The Experts below are selected from a list of 3411 Experts worldwide ranked by ideXlab platform

Thomas A. Courtade - One of the best experts on this subject based on the ideXlab platform.

  • Partial DNA Assembly: A rate-distortion perspective
    2016 IEEE International Symposium on Information Theory (ISIT), 2016
    Co-Authors: Ilan Shomorony, Govinda M. Kamath, Thomas A. Courtade
    Abstract:

    Earlier formulations of the DNA Assembly problem were all in the context of perfect Assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very often the case that the read data is not sufficiently rich to permit unambiguous reconstruction of the original sequence. While a natural generalization of the perfect Assembly formulation to these cases would be to consider a rate-distortion framework, partial assemblies are usually represented in terms of an Assembly graph, making the definition of a distortion measure challenging. In this work, we introduce a distortion function for Assembly graphs that can be understood as the logarithm of the number of Eulerian cycles in the Assembly graph, each of which correspond to a candidate Assembly that could have generated the observed reads. We also introduce an algorithm for the construction of an Assembly graph and analyze its performance on real genomes.

  • ISIT - Partial DNA Assembly: A rate-distortion perspective
    2016 IEEE International Symposium on Information Theory (ISIT), 2016
    Co-Authors: Ilan Shomorony, Govinda M. Kamath, Thomas A. Courtade
    Abstract:

    Earlier formulations of the DNA Assembly problem were all in the context of perfect Assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very often the case that the read data is not sufficiently rich to permit unambiguous reconstruction of the original sequence. While a natural generalization of the perfect Assembly formulation to these cases would be to consider a rate-distortion framework, partial assemblies are usually represented in terms of an Assembly graph, making the definition of a distortion measure challenging. In this work, we introduce a distortion function for Assembly graphs that can be understood as the logarithm of the number of Eulerian cycles in the Assembly graph, each of which correspond to a candidate Assembly that could have generated the observed reads. We also introduce an algorithm for the construction of an Assembly graph and analyze its performance on real genomes.

Jed Dean - One of the best experts on this subject based on the ideXlab platform.

  • rapid and reliable DNA Assembly via ligase cycling reaction
    ACS Synthetic Biology, 2014
    Co-Authors: Leslie H. Stanton, Todd Slaby, Darren Platt, Elaine B. Shapland, Zach Serber, Jed Dean, Maxime Durot, Kedar G Patel, Victor Holmes, Jack D Newman
    Abstract:

    Assembly of DNA parts into DNA constructs is a foundational technology in the emerging field of synthetic biology. An efficient DNA Assembly method is particularly important for high-throughput, automated DNA Assembly in biofabrication facilities and therefore we investigated one-step, scarless DNA Assembly via ligase cycling reaction (LCR). LCR Assembly uses single-stranded bridging oligos complementary to the ends of neighboring DNA parts, a thermostable ligase to join DNA backbones, and multiple denaturation–annealing–ligation temperature cycles to assemble complex DNA constructs. The efficiency of LCR Assembly was improved ca. 4-fold using designed optimization experiments and response surface methodology. Under these optimized conditions, LCR enabled one-step Assembly of up to 20 DNA parts and up to 20 kb DNA constructs with very few single-nucleotide polymorphisms (<1 per 25 kb) and insertions/deletions (<1 per 50 kb). Experimental comparison of various sequence-independent DNA Assembly methods show...

  • Rapid and reliable DNA Assembly via ligase cycling reaction
    ACS Synthetic Biology, 2014
    Co-Authors: Stefan De Kok, Leslie H. Stanton, Todd Slaby, Victor F. Holmes, Darren Platt, Elaine B. Shapland, Zach Serber, Maxime Durot, Kedar G Patel, Jed Dean
    Abstract:

    Assembly of DNA parts into DNA constructs is a foundational technology in the emerging field of synthetic biology. An efficient DNA Assembly method is particularly important for high-throughput, automated DNA Assembly in biofabrication facilities and therefore we investigated one-step, scarless DNA Assembly via ligase cycling reaction (LCR). LCR Assembly uses single-stranded bridging oligos complementary to the ends of neighboring DNA parts, a thermostable ligase to join DNA backbones, and multiple denaturation-annealing-ligation temperature cycles to assemble complex DNA constructs. The efficiency of LCR Assembly was improved ca. 4-fold using designed optimization experiments and response surface methodology. Under these optimized conditions, LCR enabled one-step Assembly of up to 20 DNA parts and up to 20 kb DNA constructs with very few single-nucleotide polymorphisms (

