Results 1 to 10 of about 1,172,908 (168)
Strainberry: automated strain separation in low-complexity metagenomes using long reads
Nature Communications, 2021 Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and ...
Riccardo Vicedomini +3 more
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decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
Microbiome, 2023 Background The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources.
Camila Duitama González +5 more
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Mapping-friendly sequence reductions: Going beyond homopolymer compression
iScience, 2022 Summary: Sequencing errors continue to pose algorithmic challenges to methods working with sequencing data. One of the simplest and most prevalent techniques for ameliorating the detrimental effects of homopolymer expansion/contraction errors present in ...
Luc Blassel, Paul Medvedev, Rayan Chikhi
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SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction [PDF]
PeerJ, 2023 Biological sequence data mining is hot spot in bioinformatics. A biological sequence can be regarded as a set of characters. Time series is similar to biological sequences in terms of both representation and mechanism.
Wu Yan +5 more
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HostPhinder: A Phage Host Prediction Tool
Viruses, 2016 The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput ...
Julia Villarroel +6 more
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RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery
iScience, 2021 Summary: Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using
Nitesh Kumar Sharma +5 more
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Localization of T cell clonotypes using the Visium spatial transcriptomics platform
STAR Protocols, 2022 Summary: We present a protocol to localize T cell receptor clones using the Visium spatial transcriptomics platform. This approach permits simultaneous localization of both gene expression and T cell clonotypes in situ within tissue sections.
William H. Hudson, Lisa J. Sudmeier
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What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?
Viruses, 2015 Phage therapy, a practice widespread in Eastern Europe, has untapped potential in the combat against antibiotic-resistant bacterial infections. However, technology transfer to Western medicine is proving challenging. Bioinformatics analysis could help to
Henrike Zschach +11 more
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iScience, 2021 Summary: Large-scale mapping of antigens and epitopes is pivotal for developing immunotherapies but challenging, especially for eukaryotic pathogens, owing to their large genomes. Here, we developed an integrated platform for genome phage display (gPhage)
André Azevedo Reis Teixeira +16 more
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Rapid Nickel-based Isolation of Extracellular Vesicles from Different Biological Fluids
Bio-Protocol, 2020 Extracellular vesicles (EVs) are membranous structures that cells massively release in extracellular fluids. EVs are cargo of cellular components such as lipids, proteins, and nucleic acids that can work as a formidable source in liquid biopsy studies ...
Michela Notarangelo +8 more
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