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  • 1
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    pIRS: Profile-based Illumina pair-end reads simulator (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-22
    Description: Motivation: The next-generation high-throughput sequencing technologies, especially from Illumina, have been widely used in re-sequencing and de novo assembly studies. However, there is no existing software that can simulate Illumina reads with real error and quality distributions and coverage bias yet, which is very useful in relevant software development and study designing of sequencing projects. Results: We provide a software package, pIRS (profile-based Illumina pair-end reads simulator), which simulates Illumina reads with empirical Base-Calling and GC%-depth profiles trained from real re-sequencing data. The error and quality distributions as well as coverage bias patterns of simulated reads using pIRS fit the properties of real sequencing data better than existing simulators. In addition, pIRS also comes with a tool to simulate the heterozygous diploid genomes. Availability: pIRS is written in C++ and Perl, and is freely available at ftp://ftp.genomics.org.cn/pub/pIRS/ . Contact: fanweisz09@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    AISAIC: a software suite for accurate identification of significant aberrations in cancers (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-29
    Description: :  Accurate identification of significant aberrations in cancers (AISAIC) is a systematic effort to discover potential cancer-driving genes such as oncogenes and tumor suppressors. Two major confounding factors against this goal are the normal cell contamination and random background aberrations in tumor samples. We describe a Java AISAIC package that provides comprehensive analytic functions and graphic user interface for integrating two statistically principled in silico approaches to address the aforementioned challenges in DNA copy number analyses. In addition, the package provides a command-line interface for users with scripting and programming needs to incorporate or extend AISAIC to their customized analysis pipelines. This open-source multiplatform software offers several attractive features: (i) it implements a user friendly complete pipeline from processing raw data to reporting analytic results; (ii) it detects deletion types directly from copy number signals using a Bayes hypothesis test; (iii) it estimates the fraction of normal contamination for each sample; (iv) it produces unbiased null distribution of random background alterations by iterative aberration-exclusive permutations; and (v) it identifies significant consensus regions and the percentage of homozygous/hemizygous deletions across multiple samples. AISAIC also provides users with a parallel computing option to leverage ubiquitous multicore machines. Availability and implementation:  AISAIC is available as a Java application, with a user’s guide and source code, at https://code.google.com/p/aisaic/ . Contact:   yug@vt.edu Supplementary information:   Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Designing electromechanical metamaterial with full nonzero piezoelectric coefficients (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Designing topological and geometrical structures with extended unnatural parameters (negative, near-zero, ultrahigh, or tunable) and counterintuitive properties is a big challenge in the field of metamaterials, especially for relatively unexplored materials with multiphysics coupling effects. For natural piezoelectric ceramics, only five nonzero elements in the piezoelectric matrix exist, which has impeded the design and application of piezoelectric devices for decades. Here, we introduce a methodology, inspired by quasi-symmetry breaking, realizing artificial anisotropy by metamaterial design to excite all the nonzero elements in contrast to zero values in natural materials. By elaborately programming topological structures and geometrical dimensions of the unit elements, we demonstrate, theoretically and experimentally, that tunable nonzero or ultrahigh values of overall effective piezoelectric coefficients can be obtained. While this work focuses on generating piezoelectric parameters of ceramics, the design principle should be inspirational to create unnatural apparent properties of other multiphysics coupling metamaterials.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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