New era of artificial intelligence and machine learning-based detection, diagnosis, and therapeutics in Parkinson's disease

R Gupta, S Kumari, A Senapati, RK Ambasta… - Ageing research …, 2023 - Elsevier
Parkinson's disease (PD) is characterized by the loss of neuronal cells, which leads to
synaptic dysfunction and cognitive defects. Despite the advancements in treatment …

[HTML][HTML] Enhancing phage therapy through synthetic biology and genome engineering

BR Lenneman, J Fernbach, MJ Loessner, TK Lu… - Current Opinion in …, 2021 - Elsevier
Highlights•Synthetic biology enables efficient phage genome engineering.•Phages with
tunable host range and antimicrobial payload delivery enhance efficacy.•Phage design …

[HTML][HTML] Identification of mobile genetic elements with geNomad

AP Camargo, S Roux, F Schulz, M Babinski, Y Xu… - Nature …, 2023 - nature.com
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …

[HTML][HTML] Thousands of previously unknown phages discovered in whole-community human gut metagenomes

S Benler, N Yutin, D Antipov, M Rayko, S Shmakov… - Microbiome, 2021 - Springer
Background Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in
structuring human gut microbiomes; yet, the gut virome is far from being fully characterized …

[HTML][HTML] Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort

S Nishijima, N Nagata, Y Kiguchi, Y Kojima… - Nature …, 2022 - nature.com
Indigenous bacteriophage communities (virome) in the human gut have a huge impact on
the structure and function of gut bacterial communities (bacteriome), but virome variation at a …

[HTML][HTML] Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework

Y Zhu, J Shang, C Peng, Y Sun - Frontiers in microbiology, 2022 - frontiersin.org
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse
entities in the biosphere. There is accumulating evidence revealing their important roles in …

[HTML][HTML] Genome binning of viral entities from bulk metagenomics data

J Johansen, DR Plichta, JN Nissen… - Nature …, 2022 - nature.com
Despite the accelerating number of uncultivated virus sequences discovered in
metagenomics and their apparent importance for health and disease, the human gut virome …

[HTML][HTML] Incorporating machine learning into established bioinformatics frameworks

N Auslander, AB Gussow, EV Koonin - International journal of molecular …, 2021 - mdpi.com
The exponential growth of biomedical data in recent years has urged the application of
numerous machine learning techniques to address emerging problems in biology and …

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

AL Borges, YC Lou, R Sachdeva, B Al-Shayeb… - Nature …, 2022 - nature.com
Bacteriophages (phages) are obligate parasites that use host bacterial translation
machinery to produce viral proteins. However, some phages have alternative genetic codes …

[HTML][HTML] Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

D Boeckaerts, M Stock, B Criel, H Gerstmans… - Scientific reports, 2021 - nature.com
Nowadays, bacteriophages are increasingly considered as an alternative treatment for a
variety of bacterial infections in cases where classical antibiotics have become ineffective …