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  1. Book ; Online: Silhouette Aggregation

    Vardakas, Georgios / Pavlopoulos, John / Likas, Aristidis

    From Micro to Macro

    2024  

    Abstract: Silhouette coefficient is an established internal clustering evaluation measure that produces a score per data point, assessing the quality of its clustering assignment. To assess the quality of the clustering of the whole dataset, the scores of all the ... ...

    Abstract Silhouette coefficient is an established internal clustering evaluation measure that produces a score per data point, assessing the quality of its clustering assignment. To assess the quality of the clustering of the whole dataset, the scores of all the points in the dataset are either (micro) averaged into a single value or averaged at the cluster level and then (macro) averaged. As we illustrate in this work, by using a synthetic example, the micro-averaging strategy is sensitive both to cluster imbalance and outliers (background noise) while macro-averaging is far more robust to both. Furthermore, the latter allows cluster-balanced sampling which yields robust computation of the silhouette score. By conducting an experimental study on eight real-world datasets, estimating the ground truth number of clusters, we show that both coefficients, micro and macro, should be considered.
    Keywords Computer Science - Machine Learning ; Computer Science - Artificial Intelligence
    Subject code 310
    Publishing date 2024-01-11
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: Corrigendum: A guide to conquer the biological network era using graph theory.

    Koutrouli, Mikaela / Karatzas, Evangelos / Paez-Espino, David / Pavlopoulos, Georgios A

    Frontiers in bioengineering and biotechnology

    2023  Volume 11, Page(s) 1182500

    Abstract: This corrects the article DOI: 10.3389/fbioe.2020.00034.]. ...

    Abstract [This corrects the article DOI: 10.3389/fbioe.2020.00034.].
    Language English
    Publishing date 2023-03-31
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2719493-0
    ISSN 2296-4185
    ISSN 2296-4185
    DOI 10.3389/fbioe.2023.1182500
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Protocol for unbiased, consolidated variant calling from whole exome sequencing data.

    Verrou, Kleio-Maria / Pavlopoulos, Georgios A / Moulos, Panagiotis

    STAR protocols

    2022  Volume 3, Issue 2, Page(s) 101418

    Abstract: Whole Exome Sequencing (WES) is used for querying DNA variants using the protein coding parts of genomes (exomes). However, WES analysis can be challenging because of the complexity of the data. Here, we describe a consolidated protocol for unbiased WES ... ...

    Abstract Whole Exome Sequencing (WES) is used for querying DNA variants using the protein coding parts of genomes (exomes). However, WES analysis can be challenging because of the complexity of the data. Here, we describe a consolidated protocol for unbiased WES analysis. The protocol uses three variant callers (HaplotypeCaller, FreeBayes, and DeepVariant), which have different underlying models. We provide detailed execution steps, as well as basic variant filtering, annotation, visualization, and consolidation aspects.
    MeSH term(s) Exome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Whole Exome Sequencing
    Language English
    Publishing date 2022-05-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.101418
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data.

    Tzaferis, Christos / Karatzas, Evangelos / Baltoumas, Fotis A / Pavlopoulos, Georgios A / Kollias, George / Konstantopoulos, Dimitris

    Computational and structural biotechnology journal

    2023  Volume 21, Page(s) 5382–5393

    Abstract: Analysis and interpretation of high-throughput transcriptional and chromatin accessibility data at single-cell (sc) resolution are still open challenges in the biomedical field. The existence of countless bioinformatics tools, for the different ... ...

    Abstract Analysis and interpretation of high-throughput transcriptional and chromatin accessibility data at single-cell (sc) resolution are still open challenges in the biomedical field. The existence of countless bioinformatics tools, for the different analytical steps, increases the complexity of data interpretation and the difficulty to derive biological insights. In this article, we present SCALA, a bioinformatics tool for analysis and visualization of single-cell RNA sequencing (scRNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) datasets, enabling either independent or integrative analysis of the two modalities. SCALA combines standard types of analysis by integrating multiple software packages varying from quality control to the identification of distinct cell populations and cell states. Additional analysis options enable functional enrichment, cellular trajectory inference, ligand-receptor analysis, and regulatory network reconstruction. SCALA is fully parameterizable, presenting data in tabular format and producing publication-ready visualizations. The different available analysis modules can aid biomedical researchers in exploring, analyzing, and visualizing their data without any prior experience in coding. We demonstrate the functionality of SCALA through two use-cases related to TNF-driven arthritic mice, handling both scRNA-seq and scATAC-seq datasets. SCALA is developed in R, Shiny and JavaScript and is mainly available as a standalone version, while an online service of more limited capacity can be found at http://scala.pavlopouloslab.info or https://scala.fleming.gr.
    Language English
    Publishing date 2023-10-20
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2023.10.032
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Bimodal optical and optoacoustic multiview microscope in the frequency-domain.

