Publications by Hyunjin Shim | EPFL Graph Search

Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network

Recent studies reveal that even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce multiple time-poi ...

2019

Likelihood-free Inference of Population Genetic Parameters from Time-Sampled Genetic Data

Hyunjin Shim

This thesis consists of five papers published in peer-reviewed journals, two of which focus on method development of time-serial inference, represented by publications in methodology journals, and three others that describe collaborative data applications ...

EPFL2018

Experimental adaptation of human echovirus 11 to ultraviolet radiation leads to tolerance to disinfection and resistance to ribavirin

Tamar Kohn, Anna Carratala Ripolles, Virginie Bachmann, Jeffrey David Jensen, Qingxia Zhong, Hyunjin Shim

Ultraviolet light in the UVC range is a commonly used disinfectant to control viruses in clinical settings and water treatment. Here, we employed an experimental evolution approach to investigate the adaptation of human echovirus 11 to disinfection by UVC, ...

2017

Resistance of echovirus 11 to ClO2 is associated with enhanced host receptor use, altered entry routes and high fitness

Tamar Kohn, Anna Carratala Ripolles, Virginie Bachmann, Jeffrey David Jensen, Qingxia Zhong, Hyunjin Shim

Waterborne viruses can exhibit resistance to common water disinfectants, yet the mechanisms that allow them to tolerate disinfection are poorly understood. Here, we generated echovirus 11 (E11) with resistance to chlorine dioxide (ClO2) by experimental evo ...

Amer Chemical Soc2017

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy

Jeffrey David Jensen, Claudia Bank, Matthieu Foll, Sebastian Matuszewski, Hyunjin Shim

The rapid evolution of drug resistance remains a critical public health concern. The treatment of influenza A virus (IAV) has proven particularly challenging, due to the ability of the virus to develop resistance against current antivirals and vaccines. He ...

Wiley-Blackwell2016

Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data

Jeffrey David Jensen, Matthieu Foll, Sebastian Matuszewski, Hyunjin Shim, Stefan Jean Laurent

During his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for the observed change in allele frequencies. This model has since been invoked in a number of ...

Genetics Society of America2016

WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data

Jeffrey David Jensen, Hyunjin Shim, Matthieu Foll

With novel developments in sequencing technologies, time-sampled data are becoming more available and accessible. Naturally, there have been efforts in parallel to infer population genetic parameters from these data sets. Here, we compare and analyse four ...

Wiley-Blackwell2015

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

Jeffrey David Jensen, Claudia Bank, Matthieu Foll, Hyunjin Shim, Gregory Bruce Ewing, Anna Ferrer Admetlla

Author Summary In recent years, considerable attention has been given to the evolution of drug resistance in the influenza A H1N1 strain. As a major annual cause of morbidity and mortality, combined with the rapid global spread of drug resistance, influenz ...

Public Library of Science2014