Tootfinder

Scientists think they know why humans don't have tails-- jumping genes and mutations. A wild read https://www.livescience.com/health/genetics/we-finally-know-why-humans-dont-have-tails

We finally know why humans don't have tails
Researchers discover a potential genetic connection between humans' tail loss and a type of birth defect.

Rooted mutation groups and finite type cluster algebras
Ibrahim Saleh
https://arxiv.org/abs/2402.17027 https://arxiv.org/pdf/2402.170…

Rooted mutation groups and finite type cluster algebras
For a fixed seed $(X, Q)$, a \emph{rooted mutation loop} is a sequence of mutations that preserves $(X, Q)$. The group generated by all rooted mutation loops is called \emph{rooted mutation group} and will be denoted by $\mathcal{M}(Q)$. Let $\mathcal{M}$ be the global mutation group. In this article, we show that two finite type cluster algebras $\mathcal{A}(Q)$ and $\mathcal{A}(Q')$ are isomorphic if and only if their rooted mutation groups are isomorphic and the sets $\mathcal{M}/\mathcal{M}…

Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating
Jakub Svoboda, Soham Joshi, Josef Tkadlec, Krishnendu Chatterjee
https://arXiv.org/abs/2401.14914

Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating
Populations evolve by accumulating advantageous mutations. Every population has some spatial structure that can be modeled by an underlying network. The network then influences the probability that new advantageous mutations fixate. Amplifiers of selection are networks that increase the fixation probability of advantageous mutants, as compared to the unstructured fully-connected network. Whether or not a network is an amplifier depends on the choice of the random process that governs the evolut…

SAM-dPCR: Real-Time and High-throughput Absolute Quantification of Biological Samples Using Zero-Shot Segment Anything Model
Yuanyuan Wei, Shanhang Luo, Changran Xu, Yingqi Fu, Qingyue Dong, Yi Zhang, Fuyang Qu, Guangyao Cheng, Yi-Ping Ho, Ho-Pui Ho, Wu Yuan
https://arxiv.org/abs/2403.18826<…

SAM-dPCR: Real-Time and High-throughput Absolute Quantification of Biological Samples Using Zero-Shot Segment Anything Model
Digital PCR (dPCR) has revolutionized nucleic acid diagnostics by enabling absolute quantification of rare mutations and target sequences. However, current detection methodologies face challenges, as flow cytometers are costly and complex, while fluorescence imaging methods, relying on software or manual counting, are time-consuming and prone to errors. To address these limitations, we present SAM-dPCR, a novel self-supervised learning-based pipeline that enables real-time and high-throughput a…

Reduction of the effective population size in a branching particle system in the moderate mutation-selection regime
Florin Boenkost, Ksenia A Khudiakova, Julie Tourniaire
https://arxiv.org/abs/2404.17527

Reduction of the effective population size in a branching particle system in the moderate mutation-selection regime
We consider a system of particles performing a one-dimensional dyadic branching Brownian motion with positive drift $β\in(0,1)$, branching rate 1/2, killed at $L(β)>0$, and reflected at 0. The killing boundary $L(β)$ is chosen so that the total population size is approximately constant, proportional to $N\in\mathbb{N}$. This branching system is interpreted as a population accumulating deleterious mutations. We prove that, when the typical width of the cloud of particles is of order $c\log(…

This https://arxiv.org/abs/2310.11057 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

Mutations of noncommutative crepant resolutions in geometric invariant theory
Let $X$ be a generic quasi-symmetric representation of a connected reductive group $G$. The GIT quotient stack $\mathfrak{X}=[X^{\rm ss}(\ell)/G]$ with respect to a generic $\ell$ is a (stacky) crepant resolution of the affine quotient $X/G$, and it is derived equivalent to a noncommutative crepant resolution (=NCCR) of $X/G$. Halpern-Leistner and Sam showed that the derived category $\mathrm{D}^b(\mathrm{coh}~\mathfrak{X})$ is equivalent to certain subcategories of $\mathrm{D}^b(\mathrm{coh}~[…

This https://arxiv.org/abs/2403.09436 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

