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  1. Article ; Online: Benchmarking Metagenomics Tools for Taxonomic Classification.

    Ye, Simon H / Siddle, Katherine J / Park, Daniel J / Sabeti, Pardis C

    Cell

    2019  Volume 178, Issue 4, Page(s) 779–794

    Abstract: Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the ... ...

    Abstract Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
    MeSH term(s) Bacteria/classification ; Bacteria/genetics ; Benchmarking/methods ; Databases, Genetic ; Fungi/classification ; Fungi/genetics ; Metagenome/genetics ; Metagenomics/methods ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Software ; Viruses/classification ; Viruses/genetics
    Language English
    Publishing date 2019-08-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2019.07.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Benchmarking Metagenomics Tools for Taxonomic Classification

    Ye, Simon H / Siddle, Katherine J / Park, Daniel J / Sabeti, Pardis C

    Cell. 2019 Aug. 08, v. 178, no. 4

    2019  

    Abstract: Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the ... ...

    Abstract Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of these data. The fast pace of development of these tools and the complexity of metagenomic data make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
    Keywords computer software ; data collection ; metagenomics
    Language English
    Dates of publication 2019-0808
    Size p. 779-794.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2019.07.010
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Reversible, opto-mechanically induced spin-switching in a nanoribbon-spiropyran hybrid material.

    Wong, Bryan M / Ye, Simon H / O'Bryan, Greg

    Nanoscale

    2012  Volume 4, Issue 4, Page(s) 1321–1327

    Abstract: It has recently been shown that electronic transport in zigzag graphene nanoribbons becomes spin-polarized upon application of an electric field across the nanoribbon width. However, the electric fields required to experimentally induce this magnetic ... ...

    Abstract It has recently been shown that electronic transport in zigzag graphene nanoribbons becomes spin-polarized upon application of an electric field across the nanoribbon width. However, the electric fields required to experimentally induce this magnetic state are typically large and difficult to apply in practice. Here, using both first-principles density functional theory (DFT) and time-dependent DFT, we show that a new spiropyran-based, mechanochromic polymer noncovalently deposited on a nanoribbon can collectively function as a dual opto-mechanical switch for modulating its own spin-polarization. These calculations demonstrate that upon mechanical stress or photoabsorption, the spiropyran chromophore isomerizes from a closed-configuration ground-state to a zwitterionic excited-state, resulting in a large change in dipole moment that alters the electrostatic environment of the nanoribbon. We show that the electronic spin-distribution in the nanoribbon-spiropyran hybrid material can be reversibly modulated via noninvasive optical and mechanical stimuli without the need for large external electric fields. Our results suggest that the reversible spintronic properties inherent to the nanoribbon-spiropyran material allow the possibility of using this hybrid structure as a resettable, molecular-logic quantum sensor where opto-mechanical stimuli are used as inputs and the spin-polarized current induced in the nanoribbon substrate is the measured output.
    Language English
    Publishing date 2012-02-21
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2515664-0
    ISSN 2040-3372 ; 2040-3364
    ISSN (online) 2040-3372
    ISSN 2040-3364
    DOI 10.1039/c2nr11543c
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Self-assembled cyclic oligothiophene nanotubes

    Wong, Bryan M. / Ye, Simon H.

    electronic properties from a dispersion-corrected hybrid functional

    2011  

    Abstract: The band structure and size-scaling of electronic properties in self-assembled cyclic oligothiophene nanotubes are investigated using density functional theory (DFT) for the first time. In these unique tubular aggregates, the {\pi}-{\pi} stacking ... ...

    Abstract The band structure and size-scaling of electronic properties in self-assembled cyclic oligothiophene nanotubes are investigated using density functional theory (DFT) for the first time. In these unique tubular aggregates, the {\pi}-{\pi} stacking interactions between adjacent monomers provide pathways for charge transport and energy migration along the periodic one-dimensional nanostructure. In order to simultaneously describe both the {\pi}-{\pi} stacking interactions and the global electronic band structure of these nanotubes, we utilize a dispersion-corrected B3LYP-D hybrid functional in conjunction with all-electron basis sets and one-dimensional periodic boundary conditions. Based on our B3LYP-D calculations, we present simple analytical formulas for estimating the fundamental band gaps of these unique nanotubes as a function of size and diameter. Our results on these molecular nanostructures indicate that all of the oligothiophene nanotubes are direct-gap semiconductors with band gaps ranging from 0.9 eV - 3.3 eV, depending on tube diameter and oligothiophene orientation. These nanotubes have cohesive energies of up to 2.43 eV per monomer, indicating future potential use in organic electronic devices due to their tunable electronic band structure and high structural stability.

    Comment: Accepted by Physical Review B
    Keywords Condensed Matter - Mesoscale and Nanoscale Physics ; Condensed Matter - Materials Science ; Physics - Atomic and Molecular Clusters
    Subject code 541
    Publishing date 2011-08-08
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Massively multiplexed nucleic acid detection with Cas13.

    Ackerman, Cheri M / Myhrvold, Cameron / Thakku, Sri Gowtham / Freije, Catherine A / Metsky, Hayden C / Yang, David K / Ye, Simon H / Boehm, Chloe K / Kosoko-Thoroddsen, Tinna-Sólveig F / Kehe, Jared / Nguyen, Tien G / Carter, Amber / Kulesa, Anthony / Barnes, John R / Dugan, Vivien G / Hung, Deborah T / Blainey, Paul C / Sabeti, Pardis C

    Nature

    2020  Volume 582, Issue 7811, Page(s) 277–282

    Abstract: The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection ... ...

