The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

David C Page - One of the best experts on this subject based on the ideXlab platform.

  • Shims 3 0 highly efficient single haplotype iterative mapping and sequencing using ultra long nanopore reads
    bioRxiv, 2020
    Co-Authors: Daniel W Bellott, Tingjan Cho, Jennifer F Hughes, Helen Skaletsky, David C Page, Emily K Jackson
    Abstract:

    The reference sequence of structurally complex regions can only be obtained through a highly accurate clone-based approach that we call Single-Haplotype Iterative Mapping and Sequencing (Shims). In recent years, improvements to Shims have reduced the cost and time required by two orders of magnitude, but internally repetitive clones still require extensive manual effort to transform draft assemblies into reference-quality finished sequences. Here we introduce Shims 3.0, using ultra-long nanopore reads to resolve internally repetitive structures and minimize the need for manual finishing of Illumina-based draft assemblies. This protocol proceeds from clone-picking to finished assemblies in 2 weeks for about 80 dollars per clone. We have used Shims 3.0 to finish the structurally complex TSPY array on the human Y chromosome, which could not be resolved by previous sequencing methods. Our protocol provides access to structurally complex regions that would otherwise be inaccessible from whole-genome shotgun data or require an impractical amount of manual effort to generate an accurate assembly.

  • cost effective high throughput single haplotype iterative mapping and sequencing for complex genomic structures
    Nature Protocols, 2018
    Co-Authors: Daniel W Bellott, Tingjan Cho, Jennifer F Hughes, Helen Skaletsky, David C Page
    Abstract:

    This protocol describes Shims 2.0, a method to generate accurate reference sequences from structurally complex genomic regions in a cost-effective, high-throughput manner. The reference sequences of structurally complex regions can be obtained only through highly accurate clone-based approaches. We and others have successfully used single-haplotype iterative mapping and sequencing (Shims) 1.0 to assemble structurally complex regions across the sex chromosomes of several vertebrate species and to allow for targeted improvements to the reference sequences of human autosomes. However, Shims 1.0 is expensive and time consuming, requiring resources that only a genome center can provide. Here we introduce Shims 2.0, an improved Shims protocol that allows even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library-preparation protocol, and taking advantage of inexpensive high-throughput short-read-sequencing technologies, a small laboratory with both molecular biology and bioinformatics experience can sequence and assemble 192 large-insert bacterial artificial chromosome (BAC) or fosmid clones in 1 week. In Shims 2.0, in contrast to other pooling strategies, each clone is sequenced with a unique barcode, thus enabling clones containing nearly identical sequences to be multiplexed in a single sequencing run and assembled separately. Relative to Shims 1.0, Shims 2.0 decreases the required cost and time by two orders of magnitude while preserving high sequencing accuracy.

  • cost effective high throughput single haplotype iterative mapping and sequencing for complex genomic structures
    bioRxiv, 2017
    Co-Authors: Daniel W Bellott, Tingjan Cho, Jennifer F Hughes, Helen Skaletsky, David C Page
    Abstract:

    Reference sequence of structurally complex regions can only be obtained through highly accurate clone-based approaches. We and others have successfully employed Single-Haplotype Iterative Mapping and Sequencing (Shims 1.0) to assemble structurally complex regions across the sex chromosomes of several vertebrate species and in targeted improvements to the reference sequences of human autosomes. However, Shims 1.0 was expensive and time consuming, requiring the resources that only a genome center could command. Here we introduce Shims 2.0, an improved Shims protocol to allow even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library preparation protocol, and taking advantage of high-throughput, inexpensive, short-read sequencing technologies, a small group can sequence and assemble hundreds of clones in a week. Relative to Shims 1.0, Shims 2.0 reduces the cost and time required by two orders of magnitude, while preserving high sequencing accuracy.

Qi Zhen Chen - One of the best experts on this subject based on the ideXlab platform.

