RNA Design Using incaRNAfbinv Demonstrated with the Identification of Functional RNA Motifs in Hepatitis Delta Virus.

Computational RNA design was introduced in the 1990s by Vienna's RNAinverse, which is a simple inverse RNA folding solver. Further developments and contemporary RNA design techniques, in addition to improved efficiency, offer more precise control over the designed sequences. incaRNAfbinv (incaRNAtion with RNA fragment-based inverse) is one such extension that builds upon RNAinverse and includes coarse-graining manipulations.

Modeling the Interplay between HDV and HBV in Chronic HDV/HBV Patients.

Hepatitis D virus is an infectious subviral agent that can only propagate in people infected with hepatitis B virus. In this study, we modified and further developed a recent model for early hepatitis D virus and hepatitis B virus kinetics to better reproduce hepatitis D virus and hepatitis B virus kinetics measured in infected patients during anti-hepatitis D virus treatment. The analytical solutions were provided to highlight the new features of the modified model.

Advances in Parameter Estimation and Learning from Data for Mathematical Models of Hepatitis C Viral Kinetics.

Mathematical models, some of which incorporate both intracellular and extracellular hepatitis C viral kinetics, have been advanced in recent years for studying HCV-host dynamics, antivirals mode of action, and their efficacy. The standard ordinary differential equation (ODE) hepatitis C virus (HCV) kinetic model keeps track of uninfected cells, infected cells, and free virus. In multiscale models, a fourth partial differential equation (PDE) accounts for the intracellular viral RNA (vRNA) kinetics in an infected cell.

IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations.

Background: RNA deleterious point mutation prediction was previously addressed with programs such as RNAmute and MultiRNAmute. The purpose of these programs is to predict a global conformational rearrangement of the secondary structure of a functional RNA molecule, thereby disrupting its function. RNAmute was designed to deal with only single point mutations in a brute force manner, while in MultiRNAmute an efficient approach to deal with multiple point mutations was developed.

Modeling-Based Response-Guided DAA Therapy for Chronic Hepatitis C to Identify Individuals for Shortening Treatment Duration.

Shortening duration of direct-acting antiviral therapy for chronic hepatitis C could provide cost savings, reduce medication exposure, and foster adherence and treatment completion in special populations. The current analysis indicates that measuring hepatitis C virus at baseline and on days 7 and 14 of therapy can identify patients for shortening therapy duration.