    Abstract The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples
    MeSH term(s) Animals ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; CRISPR-Associated Proteins/metabolism ; CRISPR-Cas Systems/genetics ; Drug Resistance, Viral/genetics ; Genome, Viral/genetics ; HIV/classification ; HIV/genetics ; HIV/isolation & purification ; Humans ; Influenza A virus/classification ; Influenza A virus/genetics ; Influenza A virus/isolation & purification ; Microfluidic Analytical Techniques/instrumentation ; Microfluidic Analytical Techniques/methods ; RNA, Guide, CRISPR-Cas Systems/genetics ; SARS-CoV-2 ; Sensitivity and Specificity ; Virus Diseases/diagnosis ; Virus Diseases/virology
    Chemical Substances CRISPR-Associated Proteins ; RNA, Guide, CRISPR-Cas Systems
    Keywords covid19
    Language English
    Publishing date 2020-04-29
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-020-2279-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Massively multiplexed nucleic acid detection with Cas13

    Ackerman, Cheri M / Myhrvold, Cameron / Thakku, Sri Gowtham / Freije, Catherine A / Metsky, Hayden C / Yang, David K / Ye, Simon H / Boehm, Chloe K / Kosoko-Thoroddsen, Tinna-Sólveig F / Kehe, Jared / Nguyen, Tien G / Carter, Amber / Kulesa, Anthony / Barnes, John R / Dugan, Vivien G / Hung, Deborah T / Blainey, Paul C / Sabeti, Pardis C

    Nature

    Abstract: The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection ... ...

    Abstract The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples1-3 while simultaneously testing for many pathogens4-6. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents7 self-organize in a microwell array8 to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health9-11.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #32349121
    Database COVID19

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  7. Article ; Online: Massively multiplexed nucleic acid detection using Cas13

    Ackerman, Cheri M. / Myhrvold, Cameron / Thakku, Sri Gowtham / Freije, Catherine A. / Metsky, Hayden C. / Yang, David K. / Ye, Simon H. / Boehm, Chloe K. / Kosoko-Thoroddsen, Tinna-Sólveig F. / Kehe, Jared / Nguyen, Tien G. / Carter, Amber / Kulesa, Anthony / Barnes, John R. / Dugan, Vivien G. / Hung, Deborah T. / Blainey, Paul C. / Sabeti, Pardis C.

    Nature

    2019  

    Abstract: The overwhelming majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection ... ...

    Abstract The overwhelming majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples while simultaneously testing for many pathogens. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanoliter droplets containing CRISPR-based nucleic acid detection reagents self-organize in a microwell array to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of >4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with ≥10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. CARMEN’s intrinsic multiplexing and throughput capabilities make it practical to scale, as miniaturization decreases reagent cost per test >300-fold. Scalable, highly-multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health. ©2020
    Keywords Multidisciplinary ; covid19
    Publisher Springer Science and Business Media LLC
    Publishing country us
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Zika virus evolution and spread in the Americas.

    Metsky, Hayden C / Matranga, Christian B / Wohl, Shirlee / Schaffner, Stephen F / Freije, Catherine A / Winnicki, Sarah M / West, Kendra / Qu, James / Baniecki, Mary Lynn / Gladden-Young, Adrianne / Lin, Aaron E / Tomkins-Tinch, Christopher H / Ye, Simon H / Park, Daniel J / Luo, Cynthia Y / Barnes, Kayla G / Shah, Rickey R / Chak, Bridget / Barbosa-Lima, Giselle /
    Delatorre, Edson / Vieira, Yasmine R / Paul, Lauren M / Tan, Amanda L / Barcellona, Carolyn M / Porcelli, Mario C / Vasquez, Chalmers / Cannons, Andrew C / Cone, Marshall R / Hogan, Kelly N / Kopp, Edgar W / Anzinger, Joshua J / Garcia, Kimberly F / Parham, Leda A / Ramírez, Rosa M Gélvez / Montoya, Maria C Miranda / Rojas, Diana P / Brown, Catherine M / Hennigan, Scott / Sabina, Brandon / Scotland, Sarah / Gangavarapu, Karthik / Grubaugh, Nathan D / Oliveira, Glenn / Robles-Sikisaka, Refugio / Rambaut, Andrew / Gehrke, Lee / Smole, Sandra / Halloran, M Elizabeth / Villar, Luis / Mattar, Salim / Lorenzana, Ivette / Cerbino-Neto, Jose / Valim, Clarissa / Degrave, Wim / Bozza, Patricia T / Gnirke, Andreas / Andersen, Kristian G / Isern, Sharon / Michael, Scott F / Bozza, Fernando A / Souza, Thiago M L / Bosch, Irene / Yozwiak, Nathan L / MacInnis, Bronwyn L / Sabeti, Pardis C

    Nature

    2017  Volume 546, Issue 7658, Page(s) 411–415

    Abstract: Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here ... ...

    Abstract Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.
    MeSH term(s) Animals ; Brazil/epidemiology ; Colombia/epidemiology ; Culicidae/virology ; Disease Outbreaks/statistics & numerical data ; Genome, Viral/genetics ; Geographic Mapping ; Honduras/epidemiology ; Humans ; Metagenome/genetics ; Molecular Epidemiology ; Mosquito Vectors/virology ; Mutation ; Phylogeny ; Public Health Surveillance ; Puerto Rico/epidemiology ; United States/epidemiology ; Zika Virus/classification ; Zika Virus/genetics ; Zika Virus/isolation & purification ; Zika Virus/pathogenicity ; Zika Virus Infection/diagnosis ; Zika Virus Infection/epidemiology ; Zika Virus Infection/transmission ; Zika Virus Infection/virology
    Language English
    Publishing date 2017-05-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/nature22402
    Database MEDical Literature Analysis and Retrieval System OnLINE

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