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- Olson, Nathan D., et al.
(författare)
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precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
- 2020
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 2. |
- Olson, Nathan D., et al.
(författare)
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PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
- 2022
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Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 2:5, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
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| 6. |
- Barman, Snigdha Roy, et al.
(författare)
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Dendrimer as a multifunctional capping agent for metal nanoparticles for use in bioimaging, drug delivery and sensor applications
- 2018
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Ingår i: Journal of materials chemistry. B. - : ROYAL SOC CHEMISTRY. - 2050-750X .- 2050-7518. ; 6:16, s. 2368-2384
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Forskningsöversikt (refereegranskat)abstract
- Advances in nanoparticle research, particularly in the domain of surface-engineered, function-oriented nanoparticles, have had a profound effect in many areas of scientific research and aided in bringing unprecedented developments forward, particularly in the biomedical field. Surface modifiers/capping agents have a direct bearing on the major properties of metal nanoparticles (MNPs), ranging from their physico-chemical properties to their stability and functional applications. Among the different classes of capping agents, dendrimers have gained traction as effective multifunctional capping agents for MNPs due to their unique structural qualities, dendritic effect and polydentate nature. Dendrimer-coated metal nanoparticles (DC-MNPs) are typically produced by both (i) a one-pot strategy, where metal ions are reduced in the presence of dendrimer molecules and (ii) a multi-pot strategy, where a sequence of reactions involving the reduction of metal ions, activation, conjugation and purification steps are involved. These DC-MNPs have shown remarkable ability to stabilize MNPs by means of electrostatic interactions, coordination chemistry or covalent attachment, due to them entailing a large number of sites at which further molecular moieties can be conjugated. This review article is an attempt to consolidate the on-going work, particularly over the last five years, in the field of the synthesis of dendrimer-coated MNPs and their potential applications in bioimaging, drug delivery and biochemical sensors.
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