Search Results - "BMC genomics"

The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation by Chicco, Davide, Jurman, Giuseppe

“…To evaluate binary classifications and their confusion matrices, scientific researchers can employ several statistical rates, accordingly to the goal of the…”
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Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics by Street, Kelly, Risso, Davide, Fletcher, Russell B, Das, Diya, Ngai, John, Yosef, Nir, Purdom, Elizabeth, Dudoit, Sandrine

“…Single-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants…”
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Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress by Xie, Tao, Chen, Chengjie, Li, Chuhao, Liu, Jiarou, Liu, Chaoyang, He, Yehua

“…WRKY proteins comprise a large family of transcription factors that play important roles in many aspects of physiological processes and adaption to…”
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Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential by Pal, Chandan, Bengtsson-Palme, Johan, Kristiansson, Erik, Larsson, D G Joakim

“…Antibacterial biocides and metals can co-select for antibiotic resistance when bacteria harbour resistance or tolerance genes towards both types of compounds…”
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Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array by Mansell, Georgina, Gorrie-Stone, Tyler J, Bao, Yanchun, Kumari, Meena, Schalkwyk, Leonard S, Mill, Jonathan, Hannon, Eilis

“…There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the…”
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How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species by Meyermans, R, Gorssen, W, Buys, N, Janssens, S

“…PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade,…”
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A review of deep learning applications for genomic selection by Montesinos-López, Osval Antonio, Montesinos-López, Abelardo, Pérez-Rodríguez, Paulino, Barrón-López, José Alberto, Martini, Johannes W R, Fajardo-Flores, Silvia Berenice, Gaytan-Lugo, Laura S, Santana-Mancilla, Pedro C, Crossa, José

“…Several conventional genomic Bayesian (or no Bayesian) prediction methods have been proposed including the standard additive genetic effect model for which the…”
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The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity by Verde, Ignazio, Jenkins, Jerry, Dondini, Luca, Micali, Sabrina, Pagliarani, Giulia, Vendramin, Elisa, Paris, Roberta, Aramini, Valeria, Gazza, Laura, Rossini, Laura, Bassi, Daniele, Troggio, Michela, Shu, Shengqiang, Grimwood, Jane, Tartarini, Stefano, Dettori, Maria Teresa, Schmutz, Jeremy

“…The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes…”
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Evolution and comparative genomics of the most common Trichoderma species by Kubicek, Christian P, Steindorff, Andrei S, Chenthamara, Komal, Manganiello, Gelsomina, Henrissat, Bernard, Zhang, Jian, Cai, Feng, Kopchinskiy, Alexey G, Kubicek, Eva M, Kuo, Alan, Baroncelli, Riccardo, Sarrocco, Sabrina, Noronha, Eliane Ferreira, Vannacci, Giovanni, Shen, Qirong, Grigoriev, Igor V, Druzhinina, Irina S

“…The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many…”
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A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency by Edwards, K D, Fernandez-Pozo, N, Drake-Stowe, K, Humphry, M, Evans, A D, Bombarely, A, Allen, F, Hurst, R, White, B, Kernodle, S P, Bromley, J R, Sanchez-Tamburrino, J P, Lewis, R S, Mueller, L A

“…Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco…”
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Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks by Pan, Xiaoyong, Rijnbeek, Peter, Yan, Junchi, Shen, Hong-Bin

“…RNA regulation is significantly dependent on its binding protein partner, known as the RNA-binding proteins (RBPs). Unfortunately, the binding preferences for…”
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SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare? by Balvočiūtė, Monika, Huson, Daniel H

“…A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely…”
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A new approach for efficient genotype imputation using information from relatives by Sargolzaei, Mehdi, Chesnais, Jacques P, Schenkel, Flavio S

“…Genotype imputation can help reduce genotyping costs particularly for implementation of genomic selection. In applications entailing large populations,…”
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Seamless integration of image and molecular analysis for spatial transcriptomics workflows by Bergenstråhle, Joseph, Larsson, Ludvig, Lundeberg, Joakim

“…Recent advancements in in situ gene expression technologies constitute a new and rapidly evolving field of transcriptomics. With the recent launch of the 10x…”
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ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases by Shen, Li, Shao, Ningyi, Liu, Xiaochuan, Nestler, Eric

“…Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest…”
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SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events by Bergstrom, Erik N, Huang, Mi Ni, Mahto, Uma, Barnes, Mark, Stratton, Michael R, Rozen, Steven G, Alexandrov, Ludmil B

“…Cancer genomes are peppered with somatic mutations imprinted by different mutational processes. The mutational pattern of a cancer genome can be used to…”
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Better prediction of functional effects for sequence variants by Hecht, Maximilian, Bromberg, Yana, Rost, Burkhard

“…Elucidating the effects of naturally occurring genetic variation is one of the major challenges for personalized health and personalized medicine. Here, we…”
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CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers by Ounit, Rachid, Wanamaker, Steve, Close, Timothy J, Lonardi, Stefano

“…The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively…”
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TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees by Mai, Uyen, Mirarab, Siavash

“…Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when…”
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HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly by Sim, Sheina B, Corpuz, Renee L, Simmonds, Tyler J, Geib, Scott M

“…Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large…”
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