Emergent time scales of epistasis in protein evolution
We introduce a data-driven epistatic model of protein evolution, capable of generating evolutionary trajectories spanning very different time scales reaching from individual mutations to diverged homologs. Our in silico evolution encompasses random nucleotide mutations, insertions and deletions, and models selection using a fitness landscape, which is inferred via a generative probabilistic model for protein families. We show that the proposed framework accurately reproduces the sequence statis…

MMT: Mutation Testing of Java Bytecode with Model Transformation -- An Illustrative Demonstration
Christoph Bockisch, Gabriele Taentzer, Daniel Neufeld
https://arxiv.org/abs/2404.14097

MMT: Mutation Testing of Java Bytecode with Model Transformation -- An Illustrative Demonstration
Mutation testing is an approach to check the robustness of test suites. The program code is slightly changed by mutations to inject errors. A test suite is robust enough if it finds such errors. Tools for mutation testing usually integrate sets of mutation operators such as, for example, swapping arithmetic operators; modern tools typically work with compiled code such as Java bytecode. In this case, the mutations must be defined in such a way that the mutated program still can be loaded and ex…

Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating
Jakub Svoboda, Soham Joshi, Josef Tkadlec, Krishnendu Chatterjee
https://arXiv.org/abs/2401.14914

Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating
Populations evolve by accumulating advantageous mutations. Every population has some spatial structure that can be modeled by an underlying network. The network then influences the probability that new advantageous mutations fixate. Amplifiers of selection are networks that increase the fixation probability of advantageous mutants, as compared to the unstructured fully-connected network. Whether or not a network is an amplifier depends on the choice of the random process that governs the evolut…

This https://arxiv.org/abs/2303.06704 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_nli…

Birational Weyl group actions via mutation combinatorics in cluster algebras
A cluster algebra is an algebraic structure generated by operations of a quiver (a directed graph) called the mutations and their associated simple birational mappings. By using a graph-combinatorial approach, we present a systematic way to derive a tropical, i.e. subtraction-free birational, representation of Weyl groups from cluster algebras. Our result provides a broad class of Weyl group actions including previously known examples acting on certain rational varieties [28, 30] and hence it i…

This https://arxiv.org/abs/2306.08142 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

Latent mutations in the ancestries of alleles under selection
We consider a single genetic locus with two alleles $A_1$ and $A_2$ in a large haploid population. The locus is subject to selection and two-way, or recurrent, mutation. Assuming the allele frequencies follow a Wright-Fisher diffusion and have reached stationarity, we describe the asymptotic behaviors of the conditional gene genealogy and the latent mutations of a sample with known allele counts, when the count $n_1$ of allele $A_1$ is fixed, and when either or both the sample size $n$ and the …

Criticality in the Luria-Delbr\"uck model with an arbitrary mutation rate
Deng Pan, Jie Lin, Ariel Amir
https://arxiv.org/abs/2402.13339 https://

Criticality in the Luria-Delbrück model with an arbitrary mutation rate
The Luria-Delbrück model is a classic model of population dynamics with random mutations, that has been used historically to prove that random mutations drive evolution. In typical scenarios, the relevant mutation rate is exceedingly small, and mutants are counted only at the final time point. Here, inspired by recent experiments on DNA repair, we study a mathematical model that is formally equivalent to the Luria-Delbrück setup, with the repair rate $p$ playing the role of mutation rate, alb…

This https://arxiv.org/abs/2302.06573 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

Propagation of weakly advantageous mutations in cancer cell population
Research into somatic mutations in cancer cell DNA and their role in tumour growth and progression between successive stages is crucial for improving our understanding of cancer evolution. Mathematical and computer modelling can provide valuable insights into the scenarios of cancer growth, the roles of somatic mutations, and the types and strengths of evolutionary forces they introduce. Previous studies have developed mathematical models of cancer evolution, incorporating driver and passenger …

This https://arxiv.org/abs/2110.07696 has been replaced.
link: https://scholar.google.com/scholar?q=a

