The Experts below are selected from a list of 351054 Experts worldwide ranked by ideXlab platform

Golnaz Vahedi - One of the best experts on this subject based on the ideXlab platform.

  • a cosine similarity based method to infer variability of chromatin accessibility at the single cell level
    Frontiers in Genetics, 2018
    Co-Authors: Georgios Georgakilas, John L Johnson, Golnaz Vahedi
    Abstract:

    Cellular identity between generations of developing cells is propagated through the epigenome particularly via the accessible parts of the chromatin. It is now possible to measure chromatin accessibility at single-cell resolution using single-cell assay for transposase accessible chromatin (scATAC-seq), which can reveal the regulatory variation behind the phenotypic variation. However, single-cell chromatin accessibility data are sparse, binary, and high dimensional, leading to unique computational challenges. To overcome these difficulties, we developed PRISM, a computational workflow that quantifies cell-to-cell chromatin accessibility variation while controlling for technical biases. PRISM is a novel multidimensional scaling-based method using angular cosine distance metrics coupled with distance from the spatial centroid. PRISM takes differences in accessibility at each genomic region between single cells into account. Using data generated in our lab and publicly available, we showed that PRISM outperforms an Existing Algorithm, which relies on the aggregate of signal across a set of genomic regions. PRISM showed robustness to noise in cells with low coverage for measuring chromatin accessibility. Our approach revealed the previously undetected accessibility variation where accessible sites differ between cells but the total number of accessible sites is constant. We also showed that PRISM, but not an Existing Algorithm, can find suppressed heterogeneity of accessibility at CTCF binding sites. Our updated approach uncovers new biological results with profound implications on the cellular heterogeneity of chromatin architecture.

  • a cosine similarity based method to infer variability of chromatin accessibility at the single cell level
    bioRxiv, 2018
    Co-Authors: Georgios Georgakilas, John L Johnson, Golnaz Vahedi
    Abstract:

    Cellular identity between generations of developing cells is propagated through the epigenome particularly via the accessible parts of the chromatin. It is now possible to measure chromatin accessibility at single-cell resolution using single-cell assay for transposase accessible chromatin (scATAC-seq), which can reveal the regulatory variation behind the phenotypic variation. However, single-cell chromatin accessibility data are sparse, binary, and high dimensional, leading to unique computational challenges. To overcome these difficulties, we developed PRISM a computational workflow and R package (https://github.com/stanleycai123/PRISM) that quantifies cell-to-cell chromatin accessibility variation while controlling for technical biases. Using data generated in our lab or publically available, we show that PRISM outperforms an Existing Algorithm, which relies on the aggregate of signal across a set of genomic regions. PRISM shows robustness to noise in low accessibility cells and reveals previously masked accessibility variation where accessible sites differ between cells but total number of accessible sites is constant. We also show that PRISM, but not an Existing Algorithm, finds suppressed heterogeneity of accessibility at CTCF binding sites. PRISM is a novel multidimensional scaling-based method using angular cosine distance metrics coupled with distance from the spatial centroid. PRISM takes differences in accessibility at each genomic region between single cells into account. This updated approach uncovers new biological results with profound implications on the cellular heterogeneity of chromatin architecture.

Georgios Georgakilas - One of the best experts on this subject based on the ideXlab platform.

  • a cosine similarity based method to infer variability of chromatin accessibility at the single cell level
    Frontiers in Genetics, 2018
    Co-Authors: Georgios Georgakilas, John L Johnson, Golnaz Vahedi
    Abstract:

    Cellular identity between generations of developing cells is propagated through the epigenome particularly via the accessible parts of the chromatin. It is now possible to measure chromatin accessibility at single-cell resolution using single-cell assay for transposase accessible chromatin (scATAC-seq), which can reveal the regulatory variation behind the phenotypic variation. However, single-cell chromatin accessibility data are sparse, binary, and high dimensional, leading to unique computational challenges. To overcome these difficulties, we developed PRISM, a computational workflow that quantifies cell-to-cell chromatin accessibility variation while controlling for technical biases. PRISM is a novel multidimensional scaling-based method using angular cosine distance metrics coupled with distance from the spatial centroid. PRISM takes differences in accessibility at each genomic region between single cells into account. Using data generated in our lab and publicly available, we showed that PRISM outperforms an Existing Algorithm, which relies on the aggregate of signal across a set of genomic regions. PRISM showed robustness to noise in cells with low coverage for measuring chromatin accessibility. Our approach revealed the previously undetected accessibility variation where accessible sites differ between cells but the total number of accessible sites is constant. We also showed that PRISM, but not an Existing Algorithm, can find suppressed heterogeneity of accessibility at CTCF binding sites. Our updated approach uncovers new biological results with profound implications on the cellular heterogeneity of chromatin architecture.

