Related papers: Simulating transgenerational hologenomes under sel…
In this paper, we develop a generalized theory of convolutional signal processing and neural networks for Reproducing Kernel Hilbert Spaces (RKHS). Leveraging the theory of algebraic signal processing (ASP), we show that any RKHS allows the…
One of the primary objectives of satellite remote sensing is to capture the complex dynamics of the Earth environment, which encompasses tasks such as reconstructing continuous cloud-free image sequences, detecting land cover changes, and…
Feature selection is indispensable in microbiome data analysis, but it can be particularly challenging as microbiome data sets are high-dimensional, underdetermined, sparse and compositional. Great efforts have recently been made on…
We argue that embryological morphogenesis provides a model of how massive swarms of microscopic agents can be coordinated to assemble complex, multiscale hierarchical structures. This is accomplished by understanding natural morphogenetic…
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes…
We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is…
Cosmological simulations are essential for inferring cosmological and galaxy population properties based on forward-modelling, but this typically requires finding the population of (sub)haloes and galaxies that they contain. The properties…
Theoretical descriptions of the stepping-stone model, a cornerstone of spatial population genetics, have long overlooked diffusive noise arising from migration dynamics. We derive an exact fluctuating hydrodynamic description of this model…
Molecular and morphological characters, as important parts of biological taxonomy, are contradictory but need to be integrated. Organism's image recognition and bioinformatics are emerging and hot problems nowadays but with a gap between…
Cis-regulatory modules (CRMs) composed of multiple transcription factor binding sites (TFBSs) control gene expression in eukaryotic genomes. Comparative genomic studies have shown that these regulatory elements are more conserved across…
A time series forecasting model--which is typically built on a single time series--is known as a local time series model (tsLM). In contrast, a forecasting model trained on multiple time series is referred to as a global time series model…
The identification of reproducible biological patterns from high-dimensional data is a bottleneck for understanding the biology of complex illnesses such as schizophrenia. To address this, we developed a biologically informed, multi-stage…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics…
One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of…
Traditional robotic systems require complex implementations that are not always accessible or easy to use for Human-Robot Interaction (HRI) application developers. With the aim of simplifying the implementation of HRI applications, this…
The Stochastic Calculus of Looping Sequences (SCLS) is a recently proposed modelling language for the representation and simulation of biological systems behaviour. It has been designed with the aim of combining the simplicity of notation…
The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of…