Integrating Fréchet distance and AI reveals the evolutionary trajectory and origin of SARS-CoV-2
A genome, composed of a precisely ordered sequence of four nucleotides (ATCG), encompasses a multitude of specific genome features like AAA motif. Mutations occurring within a genome disrupt the sequential order and composition of these features, thereby influencing the evolutionary trajectories and yielding variants. The evolutionary relatedness between a variant and its ancestor can be estimated by assessing evolutionary distances across a spectrum of genome features. This study develops a no…

This https://arxiv.org/abs/2402.12943 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

On some dynamical features of the complete Moran model for neutral evolution in the presence of mutations
We present a version of the classical Moran model, in which mutations are taken into account; the possibility of mutations was introduced by Moran in his seminal paper, but it is more often overlooked in discussing the Moran model. For this model, fixation is prevented by mutation, and we have an ergodic Markov process; the equilibrium distribution for such a process was determined by Moran. The problems we consider in this paper are those of first hitting either one of the ``pure'' (uniform po…

The Geometry of GTPs and 5d SCFTs
Guillermo Arias-Tamargo, Sebasti\'an Franco, Diego Rodr\'iguez-G\'omez
https://arxiv.org/abs/2403.09776 https…

The Geometry of GTPs and 5d SCFTs
We make progress in understanding the geometry associated to the Generalized Toric Polygons (GTPs) encoding the Physics of 5d Superconformal Field Theories (SCFTs), by exploiting the connection between Hanany-Witten transitions and the mathematical notion of polytope mutations. From this correspondence, it follows that the singular geometry associated to a GTP is identical to that obtained by regarding it as a standard toric diagram, but with some of its resolutions frozen in way that can be de…

LLM Guided Evolution - The Automation of Models Advancing Models
Clint Morris, Michael Jurado, Jason Zutty
https://arxiv.org/abs/2403.11446 https://…

LLM Guided Evolution - The Automation of Models Advancing Models
In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Though…

This https://arxiv.org/abs/2110.07696 has been replaced.
link: https://scholar.google.com/scholar?q=a

Integrating Fréchet distance and AI reveals the evolutionary trajectory and origin of SARS-CoV-2
A genome, composed of a precisely ordered sequence of four nucleotides (ATCG), encompasses a multitude of specific genome features like AAA motif. Mutations occurring within a genome disrupt the sequential order and composition of these features, thereby influencing the evolutionary trajectories and yielding variants. The evolutionary relatedness between a variant and its ancestor can be estimated by assessing evolutionary distances across a spectrum of genome features. This study develops a no…

Emergent time scales of epistasis in protein evolution
Leonardo Di Bari, Matteo Bisardi, Sabrina Cotogno, Martin Weigt, Francesco Zamponi
https://arxiv.org/abs/2403.09436

Emergent time scales of epistasis in protein evolution
We introduce a data-driven epistatic model of protein evolution, capable of generating evolutionary trajectories spanning very different time scales reaching from individual mutations to diverged homologs. Our in silico evolution encompasses random nucleotide mutations, insertions and deletions, and models selection using a fitness landscape, which is inferred via a generative probabilistic model for protein families. We show that the proposed framework accurately reproduces the sequence statis…

The Geometry of GTPs and 5d SCFTs
Guillermo Arias-Tamargo, Sebasti\'an Franco, Diego Rodr\'iguez-G\'omez
https://arxiv.org/abs/2403.09776 https…

The Geometry of GTPs and 5d SCFTs
We make progress in understanding the geometry associated to the Generalized Toric Polygons (GTPs) encoding the Physics of 5d Superconformal Field Theories (SCFTs), by exploiting the connection between Hanany-Witten transitions and the mathematical notion of polytope mutations. From this correspondence, it follows that the singular geometry associated to a GTP is identical to that obtained by regarding it as a standard toric diagram, but with some of its resolutions frozen in way that can be de…

This https://arxiv.org/abs/2303.11342 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

An agent-based modelling framework to study growth mechanisms in EGFR-L858R mutant alveolar type II cells
Mutations in the epidermal growth factor receptor (EGFR) are common in non-small cell lung cancer (NSCLC), particularly in never-smoker patients. However, these mutations are not always carcinogenic, and have recently been reported in histologically normal lung tissue from patients with and without lung cancer. To investigate the outcome of EGFR mutation in healthy lung stem cells, we grew murine alveolar type-II organoids monoclonally in a 3D Matrigel. Our experiments showed that the \textit{E…

