The Experts below are selected from a list of 324 Experts worldwide ranked by ideXlab platform
Uwe Roesler - One of the best experts on this subject based on the ideXlab platform.
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establishment of a matrix assisted laser desorption ionization time of flight mass spectrometry database for rapid identification of infectious achlorophyllous green micro algae of the genus prototheca
Clinical Microbiology and Infection, 2012Co-Authors: Jayaseelan Murugaiyan, Jennifer Ahrholdt, V Kowbel, Uwe RoeslerAbstract:Abstract The possibility of using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of pathogenic and non-pathogenic species of the genus Prototheca has been recently demonstrated. A unique reference database of MALDI-TOF MS profiles for type and reference strains of the six generally accepted Prototheca species was established. The database quality was reinforced after the acquisition of 27 spectra for selected Prototheca strains, with three biological and technical replicates for each of 18 type and reference strains of Prototheca and four strains of Chlorella . This provides reproducible and unique spectra covering a wide m/z range (2000–20 000 Da) for each of the strains used in the present study. The reproducibility of the spectra was further confirmed by employing composite correlation index calculation and main spectra library (MSP) Dendrogram creation, available with MALDI Biotyper software. The MSP Dendrograms obtained were comparable with the 18S rDNA sequence-based Dendrograms. These reference spectra were successfully added to the Bruker database, and the efficiency of identification was evaluated by cross-reference-based and unknown Prototheca identification. It is proposed that the addition of further strains would reinforce the reference spectra library for rapid identification of Prototheca strains to the genus and species/genotype level.
Donna J. Peuquet - One of the best experts on this subject based on the ideXlab platform.
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constructing overview detail Dendrogram matrix views
IEEE Transactions on Visualization and Computer Graphics, 2009Co-Authors: Jin Chen, Alan M. Maceachren, Donna J. PeuquetAbstract:A Dendrogram that visualizes a clustering hierarchy is often integrated with a re-orderable matrix for pattern identification. The method is widely used in many research fields including biology, geography, statistics, and data mining. However, most Dendrograms do not scale up well, particularly with respect to problems of graphical and cognitive information overload. This research proposes a strategy that links an overview Dendrogram and a detail-view Dendrogram, each integrated with a re-orderable matrix. The overview displays only a user-controlled, limited number of nodes that represent the ldquoskeletonrdquo of a hierarchy. The detail view displays the sub-tree represented by a selected meta-node in the overview. The research presented here focuses on constructing a concise overview Dendrogram and its coordination with a detail view. The proposed method has the following benefits: dramatic alleviation of information overload, enhanced scalability and data abstraction quality on the Dendrogram, and the support of data exploration at arbitrary levels of detail. The contribution of the paper includes a new metric to measure the ldquoimportancerdquo of nodes in a Dendrogram; the method to construct the concise overview Dendrogram from the dynamically-identified, important nodes; and measure for evaluating the data abstraction quality for Dendrograms. We evaluate and compare the proposed method to some related existing methods, and demonstrating how the proposed method can help users find interesting patterns through a case study on county-level U.S. cervical cancer mortality and demographic data.
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Constructing Overview + Detail Dendrogram-Matrix Views
IEEE transactions on visualization and computer graphics, 2009Co-Authors: Jin Chen, Alan M. Maceachren, Donna J. PeuquetAbstract:A Dendrogram that visualizes a clustering hierarchy is often integrated with a re-orderable matrix for pattern identification. The method is widely used in many research fields including biology, geography, statistics, and data mining. However, most Dendrograms do not scale up well, particularly with respect to problems of graphical and cognitive information overload. This research proposes a strategy that links an overview Dendrogram and a detail-view Dendrogram, each integrated with a re-orderable matrix. The overview displays only a user-controlled, limited number of nodes that represent the ldquoskeletonrdquo of a hierarchy. The detail view displays the sub-tree represented by a selected meta-node in the overview. The research presented here focuses on constructing a concise overview Dendrogram and its coordination with a detail view. The proposed method has the following benefits: dramatic alleviation of information overload, enhanced scalability and data abstraction quality on the Dendrogram, and the support of data exploration at arbitrary levels of detail. The contribution of the paper includes a new metric to measure the ldquoimportancerdquo of nodes in a Dendrogram; the method to construct the concise overview Dendrogram from the dynamically-identified, important nodes; and measure for evaluating the data abstraction quality for Dendrograms. We evaluate and compare the proposed method to some related existing methods, and demonstrating how the proposed method can help users find interesting patterns through a case study on county-level U.S. cervical cancer mortality and demographic data.
Jayaseelan Murugaiyan - One of the best experts on this subject based on the ideXlab platform.
