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Bioinformatics

The Experts below are selected from a list of 675792 Experts worldwide ranked by ideXlab platform

Galeb Abuali – 1st expert on this subject based on the ideXlab platform

  • assessment of variation in microbial community amplicon sequencing by the microbiome quality control mbqc project consortium
    Nature Biotechnology, 2017
    Co-Authors: Rashmi Sinha, Galeb Abuali, Emily Vogtmann, Anthony A Fodor, Amnon Amir, Emma Schwager, Boyu Ren, Jonathan Crabtree

    Abstract:

    The Microbiome Quality Control project consortium reports outcomes of a baseline study (MBQC) that will guide future improvements in reproducibility of microbiome analyses. In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine Bioinformatics protocols. Variability depended most on biospecimen type and origin, followed by DNA extraction, sample handling environment, and Bioinformatics. Analysis of artificial community specimens revealed differences in extraction efficiency and bioinformatic classification. These results may guide researchers in experimental design choices for gut microbiome studies.

  • assessment of variation in microbial community amplicon sequencing by the microbiome quality control mbqc project consortium
    Nature Biotechnology, 2017
    Co-Authors: Rashmi Sinha, Galeb Abuali, Emily Vogtmann, Anthony A Fodor, Amnon Amir, Emma Schwager, Jonathan Crabtree, Christian C Abnet

    Abstract:

    In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine Bioinformatics protocols. Variability depended most on biospecimen type and origin, followed by DNA extraction, sample handling environment, and Bioinformatics. Analysis of artificial community specimens revealed differences in extraction efficiency and bioinformatic classification. These results may guide researchers in experimental design choices for gut microbiome studies.

Emma Schwager – 2nd expert on this subject based on the ideXlab platform

  • assessment of variation in microbial community amplicon sequencing by the microbiome quality control mbqc project consortium
    Nature Biotechnology, 2017
    Co-Authors: Rashmi Sinha, Galeb Abuali, Emily Vogtmann, Anthony A Fodor, Amnon Amir, Emma Schwager, Boyu Ren, Jonathan Crabtree

    Abstract:

    The Microbiome Quality Control project consortium reports outcomes of a baseline study (MBQC) that will guide future improvements in reproducibility of microbiome analyses. In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine Bioinformatics protocols. Variability depended most on biospecimen type and origin, followed by DNA extraction, sample handling environment, and Bioinformatics. Analysis of artificial community specimens revealed differences in extraction efficiency and bioinformatic classification. These results may guide researchers in experimental design choices for gut microbiome studies.

  • assessment of variation in microbial community amplicon sequencing by the microbiome quality control mbqc project consortium
    Nature Biotechnology, 2017
    Co-Authors: Rashmi Sinha, Galeb Abuali, Emily Vogtmann, Anthony A Fodor, Amnon Amir, Emma Schwager, Jonathan Crabtree, Christian C Abnet

    Abstract:

    In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine Bioinformatics protocols. Variability depended most on biospecimen type and origin, followed by DNA extraction, sample handling environment, and Bioinformatics. Analysis of artificial community specimens revealed differences in extraction efficiency and bioinformatic classification. These results may guide researchers in experimental design choices for gut microbiome studies.

Vikram Alva – 3rd expert on this subject based on the ideXlab platform

  • a completely reimplemented mpi Bioinformatics toolkit with a new hhpred server at its core
    Journal of Molecular Biology, 2017
    Co-Authors: Lukas Zimmermann, Andrei N Lupas, Johannes Soding, Andrew Stephens, Jonas M Kubler, Marko Lozajic, Felix Gabler, Vikram Alva

    Abstract:

    Abstract The MPI Bioinformatics Toolkit ( https://toolkit.tuebingen.mpg.de ) is a free, one-stop web service for protein bioinformatic analysis. It currently offers 34 interconnected external and in-house tools, whose functionality covers sequence similarity searching, alignment construction, detection of sequence features, structure prediction, and sequence classification. This breadth has made the Toolkit an important resource for experimental biology and for teaching bioinformatic inquiry. Recently, we replaced the first version of the Toolkit, which was released in 2005 and had served around 2.5 million queries, with an entirely new version, focusing on improved features for the comprehensive analysis of proteins, as well as on promoting teaching. For instance, our popular remote homology detection server, HHpred, now allows pairwise comparison of two sequences or alignments and offers additional profile HMMs for several model organisms and domain databases. Here, we introduce the new version of our Toolkit and its application to the analysis of proteins.

  • the mpi Bioinformatics toolkit as an integrative platform for advanced protein sequence and structure analysis
    Nucleic Acids Research, 2016
    Co-Authors: Vikram Alva, Johannes Soding, Andrei N Lupas

    Abstract:

    The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art Bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAST+, HMMER3, MUSCLE) and internally (e.g. HHpred, HHblits, PCOILS). While a beta version of the Toolkit was released 10 years ago, the current production-level release has been available since 2008 and has serviced more than 1.6 million external user queries. The usage of the Toolkit has continued to increase linearly over the years, reaching more than 400 000 queries in 2015. In fact, through the breadth of its tools and their tight interconnection, the Toolkit has become an excellent platform for experimental scientists as well as a useful resource for teaching bioinformatic inquiry to students in the life sciences. In this article, we report on the evolution of the Toolkit over the last ten years, focusing on the expansion of the tool repertoire (e.g. CS-BLAST, HHblits) and on infrastructural work needed to remain operative in a changing web environment.