  • High-throughput, cost-effective verification of structural DNA Assembly
    Nucleic Acids Research, 2013
    Co-Authors: Yandi Dharmadi, Todd Slaby, Elaine B. Shapland, Jed Dean, Kedar G Patel, Daniel Hollis, Nicole Klinkner, Sunil S. Chandran
    Abstract:

    : DNA 'Assembly' from 'building blocks' remains a cornerstone in synthetic biology, whether it be for gene synthesis (∼ 1 kb), pathway engineering (∼ 10 kb) or synthetic genomes (>100 kb). Despite numerous advances in the techniques used for DNA Assembly, verification of the Assembly is still a necessity, which becomes cost-prohibitive and a logistical challenge with increasing scale. Here we describe for the first time a comprehensive, high-throughput solution for structural DNA Assembly verification by restriction digest using exhaustive in silico enzyme screening, rolling circle amplification of plasmid DNA, capillary electrophoresis and automated digest pattern recognition. This low-cost and robust methodology has been successfully used to screen over 31 000 clones of DNA constructs at

Ilan Shomorony - One of the best experts on this subject based on the ideXlab platform.

  • Partial DNA Assembly: A rate-distortion perspective
    2016 IEEE International Symposium on Information Theory (ISIT), 2016
    Co-Authors: Ilan Shomorony, Govinda M. Kamath, Thomas A. Courtade
    Abstract:

    Earlier formulations of the DNA Assembly problem were all in the context of perfect Assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very often the case that the read data is not sufficiently rich to permit unambiguous reconstruction of the original sequence. While a natural generalization of the perfect Assembly formulation to these cases would be to consider a rate-distortion framework, partial assemblies are usually represented in terms of an Assembly graph, making the definition of a distortion measure challenging. In this work, we introduce a distortion function for Assembly graphs that can be understood as the logarithm of the number of Eulerian cycles in the Assembly graph, each of which correspond to a candidate Assembly that could have generated the observed reads. We also introduce an algorithm for the construction of an Assembly graph and analyze its performance on real genomes.

  • ISIT - Partial DNA Assembly: A rate-distortion perspective
    2016 IEEE International Symposium on Information Theory (ISIT), 2016
    Co-Authors: Ilan Shomorony, Govinda M. Kamath, Thomas A. Courtade
    Abstract:

    Earlier formulations of the DNA Assembly problem were all in the context of perfect Assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is very often the case that the read data is not sufficiently rich to permit unambiguous reconstruction of the original sequence. While a natural generalization of the perfect Assembly formulation to these cases would be to consider a rate-distortion framework, partial assemblies are usually represented in terms of an Assembly graph, making the definition of a distortion measure challenging. In this work, we introduce a distortion function for Assembly graphs that can be understood as the logarithm of the number of Eulerian cycles in the Assembly graph, each of which correspond to a candidate Assembly that could have generated the observed reads. We also introduce an algorithm for the construction of an Assembly graph and analyze its performance on real genomes.

Leslie H. Stanton - One of the best experts on this subject based on the ideXlab platform.

  • rapid and reliable DNA Assembly via ligase cycling reaction
    ACS Synthetic Biology, 2014
    Co-Authors: Leslie H. Stanton, Todd Slaby, Darren Platt, Elaine B. Shapland, Zach Serber, Jed Dean, Maxime Durot, Kedar G Patel, Victor Holmes, Jack D Newman
    Abstract:

    Assembly of DNA parts into DNA constructs is a foundational technology in the emerging field of synthetic biology. An efficient DNA Assembly method is particularly important for high-throughput, automated DNA Assembly in biofabrication facilities and therefore we investigated one-step, scarless DNA Assembly via ligase cycling reaction (LCR). LCR Assembly uses single-stranded bridging oligos complementary to the ends of neighboring DNA parts, a thermostable ligase to join DNA backbones, and multiple denaturation–annealing–ligation temperature cycles to assemble complex DNA constructs. The efficiency of LCR Assembly was improved ca. 4-fold using designed optimization experiments and response surface methodology. Under these optimized conditions, LCR enabled one-step Assembly of up to 20 DNA parts and up to 20 kb DNA constructs with very few single-nucleotide polymorphisms (<1 per 25 kb) and insertions/deletions (<1 per 50 kb). Experimental comparison of various sequence-independent DNA Assembly methods show...

