Tootfinder

Unleashing the power of computational insights in revealing the complexity of biological systems in the new era of spatial multi-omics
Zhiwei Fan, Tiangang Wang, Kexin Huang, Binwu Ying, Xiaobo Zhou
https://arxiv.org/abs/2509.13376

Unleashing the power of computational insights in revealing the complexity of biological systems in the new era of spatial multi-omics
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping of cellular heterogeneity, tissue architecture, and dynamic biological processes in developmental biology, neuroscience, oncology, and evolutionary studies. This review highlights a systematic overview of the continuous advancements in both technology and co…

A High-Order Cumulant Extension of Quasi-Linkage Equilibrium
Kai S. Shimagaki, Jorge Fernandez-de-Cossio-Diaz, R\'emi Monasson, Simona Cocco, John P. Barton
https://arxiv.org/abs/2509.10987

A High-Order Cumulant Extension of Quasi-Linkage Equilibrium
A central question in evolutionary biology is how to quantitatively understand the dynamics of genetically diverse populations. Modeling the genotype distribution is challenging, as it ultimately requires tracking all correlations (or cumulants) among alleles at different loci. The quasi-linkage equilibrium (QLE) approximation simplifies this by assuming that correlations between alleles at different loci are weak -- i.e., low linkage disequilibrium -- allowing their dynamics to be modeled pert…

Expected and minimal values of a universal tree balance index
Veselin Manojlovi\'c, Armaan Ahmed, Yannick Viossat, Robert Noble
https://arxiv.org/abs/2507.08615

Expected and minimal values of a universal tree balance index
Although the analysis of rooted tree shape has wide-ranging applications, notions of tree balance have developed independently in different domains. In computer science, a balanced tree is one that enables efficient updating and retrieval of data, whereas in biology tree balance quantifies bias in evolutionary processes. The lack of a precise connection between these concepts has stymied the development of universal indices and general results. We recently introduced a new tree balance index, $…

Replaced article(s) found for cs.NE. https://arxiv.org/list/cs.NE/new
[1/1]:
- Synthetic Biology meets Neuromorphic Computing: Towards a bio-inspired Olfactory Perception System
Kevin Max, Larissa Sames, Shimeng Ye, Jan Steink\"uhler, Federico Corradi

An Approximate Maximum Likelihood Estimator for Discretely Observed Linear Birth-and-Death Processes
Xiaochen Long, Marek Kimmel
https://arxiv.org/abs/2508.07527 https://…

An Approximate Maximum Likelihood Estimator for Discretely Observed Linear Birth-and-Death Processes
Linear birth-and-death processes (LBDPs) are foundational stochastic models in population dynamics, evolutionary biology, and hematopoiesis. Estimating parameters from discretely observed data is computationally demanding due to irregular sampling, noise, and missing values. We propose a novel approximate maximum likelihood estimator (MLE) for LBDPs based on a Gaussian approximation to transition probabilities. The approach transforms estimation into a univariate optimization problem, achieving…

Evolution, the mother of age-related diseases
Alessandro Fontana
https://arxiv.org/abs/2509.08806 https://arxiv.org/pdf/2509.08806

Evolution, the mother of age-related diseases
The evolutionary origins of ageing and age-associated diseases continue to pose a fundamental question in biology. This study is concerned with a recently proposed framework, which conceptualises development and ageing as a continuous process, driven by genetically encoded epigenetic changes in target sets of cells. According to the Evolvable Soma Theory of Ageing (ESTA), ageing reflects the cumulative manifestation of epigenetic changes that are predominantly expressed during the post-reproduc…

Tumorigenesis as a trauma response: the fragmentation of morphogenetic memory drives neoplastic dissociation
Jordan Strasser
https://arxiv.org/abs/2508.20363 https://

Tumorigenesis as a trauma response: the fragmentation of morphogenetic memory drives neoplastic dissociation
The mitigation of stress is a key challenge for all biological systems. Conditions of unresolvable stress have been associated with a diverse array of pathologies, from cancer to post-traumatic stress disorder (PTSD). Here, I unify insights from evolutionary and developmental biology with trauma psychology to present a novel framework for tumorigenesis which synthesizes stress-perception, tissue dysfunction, and the hallmarks of neoplastic growth. This view carries therapeutic implications, sug…

Characterizing (multi-)semi-directed phylogenetic networks
Niels Holtgrefe, Katharina T. Huber, Leo van Iersel, Mark Jones, Vincent Moulton
https://arxiv.org/abs/2507.18772 http…

Characterizing (multi-)semi-directed phylogenetic networks
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on a special class of such networks called semi-directed networks. These graphs are defined as mixed graphs that can be obtained by de-orienting some of the arcs in some rooted phylogenetic network, that is, a directed acyclic graph whose leaves correspond to a …

Distinguishing Phylogenetic Level-2 Networks with Quartets and Inter-Taxon Quartet Distances
Niels Holtgrefe, Elizabeth S. Allman, Hector Ba\~nos, Leo van Iersel, Vincent Moulton, John A. Rhodes, Kristina Wicke
https://arxiv.org/abs/2507.17308

Distinguishing Phylogenetic Level-2 Networks with Quartets and Inter-Taxon Quartet Distances
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been limited to phylogenetic level-1 networks, which allow no interdependence between reticulate events. In this work, we establish the theoretical foundations for a statistically consistent inference method for a much broader class: semi-directed level-2 networks …

phylo2vec: a library for vector-based phylogenetic tree manipulation
Neil Scheidwasser, Ayush Nag, Matthew J Penn, Anthony MV Jakob, Frederik M{\o}lkj{\ae}r Andersen, Mark P Khurana, Landung Setiawan, Madeline Gordon, David A Duch\^ene, Samir Bhatt
https://arxiv.org/abs/2506.19490

phylo2vec: a library for vector-based phylogenetic tree manipulation
Phylogenetics is a fundamental component of many analysis frameworks in biology as well as linguistics to study the evolutionary relationships of different entities. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has underscored the necessity for phylogenetic software to handle large datasets of genomes or phylogenetic trees. While significant efforts have focused on scaling optimisation algorithms, visualization, and lineage identification, an emerging body of researc…