    Mylonakis, Mikis / Tserevelakis, George J / Vlachos, Georgios / Fanouraki, Eleftheria / Pavlopoulos, Anastasios / Pavlidis, Michalis / Zacharakis, Giannis

    Optics letters

    2024  Volume 49, Issue 3, Page(s) 462–465

    Abstract: Hybrid fluorescence and optoacoustic microscopy systems have recently emerged as powerful imaging modalities concurrently capturing both radiative and non-radiative molecular relaxations in biological tissues. Nevertheless, such approaches provide ... ...

    Abstract Hybrid fluorescence and optoacoustic microscopy systems have recently emerged as powerful imaging modalities concurrently capturing both radiative and non-radiative molecular relaxations in biological tissues. Nevertheless, such approaches provide limited information as specimens are imaged exclusively from one side, not permitting the acquisition of their full anatomical, structural, or functional features in multiple views of interest. Herein we present a bimodal optical and optoacoustic multiview (BOOM) cost-efficient microscope operating in the frequency-domain for the comprehensive label-free imaging of established and emerging model organisms. Thus, the capabilities of BOOM microscopy have been proven suitable for highly demanding observations in developmental biology and embryology.
    MeSH term(s) Microscopy/methods
    Language English
    Publishing date 2024-02-01
    Publishing country United States
    Document type Journal Article
    ISSN 1539-4794
    ISSN (online) 1539-4794
    DOI 10.1364/OL.510384
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: MPRAbase: A Massively Parallel Reporter Assay Database.

    Zhao, Jingjing / Baltoumas, Fotis A / Konnaris, Maxwell A / Mouratidis, Ioannis / Liu, Zhe / Sims, Jasmine / Agarwal, Vikram / Pavlopoulos, Georgios A / Georgakopoulos-Soares, Ilias / Ahituv, Nadav

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene regulatory activity. There are several different variations of MPRA technology and ... ...

    Abstract Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene regulatory activity. There are several different variations of MPRA technology and they are used for numerous applications, including regulatory element discovery, variant effect measurement, saturation mutagenesis, synthetic regulatory element generation or characterization of evolutionary gene regulatory differences. Despite their many designs and uses, there is no comprehensive database that incorporates the results of these experiments. To address this, we developed MPRAbase, a manually curated database that currently harbors 129 experiments, encompassing 17,718,677 elements tested across 35 cell types and 4 organisms. The MPRAbase web interface (http://www.mprabase.com) serves as a centralized user-friendly repository to download existing MPRA data for independent analysis and is designed with the ability to allow researchers to share their published data for rapid dissemination to the community.
    Language English
    Publishing date 2023-11-22
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.11.19.567742
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Protocol for unbiased, consolidated variant calling from whole exome sequencing data

    Kleio-Maria Verrou / Georgios A. Pavlopoulos / Panagiotis Moulos

    STAR Protocols, Vol 3, Iss 2, Pp 101418- (2022)

    2022  

    Abstract: Summary: Whole Exome Sequencing (WES) is used for querying DNA variants using the protein coding parts of genomes (exomes). However, WES analysis can be challenging because of the complexity of the data. Here, we describe a consolidated protocol for ... ...

    Abstract Summary: Whole Exome Sequencing (WES) is used for querying DNA variants using the protein coding parts of genomes (exomes). However, WES analysis can be challenging because of the complexity of the data. Here, we describe a consolidated protocol for unbiased WES analysis. The protocol uses three variant callers (HaplotypeCaller, FreeBayes, and DeepVariant), which have different underlying models. We provide detailed execution steps, as well as basic variant filtering, annotation, visualization, and consolidation aspects. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
    Keywords Bioinformatics ; Genetics ; Genomics ; Science (General) ; Q1-390
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization.

    Koutrouli, Mikaela / Karatzas, Evangelos / Papanikolopoulou, Katerina / Pavlopoulos, Georgios A

    Genomics, proteomics & bioinformatics

    2021  Volume 20, Issue 3, Page(s) 578–586

    Abstract: The Network Makeup Artist (NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g., Gene Ontology, Pathway enrichment, ...

