John Favate

Graduate Student
Google Scholar

I am a graduate student in the microbiology and molecular genetics PhD program. I received my undergraduate degree in biology with a minor in biochemistry from the University of Delaware where I studied paracrine signaling interactions between metastatic prostate cancer and bone stromal cells in the lab of Robert Sikes.

I then received my masters in biomedical sciences from Rutgers University where I studied the role of SOX9 in lung cancer in the lab of Sharon Pine. I was also a visiting scientist at the American Museum of Natural History where, in the lab of Eunsoo Kim I studied the environmental conditions and molecular mechanisms that may have led to the initial endosymbiotic event that created the first photosynthetic Eukaryotes.

The overarching theme of my current research is to understand the degree and molecular mechanisms by which changes in gene regulation affect evolutionary processes such as adaptation.


NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes. Sharma et al. Commun Biol 2023

Linking genotypic and phenotypic changes in the LTEE using metabolomics. Favate et al. eLife 2023

IMP1/IGF2BP1 in human colorectal cancer extracellular vesicles. Kuhn et al. Am. J. Physiol. 2022

The landscape of transcriptional and translational changes over 22 years of bacterial adaptation. Favate et al. eLife 2022

The hypoxia response pathway promotes PEP carboxykinase and gluconeogenesis in C. elegans. Vora et al. Nature Comm. 2022

riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow. Cope et al. Bioinformatics 2022

Exploring ribosome-positioning on translating transcripts with ribosome-profiling. Cope et al. MiMB 2021

The gastrin-releasing peptide regulates stress-enhanced fear and dopamine signaling. Morishita et al. bioRxiv 2021

O-GlcNAcylation alters the selection of mRNAs for translation and promotes 4E-BP1–dependent mitochondrial dysfunction in the retina. Dierschke et al. Jour Biol Chem 2019