cohn, Tong Zhu, Lining Guo, Danny C Alexander, Yong-Mei Bi, others (2014). Metabolic and co-expression network-based analyses associated with nitrate response in rice. BMC Genomics.