    Abstract The Network Makeup Artist (NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g., Gene Ontology, Pathway enrichment, community detection, or clustering results) can be uploaded and visualized in a network, either as colored pie-chart nodes or as color-filled areas in a 2D/3D Venn-diagram-like style. In the case where no annotation exists, algorithms for automated community detection are offered. Users can adjust the network views using standard layout algorithms or allow NORMA to slightly modify them for visually better group separation. Once a network view is set, users can interactively select and highlight any group of interest in order to generate publication-ready figures. Briefly, with NORMA, users can encode three types of information simultaneously. These are 1) the network, 2) the communities or annotations of interest, and 3) node categories or expression values. Finally, NORMA offers basic topological analysis and direct topological comparison across any of the selected networks. NORMA service is available at http://norma.pavlopouloslab.info, whereas the code is available at https://github.com/PavlopoulosLab/NORMA.
    MeSH term(s) Software ; Algorithms
    Language English
    Publishing date 2021-06-24
    Publishing country China
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2240213-5
    ISSN 2210-3244 ; 1672-0229
    ISSN (online) 2210-3244
    ISSN 1672-0229
    DOI 10.1016/j.gpb.2021.02.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  9. Article ; Online: NORMA

    Mikaela Koutrouli / Evangelos Karatzas / Katerina Papanikolopoulou / Georgios A. Pavlopoulos

    Genomics, Proteomics & Bioinformatics, Vol 20, Iss 3, Pp 578-

    The Network Makeup Artist — A Web Tool for Network Annotation Visualization

    2022  Volume 586

    Abstract: The Network Makeup Artist (NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g., Gene Ontology, Pathway enrichment, ...

    Abstract The Network Makeup Artist (NORMA) is a web tool for interactive network annotation visualization and topological analysis, able to handle multiple networks and annotations simultaneously. Precalculated annotations (e.g., Gene Ontology, Pathway enrichment, community detection, or clustering results) can be uploaded and visualized in a network, either as colored pie-chart nodes or as color-filled areas in a 2D/3D Venn-diagram-like style. In the case where no annotation exists, algorithms for automated community detection are offered. Users can adjust the network views using standard layout algorithms or allow NORMA to slightly modify them for visually better group separation. Once a network view is set, users can interactively select and highlight any group of interest in order to generate publication-ready figures. Briefly, with NORMA, users can encode three types of information simultaneously. These are 1) the network, 2) the communities or annotations of interest, and 3) node categories or expression values. Finally, NORMA offers basic topological analysis and direct topological comparison across any of the selected networks. NORMA service is available at http://norma.pavlopouloslab.info, whereas the code is available at https://github.com/PavlopoulosLab/NORMA.
    Keywords Network annotation ; Visualization ; Topological analysis ; Community detection ; Functional enrichment visualization ; Biology (General) ; QH301-705.5
    Subject code 000
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: The network makeup artist (NORMA-2.0): distinguishing annotated groups in a network using innovative layout strategies.

    Karatzas, Evangelos / Koutrouli, Mikaela / Baltoumas, Fotis A / Papanikolopoulou, Katerina / Bouyioukos, Costas / Pavlopoulos, Georgios A

    Bioinformatics advances

    2022  Volume 2, Issue 1, Page(s) vbac036

    Abstract: Motivation: Network biology is a dominant player in today's multi-omics era. Therefore, the need for visualization tools which can efficiently cope with intra-network heterogeneity emerges.: Results: NORMA-2.0 is a web application which uses ... ...

    Abstract Motivation: Network biology is a dominant player in today's multi-omics era. Therefore, the need for visualization tools which can efficiently cope with intra-network heterogeneity emerges.
    Results: NORMA-2.0 is a web application which uses efficient layouts to group together areas of interest in a network. In this version, NORMA-2.0 utilizes three different strategies to make such groupings as distinct as possible while it preserves all of the properties from its first version where one can handle multiple networks and annotation files simultaneously.
    Availability and implementation: The web resource is available at http://norma.pavlopouloslab.info/. The source code is freely available at https://github.com/PavlopoulosLab/NORMA.
    Language English
    Publishing date 2022-05-13
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbac036
    Database MEDical Literature Analysis and Retrieval System OnLINE

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