Related papers: Multiple Comparative Metagenomics using Multiset k…
Species complexes are groups of closely related populations exchanging genes through dispersal. We study the dynamics of the structure of species complexes in a class of metapopulation models where demes can exchange genetic material…
Microbiomes, which are collections of interacting microbes in an environment, often substantially impact the environmental patches or living hosts that they occupy. In microbiome models, it is important to consider both the local dynamics…
The main objective of the Multiple Kernel k-Means (MKKM) algorithm is to extract non-linear information and achieve optimal clustering by optimizing base kernel matrices. Current methods enhance information diversity and reduce redundancy…
Metabarcoding on amplicons is rapidly expanding as a method to produce molecular based inventories of microbial communities. Here, we work on freshwater diatoms, which are microalgae possibly inventoried both on a morphological and a…
1. Understanding the mechanisms underlying biological systems, and ultimately, predicting their behaviours in a changing environment requires overcoming the gap between mathematical models and experimental or observational data.…
The delimitation of biological species, i.e., deciding which individuals belong to the same species and whether and how many different species are represented in a data set, is key to the conservation of biodiversity. Much existing work…
Ecosystem approach to fisheries requires a thorough understanding of fishing impacts on ecosystem status and processes as well as predictive tools such as ecosystem models to provide useful information for management. The credibility of…
Measuring inter-dataset similarity is an important task in machine learning and data mining with various use cases and applications. Existing methods for measuring inter-dataset similarity are computationally expensive, limited, or…
To analyse a very large data set containing lengthy variables, we adopt a sequential estimation idea and propose a parallel divide-and-conquer method. We conduct several conventional sequential estimation procedures separately, and properly…
We propose a family of near-metrics based on local graph diffusion to capture similarity for a wide class of data sets. These quasi-metametrics, as their names suggest, dispense with one or two standard axioms of metric spaces, specifically…
We introduce an effective strategy to generate an annotated synthetic dataset of microbiological images of Petri dishes that can be used to train deep learning models in a fully supervised fashion. The developed generator employs…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
In generating large quantities of DNA data, high-throughput sequencing technologies require advanced bioinformatics infrastructures for efficient data analysis. k-mer counting, the process of quantifying the frequency of fixed-length k DNA…
A computational framework utilizes the traditional similarity measures for mining the significant relationships in biological annotations is recently proposed by Tatiana V. Karpinets et al. [2]. In this paper, an improved approximation…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…
Biodiversity is declining at an unprecedented rate, impacting ecosystem services necessary to ensure food, water, and human health and well-being. Understanding the distribution of species and their habitats is crucial for conservation…
Data acquisition in animal ecology is rapidly accelerating due to inexpensive and accessible sensors such as smartphones, drones, satellites, audio recorders and bio-logging devices. These new technologies and the data they generate hold…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…