Emily Rogers's research while affiliated with Georgia Institute of Technology and other places
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Publications (4)
Understanding how RNA secondary structure prediction methods depend on the underlying nearest-neighbor thermodynamic model remains a fundamental challenge in the field. Minimum free energy (MFE) predictions are known to be “ill conditioned” in that small changes to the thermodynamic model can result in significantly different optimal structures. He...
A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular...
As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been f...
Citations
... There are several implementations of NNTM; some of the popular ones include RNAStructure [25], GTfold [31], UNAfold [23], and ViennaRNA package [22]. However, NNTM has been shown to be ill-conditioned [17,18,26]. That is, for a given sequence, signi cantly di erent secondary structures might exhibit very similar energies. ...
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... Here, the current work expands on Tapp's secondary structure analysis by adapting existing motif identification and multiple protein sequence alignment tools in order to score the occurrence of both dominant and suboptimal secondary structure elements and to identify shared domains where particular secondary structure features predominate. Notably, while analytical tools for aligning pairs [42,43] as well as groups [44][45][46] of RNA secondary structure features and even suboptimal self-hybridized structures [47,48] are available, these tools generally presume an evolutionary connection between biologically relevant RNA sequences [49]. Additionally, some RNA alignment programs take into account secondary structure features such as pseudoknots [50] more widely reported in RNA sequences. ...
... There have been substantial advances in methods to characterize RNA dynamic ensembles in vitro (Salmon et al., 2014;Xue et al., 2015;Shi et al., 2016;Tian and Das, 2016;Nichols et al., 2018). However, despite significant progress (Mahen et al., 2005(Mahen et al., , 2010Spitale et al., 2013;Rogers and Heitsch, 2014;Ruminski et al., 2016;Watters et al., 2016;Lee et al., 2017;Li and Aviran, 2018;Woods et al., 2017;Spasic et al., 2018), probing RNA dynamics in vivo remains challenging. Transcriptomewide structure probing experiments indicate that the cellular environment can affect RNA folding relative to in vitro (Beaudoin et al., 2018;Mustoe et al., 2018;Sun et al., 2019). ...
