Related papers: Viral Hitchhikers and Macroevolution: A Novel Hypo…
HIV is a retrovirus that attacks the human immune system and can lead to death without proper treatment. In collaboration with the WHO and Wits University, we study how to improve the efficiency of HIV testing with the goal of eventual…
We introduce Evolutionary Ensemble (EvE), a decentralized framework that organizes existing, highly capable coding agents into a live, co-evolving system for algorithmic discovery. Rather than reinventing the wheel within the "LLMs as…
Gene-environment interactions have important implications to elucidate the genetic basis of complex diseases beyond the joint function of multiple genetic factors and their interactions (or epistasis). In the past, G$\times$E interactions…
Understanding the host-specificity of different families of viruses sheds light on the origin of, e.g., SARS-CoV-2, rabies, and other such zoonotic pathogens in humans. It enables epidemiologists, medical professionals, and policymakers to…
The profound impact of Darwin's theory of evolution on biology has led to the acceptance of the theory in many complex systems that lie well beyond its original domain. Culture is one example that also exhibits key Darwinian evolutionary…
Climate change is reshaping species interactions and movement across fragmented landscapes. Despite this, most mathematical models assume random diffusion, overlooking the influence of directed movement. Here, we develop a graph based…
While small single stranded viral shells encapsidate their genome spontaneously, many large viruses, such as the Herpes virus or Infectious Bursal Disease Virus (IBDV), typically require a template, consisting of either scaffolding proteins…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
Epidemics on complex networks is a widely investigated topic in the last few years, mainly due to the last pandemic events. Usually, real contact networks are dynamic, hence much effort has been invested in studying epidemics on evolving…
The propagations of diseases, behaviors and information in real systems are rarely independent of each other, but they are coevolving with strong interactions. To uncover the dynamical mechanisms, the evolving spatiotemporal patterns and…
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers,…
In data-driven drug discovery, designing molecular descriptors is a very important task. Deep generative models such as variational autoencoders (VAEs) offer a potential solution by designing descriptors as probabilistic latent vectors…
We analyze how temporal variability in local demography and dispersal combine to affect the rate of spread of an invading species. Our model combines state-structured local demography (specified by an integral or matrix projection model)…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
We explore the connection between migration patterns and emergent behaviors of evolving populations in spatially heterogeneous environments. Despite extensive studies in ecologically and medically important systems, a unifying framework…
We consider a model for an epidemic in a population that occupies geographically distinct locations. The disease is spread within subpopulations by contacts between infective and susceptible individuals, and is spread between subpopulations…
Understanding how viral mutant spectra organize and explore genotype space is essential for unraveling the mechanisms driving evolution at the finest scale. Here we use deep-sequencing data of an amplicon in the A2 protein of the RNA…
Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, because the higher resolution of these data compared to standard Sanger sequencing provide evidence into the direction of infectious…
Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer…
We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the…