Probing RNA structure and dynamics using nanopore and next generation sequencing.

It has become increasingly evident that the structures RNAs adopt are conformationally dynamic; the various structured states that RNAs sample govern their interactions with other nucleic acids, proteins, and ligands to regulate a myriad of biological processes. Although several biophysical approaches have been developed and used to study the dynamic landscape of structured RNAs, technical limitations have limited their application to all classes of RNA due to variable size and flexibility. Recent advances combining chemical probing experiments with next-generation- and direct sequencing have emerged as an alternative approach to exploring the conformational dynamics of RNA.

Application of Network Analysis to Uncover Variables Contributing to Functional Recovery after Stroke.

To estimate network structures to discover the interrelationships among variables and distinguish the difference between networks. Three hundred and forty-eight stroke patients were enrolled in this retrospective study. A network analysis was used to investigate the association between those variables.

Nuclease resistance and protein recognition properties of DNA and hybrid PNA-DNA four-way junctions.

Nucleic acids possess unique biochemical features that make them ideal candidates to inhibit "difficult to target" proteins. The limited stability of nucleic acids in vivo presents a major obstacle to their development as drugs. Here, immobile four-way junctions (4WJs) are used to target the DNA-binding cytokine, High Mobility Group B1.

Minimum redundancy maximal relevance gene selection of apoptosis pathway genes in peripheral blood mononuclear cells of HIV-infected patients with antiretroviral therapy-associated mitochondrial toxicity.

Background: We previously identified differentially expressed genes on the basis of false discovery rate adjusted P value using empirical Bayes moderated tests. However, that approach yielded a subset of differentially expressed genes without accounting for redundancy between the selected genes.

Methods: This study is a secondary analysis of a case-control study of the effect of antiretroviral therapy on apoptosis pathway genes comprising of 16 cases (HIV infected with mitochondrial toxicity) and 16 controls (uninfected).