Florian Pflug
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View article: Fast and exact stochastic simulations of epidemics on static and temporal networks
Fast and exact stochastic simulations of epidemics on static and temporal networks Open
Epidemic models on complex networks are widely used to assess how the social structure of a population affects epidemic spreading. However, their numerical simulation can be computationally heavy, especially for large networks. In this pap…
View article: Fast and exact simulations of stochastic epidemics on static and temporal networks
Fast and exact simulations of stochastic epidemics on static and temporal networks Open
Epidemic models on complex networks have been widely used to study how the social structure of a population affect the spreading of epidemics. However, their numerical simulation can be computationally heavy, especially for large networks.…
View article: Genomic GC bias correction improves species abundance estimation from metagenomic data
Genomic GC bias correction improves species abundance estimation from metagenomic data Open
Metagenomic sequencing measures the species composition of microbial communities, and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial comm…
View article: Exponential rate of epidemic spreading on complex networks
Exponential rate of epidemic spreading on complex networks Open
The initial phase of an epidemic is often characterized by an exponential increase in the number of infected individuals. In this paper, we predict the exponential spreading rate of an epidemic on a complex network. We first find an expres…
View article: Neutral competition explains the clonal composition of neural organoids
Neutral competition explains the clonal composition of neural organoids Open
Neural organoids model the development of the human brain and are an indispensable tool for studying neurodevelopment. Whole-organoid lineage tracing has revealed the number of progenies arising from each initial stem cell to be highly div…
View article: Genome replication in asynchronously growing microbial populations
Genome replication in asynchronously growing microbial populations Open
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and g…
View article: Critical Growth of Cerebral Tissue in Organoids: Theory and Experiments
Critical Growth of Cerebral Tissue in Organoids: Theory and Experiments Open
We develop a Fokker-Planck theory of tissue growth with three types of cells (symmetrically dividing, asymmetrically dividing, and nondividing) as main agents to study the growth dynamics of human cerebral organoids. Fitting the theory to …
View article: Genome replication in asynchronously growing microbial populations
Genome replication in asynchronously growing microbial populations Open
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and g…
View article: Genome replication in asynchronously growing microbial populations
Genome replication in asynchronously growing microbial populations Open
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and g…
View article: Critical growth of cerebral tissue in organoids: theory and experiments
Critical growth of cerebral tissue in organoids: theory and experiments Open
We develop a Fokker-Planck theory of tissue growth with three types of cells (symmetrically dividing, asymmetrically dividing and non-dividing) as main agents to study the growth dynamics of human cerebral organoids. Fitting the theory to …
View article: Neutral competition explains the clonal composition of neural organoids
Neutral competition explains the clonal composition of neural organoids Open
Summary Cerebral organoids model the development of the human brain and are an indispensable tool for studying neurodevelopment. Whole-organoid lineage tracing has revealed the number of progeny arising from each initial stem cell to be hi…
View article: A human tissue screen identifies a regulator of ER secretion as a brain-size determinant
A human tissue screen identifies a regulator of ER secretion as a brain-size determinant Open
Functional screen for microcephaly genes Genetic screens are widely used to identify regulators in biological processes. Human screens are currently limited to two-dimensional cell cultures, which lack the ability to score tissue-dependent…
View article: Insertion Pool Sequencing for Insertional Mutant Analysis in Complex Host‐Microbe Interactions
Insertion Pool Sequencing for Insertional Mutant Analysis in Complex Host‐Microbe Interactions Open
Insertional mutant libraries of microorganisms can be applied in negative depletion screens to decipher gene functions. Because of underrepresentation in colonized tissue, one major bottleneck is analysis of species that colonize hosts. To…
View article: In vivo insertion pool sequencing identifies virulence factors in a complex fungal–host interaction
In vivo insertion pool sequencing identifies virulence factors in a complex fungal–host interaction Open
Large-scale insertional mutagenesis screens can be powerful genome-wide tools if they are streamlined with efficient downstream analysis, which is a serious bottleneck in complex biological systems. A major impediment to the success of nex…
View article: TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers
TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers Open
Motivation Counting molecules using next-generation sequencing (NGS) suffers from PCR amplification bias, which reduces the accuracy of many quantitative NGS-based experimental methods such as RNA-Seq. This is true even if molecules are ma…
View article: TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers
TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers Open
Counting DNA or RNA molecules using next-generation sequencing (NGS) suffers from amplification biases. Counting unique molecular identifiers (UMIs) instead of reads is still prone to over-estimation due to amplification and sequencing art…
View article: Linking speech enhancement and error concealment based on recursive MMSE estimation
Linking speech enhancement and error concealment based on recursive MMSE estimation Open
Speech enhancement and error concealment have seen a considerable progress over the past decades. Although both fields deal with distorted speech signals, there has rarely been an attempt to relate respective approaches to each other. In t…