Related papers: Therapeutic Interfering Particles Exploiting Viral…
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments.…
Microbes and pathogens play a detrimental role in healing wounds, causing infections like impetigo through bodily fluids and skin and entering the bloodstream through the wounds, thereby hindering the healing process and tissue…
Small interfering RNA (siRNA) is a short double-stranded RNA molecule (about 21-23 nucleotides) with the potential to cure diseases by silencing the function of target genes. Due to its well-understood mechanism, many siRNA-based drugs have…
Segmentation of very large images is a common problem in microscopy, medical imaging or remote sensing. The problem is usually addressed by sliding window inference, which can theoretically lead to seamlessly stitched predictions. However,…
Antibodies are versatile proteins that can bind to pathogens and provide effective protection for human body. Recently, deep learning-based computational antibody design has attracted popular attention since it automatically mines the…
Human immunodeficiency virus (HIV) capsid proteins spontaneously assemble around the genome into a protective protein shell called the capsid, which can take on a variety of shapes broadly classified as conical, cylindrical and irregular.…
Protein inverse folding is a fundamental problem in bioinformatics, aiming to recover the amino acid sequences from a given protein backbone structure. Despite the success of existing methods, they struggle to fully capture the intricate…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
Cytotoxic T-lymphocytes (CTLs) recognize viral protein fragments displayed by major histocompatibility complex (MHC) molecules on the surface of virally infected cells and generate an anti-viral response that can kill the infected cells.…
Messenger RNA (mRNA) sequences as therapeutics require optimized design to ensure efficient translation, structural stability, and minimal immunogenicity. This study presents a two-stage in-silico framework that integrates deep learning and…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
Mobile genetic elements (e.g., endogenous viruses, LINEs, SINEs) can transfer between genomes, even between species, triggering dramatic genetic changes. Endogenous viral elements (EVEs) arise when infectious viruses integrate into the host…
Replicability is a lynchpin for credible discoveries. The partial conjunction (PC) p-value, which combines individual base p-values from multiple similar studies, can gauge whether a feature of interest exhibits replicated signals across…
The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that…
The integration of machine learning methods into bioinformatics provides particular benefits in identifying how therapeutics effective in one context might have utility in an unknown clinical context or against a novel pathology. We aim to…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
Bacterial resistance to antibiotic treatment is a huge concern: introduction of any new antibiotic is shortly followed by the emergence of resistant bacterial isolates in the clinic. This issue is compounded by a severe lack of new…
In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses…
Pilot contamination, caused by the reuse of pilots among interfering cells, remains as a significant obstacle that limits the performance of massive multi-input multi-output antenna systems. To handle this problem, less aggressive reuse of…
Viruses self-assemble from identical capsid proteins and their genome consisting, for example, of a long single stranded (ss) RNA. For a big class of T = 3 viruses capsid proteins have long positive N-terminal tails. We explore the role…