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establishment of a matrix assisted laser desorption ionization time of flight mass spectrometry database for rapid identification of infectious achlorophyllous green micro algae of the genus prototheca
Clinical Microbiology and Infection, 2012Co-Authors: Jayaseelan Murugaiyan, Jennifer Ahrholdt, V Kowbel, Uwe RoeslerAbstract:Abstract The possibility of using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of pathogenic and non-pathogenic species of the genus Prototheca has been recently demonstrated. A unique reference database of MALDI-TOF MS profiles for type and reference strains of the six generally accepted Prototheca species was established. The database quality was reinforced after the acquisition of 27 spectra for selected Prototheca strains, with three biological and technical replicates for each of 18 type and reference strains of Prototheca and four strains of Chlorella . This provides reproducible and unique spectra covering a wide m/z range (2000–20 000 Da) for each of the strains used in the present study. The reproducibility of the spectra was further confirmed by employing composite correlation index calculation and main spectra library (MSP) Dendrogram creation, available with MALDI Biotyper software. The MSP Dendrograms obtained were comparable with the 18S rDNA sequence-based Dendrograms. These reference spectra were successfully added to the Bruker database, and the efficiency of identification was evaluated by cross-reference-based and unknown Prototheca identification. It is proposed that the addition of further strains would reinforce the reference spectra library for rapid identification of Prototheca strains to the genus and species/genotype level.
Kenji Mizuguchi - One of the best experts on this subject based on the ideXlab platform.
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CLINE: a web-tool for the comparison of biological Dendrogram structures
BMC Bioinformatics, 2019Co-Authors: Rodolfo S. Allendes Osorio, Lokesh P. Tripathi, Kenji MizuguchiAbstract:Background When visually comparing the results of hierarchical clustering, the differences in the arrangements of components are of special interest. However, in a biological setting, identifying such differences becomes less straightforward, as the changes in the Dendrogram structure caused by permuting biological replicates, do not necessarily imply a different biological interpretation. Here, we introduce a visualization tool to help identify biologically similar topologies across different clustering results, even in the presence of replicates. Results Here we introduce CLINE, an open-access web application that allows users to visualize and compare multiple Dendrogram structures, by visually displaying the links between areas of similarity across multiple structures. Through the use of a single page and a simple user interface, the user is able to load and remove structures form the visualization, change some aspects of their display and set the parameters used to match cluster topology across consecutive pairs of Dendrograms. Conclusions We have implemented a web-tool that allows the users to visualize different Dendrogram structures, showing not only the structures themselves, but also linking areas of similarity across multiple structures. The software is freely available at http://mizuguchilab.org/tools/cline/ . Also, the source code, documentation and installation instructions are available on GitHub at https://github.com/RodolfoAllendes/cline/ .
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CLINE: a web-tool for the comparison of biological Dendrogram structures
BMC bioinformatics, 2019Co-Authors: Rodolfo S. Allendes Osorio, Lokesh P. Tripathi, Kenji MizuguchiAbstract:When visually comparing the results of hierarchical clustering, the differences in the arrangements of components are of special interest. However, in a biological setting, identifying such differences becomes less straightforward, as the changes in the Dendrogram structure caused by permuting biological replicates, do not necessarily imply a different biological interpretation. Here, we introduce a visualization tool to help identify biologically similar topologies across different clustering results, even in the presence of replicates. Here we introduce CLINE, an open-access web application that allows users to visualize and compare multiple Dendrogram structures, by visually displaying the links between areas of similarity across multiple structures. Through the use of a single page and a simple user interface, the user is able to load and remove structures form the visualization, change some aspects of their display and set the parameters used to match cluster topology across consecutive pairs of Dendrograms. We have implemented a web-tool that allows the users to visualize different Dendrogram structures, showing not only the structures themselves, but also linking areas of similarity across multiple structures. The software is freely available at http://mizuguchilab.org/tools/cline/ . Also, the source code, documentation and installation instructions are available on GitHub at https://github.com/RodolfoAllendes/cline/ .
Jennifer Ahrholdt - One of the best experts on this subject based on the ideXlab platform.
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establishment of a matrix assisted laser desorption ionization time of flight mass spectrometry database for rapid identification of infectious achlorophyllous green micro algae of the genus prototheca
Clinical Microbiology and Infection, 2012Co-Authors: Jayaseelan Murugaiyan, Jennifer Ahrholdt, V Kowbel, Uwe RoeslerAbstract:Abstract The possibility of using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of pathogenic and non-pathogenic species of the genus Prototheca has been recently demonstrated. A unique reference database of MALDI-TOF MS profiles for type and reference strains of the six generally accepted Prototheca species was established. The database quality was reinforced after the acquisition of 27 spectra for selected Prototheca strains, with three biological and technical replicates for each of 18 type and reference strains of Prototheca and four strains of Chlorella . This provides reproducible and unique spectra covering a wide m/z range (2000–20 000 Da) for each of the strains used in the present study. The reproducibility of the spectra was further confirmed by employing composite correlation index calculation and main spectra library (MSP) Dendrogram creation, available with MALDI Biotyper software. The MSP Dendrograms obtained were comparable with the 18S rDNA sequence-based Dendrograms. These reference spectra were successfully added to the Bruker database, and the efficiency of identification was evaluated by cross-reference-based and unknown Prototheca identification. It is proposed that the addition of further strains would reinforce the reference spectra library for rapid identification of Prototheca strains to the genus and species/genotype level.