  • a cosine similarity based method to infer variability of chromatin accessibility at the single cell level
    bioRxiv, 2018
    Co-Authors: Georgios Georgakilas, John L Johnson, Golnaz Vahedi
    Abstract:

    Cellular identity between generations of developing cells is propagated through the epigenome particularly via the accessible parts of the chromatin. It is now possible to measure chromatin accessibility at single-cell resolution using single-cell assay for transposase accessible chromatin (scATAC-seq), which can reveal the regulatory variation behind the phenotypic variation. However, single-cell chromatin accessibility data are sparse, binary, and high dimensional, leading to unique computational challenges. To overcome these difficulties, we developed PRISM a computational workflow and R package (https://github.com/stanleycai123/PRISM) that quantifies cell-to-cell chromatin accessibility variation while controlling for technical biases. Using data generated in our lab or publically available, we show that PRISM outperforms an Existing Algorithm, which relies on the aggregate of signal across a set of genomic regions. PRISM shows robustness to noise in low accessibility cells and reveals previously masked accessibility variation where accessible sites differ between cells but total number of accessible sites is constant. We also show that PRISM, but not an Existing Algorithm, finds suppressed heterogeneity of accessibility at CTCF binding sites. PRISM is a novel multidimensional scaling-based method using angular cosine distance metrics coupled with distance from the spatial centroid. PRISM takes differences in accessibility at each genomic region between single cells into account. This updated approach uncovers new biological results with profound implications on the cellular heterogeneity of chromatin architecture.

John L Johnson - One of the best experts on this subject based on the ideXlab platform.

  • a cosine similarity based method to infer variability of chromatin accessibility at the single cell level
    Frontiers in Genetics, 2018
    Co-Authors: Georgios Georgakilas, John L Johnson, Golnaz Vahedi
    Abstract:

    Cellular identity between generations of developing cells is propagated through the epigenome particularly via the accessible parts of the chromatin. It is now possible to measure chromatin accessibility at single-cell resolution using single-cell assay for transposase accessible chromatin (scATAC-seq), which can reveal the regulatory variation behind the phenotypic variation. However, single-cell chromatin accessibility data are sparse, binary, and high dimensional, leading to unique computational challenges. To overcome these difficulties, we developed PRISM, a computational workflow that quantifies cell-to-cell chromatin accessibility variation while controlling for technical biases. PRISM is a novel multidimensional scaling-based method using angular cosine distance metrics coupled with distance from the spatial centroid. PRISM takes differences in accessibility at each genomic region between single cells into account. Using data generated in our lab and publicly available, we showed that PRISM outperforms an Existing Algorithm, which relies on the aggregate of signal across a set of genomic regions. PRISM showed robustness to noise in cells with low coverage for measuring chromatin accessibility. Our approach revealed the previously undetected accessibility variation where accessible sites differ between cells but the total number of accessible sites is constant. We also showed that PRISM, but not an Existing Algorithm, can find suppressed heterogeneity of accessibility at CTCF binding sites. Our updated approach uncovers new biological results with profound implications on the cellular heterogeneity of chromatin architecture.

