Related papers: CONCOCT: Clustering cONtigs on COverage and Compos…

High-throughput sequencing technology provides unprecedented opportunities to quantitatively explore human gut microbiome and its relation to diseases. Microbiome data are compositional, sparse, noisy, and heterogeneous, which pose serious…

We herein introduce a new method of interpretable clustering that uses unsupervised binary trees. It is a three-stage procedure, the first stage of which entails a series of recursive binary splits to reduce the heterogeneity of the data…

Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates…

Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…

The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

Medical coding translates professionally written medical reports into standardized codes, which is an essential part of medical information systems and health insurance reimbursement. Manual coding by trained human coders is time-consuming…

We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…

While Retrieval-Augmented Generation (RAG) has emerged as a promising paradigm for boosting large language models (LLMs) in knowledge-intensive tasks, it often overlooks the crucial aspect of text chunking within its workflow. This paper…

Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…

When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can…

Compact Genetic Algorithms (cGAs) are condensed variants of classical Genetic Algorithms (GAs) that use a probability vector representation of the population instead of the complete population. cGAs have been shown to significantly reduce…

Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…

Crohn's disease (CD) is associated with an ecological imbalance of the intestinal microbiota, consisting of hundreds of species. The underlying complexity as well as individual differences between patients contributes to the difficulty to…

Image compositing is a method used to generate realistic yet fake imagery by inserting contents from one image to another. Previous work in compositing has focused on improving appearance compatibility of a user selected foreground segment…

Obtaining effective representations of DNA sequences is crucial for genome analysis. Metagenomic binning, for instance, relies on genome representations to cluster complex mixtures of DNA fragments from biological samples with the aim of…

Computed Tomography (CT) is an imaging technique where information about an object are collected at different angles (called projections or scans). Then the cross-sectional image showing the internal structure of the slice is produced by…

Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of…

Clustering is a concept used in a huge variety of applications. We review a conceptually very simple algorithm for hierarchical clustering called in the following the {\it mutual information clustering} (MIC) algorithm. It uses mutual…

Concolic testing is a popular dynamic validation technique that can be used for both model checking and automatic test case generation. We have recently introduced concolic testing in the context of logic programming. In contrast to…