  • surface analysis using shell isolated nanoparticle enhanced raman spectroscopy
    Nature Protocols, 2013
    Co-Authors: Jianfeng Li, Xiangdong Tian, Song Bo Li, Jason R Anema, Zhilin Yang, Yong Ding, Yuan Fei Wu, Yong Ming Zeng, Qi Zhen Chen
    Abstract:

    Surface-enhanced Raman scattering (SERS) is a powerful fingerprint vibrational spectroscopy with a single-molecule detection limit, but its applications are generally restricted to 'free-electron–like' metal substrates such as Au, Ag and Cu nanostructures. We have invented a shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) technique, using Au-core silica-shell nanoparticles (Au@SiO2 NPs), which makes SERS universally applicable to surfaces with any composition and any morphology. This protocol describes how to prepare shell-isolated nanoparticles (SHINs) with different well-controlled core sizes (55 and 120 nm), shapes (nanospheres, nanorods and nanocubes) and shell thicknesses (1–20 nm). It then describes how to apply SHINs to Pt and Au single-crystal surfaces with different facets in an electrochemical environment, on Si wafer surfaces adsorbed with hydrogen, on ZnO nanorods, and on living bacteria and fruit. With this method, SHINs can be prepared for use in ∼3 h, and each subsequent procedure for SHINERS measurement requires 1–2 h.

Jason R Anema - One of the best experts on this subject based on the ideXlab platform.

  • surface analysis using shell isolated nanoparticle enhanced raman spectroscopy
    Nature Protocols, 2013
    Co-Authors: Jianfeng Li, Xiangdong Tian, Song Bo Li, Jason R Anema, Zhilin Yang, Yong Ding, Yuan Fei Wu, Yong Ming Zeng, Qi Zhen Chen
    Abstract:

    Surface-enhanced Raman scattering (SERS) is a powerful fingerprint vibrational spectroscopy with a single-molecule detection limit, but its applications are generally restricted to 'free-electron–like' metal substrates such as Au, Ag and Cu nanostructures. We have invented a shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) technique, using Au-core silica-shell nanoparticles (Au@SiO2 NPs), which makes SERS universally applicable to surfaces with any composition and any morphology. This protocol describes how to prepare shell-isolated nanoparticles (SHINs) with different well-controlled core sizes (55 and 120 nm), shapes (nanospheres, nanorods and nanocubes) and shell thicknesses (1–20 nm). It then describes how to apply SHINs to Pt and Au single-crystal surfaces with different facets in an electrochemical environment, on Si wafer surfaces adsorbed with hydrogen, on ZnO nanorods, and on living bacteria and fruit. With this method, SHINs can be prepared for use in ∼3 h, and each subsequent procedure for SHINERS measurement requires 1–2 h.

Helen Skaletsky - One of the best experts on this subject based on the ideXlab platform.

  • Shims 3 0 highly efficient single haplotype iterative mapping and sequencing using ultra long nanopore reads
    bioRxiv, 2020
    Co-Authors: Daniel W Bellott, Tingjan Cho, Jennifer F Hughes, Helen Skaletsky, David C Page, Emily K Jackson
    Abstract:

    The reference sequence of structurally complex regions can only be obtained through a highly accurate clone-based approach that we call Single-Haplotype Iterative Mapping and Sequencing (Shims). In recent years, improvements to Shims have reduced the cost and time required by two orders of magnitude, but internally repetitive clones still require extensive manual effort to transform draft assemblies into reference-quality finished sequences. Here we introduce Shims 3.0, using ultra-long nanopore reads to resolve internally repetitive structures and minimize the need for manual finishing of Illumina-based draft assemblies. This protocol proceeds from clone-picking to finished assemblies in 2 weeks for about 80 dollars per clone. We have used Shims 3.0 to finish the structurally complex TSPY array on the human Y chromosome, which could not be resolved by previous sequencing methods. Our protocol provides access to structurally complex regions that would otherwise be inaccessible from whole-genome shotgun data or require an impractical amount of manual effort to generate an accurate assembly.

