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View article: <i>μ</i> Seq: Universal mutation rate quantification via deep sequencing of a single clonal expansion
<i>μ</i> Seq: Universal mutation rate quantification via deep sequencing of a single clonal expansion Open
Quantifying mutational processes is crucial for understanding evolution, especially in clinical and experimental settings, but remains challenging. Current methods are labor-intensive and often lack robustness, resulting in inconsistent or…
View article: Evolutionary adaptation to hyperstable microtubules selectively targets tubulins and is empowered by the spindle assembly checkpoint
Evolutionary adaptation to hyperstable microtubules selectively targets tubulins and is empowered by the spindle assembly checkpoint Open
Microtubules are polymers required for chromosome segregation. Their drug-induced hyperstabilization impairs chromosome segregation and is an established anti-cancer therapy. How cells respond to microtubule hyperstabilization, however, is…
View article: Optimal treatment for drug-induced cancer persisters involves release periods and intermediate drug doses
Optimal treatment for drug-induced cancer persisters involves release periods and intermediate drug doses Open
Targeted cancer therapies often induce a reversible drug-tolerant state in subpopulations of cells, akin to bacterial persistence. Precise characterization of these “cancer persisters” may inform the design of more effective treatment stra…
View article: Heterogeneity and evolution of DNA mutation rates in microsatellite stable colorectal cancer
Heterogeneity and evolution of DNA mutation rates in microsatellite stable colorectal cancer Open
DNA sequence mutability in tumors with chromosomal instability is conventionally believed to remain uniform, constant, and low, based on the assumption that further mutational accrual in a context of marked aneuploidy is evolutionarily dis…
View article: Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer
Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer Open
The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics w…
View article: Clonal cooperation through soluble metabolite exchange facilitates metastatic outgrowth by modulating Allee effect
Clonal cooperation through soluble metabolite exchange facilitates metastatic outgrowth by modulating Allee effect Open
Cancers feature substantial intratumoral heterogeneity of genetic and phenotypically distinct lineages. Although interactions between coexisting lineages are emerging as a potential contributor to tumor evolution, the extent and nature of …
View article: A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains
A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains Open
The early development of aneuploidy from an accidental chromosome missegregation shows contrasting effects. On the one hand, it is associated with significant cellular stress and decreased fitness. On the other hand, it often carries a ben…
View article: Metacommunity Structure Preserves Genome Diversity in the Presence of Gene-specific Selective Sweeps
Metacommunity Structure Preserves Genome Diversity in the Presence of Gene-specific Selective Sweeps Open
The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics w…
View article: A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains
A fitness trade-off explains the early fate of yeast aneuploids with chromosome gains Open
The early development of aneuploidy from an accidental chromosome missegregation shows contrasting effects. On the one hand, it is associated to significant cellular stress and decreased fitness. On the other hand, it often carries a benef…
View article: A modified fluctuation-test framework characterizes the population dynamics and mutation rate of colorectal cancer persister cells
A modified fluctuation-test framework characterizes the population dynamics and mutation rate of colorectal cancer persister cells Open
Compelling evidence shows that cancer persister cells represent a major limit to the long-term efficacy of targeted therapies. However, the phenotype and population dynamics of cancer persister cells remain unclear. We developed a quantita…
View article: Adaptive ratchets and the evolution of molecular complexity
Adaptive ratchets and the evolution of molecular complexity Open
Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or pept…
View article: Epistasis, aneuploidy, and functional mutations underlie evolution of resistance to induced microtubule depolymerization
Epistasis, aneuploidy, and functional mutations underlie evolution of resistance to induced microtubule depolymerization Open
View article: Drug-induced colorectal cancer persister cells show increased mutation rate
Drug-induced colorectal cancer persister cells show increased mutation rate Open
Compelling evidence shows that cancer persister cells limit the efficacy of targeted therapies. However, it is unclear whether persister cells are induced by anticancer drugs, and if their mutation rate quantitatively increases during trea…
View article: Adaptive evolution of hybrid bacteria by horizontal gene transfer
Adaptive evolution of hybrid bacteria by horizontal gene transfer Open
Significance In a parallel evolution experiment, we probe lateral gene transfer between two Bacillus subtilis lineages close to the species boundary. We show that laboratory evolution by horizontal gene transfer can rapidly generate hybrid…
View article: Epistasis, aneuploidy, and gain-of-function mutations underlie the evolution of resistance to induced microtubule depolymerization
Epistasis, aneuploidy, and gain-of-function mutations underlie the evolution of resistance to induced microtubule depolymerization Open
Microtubules, polymers of alpha- and beta-tubulin, are essential cellular components. When microtubule polymerization is hindered, cells are delayed in mitosis, but eventually they manage to proliferate with massive chromosome missegregati…
View article: Adaptive evolution of hybrid bacteria by horizontal gene transfer
Adaptive evolution of hybrid bacteria by horizontal gene transfer Open
Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient organi…
View article: Copystree
Copystree Open
The reconstruction of phylogenies of cultural artefacts represents an open problem that mixes theoretical and computational challenges. Existing benchmarks rely on simulated phylogenies, where hypotheses on the underlying evolutionary mech…
View article: Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology
Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology Open