On some dynamical features of the complete Moran model for neutral evolution in the presence of mutations
Giuseppe Gaeta
https://arxiv.org/abs/2402.12943 h…

On some dynamical features of the complete Moran model for neutral evolution in the presence of mutations
We present a version of the classical Moran model, in which mutations are taken into account; the possibility of mutations was introduced by Moran in his seminal paper, but it is more often overlooked in discussing the Moran model. For this model, fixation is prevented by mutation, and we have an ergodic Markov process; the equilibrium distribution for such a process was determined by Moran. The problems we consider in this paper are those of first hitting either one of the ``pure'' (uniform po…

Evaluation of simulation methods for tumor subclonal reconstruction
Jiaying Lai, Yunzhou Liu, Robert B. Scharpf, Rachel Karchin
https://arxiv.org/abs/2402.09599

Evaluation of simulation methods for tumor subclonal reconstruction
Most neoplastic tumors originate from a single cell, and their evolution can be genetically traced through lineages characterized by common alterations such as small somatic mutations (SSMs), copy number alterations (CNAs), structural variants (SVs), and aneuploidies. Due to the complexity of these alterations in most tumors and the errors introduced by sequencing protocols and calling algorithms, tumor subclonal reconstruction algorithms are necessary to recapitulate the DNA sequence compositi…

This https://arxiv.org/abs/2206.09400 has been replaced.
link: https://scholar.google.com/scholar?q=a

Ideal mutations in triangulated categories and generalized Auslander-Reiten theory
We introduce the notion of ideal mutations in a triangulated category, which generalizes the version of Iyama and Yoshino \cite{iyama2008mutation} by replacing approximations by objects of a subcategory with approximations by morphisms of an ideal. As applications, for a Hom-finite Krull-Schmidt triangulated category $\mathcal{T}$ over an algebraically closed field $K$. (1) We generalize a theorem of Jorgensen \cite[Theorem 3.3]{jorgensen2010quotients} to a more general setting; (2) We provide …

This https://arxiv.org/abs/2306.08142 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

Latent mutations in the ancestries of alleles under selection
We consider a single genetic locus with two alleles $A_1$ and $A_2$ in a large haploid population. The locus is subject to selection and two-way, or recurrent, mutation. Assuming the allele frequencies follow a Wright-Fisher diffusion and have reached stationarity, we describe the asymptotic behaviors of the conditional gene genealogy and the latent mutations of a sample with known allele counts, when the count $n_1$ of allele $A_1$ is fixed, and when either or both the sample size $n$ and the …

Locuaz: an in-silico platform for antibody fragments optimization
German P. Barletta (1 CONCEPT, Istituto Italiano di Teconologia, Genova, Italy), Rika Tandiana (1 CONCEPT, Istituto Italiano di Teconologia, Genova, Italy), Miguel Soler (1 CONCEPT, Istituto Italiano di Teconologia, Genova, Italy), Sara Fortuna (1 CONCEPT, Istituto Italiano di Teconologia, Genova, Italy), Walter Rocchia

Locuaz: an in-silico platform for antibody fragments optimization
Motivation: Engineering high-affinity binders targeting specific antigenic determinants remains a challenging and often daunting task, requiring extensive experimental screening. Computational methods have the potential to accelerate this process, reducing costs and time, but only if they demonstrate broad applicability and efficiency in exploring mutations, evaluating affinity, and pruning unproductive mutation paths. Results: In response to these challenges, we introduce a new computational p…

A Flexible Evolutionary Algorithm With Dynamic Mutation Rate Archive
Martin S. Krejca, Carsten Witt
https://arxiv.org/abs/2404.04015 https://

A Flexible Evolutionary Algorithm With Dynamic Mutation Rate Archive
We propose a new, flexible approach for dynamically maintaining successful mutation rates in evolutionary algorithms using $k$-bit flip mutations. The algorithm adds successful mutation rates to an archive of promising rates that are favored in subsequent steps. Rates expire when their number of unsuccessful trials has exceeded a threshold, while rates currently not present in the archive can enter it in two ways: (i) via user-defined minimum selection probabilities for rates combined with a su…

