Tijana Milenković

Enhancing gene co-expression network inference for the malaria parasite Plasmodium falciparum

This paper evaluates multiple gene co-expression network inference methods for Plasmodium falciparum to improve functional annotation of its genes.

Synonymous codon substitutions regulate transcription and translation of an upstream gene

The paper shows that synonymous codon substitutions in E. coli can upregulate an upstream gene through cryptic transcription, challenging the view that synonymous mutations have no phenotypic effects.

Analysis of computational codon usage models and their association with translationally slow codons

The paper evaluates five computational codon usage models for their ability to predict translational slowdowns using ribosome footprint data from S. cerevisiae, finding strong associations but also highlighting inconsistencies in RFP data.