|Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case–control study using centralized ultrasensitive 454 …|
A Cozzi-Lepri, M Noguera-Julian, F Di Giallonardo, R Schuurman, ...
Journal of antimicrobial chemotherapy 70 (3), 930-940, 2014
|Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations|
FD Giallonardo, A Töpfer, M Rey, S Prabhakaran, Y Duport, C Leemann, ...
Nucleic acids research 42 (14), e115-e115, 2014
|Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination|
F Di Giallonardo, O Zagordi, Y Duport, C Leemann, B Joos, ...
PloS one 8 (9), e74249, 2013
|Virological factors that increase the transmissibility of emerging human viruses|
JL Geoghegan, AM Senior, F Di Giallonardo, EC Holmes
Proceedings of the National Academy of Sciences 113 (15), 4170-4175, 2016
|Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells|
CF Althaus, V Vongrad, B Niederöst, B Joos, F Di Giallonardo, P Rieder, ...
Retrovirology 9 (1), 27, 2012
|EH3 (ABHD9): the first member of a new epoxide hydrolase family with high activity for fatty acid epoxides|
M Decker, M Adamska, A Cronin, F Di Giallonardo, J Burgener, ...
Journal of lipid research 53 (10), 2038-2045, 2012
|Distinct viral lineages from fish and amphibians reveal the complex evolutionary history of hepadnaviruses|
JA Dill, AC Camus, JH Leary, F Di Giallonardo, EC Holmes, TFF Ng
Journal of virology 90 (17), 7920-7933, 2016
|RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation|
JAC Wilson, NA Prow, WA Schroder, JJ Ellis, HE Cumming, LJ Gearing, ...
PLoS pathogens 13 (2), e1006155, 2017
|Viral biocontrol: grand experiments in disease emergence and evolution|
F Di Giallonardo, EC Holmes
Trends in microbiology 23 (2), 83-90, 2015
|A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory|
D Seifert, F Di Giallonardo, KJ Metzner, HF Günthard, N Beerenwinkel
Genetics 199 (1), 191-203, 2015
|Fluid spatial dynamics of West Nile virus in the United States: rapid spread in a permissive host environment|
F Di Giallonardo, JL Geoghegan, DE Docherty, RG McLean, MC Zody, ...
Journal of virology 90 (2), 862-872, 2016
|An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing|
BB Simen, MS Braverman, I Abbate, J Aerssens, Y Bidet, O Bouchez, ...
Journal of virological methods 204, 31-37, 2014
|Substitution model adequacy and assessing the reliability of estimates of virus evolutionary rates and time scales|
S Duchêne, F Di Giallonardo, EC Holmes
Molecular biology and evolution 33 (1), 255-267, 2015
|In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing|
SA Knoepfel, F Di Giallonardo, M Däumer, A Thielen, KJ Metzner
Journal of virological methods 171 (2), 329-338, 2011
|A comprehensive analysis of primer IDs to study heterogeneous HIV-1 populations|
D Seifert, F Di Giallonardo, A Töpfer, J Singer, S Schmutz, HF Günthard, ...
Journal of molecular biology 428 (1), 238-250, 2016
|Dinucleotide composition in animal RNA viruses is shaped more by virus family than by host species|
F Di Giallonardo, TE Schlub, M Shi, EC Holmes
Journal of virology 91 (8), e02381-16, 2017
|Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants|
M Noguera-Julian, A Cozzi-Lepri, F Di Giallonardo, R Schuurman, ...
Clinical microbiology and infection 22 (2), 191-200, 2016
|Cross-validation to select Bayesian hierarchical models in phylogenetics|
S Duchêne, DA Duchêne, F Di Giallonardo, JS Eden, JL Geoghegan, ...
BMC evolutionary biology 16 (1), 115, 2016
|Reappearance of minority K103N HIV-1 variants after interruption of ART initiated during primary HIV-1 infection|
KJ Metzner, C Leemann, F Di Giallonardo, C Grube, AU Scherrer, ...
PLoS One 6 (7), e21734, 2011
|A follow-up of the multicenter collaborative study on HIV-1 drug resistance and tropism testing using 454 ultra deep pyrosequencing|
EPS John, BB Simen, GS Turenchalk, MS Braverman, I Abbate, ...
PloS one 11 (1), e0146687, 2016