Two fitness inference schemes compared using allele frequencies from 1,068,391 sequences sampled in the UK during the COVID-19 pandemic
Hong-Li Zeng, Cheng-Long Yang, Bo Jing, John Barton, Erik Aurell
https://arxiv.org/abs/2403.14202

Two fitness inference schemes compared using allele frequencies from 1,068,391 sequences sampled in the UK during the COVID-19 pandemic
Throughout the course of the SARS-CoV-2 pandemic, genetic variation has contributed to the spread and persistence of the virus. For example, various mutations have allowed SARS-CoV-2 to escape antibody neutralization or to bind more strongly to the receptors that it uses to enter human cells. Here, we compared two methods that estimate the fitness effects of viral mutations using the abundant sequence data gathered over the course of the pandemic. Both approaches are grounded in population gene…

This https://arxiv.org/abs/2307.03346 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

Limit theorems for the site frequency spectrum of neutral mutations in an exponentially growing population
The site frequency spectrum (SFS) is a widely used summary statistic of genomic data. Motivated by recent evidence for the role of neutral evolution in cancer, we investigate the SFS of neutral mutations in an exponentially growing population. Using branching process techniques, we establish (first-order) almost sure convergence results for the SFS of a Galton-Watson process, evaluated either at a fixed time or at the stochastic time at which the population first reaches a certain size. We fina…

A Flexible Evolutionary Algorithm With Dynamic Mutation Rate Archive
Martin S. Krejca, Carsten Witt
https://arxiv.org/abs/2404.04015 https://

A Flexible Evolutionary Algorithm With Dynamic Mutation Rate Archive
We propose a new, flexible approach for dynamically maintaining successful mutation rates in evolutionary algorithms using $k$-bit flip mutations. The algorithm adds successful mutation rates to an archive of promising rates that are favored in subsequent steps. Rates expire when their number of unsuccessful trials has exceeded a threshold, while rates currently not present in the archive can enter it in two ways: (i) via user-defined minimum selection probabilities for rates combined with a su…

New cluster algebras from old: integrability beyond Zamolodchikov periodicity
Andrew N. W. Hone, Wookyung Kim, Takafumi Mase
https://arxiv.org/abs/2403.00721

New cluster algebras from old: integrability beyond Zamolodchikov periodicity
We consider discrete dynamical systems obtained as deformations of mutations in cluster algebras associated with finite-dimensional simple Lie algebras. The original (undeformed) dynamical systems provide the simplest examples of Zamolodchikov periodicity: they are affine birational maps for which every orbit is periodic with the same period. Following on from preliminary work by one of us with Kouloukas, here we present integrable maps obtained from deformations of cluster mutations related to…

This https://arxiv.org/abs/2309.13326 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities
During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cryptic lineages, but it is difficult to clearly identify and define novel lineages from wastewater (WW) alone. While WWGS has significant advantages in…

Guidelines for releasing a variant effect predictor
Benjamin J. Livesey, Mihaly Badonyi, Mafalda Dias, Jonathan Frazer, Sushant Kumar, Kresten Lindorff-Larsen, David M. McCandlish, Rose Orenbuch, Courtney A. Shearer, Lara Muffley, Julia Foreman, Andrew M. Glazer, Ben Lehner, Debora S. Marks, Frederick P. Roth, Alan F. Rubin, Lea M. Starita, Joseph A. Marsh

Guidelines for releasing a variant effect predictor
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein engineering. Many different VEPs have been released to date, and there is tremendous variability in their underlying algorithms and outputs, and in the ways in which the methodologies and predictions are shared. This leads to considerable challenges for end us…

Guidelines for releasing a variant effect predictor
Benjamin J. Livesey, Mihaly Badonyi, Mafalda Dias, Jonathan Frazer, Sushant Kumar, Kresten Lindorff-Larsen, David M. McCandlish, Rose Orenbuch, Courtney A. Shearer, Lara Muffley, Julia Foreman, Andrew M. Glazer, Ben Lehner, Debora S. Marks, Frederick P. Roth, Alan F. Rubin, Lea M. Starita, Joseph A. Marsh