  • a cosine similarity based method to infer variability of chromatin accessibility at the single cell level
    bioRxiv, 2018
    Co-Authors: Georgios Georgakilas, John L Johnson, Golnaz Vahedi
    Abstract:

    Cellular identity between generations of developing cells is propagated through the epigenome particularly via the accessible parts of the chromatin. It is now possible to measure chromatin accessibility at single-cell resolution using single-cell assay for transposase accessible chromatin (scATAC-seq), which can reveal the regulatory variation behind the phenotypic variation. However, single-cell chromatin accessibility data are sparse, binary, and high dimensional, leading to unique computational challenges. To overcome these difficulties, we developed PRISM a computational workflow and R package (https://github.com/stanleycai123/PRISM) that quantifies cell-to-cell chromatin accessibility variation while controlling for technical biases. Using data generated in our lab or publically available, we show that PRISM outperforms an Existing Algorithm, which relies on the aggregate of signal across a set of genomic regions. PRISM shows robustness to noise in low accessibility cells and reveals previously masked accessibility variation where accessible sites differ between cells but total number of accessible sites is constant. We also show that PRISM, but not an Existing Algorithm, finds suppressed heterogeneity of accessibility at CTCF binding sites. PRISM is a novel multidimensional scaling-based method using angular cosine distance metrics coupled with distance from the spatial centroid. PRISM takes differences in accessibility at each genomic region between single cells into account. This updated approach uncovers new biological results with profound implications on the cellular heterogeneity of chromatin architecture.

Jitendra Kumar - One of the best experts on this subject based on the ideXlab platform.

  • Both Ended Sorting Algorithm & Performance Comparison with Existing Algorithm
    2014
    Co-Authors: Arpit Goel, Anubhooti Papola, Jitendra Kumar
    Abstract:

    One of the basic areas of the computer science is Data Structure. Sorting is an important issue in Data Structure which creates the sequence of the list of items. Although numbers of sorting Algorithms are available, it is all the more necessary to select the best sorting Algorithm. Therefore, sorting problem has attracted a great deal of research as sorting technique is very often used in a large variety of important applications so as to arrange the data in ascending or descending order. This paper presents a Both Ended Sorting Algorithm which is faster or better than the bubble sort& others Algorithm. After having studied various sorting Algorithms; I came to the conclusion that there is no such sorting Algorithm which works on the basis of both end comparison right end as well as left end. The new Algorithm so is then analysed, implemented & tested. The test results obtained are then presented and compared with the traditional Sorting Algorithm. Worst case complexity is also improved as a compare to bubble sort.

  • both ended sorting Algorithm performance comparison with Existing Algorithm
    2014
    Co-Authors: Arpit Goel, Anubhooti Papola, Jitendra Kumar
    Abstract:

    One of the basic areas of the computer science is Data Structure. Sorting is an important issue in Data Structure which creates the sequence of the list of items. Although numbers of sorting Algorithms are available, it is all the more necessary to select the best sorting Algorithm. Therefore, sorting problem has attracted a great deal of research as sorting technique is very often used in a large variety of important applications so as to arrange the data in ascending or descending order. This paper presents a Both Ended Sorting Algorithm which is faster or better than the bubble sort& others Algorithm. After having studied various sorting Algorithms; I came to the conclusion that there is no such sorting Algorithm which works on the basis of both end comparison right end as well as left end. The new Algorithm so is then analysed, implemented & tested. The test results obtained are then presented and compared with the traditional Sorting Algorithm. Worst case complexity is also improved as a compare to bubble sort.

Marc Streit - One of the best experts on this subject based on the ideXlab platform.

  • Opening the Black Box: Strategies for Increased User Involvement in Existing Algorithm Implementations
    IEEE transactions on visualization and computer graphics, 2014
    Co-Authors: Thomas Muhlbacher, Harald Piringer, Samuel Gratzl, Michael Sedlmair, Marc Streit
    Abstract:

    An increasing number of interactive visualization tools stress the integration with computational software like MATLAB and R to access a variety of proven Algorithms. In many cases, however, the Algorithms are used as black boxes that run to completion in isolation which contradicts the needs of interactive data exploration. This paper structures, formalizes, and discusses possibilities to enable user involvement in ongoing computations. Based on a structured characterization of needs regarding intermediate feedback and control, the main contribution is a formalization and comparison of strategies for achieving user involvement for Algorithms with different characteristics. In the context of integration, we describe considerations for implementing these strategies either as part of the visualization tool or as part of the Algorithm, and we identify requirements and guidelines for the design of Algorithmic APIs. To assess the practical applicability, we provide a survey of frequently used Algorithm implementations within R regarding the fulfillment of these guidelines. While echoing previous calls for analysis modules which support data exploration more directly, we conclude that a range of pragmatic options for enabling user involvement in ongoing computations exists on both the visualization and Algorithm side and should be used.