Related papers: SICLE: A high-throughput tool for extracting evolu…
This work presents a novel approach for selecting the optimal ensemble-based classification method and features with a primarly focus on achieving generalization, based on the state-of-the-art, to provide diagnostic support for Sickle Cell…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
The surging amount of biomedical literature & digital clinical records presents a growing need for text mining techniques that can not only identify but also semantically relate entities in unstructured data. In this paper we propose a text…
This paper presents the ReXCL tool, which automates the extraction and classification processes in requirement engineering, enhancing the software development lifecycle. The tool features two main modules: Extraction, which processes raw…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
Citizen science is a powerful analysis tool, capable of processing large amounts of data in a very short time. To bridge the gap between classification data products from web-based citizen science platforms to statistically robust signal…
Microbial communities play important roles in the function and maintenance of various biosystems, ranging from human body to the environment. Current methods for analysis of microbial communities are typically based on taxonomic…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
As a result of decades of research, Windows malware detection is approached through a plethora of techniques. However, there is an ongoing mismatch between academia -- which pursues an optimal performances in terms of detection rate and low…
To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…
In this paper we identify several serious problems that arise in the use of syntactic data from the SSWL database for the purpose of computational phylogenetic reconstruction. We show that the most naive approach fails to produce reliable…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…
Ecological networks offer powerful insights into community function, but without first characterizing these networks accurately, our ability to detect and interpret changes under environmental stress is limited. We develop an approach to…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
The progenitors for many types of supernovae (SNe) are still unknown, and an approach to diagnose their physical origins is to investigate the light curve brightness and shape of a large set of SNe. However, it is often difficult to compare…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
Document-level Relation Extraction (DocRE) involves identifying relations between entities across multiple sentences in a document. Evidence sentences, crucial for precise entity pair relationships identification, enhance focus on essential…