Guidelines for releasing a variant effect predictor
Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein engineering. Many different VEPs have been released to date, and there is tremendous variability in their underlying algorithms and outputs, and in the ways in which the methodologies and predictions are shared. This leads to considerable challenges for end us…

Lotka-Volterra Model with Mutations and Generative Adversarial Networks
S. V. Kozyrev
https://arxiv.org/abs/2402.19035 https://arxiv.…

Lotka-Volterra Model with Mutations and Generative Adversarial Networks
A model of population genetics of the Lotka-Volterra type with mutations on a statistical manifold is introduced. Mutations in the model are described by diffusion on a statistical manifold with a generator in the form of a Laplace-Beltrami operator with a Fisher-Rao metric, that is, the model combines population genetics and information geometry. This model describes a generalization of the model of machine learning theory, the model of generative adversarial network (GAN), to the case of popu…

The curious case of A31P, a topology-switching mutant of the Repressor of Primer protein : A molecular dynamics study of its folding and misfolding
Olympia-Dialekti Vouzina, Alexandros Tafanidis, Nicholas M. Glykos
https://arxiv.org/abs/2404.01405

The curious case of A31P, a topology-switching mutant of the Repressor of Primer protein : A molecular dynamics study of its folding and misfolding
The effect of mutations on protein structures is usually rather localized and minor. Finding a mutation that can single-handedly change the fold and/or topology of a protein structure is a rare exception. The A31P mutant of the homodimeric Repressor of Primer (Rop) protein is one such exception: This single mutation -and as demonstrated by two independent crystal structure determinations- can convert the canonical (left-handed/all-antiparallel) 4-alpha-helical bundle of Rop, to a new form (righ…

Concepts and methods for predicting viral evolution
Matthijs Meijers, Denis Ruchnewitz, Jan Eberhardt, Malancha Karmakar, Marta {\L}uksza, Michael L\"assig
https://arxiv.org/abs/2403.12684

Concepts and methods for predicting viral evolution
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral is…

This https://arxiv.org/abs/2112.12675 has been replaced.
link: https://scholar.google.com/scholar?q=a

A general multi-scale description of metastable adaptive motion across fitness valleys
We consider a stochastic individual-based model of adaptive dynamics on a finite trait graph $G=(V,E)$. The evolution is driven by a linear birth rate, a density dependent logistic death rate an the possibility of mutations along the (possibly directed) edges in $E$. We study the limit of small mutation rates for a simultaneously diverging population size. Closing the gap between the works of Bovier, Coquille and Smadi (2019) and Coquille, Kraut and Smadi (2021), we give a precise description o…

Concepts and methods for predicting viral evolution
Matthijs Meijers, Denis Ruchnewitz, Jan Eberhardt, Malancha Karmakar, Marta {\L}uksza, Michael L\"assig
https://arxiv.org/abs/2403.12684

Concepts and methods for predicting viral evolution
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral is…

Nuclear compensatory evolution driven by mito-nuclear incompatibilities
D\'ebora Princepe, Marcus A. M. de Aguiar
https://arxiv.org/abs/2403.10411 http…

Nuclear compensatory evolution driven by mito-nuclear incompatibilities
Mitochondrial function relies on the coordinated expression of mitochondrial and nuclear genes, exhibiting remarkable resilience regardless the susceptibility of mitochondrial DNA (mtDNA) to accumulate harmful mutations. A suggested mechanism for preserving this mito-nuclear compatibility is the nuclear compensation, where deleterious mitochondrial alleles drive compensatory changes in nuclear genes. However, prevalence and conditioning factors for this phenomenon remain debated, with empirical…

This https://arxiv.org/abs/2309.02148 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

The canonical equation of adaptive dynamics in individual-based models with power law mutation rates
In this paper, we consider an individual-based model with power law mutation probability. In this setting, we use the large population limit with a subsequent ``small mutations'' limit to derive the canonical equation of adaptive dynamics. For a one-dimensional trait space this corresponds to well established results and we can formulate a criterion for evolutionary branching in the spirit of Champagnat and Méléard (2011). In higher dimensional trait spaces, we find that the speed at which th…