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In this manuscript we describe the investigation of the SARS-CoV2 membrane fusion timescale by means of small-angle neutron scattering (SANS) using hydrogen/deuterium contrast variation. After the successful production of virus-like…
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies,…
The rapid evolution and global impact of coronaviruses, notably SARS-CoV-1 and SARS-CoV-2, underscore the importance of understanding their molecular mechanisms in detail. This study focuses on the receptor-binding motif (RBM) within the…
Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that…
This paper presents a federated learning (FL) approach to train an AI model for SARS-Cov-2 variant classification. We analyze the SARS-CoV-2 spike sequences in a distributed way, without data sharing, to detect different variants of this…
In the field of computer graphics, the use of vector graphics, particularly Scalable Vector Graphics (SVG), represents a notable development from traditional pixel-based imagery. SVGs, with their XML-based format, are distinct in their…
The ICTV develops, refines and maintains a universal virus taxonomy; Order is the highest taxon in the branching hierarchy of recognised viral taxa. Historically, ICTV (sub)committees have classified viruses on the basis of morphological…
The COVID-19 pandemic has stimulated the scientific world to intensify virus-related studies, aimed at the development of quick and safe ways of detecting viruses in human body, studying the virus-antibody and virus-cell interactions, and…
The COVID-19 pandemic has profoundly affected global health, driven by the remarkable transmissibility and mutational adaptability of the SARS-CoV-2 virus. Although five variants of concern, Alpha, Beta, Gamma, Delta, and Omicron, have been…
Pattern detection and string matching are fundamental problems in computer science and the accelerated expansion of bioinformatics and computational biology have made them a core topic for both disciplines. The SARS-CoV-2 pandemic has made…
COVID-19 pandemic, is still unknown and is an important open question. There are speculations that bats are a possible origin. Likewise, there are many closely related (corona-) viruses, such as SARS, which was found to be transmitted…
Scaling visual generation models is essential for real-world content creation, yet requires substantial training and computational expenses. Alternatively, test-time scaling has garnered growing attention due to resource efficiency and…
Scalable Vector Graphics (SVG) is a code-based representation for 2D visuals. Leveraging recent advances in large language models (LLMs), we study text-to-SVG generation and address two persistent gaps: weak generalization and poor…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome -- millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of…
With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover low-frequency variants in the genome. However, due to the errors in…
In light of the continuing emergence of new SARS-CoV-2 variants and vaccines, we create a simulation framework for exploring possible infection trajectories under various scenarios. The situations of primary interest involve the interaction…
Surges that have been observed at different periods in the number of COVID-19 cases are associated with the emergence of multiple SARS-CoV-2 (Severe Acute Respiratory Virus) variants. The design of methods to support laboratory detection…
During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to…
In industrial settings, weakly supervised (WS) methods are usually preferred over their fully supervised (FS) counterparts as they do not require costly manual annotations. Unfortunately, the segmentation masks obtained in the WS regime are…