The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Wolf Reik - One of the best experts on this subject based on the ideXlab platform.
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comparison of whole genome bisulfite sequencing Library preparation strategies identifies sources of biases affecting dna methylation data
Genome Biology, 2018Co-Authors: Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V Berrens, Miguel R Branco, Wolf ReikAbstract:Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS Library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of Standard Library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. We show that amplification-free Library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets.
Mirna Willer - One of the best experts on this subject based on the ideXlab platform.
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Standard Library metadata models and structures for the semantic web
Library Hi Tech News, 2011Co-Authors: Gordon Dunsire, Mirna WillerAbstract:Purpose – There has been a significant increase in activity over the past few years to integrate Library metadata with the Semantic Web. While much of this has involved the development of controlled vocabularies as “linked data”, there have recently been concerted attempts to represent Standard Library models for bibliographic metadata in forms that are compatible with Semantic Web technologies. This paper aims to give an overview of these initiatives, describing relationships between them in the context of the Semantic Web.Design/methodology/approach – The paper focusses on Standards created and maintained by the International Federation of Library Associations and Institutions, including Functional Requirements for Bibliographic Records, Functional Requirements for Authority Data, and International Standard Bibliographic Description. It also covers related Standards and models such as RDA – Resource Description and Access, REICAT (the new Italian cataloguing rules) and CIDOC Conceptual Reference Model, ...
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initiatives to make Standard Library metadata models and structures available to the semantic web
2010Co-Authors: Gordon Dunsire, Mirna WillerAbstract:This paper describes recent initiatives to make Standard Library metadata models and structures available to the Semantic Web, including IFLA Standards such as Functional Requirements for Bibliographic Records (FRBR), Functional Requirements for Authority Data (FRAD), and International Standard Bibliographic Description (ISBD) along with the infrastructure that supports them. The FRBR Review Group is currently developing representations of FRAD and the entityrelationship model of FRBR in resource description framework (RDF) applications, using a combination of RDF, RDF Schema (RDFS), Simple Knowledge Organisation System (SKOS) and Web Ontology Language (OWL), cross-relating both models where appropriate. The ISBD/XML Task Group is investigating the representation of ISBD in RDF. The IFLA Namespaces project is developing an administrative and technical infrastructure to support such initiatives and encourage uptake of Standards by other agencies. The paper describes similar initiatives with related external Standards such as RDA – resource description and access, REICAT (the new Italian cataloguing rules) and CIDOC Conceptual Reference Model (CRM). The DCMI RDA Task Group is working with the Joint Steering Committee for RDA to develop Semantic Web representations of RDA structural elements, which are aligned with FRBR and FRAD, and controlled metadata content vocabularies. REICAT is also based on FRBR, and an object-oriented version of FRBR has been
Guido Van Rossum - One of the best experts on this subject based on the ideXlab platform.
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python programming language
USENIX Annual Technical Conference, 2007Co-Authors: Guido Van RossumAbstract:Python is an interpreted, general purpose language. An interpreted language is a language that needs to be interpreted by an interpreter. The program codes written using an interpreted language are supposed to be executed using an interpreter. The interpreter performs various functions. For example, the interpreter executes the source of the programming language directly. So, the interpreter translates the source code into a code that can be understood by the user. In addition, python is a high level programming language .The design philosophy of python enforces code readability. Python is aimed at combining remarkable power with a clear syntax. The Standard Library of python is large and comprehensive. Python is different from other languages.
Nelly Olova - One of the best experts on this subject based on the ideXlab platform.
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comparison of whole genome bisulfite sequencing Library preparation strategies identifies sources of biases affecting dna methylation data
Genome Biology, 2018Co-Authors: Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V Berrens, Miguel R Branco, Wolf ReikAbstract:Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS Library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of Standard Library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. We show that amplification-free Library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets.
Stefano Zacchiroli - One of the best experts on this subject based on the ideXlab platform.
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a content based mathematical search engine whelp
Lecture Notes in Computer Science, 2006Co-Authors: Andrea Asperti, Ferruccio Guidi, Claudio Sacerdoti Coen, Enrico Tassi, Stefano ZacchiroliAbstract:The prototype of a content based search engine for mathematical knowledge supporting a small set of queries requiring matching and/or typing operations is described. The prototype - called Whelp -exploits a metadata approach for indexing the information that looks far more flexible than traditional indexing techniques for structured expressions like substitution, discrimination, or context trees. The prototype has been instantiated to the Standard Library of the Coq proof assistant extended with many user contributions.