  • cost effective high throughput single haplotype iterative mapping and sequencing for complex genomic structures
    Nature Protocols, 2018
    Co-Authors: Daniel W Bellott, Tingjan Cho, Jennifer F Hughes, Helen Skaletsky, David C Page
    Abstract:

    This protocol describes Shims 2.0, a method to generate accurate reference sequences from structurally complex genomic regions in a cost-effective, high-throughput manner. The reference sequences of structurally complex regions can be obtained only through highly accurate clone-based approaches. We and others have successfully used single-haplotype iterative mapping and sequencing (Shims) 1.0 to assemble structurally complex regions across the sex chromosomes of several vertebrate species and to allow for targeted improvements to the reference sequences of human autosomes. However, Shims 1.0 is expensive and time consuming, requiring resources that only a genome center can provide. Here we introduce Shims 2.0, an improved Shims protocol that allows even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library-preparation protocol, and taking advantage of inexpensive high-throughput short-read-sequencing technologies, a small laboratory with both molecular biology and bioinformatics experience can sequence and assemble 192 large-insert bacterial artificial chromosome (BAC) or fosmid clones in 1 week. In Shims 2.0, in contrast to other pooling strategies, each clone is sequenced with a unique barcode, thus enabling clones containing nearly identical sequences to be multiplexed in a single sequencing run and assembled separately. Relative to Shims 1.0, Shims 2.0 decreases the required cost and time by two orders of magnitude while preserving high sequencing accuracy.

  • cost effective high throughput single haplotype iterative mapping and sequencing for complex genomic structures
    bioRxiv, 2017
    Co-Authors: Daniel W Bellott, Tingjan Cho, Jennifer F Hughes, Helen Skaletsky, David C Page
    Abstract:

    Reference sequence of structurally complex regions can only be obtained through highly accurate clone-based approaches. We and others have successfully employed Single-Haplotype Iterative Mapping and Sequencing (Shims 1.0) to assemble structurally complex regions across the sex chromosomes of several vertebrate species and in targeted improvements to the reference sequences of human autosomes. However, Shims 1.0 was expensive and time consuming, requiring the resources that only a genome center could command. Here we introduce Shims 2.0, an improved Shims protocol to allow even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library preparation protocol, and taking advantage of high-throughput, inexpensive, short-read sequencing technologies, a small group can sequence and assemble hundreds of clones in a week. Relative to Shims 1.0, Shims 2.0 reduces the cost and time required by two orders of magnitude, while preserving high sequencing accuracy.

Marco Pritoni - One of the best experts on this subject based on the ideXlab platform.

  • Of impacts, agents, and functions: An interdisciplinary meta-review of smart home energy management systems research
    Energy Research & Social Science, 2020
    Co-Authors: Claire Mcilvennie, Angela Sanguinetti, Marco Pritoni
    Abstract:

    Abstract Smart home energy management technologies (SHEMS) have long been viewed as a promising opportunity to manage the way households use energy. Research on this topic has emerged across a variety of disciplines, focusing on different pieces of the SHEMS puzzle without offering a holistic vision of how these technologies and their users will influence home energy use moving forward. This paper presents the results of a systematic, interdisciplinary meta-review of SHEMS literature, assessing the extent to which it discusses the role of various SHEMS components in driving energy benefits. Results reveal a bias towards technical perspectives and controls approaches that seek to drive energy impacts such as load management and energy savings through SHEMS without user or third-party participation. Not only are techno-centric approaches more common, there is also a lack of integration of these approaches with user-centric, information-based solutions for driving energy impacts. These results suggest future work should investigate more holistic solutions for optimal impacts on household energy use. We hope these results will provoke a broader discussion about how to advance research on SHEMS to capitalize on their potential contributions to demand-side management initiatives moving forward.