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Spider silks are remarkable materials characterized by superb mechanical properties such as strength, extensibility and lightweightedness. Yet, to date, limited models are available to fully explore sequence-property relationships for…
The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail unlike any virus before it.…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
Widely used models in genetics include the Wright-Fisher diffusion and its moment dual, Kingman's coalescent. Each has a multilocus extension but under neither extension is the sampling distribution available in closed-form, and their…
Data replication is used in distributed systems to maintain up-to-date copies of shared data across multiple computers in a network. However, despite decades of research, algorithms for achieving consistency in replicated systems are still…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
Genomic aberrations, such as somatic copy number alterations, are frequently observed in tumor tissue. Recurrent aberrations, occurring in the same region across multiple subjects, are of interest because they may highlight genes associated…
Complexity has been a recurrent research topic in cellular automata because they represent systems where complex behaviors emerge from simple local interactions. A significant amount of previous research has been conducted proposing…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
In cancer research, clustering techniques are widely used for exploratory analyses and dimensionality reduction, playing a critical role in the identification of novel cancer subtypes, often with direct implications for patient management.…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
A large offspring number diploid biparental multilocus population model of Moran type is our object of study. At each timestep, a pair of diploid individuals drawn uniformly at random contribute offspring to the population. The number of…
The optimizations of the track fittings require complex simulations of silicon strip detectors to be compliant with the fundamental properties of the hit heteroscedasticity. Many different generations of random numbers must be available…
We review recent progress in the understanding of the role of multiple- and simultaneous multiple merger coalescents as models for the genealogy in idealised and real populations with exceptional reproductive behaviour. In particular, we…
Protein design using structure prediction models such as AlphaFold2 has shown remarkable success, but existing approaches like relaxed sequence optimization (RSO) rely on single-path gradient descent and ignore sequence-space constraints,…
Post-training improves instruction-following and helpfulness of large language models (LLMs) but often reduces generation diversity, which leads to repetitive outputs in open-ended settings, a phenomenon known as mode collapse. Motivated by…
Locating recombination hotspots in genomic data is an important but difficult task. Current methods frequently rely on estimating complicated models at high computational cost. In this paper we develop an extremely fast, scalable method for…
Recent experimental evidence suggests that acute myeloid leukemias may originate from multiple clones of malignant cells. Nevertheless it is not known how the observed clones may differ with respect to cell properties such as proliferation…
Strongly log-concave (SLC) distributions are a rich class of discrete probability distributions over subsets of some ground set. They are strictly more general than strongly Rayleigh (SR) distributions such as the well-known determinantal…
In this work we present a model for computation of random processes in digital computers which solves the problem of periodic sequences and hidden errors produced by correlations. We show that systems with non-invertible non-linearities can…