  • Rapid and reliable DNA Assembly via ligase cycling reaction
    ACS Synthetic Biology, 2014
    Co-Authors: Stefan De Kok, Leslie H. Stanton, Todd Slaby, Victor F. Holmes, Darren Platt, Elaine B. Shapland, Zach Serber, Maxime Durot, Kedar G Patel, Jed Dean
    Abstract:

    Assembly of DNA parts into DNA constructs is a foundational technology in the emerging field of synthetic biology. An efficient DNA Assembly method is particularly important for high-throughput, automated DNA Assembly in biofabrication facilities and therefore we investigated one-step, scarless DNA Assembly via ligase cycling reaction (LCR). LCR Assembly uses single-stranded bridging oligos complementary to the ends of neighboring DNA parts, a thermostable ligase to join DNA backbones, and multiple denaturation-annealing-ligation temperature cycles to assemble complex DNA constructs. The efficiency of LCR Assembly was improved ca. 4-fold using designed optimization experiments and response surface methodology. Under these optimized conditions, LCR enabled one-step Assembly of up to 20 DNA parts and up to 20 kb DNA constructs with very few single-nucleotide polymorphisms (

Todd Slaby - One of the best experts on this subject based on the ideXlab platform.

  • rapid and reliable DNA Assembly via ligase cycling reaction
    ACS Synthetic Biology, 2014
    Co-Authors: Leslie H. Stanton, Todd Slaby, Darren Platt, Elaine B. Shapland, Zach Serber, Jed Dean, Maxime Durot, Kedar G Patel, Victor Holmes, Jack D Newman
    Abstract:

    Assembly of DNA parts into DNA constructs is a foundational technology in the emerging field of synthetic biology. An efficient DNA Assembly method is particularly important for high-throughput, automated DNA Assembly in biofabrication facilities and therefore we investigated one-step, scarless DNA Assembly via ligase cycling reaction (LCR). LCR Assembly uses single-stranded bridging oligos complementary to the ends of neighboring DNA parts, a thermostable ligase to join DNA backbones, and multiple denaturation–annealing–ligation temperature cycles to assemble complex DNA constructs. The efficiency of LCR Assembly was improved ca. 4-fold using designed optimization experiments and response surface methodology. Under these optimized conditions, LCR enabled one-step Assembly of up to 20 DNA parts and up to 20 kb DNA constructs with very few single-nucleotide polymorphisms (<1 per 25 kb) and insertions/deletions (<1 per 50 kb). Experimental comparison of various sequence-independent DNA Assembly methods show...

  • Rapid and reliable DNA Assembly via ligase cycling reaction
    ACS Synthetic Biology, 2014
    Co-Authors: Stefan De Kok, Leslie H. Stanton, Todd Slaby, Victor F. Holmes, Darren Platt, Elaine B. Shapland, Zach Serber, Maxime Durot, Kedar G Patel, Jed Dean
    Abstract:

    Assembly of DNA parts into DNA constructs is a foundational technology in the emerging field of synthetic biology. An efficient DNA Assembly method is particularly important for high-throughput, automated DNA Assembly in biofabrication facilities and therefore we investigated one-step, scarless DNA Assembly via ligase cycling reaction (LCR). LCR Assembly uses single-stranded bridging oligos complementary to the ends of neighboring DNA parts, a thermostable ligase to join DNA backbones, and multiple denaturation-annealing-ligation temperature cycles to assemble complex DNA constructs. The efficiency of LCR Assembly was improved ca. 4-fold using designed optimization experiments and response surface methodology. Under these optimized conditions, LCR enabled one-step Assembly of up to 20 DNA parts and up to 20 kb DNA constructs with very few single-nucleotide polymorphisms (

  • High-throughput, cost-effective verification of structural DNA Assembly
    Nucleic Acids Research, 2013
    Co-Authors: Yandi Dharmadi, Todd Slaby, Elaine B. Shapland, Jed Dean, Kedar G Patel, Daniel Hollis, Nicole Klinkner, Sunil S. Chandran
    Abstract:

    : DNA 'Assembly' from 'building blocks' remains a cornerstone in synthetic biology, whether it be for gene synthesis (∼ 1 kb), pathway engineering (∼ 10 kb) or synthetic genomes (>100 kb). Despite numerous advances in the techniques used for DNA Assembly, verification of the Assembly is still a necessity, which becomes cost-prohibitive and a logistical challenge with increasing scale. Here we describe for the first time a comprehensive, high-throughput solution for structural DNA Assembly verification by restriction digest using exhaustive in silico enzyme screening, rolling circle amplification of plasmid DNA, capillary electrophoresis and automated digest pattern recognition. This low-cost and robust methodology has been successfully used to screen over 31 000 clones of DNA constructs at