282 citations · 285 across the 4 of their papers we have counts for
5 papers
Analysing high-throughput sequencing data in Python with HTSeq 2.0
Givanna H Putri, Simon Anders, Paul Theodor Pyl +2
Summary: HTSeq 2.0 provides a more extensive API including a new representation for sparse genomic data, enhancements in htseq-count to suit single cell omics, a new script for dat…
Establishment and stability of the latent HIV-1 DNA reservoir
Johanna Brodin, Fabio Zanini, Lina Thebo +4
HIV-1 infection currently cannot be cured because the virus persists as integrated proviral DNA in long-lived cells despite years of suppressive antiretroviral therapy (ART). To ch…
In-vivo mutation rates and fitness landscape of HIV-1
Fabio Zanini, Vadim Puller, Johanna Brodin +2
Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequ…
Population genomics of intrapatient HIV-1 evolution
Fabio Zanini, Johanna Brodin, Lina Thebo +4
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolv…
FFPopSim: An efficient forward simulation package for the evolution of large populations
Fabio Zanini, Richard A. Neher
The analysis of the evolutionary dynamics of a population with many polymorphic loci is challenging since a large number of possible genotypes needs to be tracked. In the absence o…