Results 1 to 10 of about 6,382,567 (173)
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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Mega-scale experimental analysis of protein folding stability in biology and design
Nature, 2023 Large-scale assays using cDNA display proteolysis are used to measure the folding stabilities of protein domains, providing a method to quantify the effects of mutations on protein folding, with applications in protein design.
Kotaro Tsuboyama +8 more
semanticscholar +1 more source
Encyclopedia of Bioinformatics and Computational Biology, 2020 This chapter explores sequence analysis (SA), which conceives the social world as happening in processes, in series of events experienced by social entities. SA refers to a set of tools used to summarize, represent, and compare sequences — i.e.
Andrey D. Prjibelski +2 more
semanticscholar +1 more source
Predicting multiple conformations via sequence clustering and AlphaFold2
Nature, 2023 AlphaFold2 (ref. 1) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein’s biological function often depends on multiple conformational substates2, and disease-causing point mutations often ...
Hannah K. Wayment-Steele +8 more
semanticscholar +1 more source
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
doaj +2 more sources
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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The EM Algorithm and the Rise of Computational Biology [PDF]
, 2010 In the past decade computational biology has grown from a cottage industry with a handful of researchers to an attractive interdisciplinary field, catching the attention and imagination of many quantitatively-minded scientists.
Citable Link +3 more
core +3 more sources