Sequence clustering
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Part 1 of ebook "Software engineering, artificial intelligence, networking and parallel/distributed computing 2011" includes the following main contents: analysis of ISSP environment II survey data using variable clustering; polar transformation system for offline handwritten character recognition; examining QoS guarantees for real-time CBR services in broadband wireless access networks; sin and sigmoid higher order neural networks for data simulations and predictions; a proposal of mouth shapes sequence code for Japanese pronunciation;...
90p khuynhlinhnguyet1009 05-04-2024 3 1 Download
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Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells.
16p vibransone 28-03-2024 2 1 Download
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Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer.
16p vicwell 29-02-2024 5 1 Download
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Ebook "Pattern recognition in bioinformatics: 5th IAPR international conference, PRIB 2010 Nijmegen, The Netherlands, September 22-24, 2010 proceedings" has two main objectives: the creation and maintenance of biological databases and the analysis of life sciences data in order to unravel the mysteries of biological function. Computer science methods such as pattern recognition, machine learning, and data mining have a great deal to offer the field of bioinformatics.
458p tachieuhoa 28-01-2024 4 2 Download
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The aim of the present study was to determine a common exonic signature to discriminate between different clinical pictures, such as non-metastatic, metastatic and non-disease (healthy), using a sustainable and novel technology in liquid biopsy.
14p vileonardodavinci 23-12-2023 4 2 Download
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Accurate imputation plays a major role in genomic studies of livestock industries, where the number of genotyped or sequenced animals is limited by costs. This study explored methods to create an ideal reference population for imputation to Next Generation Sequencing data in cattle.
12p vinarcissa 21-03-2023 4 1 Download
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Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (~70%) repetitive-sequence content was identified in the chicken genome but without indicating its genomic position.
8p vinarcissa 21-03-2023 3 1 Download
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The existence of protospacer adjacent motifs (PAMs) sequences in bacteriophage genome is critical for the recognition and function of the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) machinery system. We further elucidate the significance of PAMs and their function, particularly as a part of transcriptional regulatory regions in T4 bacteriophages.
10p vihagrid 30-01-2023 10 3 Download
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Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease defined using a number of wellestablished molecular subsets. Application of non-negative matrix factorization (NMF) to whole exome sequence data has previously been used to identify six distinct molecular clusters in DLBCL with potential clinical relevance.
10p viangelamerkel 27-07-2022 4 1 Download
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Dimensionality reduction is an indispensable analytic component for many areas of single-cell RNA sequencing (scRNA-seq) data analysis. Proper dimensionality reduction can allow for effective noise removal and facilitate many downstream analyses that include cell clustering and lineage reconstruction.
21p vielonmusk 30-01-2022 9 1 Download
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Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogenetics, and multilocus sequencing typing, have not been quantified.
6p vielonmusk 30-01-2022 45 0 Download
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Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. We apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the same RNA sites.
16p vialfrednobel 29-01-2022 15 0 Download
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The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification of their biological functions. Sparse sequence conservation in non-coding sequences and the unreliable nature of RNA structure predictions further exacerbate this conundrum.
12p vialfrednobel 29-01-2022 5 0 Download
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The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants.
20p vialfrednobel 29-01-2022 9 0 Download
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Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases.
4p vialfrednobel 29-01-2022 6 0 Download
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Single-guide RNA (sgRNA) is one of the two key components of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 genome-editing system. The current commonly used sgRNA structure has a shortened duplex compared with the native bacterial CRISPR RNA (crRNA)–transactivating crRNA (tracrRNA) duplex and contains a continuous sequence of thymines, which is the pause signal for RNA polymerase III and thus could potentially reduce transcription efficiency.
10p viaristotle 29-01-2022 12 0 Download
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Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
14p viaristotle 29-01-2022 7 0 Download
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Single-cell RNA sequencing (scRNA-seq) provides new opportunities to characterize cell populations, typically accomplished through some type of clustering analysis. Estimation of the optimal cluster number (K) is a crucial step but often ignored.
21p viarchimedes 26-01-2022 15 0 Download
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Many computational methods have been developed recently to analyze single-cell RNA-seq (scRNA-seq) data. Several benchmark studies have compared these methods on their ability for dimensionality reduction, clustering, or differential analysis, often relying on default parameters.
17p viarchimedes 26-01-2022 6 0 Download
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Single-cell RNA-sequencing (scRNAseq) and the set of attached analysis methods are evolving fast, with more than 560 software tools available to the community, roughly half of which are dedicated to tasks related to data processing such as clustering, ordering, dimension reduction, or normalization.
28p viarchimedes 26-01-2022 10 0 Download